eaogorg.files.wordpress.com · web viewgeochemistry articles – september 2019. analytical...

GEOCHEMISTRY ARTICLES – September 2019

Analytical Chemistry

Gascon, G., Negrín, J., Montoto, V.G., Acevedo, S., Lienemann, C.-P., Bouyssiere, B., 2019. Simplification of heavy matrices by liquid–solid extraction: Part II—How to separate the LMW, MMW, and HMW compounds in asphaltene fractions for V, Ni, and S compounds. Energy & Fuels 33, 8110-8117.

Küpper, H., Bokhari, S.N.H., Jaime-Pérez, N., Lyubenova, L., Ashraf, N., Andresen, E., 2019. Ultratrace metal speciation analysis by coupling of sector-field ICP-MS to high-resolution size exclusion and reversed-phase liquid chromatography. Analytical Chemistry 91, 10961-10969.

GAS CHROMATOGRAPHY/GC×GC/GC-MS

Dohmann, J.F., Thiäner, J.B., Achten, C., 2019. Ultrasensitive detection of polycyclic aromatic hydrocarbons in coastal and harbor water using GC-APLI-MS. Marine Pollution Bulletin 149, 110547.

Elie, N., Santerre, C., Touboul, D., 2019. Generation of a molecular network from electron ionization mass spectrometry data by combining MZmine2 and MetGem software. Analytical Chemistry 91, 11489-11492.

Li, M., Wang, X.R., 2019. Peak alignment of gas chromatography–mass spectrometry data with deep learning. Journal of Chromatography A 1604, 460476.

Luong, J., Hua, Y., Gras, R., Shellie, R.A., 2019. Uniformity and sensitivity improvements in comprehensive two-dimensional gas chromatography using flame ionization detection with post-column reaction. Analytical Chemistry 91, 11223-11230.

Stevenson, K.A.J.M., Blumberg, L.M., Harynuk, J.J., 2019. Thermodynamics-based retention maps to guide column choices for comprehensive multi-dimensional gas chromatography. Analytica Chimica Acta 1086, 133-141.

Weggler, B.A., Gruber, B., Dorman, F.L., 2019. Rapid screening of complex matrices: Utilizing Kendrick mass defect to enhance knowledge-based group type evaluation of multidimensional gas chromatography–high-resolution time-of-flight mass spectrometry data. Analytical Chemistry 91, 10949-10954.

Zhou, W., Zhang, H., Deng, C., Chen, Y., Liao, J., Chen, Z., Xu, J., 2019. Solvent-assisted vacuum desorption coupled with gas chromatography-tandem mass spectrometry for rapid determination of polycyclic aromatic hydrocarbons in soil samples. Journal of Chromatography A 1604, 460473.

IMAGING: AFM

Billups, W.E., Verma, M., Brinson, B.E., Vishnyakova, E., Alemany, L.B., Shammai, M., 2019. Birch reduction of asphaltenes. Synthesis of hydroasphaltenes. Energy & Fuels 33, 8040-8044.

Dias, H.P., Barros, E.V., Gomes, A.O., Moura, R.R., Pinto, F.E., Gonçalves, A.S., Aquije, G.M.F.V., Xu, Z., Romão, W., 2020. Corrosion rate studies of AISI 1020 steel using linear, cyclic, and aromatic naphthenic acid standards. Journal of Petroleum Science and Engineering 1874, 106474.

Dickinson, W.W., Aravind, S.S.J., Higgins, S.R., Berg, S., Suijkerbuijk, B.M.J.M., Schniepp, H.C., 2020. Using atomic force spectroscopy to study oil/mineral interactions at reservoir temperatures and pressures. Fuel 259, 116194.

Kaiser, K., Scriven, L.M., Schulz, F., Gawel, P., Gross, L., Anderson, H.L., 2019. An sp-hybridized molecular carbon allotrope, cyclo[18]carbon. Science 365, 1299-1301.

IMAGING: SEM, TEM, HIM

Bi, G., Lyu, C., Li, C., Chen, G., Zhang, G., Zhou, Q., Li, C., Zhao, Y., 2019. Impact of early hydrocarbon charge on the diagenetic history and reservoir quality of the Central Canyon sandstones in the Qiongdongnan Basin, South China Sea. Journal of Asian Earth Sciences 185, 104022.

Cao, T., Liu, G., Liu, H., Deng, M., Han, Y., Huang, Y., Hursthouse, A.S., 2019. Nanoscale pore characteristics of the Upper Permian mudrocks from a transitional environment in and around eastern Sichuan Basin, China. Acta Geologica Sinica - English Edition 93, 1025-1046.

Cornell, C.E., Black, R.A., Xue, M., Litz, H.E., Ramsay, A., Gordon, M., Mileant, A., Cohen, Z.R., Williams, J.A., Lee, K.K., Drobny, G.P., Keller, S.L., 2019. Prebiotic amino acids bind to and stabilize prebiotic fatty acid membranes. Proceedings of the National Academy of Sciences 116, 17239-17244.


Dill, H.G., Kus, J., Goldmann, S., Suárez-Ruiz, I., Neumann, T., Kaufhold, S., 2019. The physical-chemical regime of a sulfide-bearing semi-graphite mineral assemblage in metabasic rocks (SE Germany) – A multidisciplinary study of the missing link between impsonite and graphite. International Journal of Coal Geology 214, 103262.

Fang, C., Achal, V., 2019. Biostimulation of calcite precipitation process by bacterial community in improving cement stabilized rammed earth as sustainable material. Applied Microbiology and Biotechnology 103, 7719-7727.

Feng, G., Zhu, Y., Wang, G.G.X., Chen, S., Wang, Y., Ju, W., 2019. Supercritical methane adsorption on overmature shale: Effect of pore structure and fractal characteristics. Energy & Fuels 33, 8323-8337.

Goral, J., Walton, I., Andrew, M., Deo, M., 2019. Pore system characterization of organic-rich shales using nanoscale-resolution 3D imaging. Fuel 258, 116049.

Klein, F., Grozeva, N.G., Seewald, J.S., 2019. Abiotic methane synthesis and serpentinization in olivine-hosted fluid inclusions. Proceedings of the National Academy of Sciences 116, 17666-17672.

Lo, Y.H., Liao, C.-T., Zhou, J., Rana, A., Bevis, C.S., Gui, G., Enders, B., Cannon, K.M., Yu, Y.-S., Celestre, R., Nowrouzi, K., Shapiro, D., Kapteyn, H., Falcone, R., Bennett, C., Murnane, M., Miao, J., 2019. Multimodal x-ray and electron microscopy of the Allende meteorite. Science Advances 5, eaax3009.

Priebe, A., Utke, I., Pethö, L., Michler, J., 2019. Application of a gas-injection system during the FIB-TOF-SIMS analysis—influence of water vapor and fluorine gas on secondary ion signals and sputtering rates. Analytical Chemistry 91, 11712-11722.

Song, W., Yao, J., Wang, D., Li, Y., Sun, H., Yang, Y., 2020. Dynamic pore network modelling of real gas transport in shale nanopore structure. Journal of Petroleum Science and Engineering 184, 106506.

Tang, G., Wang, G., An, Y., Zhang, H., 2019. Graphene oxide on microbially induced calcium carbonate precipitation. International Biodeterioration & Biodegradation 145, 104767.

Wang, X., Zhu, Y., Liu, Y., Li, W., 2019. Molecular structure of kerogen in the Longmaxi shale: Insights from solid state NMR, FT-IR, XRD and HRTEM. Acta Geologica Sinica - English Edition 93, 1015-1024.

Wu, J., Zhou, W., Sun, S., Zhou, S., Shi, Z., 2019. Graptolite-derived organic matter and pore characteristics in the Wufeng-Longmaxi black shale of the Sichuan Basin and its periphery. Acta Geologica Sinica - English Edition 93, 982-995.

Yang, C., Xiong, Y., Zhang, J., Liu, Y., Chen, C., 2019. Comprehensive understanding of OM-hosted pores in transitional shale: A case study of Permian Longtan Shale in South China based on organic petrographic analysis, gas adsorption, and X-ray diffraction measurements. Energy & Fuels 33, 8055-8064.

Zhang, H., Zhu, Y., Ma, N., Zhou, C., Dang, Y., Shao, F., Jiao, J., Li, L., Wang, H., Li, M., 2019. Combined technology of PCP and nano-CT quantitative characterization of dense oil reservoir pore throat characteristics. Arabian Journal of Geosciences 12, 534.

Zhang, J., Li, X., Zhang, G., Zou, X., Wang, F., Tang, Y., 2019. Microstructural investigation of different nanopore types in marine-continental transitional shales: Examples from the Longtan formation in Southern Sichuan Basin, south China. Marine and Petroleum Geology 110, 912-927.

Zhang, S., Liu, H., Liu, Y., Wang, Y., Wang, M., Bao, Y., Hu, Q., Li, Z., Zhang, S., Yao, S., Wang, Y., Xiong, W., Liu, P., Fang, Z., 2020. Main controls and geological sweet spot

types in Paleogene shale oil rich areas of the Jiyang Depression, Bohai Bay basin, China. Marine and Petroleum Geology 111, 576-587.

Zhang, Y., He, Z., Lu, S., Jiang, S., Xiao, D., Long, S., Gao, B., Du, W., Zhao, J., Chen, G., Li, Y., 2020. Characteristics of microorganisms and origin of organic matter in Wufeng Formation and Longmaxi Formation in Sichuan Basin, South China. Marine and Petroleum Geology 111, 363-374.

Zhou, H., Luo, F., Luo, Z., Li, D., Liu, C., Li, X., 2019. Programming conventional electron microscopes for solving ultrahigh-resolution structures of small and macro-molecules. Analytical Chemistry 91, 10996-11003.

IMAGING: XRAY CT



Qiu, L., Zhou, G., Zhang, W., Han, W., 2019. Simulations on the micro-seepage rules of gas and water based on micro-CT/CFD and the related contrastive analysis. Arabian Journal of Geosciences 12, 549.

Roslin, A., Pokrajac, D., Zhou, Y., 2019. Permeability upscaling using the cubic law based on the analysis of multiresolution micro computed tomography images of intermediate rank coal. Energy & Fuels 33, 8215-8221.


LIQUID CHROMATOGRAPHY/LC-MS/SFC

Ali, I., Suhail, M., Aboul-Enein, H.Y., 2019. Advances in chiral multidimensional liquid chromatography. TrAC Trends in Analytical Chemistry 120, 115634.

Baca, M., Desmet, G., Ottevaere, H., De Malsche, W., 2019. Achieving a peak capacity of 1800 using an 8 m long pillar array column. Analytical Chemistry 91, 10932-10936.

Chen, Y., Montero, L., Schmitz, O.J., 2019. Advance in on-line two-dimensional liquid chromatography modulation technology. TrAC Trends in Analytical Chemistry 120, 115647.

Kantz, E.D., Tiwari, S., Watrous, J.D., Cheng, S., Jain, M., 2019. Deep neural networks for classification of LC-MS spectral peaks. Analytical Chemistry 91, 12407-12413.

Montero, L., Herrero, M., 2019. Two-dimensional liquid chromatography approaches in Foodomics – A review. Analytica Chimica Acta 1083, 1-18.

Seidl, C., Bell, D.S., Stoll, D.R., 2019. A study of the re-equilibration of hydrophilic interaction columns with a focus on viability for use in two-dimensional liquid chromatography. Journal of Chromatography A 1604, 460484.

Si, W., Liu, Y., Xiao, Y., Guo, Z., Jin, G., Yan, J., Shen, A., Zhou, H., Yang, F., Liang, X., 2020. An offline two-dimensional supercritical fluid chromatography × reversed phase liquid chromatography tandem quadrupole time-of-flight mass spectrometry system for comprehensive gangliosides profiling in swine brain extract. Talanta 208, 120366.

Song, C., Gao, D., Li, S., Liu, L., Chen, X., Jiang, Y., 2019. Determination and quantification of fatty acid C=C isomers by epoxidation reaction and liquid chromatography-mass spectrometry. Analytica Chimica Acta 1086, 82-89.

West, C., 2019. Recent trends in chiral supercritical fluid chromatography. TrAC Trends in Analytical Chemistry 120, 115648.

Zeng, Z., Zhou, W., Hu, N., Zou, L., Bai, B., Wang, H., 2019. Comparison of using two different labeling reagents for rapid analysis of triterpenic acids by pre-column derivatization with RP-HPLC-FLD and application to plant samples. Analytical Methods 11, 4354-4361.

MASS SPECTROSCOPY/ICR-FTMS/ORBITRAP

Editorial, 2019. The path of biomolecular mass spectrometry into open research. Nature Communications 10, 4029.

Gao, Y., Wang, W., He, C., Fang, Z., Zhang, Y., Shi, Q., 2019. Fractionation and molecular characterization of natural organic matter (NOM) by solid-phase extraction followed by FT-ICR MS and ion mobility MS. Analytical and Bioanalytical Chemistry 411, 6343-6352.

Guillemant, J., Albrieux, F., Lacoue-Nègre, M., Pereira de Oliveira, L., Joly, J.-F., Duponchel, L., 2019. Chemometric exploration of APPI(+)-FT-ICR MS data sets for a comprehensive study of aromatic sulfur compounds in gas oils. Analytical Chemistry 91, 11785-11793.

Jaggi, A., Radović, J.R., Snowdon, L.R., Larter, S.R., Oldenburg, T.B.P., 2019. Composition of the dissolved organic matter produced during in situ burning of spilled oil. Organic Geochemistry 138, 103926.

Lee, M.-H., Lee, Y.K., Derrien, M., Choi, K., Shin, K.H., Jang, K.-S., Hur, J., 2019. Evaluating the contributions of different organic matter sources to urban river water during a storm event via optical indices and molecular composition. Water Research 165, 115006.

Makarov, A., 2019. Orbitrap journey: taming the ion rings. Nature Communications 10, 3743.

Ye, Q., Zhang, Z.-T., Liu, Y.-C., Wang, Y.-H., Zhang, S., He, C., Shi, Q., Zeng, H.-X., Wang, J.-J., 2019. Spectroscopic and molecular-level characteristics of dissolved organic matter in a highly polluted urban river in South China. ACS Earth and Space Chemistry 3, 2033-2044.

Yu, Z., Liu, X., Chen, C., Liao, H., Chen, Z., Zhou, S., 2019. Molecular insights into the transformation of dissolved organic matter during hyperthermophilic composting using ESI FT-ICR MS. Bioresource Technology 292, 122007.

Yuan, R., Shen, Y., Zhu, N., Yin, C., Yuan, H., Dai, X., 2019. Pretreatment-promoted sludge fermentation liquor improves biological nitrogen removal: molecular insight into the role of dissolved organic matter. Bioresource Technology 293, 122082.

Zhang, Y., Horsfield, B., Hou, D., Noah, M., Yang, S., 2019. Impact of hydrothermal activity on organic matter quantity and quality during deposition in the Permian Dalong Formation, Southern China. Marine and Petroleum Geology 110, 901-911.

MASS SPECTROSCOPY/OTHER

De Carolis, E., Soldini, S., La Rosa, M., Nucci, F., Posteraro, B., Sanguinetti, M., 2019. Biof–hilo assay: A new MALDI–TOF mass spectrometry based method for discriminating between high- and low-biofilm-producing Candida parapsilosis isolates. Frontiers in Microbiology 10, 2046. doi: 2010.3389/fmicb.2019.02046.


Kirk, A.T., Bohnhorst, A., Raddatz, C.-R., Allers, M., Zimmermann, S., 2019. Ultra-high-resolution ion mobility spectrometry—current instrumentation, limitations, and future developments. Analytical and Bioanalytical Chemistry 411, 6229-6246.

Kulyk, D.S., Swiner, D.J., Sahraeian, T., Badu-Tawiah, A.K., 2019. Direct mass spectrometry analysis of complex mixtures by nanoelectrospray with simultaneous atmospheric pressure chemical ionization and electrophoretic separation capabilities. Analytical Chemistry 91, 11562-11568.

Löhr, K., Borovinskaya, O., Tourniaire, G., Panne, U., Jakubowski, N., 2019. Arraying of single cells for quantitative high throughput laser ablation ICP-TOF-MS. Analytical Chemistry 91, 11520-11528.

Mallah, K., Quanico, J., Raffo-Romero, A., Cardon, T., Aboulouard, S., Devos, D., Kobeissy, F., Zibara, K., Salzet, M., Fournier, I., 2019. Matrix-assisted laser desorption/ionization-mass spectrometry imaging of lipids in experimental model of traumatic brain injury detecting acylcarnitines as injury related markers. Analytical Chemistry 91, 11879-11887.

Mann, M., 2019. The ever expanding scope of electrospray mass spectrometry—a 30 year journey. Nature Communications 10, 3744.

Nguyen, S.N., Kyle, J.E., Dautel, S.E., Sontag, R., Luders, T., Corley, R., Ansong, C., Carson, J., Laskin, J., 2019. Lipid coverage in nanospray desorption electrospray ionization mass spectrometry imaging of mouse lung tissues. Analytical Chemistry 91, 11629-11635.


Qi, Y., Volmer, D.A., 2019. Chemical diversity of lignin degradation products revealed by matrix-optimized MALDI mass spectrometry. Analytical and Bioanalytical Chemistry 411, 6031-6037.

Ropartz, D., Fanuel, M., Ujma, J., Palmer, M., Giles, K., Rogniaux, H., 2019. Structure determination of large isomeric oligosaccharides of natural origin through multipass and multistage cyclic traveling-wave ion mobility mass spectrometry. Analytical Chemistry 91, 12030-12037.

METABOLOMICS/LIPIDOMICS

Caesar, L.K., Nogo, S., Naphen, C.N., Cech, N.B., 2019. Simplify: A mass spectrometry metabolomics approach to identify additives and synergists from complex mixtures. Analytical Chemistry 91, 11297-11305.

Freiburghaus, K., Largiadèr, C.R., Stettler, C., Fiedler, G.M., Bally, L., Bovet, C., 2019. Metabolomics by UHPLC–MS: benefits provided by complementary use of Q-TOF and QQQ for pathway profiling. Metabolomics 15, 120.

Kuo, T.-H., Chung, H.-H., Chang, H.-Y., Lin, C.-W., Wang, M.-Y., Shen, T.-L., Hsu, C.-C., 2019. Deep lipidomics and molecular imaging of unsaturated lipid isomers: A universal strategy initiated by mCPBA epoxidation. Analytical Chemistry 91, 11905-11915.

Sarma, S.N., Kimpe, L.E., Doyon, V.C., Blais, J.M., Chan, H.M., 2019. A metabolomics study on effects of polyaromatic compounds in oil sand extracts on the respiratory, hepatic and nervous systems using three human cell lines. Environmental Research 178, 108680.


Wu, Q., Xu, Y., Ji, H., Wang, Y., Zhang, Z., Lu, H., 2019. Enhancing coverage in LC–MS-based untargeted metabolomics by a new sample preparation procedure using mixed-mode solid-phase extraction and two derivatizations. Analytical and Bioanalytical Chemistry 411, 6189-6202.

Xia, F., Feng, R., Xu, F.-G., Su, H., He, C., Hu, Y.-J., Wan, J.-B., 2019. Quantification of phospholipid fatty acids by chemical isotope labeling coupled with atmospheric pressure gas chromatography quadrupole- time-of-flight mass spectrometry (APGC/Q-TOF MS). Analytica Chimica Acta 1082, 86-97.

Yin, Y., Wang, R., Cai, Y., Wang, Z., Zhu, Z.-J., 2019. DecoMetDIA: Deconvolution of multiplexed MS/MS spectra for metabolite identification in SWATH-MS-based untargeted metabolomics. Analytical Chemistry 91, 11897-11904.

Zhao, S., Li, H., Han, W., Chan, W., Li, L., 2019. Metabolomic coverage of chemical-group-submetabolome analysis: Group classification and four-channel chemical isotope labeling LC-MS. Analytical Chemistry 91, 12108-12115.

PUPPYOMICS

Hecht, E.E., Smaers, J.B., Dunn, W.J., Kent, M., Preuss, T.M., Gutman, D.A., 2019. Significant neuroanatomical variation among domestic dog breeds. The Journal of Neuroscience 39, 7748-7758.

Maugeri, A., Medina-Inojosa, J.R., Kunzova, S., Barchitta, M., Agodi, A., Vinciguerra, M., Lopez-Jimenez, F., 2019. Dog ownership and cardiovascular health: Results from the Kardiovize 2030 Project. Mayo Clinic Proceedings: Innovations, Quality & Outcomes 3, 268-275. O'Keefe, J.H., O'Keefe, E.L., Lavie, C.J., 2019. The human-canine bond: A heart's best friend. Mayo Clinic Proceedings: Innovations, Quality & Outcomes 3, 249-250.

Archaeological/Art Organic Chemistry

Barberis, E., Manfredi, M., Marengo, E., Zilberstein, G., Zilberstein, S., Kossolapov, A., Righetti, P.G., 2019. Leonardo's Donna Nuda unveiled. Journal of Proteomics 207, 103450.

Blanco-Zubiaguirre, L., Olivares, M., Castro, K., Carrero, J.A., García-Benito, C., García-Serrano, J.Á., Pérez-Pérez, J., Pérez-Arantegui, J., 2019. Wine markers in archeological potteries: detection by GC-MS at ultratrace levels. Analytical and Bioanalytical Chemistry 411, 6711-6722.

Davis, L.G., Madsen, D.B., Becerra-Valdivia, L., Higham, T., Sisson, D.A., Skinner, S.M., Stueber, D., Nyers, A.J., Keen-Zebert, A., Neudorf, C., Cheyney, M., Izuho, M., Iizuka, F., Burns, S.R., Epps, C.W., Willis, S.C., Buvit, I., 2019. Late Upper Paleolithic occupation at Cooper’s Ferry, Idaho, USA, ~16,000 years ago. Science 365, 891-897.

Jambrina-Enríquez, M., Herrera-Herrera, A.V., Rodríguez de Vera, C., Leierer, L., Connolly, R., Mallol, C., 2019. n-Alkyl nitriles and compound-specific carbon isotope analysis of lipid combustion residues from Neanderthal and experimental hearths: Identifying sources of organic compounds and combustion temperatures. Quaternary Science Reviews 222, 105899.

Łaciak, D., Borowski, M.P., Łydżba-Kopczyńska, B., Baron, J., Furmanek, M., 2019. Archaeometric characterisation and origin of black coatings on prehistoric pottery. Geochemistry 79, 453-466.

Lejay, M., Alexis, M.A., Quénéa, K., Anquetil, C., Bon, F., 2019. The organic signature of an experimental meat-cooking fireplace: The identification of nitrogen compounds and their archaeological potential. Organic Geochemistry 138, 103923.

Nagai, Y., Sato, F., Okamoto, S., Kamiya, Y., Honda, T., 2019. Pyrolysis behavior of Asian lacquer film in the presence of carbon nanotubes with potential application as a new sampling method. Journal of Analytical and Applied Pyrolysis 142, 104637.

Schmidt, P., Blessing, M., Rageot, M., Iovita, R., Pfleging, J., Nickel, K.G., Righetti, L., Tennie, C., 2019. Birch tar production does not prove Neanderthal behavioral complexity. Proceedings of the National Academy of Sciences 116, 17707-17711.

Schuetz, R., Maragh, J.M., Weaver, J.C., Rabin, I., Masic, A., 2019. The Temple Scroll: Reconstructing an ancient manufacturing practice. Science Advances 5, eaaw7494.

Sponheimer, M., Ryder, C.M., Fewlass, H., Smith, E.K., Pestle, W.J., Talamo, S., 2019. Saving old bones: a non-destructive method for bone collagen prescreening. Scientific Reports 9, 13928.

Stephens, L., Fuller, D., Boivin, N., Rick, T., Gauthier, N., Kay, A., Marwick, B., Geralda, C., Armstrong, D., Barton, C.M., Denham, T., Douglass, K., Driver, J., Janz, L., Roberts, P., Rogers, J.D., Thakar, H., Altaweel, M., Johnson, A.L., Sampietro Vattuone, M.M., Aldenderfer, M., Archila, S., Artioli, G., Bale, M.T., Beach, T., Borrell, F., Braje, T., Buckland, P.I., Jiménez Cano, N.G., Capriles, J.M., Diez Castillo, A., Çilingiroğlu, Ç., Negus Cleary, M., Conolly, J., Coutros, P.R., Covey, R.A., Cremaschi, M., Crowther, A., Der, L., di Lernia, S., Doershuk, J.F., Doolittle, W.E., Edwards, K.J., Erlandson, J.M., Evans, D., Fairbairn, A., Faulkner, P., Feinman, G., Fernandes, R., Fitzpatrick, S.M., Fyfe, R., Garcea, E., Goldstein, S., Goodman, R.C., Dalpoim Guedes, J., Herrmann, J., Hiscock, P., Hommel, P., Horsburgh, K.A., Hritz, C., Ives, J.W., Junno, A., Kahn, J.G., Kaufman, B., Kearns, C., Kidder, T.R., Lanoë, F., Lawrence, D., Lee, G.-A., Levin, M.J., Lindskoug, H.B., López-Sáez, J.A., Macrae, S., Marchant, R., Marston, J.M., McClure, S., McCoy, M.D., Miller, A.V., Morrison, M., Motuzaite Matuzeviciute, G., Müller, J., Nayak, A., Noerwidi, S., Peres, T.M., Peterson, C.E., Proctor, L., Randall, A.R., Renette, S., Robbins Schug, G., Ryzewski, K., Saini, R., Scheinsohn, V., Schmidt, P., Sebillaud, P., Seitsonen, O., Simpson, I.A., Sołtysiak, A., Speakman, R.J., Spengler, R.N., Steffen, M.L., Storozum, M.J., Strickland, K.M., Thompson, J., Thurston, T.L., Ulm, S., Ustunkaya, M.C., Welker, M.H., West, C., Williams, P.R., Wright, D.K., Wright, N., Zahir, M., Zerboni, A., Beaudoin, E., Munevar Garcia, S., Powell, J., Thornton, A., Kaplan, J.O., Gaillard, M.-J., Klein Goldewijk, K., Ellis, E., 2019. Archaeological assessment reveals Earth’s early transformation through land use. Science 365, 897-902.

Wade, L., 2019. Ancient site in Idaho implies first Americans came by sea. Science 365, 848-849.

Biochemistry

Alvarez, H.M., Herrero, O.M., Silva, R.A., Hernández, M.A., Lanfranconi, M.P., Villalba, M.S., 2019. Insights into the metabolism of oleaginous Rhodococcus spp. Applied and Environmental Microbiology 85, e00498-00419.

Cotruvo, J.A., 2019. The chemistry of lanthanides in biology: Recent discoveries, emerging principles, and technological applications. ACS Central Science 5, 1496-1506.

Levitan, O., Chen, M., Kuang, X., Cheong, K.Y., Jiang, J., Banal, M., Nambiar, N., Gorbunov, M.Y., Ludtke, S.J., Falkowski, P.G., Dai, W., 2019. Structural and functional analyses of photosystem II in the marine diatom Phaeodactylum tricornutum. Proceedings of the National Academy of Sciences 116, 17316-17322.

Li, C., Reimers, C.E., Alleau, Y., 2019. Inducing the attachment of cable bacteria on oxidizing electrodes. Biogeosciences Discussions 2019, 1-20.

Lovley, D.R., Walker, D.J.F., 2019. Geobacter protein nanowires. Frontiers in Microbiology 10, 2078. doi: 2010.3389/fmicb.2019.02078.

Mand, T.D., Metcalf, W.W., 2019. Energy conservation and hydrogenase function in methanogenic archaea, in particular the genus Methanosarcina. Microbiology and Molecular Biology Reviews 83, e00020-00019.

Martins, C., Rodrigo, A.P., Cabrita, L., Henriques, P., Parola, A.J., Costa, P.M., 2019. The complexity of porphyrin-like pigments in a marine annelid sheds new light on haem metabolism in aquatic invertebrates. Scientific Reports 9, 12930.

Biodegradation

Antipenko, V.R., Bakanova, O.S., Filatov, D.A., 2019. Change in the hydrocarbon composition of Ashal’chinskoe crude oil via biodegradation by indigenous soil microflora under laboratory conditions. Petroleum Chemistry 59, 961-967.

Cheng, L., Shi, S.-b., Yang, L., Zhang, Y., Dolfing, J., Sun, Y.-g., Liu, L.-y., Li, Q., Tu, B., Dai, L.-r., Shi, Q., Zhang, H., 2019. Preferential degradation of long-chain alkyl substituted hydrocarbons in heavy oil under methanogenic conditions. Organic Geochemistry 138, 103927.

Huang, H., Li, Z., Wen, Z., Han, D., Pan, R., 2019. Biodegradation influence on alkylphenanthrenes in oils from Bongor Basin, SW Chad. Scientific Reports 9, 12960.

Krolicka, A., Boccadoro, C., Nilsen, M.M., Demir-Hilton, E., Birch, J., Preston, C., Scholin, C., Baussant, T., 2019. Identification of microbial key-indicators of oil contamination at sea through tracking of oil biotransformation: An Arctic field and laboratory study. Science of The Total Environment 696, 133715.

Pereira, E., Napp, A.P., Allebrandt, S., Barbosa, R., Reuwsaat, J., Lopes, W., Kmetzsch, L., Staats, C.C., Schrank, A., Dallegrave, A., Peralba, M.d.C.R., Passaglia, L.M.P., Bento, F.M., Vainstein, M.H., 2019. Biodegradation of aliphatic and polycyclic aromatic hydrocarbons in seawater by autochthonous microorganisms. International Biodeterioration & Biodegradation 145, 104789.

Poddar, K., Sarkar, D., Sarkar, A., 2019. Construction of potential bacterial consortia for efficient hydrocarbon degradation. International Biodeterioration & Biodegradation 144, 104770.

Shahebrahimi, Y., Fazlali, A., Motamedi, H., Kord, S., 2019. Experimental insight into the effects of two asphaltene-degrading bacterial consortia on crude oil properties. Energy & Fuels 33, 8007-8013.

BIODEGRADATION PATHWAYS/GENOMICS

Gao, C., Zhang, Y., Wang, X., Lin, J., Li, Y., 2019. Geochemical characteristics and geological significance of the anaerobic biodegradation products of crude oil. Energy & Fuels 33, 8588-8595.

Sazykin, I., Makarenko, M., Khmelevtsova, L., Seliverstova, E., Rakin, A., Sazykina, M., 2019. Cyclohexane, naphthalene, and diesel fuel increase oxidative stress, CYP153, sodA, and recA gene expression in Rhodococcus erythropolis. MicrobiologyOpen 8, e00855.

Biofuels/Biomass/Bioengineering

Glasser, W.G., 2019. About making lignin great again—some lessons from the past. Frontiers in Chemistry 7, 565. doi: 510.3389/fchem.2019.00565.

Khoo, C.G., Dasan, Y.K., Lam, M.K., Lee, K.T., 2019. Algae biorefinery: Review on a broad spectrum of downstream processes and products. Bioresource Technology 292, 121964.

Liu, K., Li, S., 2020. Biosynthesis of fatty acid-derived hydrocarbons: perspectives on enzymology and enzyme engineering. Current Opinion in Biotechnology 62, 7-14.

Luan, G., Zhang, S., Lu, X., 2020. Engineering cyanobacteria chassis cells toward more efficient photosynthesis. Current Opinion in Biotechnology 62, 1-6.

Mihreteab, M., Stubblefield, B.A., Gilbert, E.S., 2019. Microbial bioconversion of thermally depolymerized polypropylene by Yarrowia lipolytica for fatty acid production. Applied Microbiology and Biotechnology 103, 7729-7740.

Pourkarimi, S., Hallajisani, A., Alizadehdakhel, A., Nouralishahi, A., 2019. Biofuel production through micro- and macroalgae pyrolysis – A review of pyrolysis methods and process parameters. Journal of Analytical and Applied Pyrolysis 142, 104599.


Biogeochemistry

Ducklow, H., Plank, T., 2019. Volcano-stimulated marine photosynthesis. Science 365, 978-979.

Durham, B.P., Boysen, A.K., Carlson, L.T., Groussman, R.D., Heal, K.R., Cain, K.R., Morales, R.L., Coesel, S.N., Morris, R.M., Ingalls, A.E., Armbrust, E.V., 2019. Sulfonate-based

networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nature Microbiology 4, 1706-1715.

Houghton, J.L., Foustoukos, D.I., Fike, D.A., 2019. The effect of O2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila. Geobiology 17, 564-576.

Khatun, S., Iwata, T., Kojima, H., Fukui, M., Aoki, T., Mochizuki, S., Naito, A., Kobayashi, A., Uzawa, R., 2019. Aerobic methane production by planktonic microbes in lakes. Science of The Total Environment 696, 133916.

Kohl, L., Koskinen, M., Rissanen, K., Haikarainen, I., Polvinen, T., Hellén, H., Pihlatie, M., 2019. Technical note: Interferences of volatile organic compounds (VOCs) on methane concentration measurements. Biogeosciences 16, 3319-3332.

Liu, S., Liu, H., Wang, Z., Cui, Y., Chen, R., Peng, Z., Yuan, S., Shi, L., 2019. Benzene promotes microbial Fe(III) reduction and flavins secretion. Geochimica et Cosmochimica Acta 264, 92-104.

Lollar, G.S., Warr, O., Telling, J., Osburn, M.R., Sherwood Lollar, B., 2019. ‘Follow the water’: Hydrogeochemical constraints on microbial investigations 2.4 km below surface at the Kidd Creek Deep Fluid and Deep Life Observatory. Geomicrobiology Journal 36, 859-872.

Pastor, A., Freixa, A., Skovsholt, L.J., Wu, N., Romaní, A.M., Riis, T., 2019. Microbial organic matter utilization in high-Arctic streams: Key enzymatic controls. Microbial Ecology 78, 539-554.

Praetzel, L.S.E., Plenter, N., Schilling, S., Schmiedeskamp, M., Broll, G., Knorr, K.-H., 2019. Organic matter and sediment properties determine in-lake variability of sediment CO2 and CH4 production and emissions of a small and shallow lake. Biogeosciences Discussions 2019, 1-39.

Rey-Sanchez, C., Bohrer, G., Slater, J.u., Li, Y.-F., Grau-Andrés, R., Hao, Y., Rich, V.I., Davies, G.M., 2019. The ratio of methanogens to methanotrophs and water-level dynamics drive methane transfer velocity in a temperate kettle-hole peat bog. Biogeosciences 16, 3207-3231.

Wilson, S.T., Hawco, N.J., Armbrust, E.V., Barone, B., Björkman, K.M., Boysen, A.K., Burgos, M., Burrell, T.J., Casey, J.R., DeLong, E.F., Dugenne, M., Dutkiewicz, S., Dyhrman, S.T., Ferrón, S., Follows, M.J., Foreman, R.K., Funkey, C.P., Harke, M.J., Henke, B.A., Hill, C.N., Hynes, A.M., Ingalls, A.E., Jahn, O., Kelly, R.L., Knapp, A.N., Letelier, R.M., Ribalet, F., Shimabukuro, E.M., Tabata, R.K.S., Turk-Kubo, K.A., White, A.E., Zehr, J.P., John, S., Karl, D.M., 2019. Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean. Science 365, 1040-1044.

Zhang, K., He, D., Cui, X., Fan, D., Xiao, S., Sun, Y., 2019. Impact of anthropogenic organic matter on the distribution patterns of sediment microbial community from the Yangtze River, China. Geomicrobiology Journal 36, 881-893.

Zhao, Y., Liu, P., Rui, J., Cheng, L., Wang, Q., Liu, X., Yuan, Q., 2020. Dark carbon fixation and chemolithotrophic microbial community in surface sediments of the cascade reservoirs, Southwest China. Science of The Total Environment 698, 134316.

Zhao, Z., Gonsior, M., Schmitt-Kopplin, P., Zhan, Y., Zhang, R., Jiao, N., Chen, F., 2019. Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity. The ISME Journal 13, 2551-2565.

BIOFILM/MICROBIAL INDUCED CORROSION


Ibarra, Y., Sanon, S., 2019. A freshwater analog for the production of Epiphyton-like microfossils. Geobiology 17, 510-522.

Liduino, V.S., Payão Filho, J.C., Cravo-Laureau, C., Lutterbach, M.T., Camporese Sérvulo, E.F., 2019. Comparison of flow regimes on biocorrosion of steel pipe weldments: Fluid characterization and pitting analysis. International Biodeterioration & Biodegradation 144, 104750.

Ramírez, G.A., Garber, A.I., Lecoeuvre, A., D’Angelo, T., Wheat, C.G., Orcutt, B.N., 2019. Ecology of subseafloor crustal biofilms. Frontiers in Microbiology 10, 1983. doi: 1910.3389/fmicb.2019.01983.

MICROBIAL MEDIATION OF MINERAL FORMATION/DEGRADATION


Li, M.-L., Liu, S.-A., Xue, C.-J., Li, D., 2019. Zinc, cadmium and sulfur isotope fractionation in a supergiant MVT deposit with bacteria. Geochimica et Cosmochimica Acta 265, 1-18.


Zhang, J., Xie, L., Huang, X., Liang, Z., Liu, B., Han, N., Xing, F., Deng, X., 2019. Enhanced calcite precipitation for crack healing by bacteria isolated under low-nitrogen conditions. Applied Microbiology and Biotechnology 103, 7971-7982.

Carbon Cycle

Ding, J., Wang, T., Piao, S., Smith, P., Zhang, G., Yan, Z., Ren, S., Liu, D., Wang, S., Chen, S., Dai, F., He, J., Li, Y., Liu, Y., Mao, J., Arain, A., Tian, H., Shi, X., Yang, Y., Zeng, N., Zhao, L., 2019. The paleoclimatic footprint in the soil carbon stock of the Tibetan permafrost region. Nature Communications 10, 4195.

Ortega, A., Geraldi, N.R., Alam, I., Kamau, A.A., Acinas, S.G., Logares, R., Gasol, J.M., Massana, R., Krause-Jensen, D., Duarte, C.M., 2019. Important contribution of macroalgae to oceanic carbon sequestration. Nature Geoscience 12, 748-754.

Pugh, T.A.M., Arneth, A., Kautz, M., Poulter, B., Smith, B., 2019. Important role of forest disturbances in the global biomass turnover and carbon sinks. Nature Geoscience 12, 730-735.

St. Pierre, K.A., St. Louis, V.L., Schiff, S.L., Lehnherr, I., Dainard, P.G., Gardner, A.S., Aukes, P.J.K., Sharp, M.J., 2019. Proglacial freshwaters are significant and previously unrecognized sinks of atmospheric CO2. Proceedings of the National Academy of Sciences 116, 17690-17695.

Climate Change


Hameau, A., Frölicher, T.L., Mignot, J., Joos, F., 2019. Is deoxygenation detectable before warming in the thermocline? Biogeosciences Discussions 2019, 1-32.

Labbé, T., Pfister, C., Brönnimann, S., Rousseau, D., Franke, J., Bois, B., 2019. The longest homogeneous series of grape harvest dates, Beaune 1354–2018, and its significance for the understanding of past and present climate. Climate of the Past 15, 1485-1501.

Carbon Sequestration

Abba, M.K., Abbas, A.J., Nasr, G.G., Al-Otaibi, A., Burby, M., Saidu, B., Suleiman, S.M., 2019. Solubility trapping as a potential secondary mechanism for CO2 sequestration during enhanced gas recovery by CO2 injection in conventional natural gas reservoirs: An experimental approach. Journal of Natural Gas Science and Engineering 71, 103002.

Amonette, J.E., Zhong, L., Darrah, T.H., Grove, B.S., Cole, D.R., 2019. Noble and major gases released from rock core materials as intrinsic tracers for detecting carbon dioxide leakage – Laboratory evaluation. International Journal of Greenhouse Gas Control 89, 76-88.

Gros, J., Schmidt, M., Dale, A.W., Linke, P., Vielstädte, L., Bigalke, N., Haeckel, M., Wallmann, K., Sommer, S., 2019. Simulating and quantifying multiple natural subsea CO2 seeps at Panarea Island (Aeolian Islands, Italy) as a proxy for potential leakage from subseabed carbon storage sites. Environmental Science & Technology 53, 10258-10268.

Huang, L., Ning, Z., Wang, Q., Qi, R., Cheng, Z., Wu, X., Zhang, W., Qin, H., 2019. Kerogen deformation upon CO2/CH4 competitive sorption: Implications for CO2 sequestration and enhanced CH4 recovery. Journal of Petroleum Science and Engineering 183, 106460.

Coal/Lignite/Peat Geochemistry

Bechtel, A., Widera, M., Woszczyk, M., 2019. Composition of lipids from the First Lusatian lignite seam of the Konin Basin (Poland): Relationships with vegetation, climate and carbon cycling during the mid-Miocene Climatic Optimum. Organic Geochemistry 138, 103908.

Eble, C.F., Greb, S.F., Williams, D.A., Hower, J.C., O’Keefe, J.M.K., 2019. Palynology, organic petrology and geochemistry of the Bell coal bed in Western Kentucky, Eastern Interior (Illinois) Basin, USA. International Journal of Coal Geology 213, 103264.



Yan, X., Dai, S., Graham, I.T., French, D., Hower, J.C., 2019. Mineralogy and geochemistry of the Palaeogene low-rank coal from the Baise Coalfield, Guangxi Province, China. International Journal of Coal Geology 214, 103282.

Zamansani, N., Rajabzadeh, M.A., Littke, R., Zieger, L., Baniasad, A., 2019. Organic petrology and geochemistry of Triassic and Jurassic coals of the Tabas Basin, Northeastern/Central Iran. International Journal of Coal Science & Technology 6, 354-371.

COAL BED METHANE

Chen, B., Stuart, F.M., Xu, S., Gyӧre, D., Liu, C., 2019. Evolution of coal-bed methane in Southeast Qinshui Basin, China: Insights from stable and noble gas isotopes. Chemical Geology 529, 119298.

Guo, Q., Fink, R., Littke, R., Zieger, L., 2019. Methane sorption behaviour of coals altered by igneous intrusion, South Sumatra Basin. International Journal of Coal Geology 214, 103250.

Li, Y., Yang, Z., Li, X., 2019. Molecular simulation study on the effect of coal rank and moisture on CO2/CH4 competitive adsorption. Energy & Fuels 33, 9087-9098.

Lu, G., Wei, C., Wang, J., Zhang, J., Quan, F., Tamehe, L.S., 2019. Variation of surface free energy in the process of methane adsorption in the nanopores of tectonically deformed coals: A case study of middle-rank tectonically deformed coals in the Huaibei coalfield. Energy & Fuels 33, 7155-7165.

Lv, D., Lu, C., Wen, Z., Song, H., Yin, S., 2019. Coal-bed methane geology of the No. 2 coal seam in Fengfeng Coalfield, North China. Arabian Journal of Geosciences 12, 529.

Xia, D., Zhang, H., Su, X., Chen, H., Li, D., 2019. Adsorption characteristics and mechanisms of coal–microorganisms in the process of biogenic methane production from highly volatile bituminous coal. Energy & Fuels 33, 8702-8710.

Zhang, J., Wei, C., Vandeginste, V., Ju, W., Qin, Z., Quan, F., Soh Tamehe, L., 2019. Experimental simulation study on water migration and methane depressurizing desorption based on nuclear magnetic resonance technology: A case study of middle-rank coals from the Panguan Syncline in the western Guizhou Region. Energy & Fuels 33, 7993-8006.

Cosmochemistry/Planetary Geochemistry

Blázquez, S., González, D., García-Sáez, A., Antiñolo, M., Bergeat, A., Caralp, F., Mereau, R., Canosa, A., Ballesteros, B., Albaladejo, J., Jiménez, E., 2019. Experimental and theoretical investigation on the OH + CH3C(O)CH3 reaction at interstellar temperatures (T = 11.7–64.4 K). ACS Earth and Space Chemistry 3, 1873-1883.

Brenan, J.M., Mungall, J.E., Bennett, N.R., 2019. Abundance of highly siderophile elements in lunar basalts controlled by iron sulfide melt. Nature Geoscience 12, 701-706.

Da Pieve, F., 2019. Physicochemical properties and complexity of amino acids beyond our biosphere: Analysis of the isoleucine group from meteorites. ACS Earth and Space Chemistry 3, 1955-1965.

Davies, M.B., Kokaia, G., 2019. Stellar encounters with giant molecular clouds. Monthly Notices of the Royal Astronomical Society 489, 5165–5180.

Falcinelli, S., Vecchiocattivi, F., Pirani, F., Alagia, M., Schio, L., Richter, R., Stranges, S., Zhaunerchyk, V., Balucani, N., Rosi, M., 2019. The fragmentation dynamics of simple organic molecules of astrochemical interest interacting with VUV photons. ACS Earth and Space Chemistry 3, 1862-1872.

Giese, C.-C., Ten Kate, I.L., Plümper, O., King, H.E., Lenting, C., Liu, Y., Tielens, A.G.G.M., 2019. The evolution of polycyclic aromatic hydrocarbons under simulated inner asteroid conditions. Meteoritics & Planetary Science 54, 1930-1950.

Gleißner, P., 2019. The Earth–Moon late-accretion conundrum. Nature Geoscience 12, 683-684.

Lee, M.R., Cohen, B.E., King, A.J., Greenwood, R.C., 2019. The diversity of CM carbonaceous chondrite parent bodies explored using Lewis Cliff 85311. Geochimica et Cosmochimica Acta 264, 224-244.


Mitri, G., Lunine, J.I., Mastrogiuseppe, M., Poggiali, V., 2019. Possible explosion crater origin of small lake basins with raised rims on Titan. Nature Geoscience 12, 791-796.

Morse, A.D., Chan, Q.H.S., 2019. Observations of cometary organics: A post Rosetta review. ACS Earth and Space Chemistry 3, 1773-1791.

Remusat, L., Bonnet, J.-Y., Bernard, S., Buch, A., Quirico, E., 2019. Molecular and isotopic behavior of insoluble organic matter of the Orgueil meteorite upon heating. Geochimica et Cosmochimica Acta 263, 235-247.

Rubin, M., Bekaert, D.V., Broadley, M.W., Drozdovskaya, M.N., Wampfler, S.F., 2019. Volatile species in comet 67P/Churyumov-Gerasimenko: Investigating the link from the ISM to the terrestrial planets. ACS Earth and Space Chemistry 3, 1792-1811.

Schmidt, F., Swiderek, P., Bredehöft, J.H., 2019. Formation of formic acid, formaldehyde, and carbon dioxide by electron-induced chemistry in ices of water and carbon monoxide. ACS Earth and Space Chemistry 3, 1974-1986.

Schuhmann, M., Altwegg, K., Balsiger, H., Berthelier, J.-J., De Keyser, J., Fuselier, S.A., Gasc, S., Gombosi, T.I., Hänni, N., Rubin, M., Sémon, T., Tzou, C.-Y., Wampfler, S.F., 2019. CHO-bearing molecules in comet 67P/Churyumov-Gerasimenko. ACS Earth and Space Chemistry 3, 1854-1861.

Soderlund, K.M., 2019. Ocean dynamics of outer solar system satellites. Geophysical Research Letters 46, 8700-8710.

Souza-Corrêa, J.A., da Costa, C.A.P., da Silveira, E.F., 2019. Compaction and destruction cross-sections for α-glycine from radiolysis process via 1.0 keV electron beam as a function of temperature. Astrobiology 19, 1123-1138.

Thiemens, M.M., Sprung, P., Fonseca, R.O.C., Leitzke, F.P., Münker, C., 2019. Early Moon formation inferred from hafnium–tungsten systematics. Nature Geoscience 12, 696-700.

Zeebe, R.E., Lourens, L.J., 2019. Solar System chaos and the Paleocene–Eocene boundary age constrained by geology and astronomy. Science 365, 926-929.

ASTROBIOLOGY

Benford, J., 2019. Looking for lurkers: Co-orbiters as SETI observables. The Astronomical Journal 158, 150.

Betts, B.H., Warmflash, D., Fraze, R.E., Friedman, L., Vorobyova, E., Lilburn, T.G., Smith, A., Rettberg, P., Jönsson, K.I., Ciftcioglu, N., Fox, G.E., Svitek, T., Kirschvinck, J.L., Moeller, R., Wassmann, M., Berger, T., 2019. Phobos LIFE (Living Interplanetary Flight Experiment). Astrobiology 19, 1177-1185.

Chan, M.A., Hinman, N.W., Potter-McIntyre, S.L., Schubert, K.E., Gillams, R.J., Awramik, S.M., Boston, P.J., Bower, D.M., Des Marais, D.J., Farmer, J.D., Jia, T.Z., King, P.L., Hazen, R.M., Léveillé, R.J., Papineau, D., Rempfert, K.R., Sánchez-Román, M., Spear, J.R., Southam, G., Stern, J.C., Cleaves, H.J., 2019. Deciphering biosignatures in planetary contexts. Astrobiology 19, 1075-1102.

García-Descalzo, L., Parro, V., García-Villadangos, M., Cockell, S.C., Moissl-Eichinger, C., Perras, A., Rettberg, P., Beblo-Vranesevic, K., Bohmeier, M., Rabbow, E., Westall, F., Gaboyer, F., Amils, R., Malki, M., Marteinsson, V., Vannier, P., Ehrenfreund, P., Monaghan, E., Riedo, A., Cabezas, P., Walter, N., Gómez, G.F., 2019. Microbial markers profile in anaerobic Mars analogue environments using the LDChip (Life Detector Chip)

antibody microarray core of the SOLID (Signs of Life Detector) platform. Microorganisms 7, 365.

Ilgrande, C., Mastroleo, F., Christiaens, M.E.R., Lindeboom, R.E.F., Prat, D., Van Hoey, O., Ambrozova, I., Coninx, I., Heylen, W., Pommerening-Roser, A., Spieck, E., Boon, N., Vlaeminck, S.E., Leys, N., Clauwaert, P., 2019. Reactivation of microbial strains and synthetic communities after a spaceflight to the International Space Station: Corroborating the feasibility of essential conversions in the MELiSSA loop. Astrobiology 19, 1167-1176.

Kingsley, I., Oliver, C., Slavich, E., 2019. Hidden in the figures: What students are telling us about the effectiveness of astrobiology outreach. Astrobiology 19, 1103-1116.

Lopez, J.V., Peixoto, R.S., Rosado, A.S., 2019. Inevitable future: space colonization beyond Earth with microbes first. FEMS Microbiology Ecology 95, fiz127.

Mojarro, A., Hachey, J., Bailey, R., Brown, M., Doebler, R., Ruvkun, G., Zuber, M.T., Carr, C.E., 2019. Nucleic acid extraction and sequencing from low-biomass synthetic Mars analog soils for in situ life detection. Astrobiology 19, 1139-1152.

Paradise, A., Menou, K., Valencia, D., Lee, C., 2019. Habitable snowballs: Temperate land conditions, liquid water, and implications for CO2 weathering. Journal of Geophysical Research: Planets 124, 2087-2100.

Royle, S.H., Watson, J.S., Zhang, Y., Chatzitheoklitos, G., Sephton, M.A., 2019. Solid phase micro extraction: Potential for organic contamination control for planetary protection of life-detection missions to the icy moons of the outer solar system. Astrobiology 19, 1153-1166.

Environmental Geochemistry


Griffero, L., Alcántara-Durán, J., Alonso, C., Rodríguez-Gallego, L., Moreno-González, D., García-Reyes, J.F., Molina-Díaz, A., Pérez-Parada, A., 2019. Basin-scale monitoring and risk assessment of emerging contaminants in South American Atlantic coastal lagoons. Science of The Total Environment 697, 134058.



Morgunova, I.P., Petrova, V.I., Litvinenko, I.V., Kursheva, A.V., Batova, G.I., Renaud, P.E., Granovitch, A.I., 2019. Hydrocarbon molecular markers in the Holocene bottom sediments

of the Barents Sea as indicators of natural and anthropogenic impacts. Marine Pollution Bulletin 149, 110587.



BIOREMEDIATION



Sazykin, I.S., Minkina, T.M., Grigoryeva, T.V., Khmelevtsova, L.E., Sushkova, S.N., Laikov, A.V., Antonenko, E.M., Ismagilova, R.K., Seliverstova, E.Y., Mandzhieva, S.S., Sazykina, M.A., 2019. PAHs distribution and cultivable PAHs degraders’ biodiversity in soils and surface sediments of the impact zone of the Novocherkassk thermal electric power plant (Russia). Environmental Earth Sciences 78, 581.

DEEPWATER HORIZON/MACONDO/OTHER OIL SPILLS


Thyng, K.M., 2019. Deepwater Horizon oil could have naturally reached Texas beaches. Marine Pollution Bulletin 149, 110527.

MICROPLASTICS

Corami, F., Rosso, B., Bravo, B., Gambaro, A., Barbante, C., 2020. A novel method for purification, quantitative analysis and characterization of microplastic fibers using Micro-FTIR. Chemosphere 238, 124564.

Danso, D., Chow, J., Streit, W.R., 2019. Plastics: Environmental and biotechnological perspectives on microbial degradation. Applied and Environmental Microbiology 85, e01095-01019.

OIL SAND PROCESS WATERS/TAILING PONDS

Loughery, J.R., Marentette, J.R., Frank, R.A., Hewitt, L.M., Parrott, J.L., Martyniuk, C.J., 2019. Transcriptome profiling in larval fathead minnow exposed to commercial naphthenic acids and extracts from fresh and aged oil sands process-affected water. Environmental Science & Technology 53, 10435-10444.

Pacheco, D.M., Bergerson, J.A., Alvarez-Majmutov, A., Chen, J., MacLean, H.L., 2019. Characterizing variability in oil sands upgrading greenhouse gas emissions intensity. Energy & Fuels 33, 8907-8919.


UNCONVENTIONALSHALE GAS-CBM RESOURCES

Casey, J.A., Goin, D.E., Rudolph, K.E., Schwartz, B.S., Mercer, D., Elser, H., Eisen, E.A., Morello-Frosch, R., 2019. Unconventional natural gas development and adverse birth outcomes in Pennsylvania: The potential mediating role of antenatal anxiety and depression. Environmental Research 177, 108598.

Evolution/Paleontology/Palynology

Ayuso-Fernández, I., Rencoret, J., Gutiérrez, A., Ruiz-Dueñas, F.J., Martínez, A.T., 2019. Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants. Proceedings of the National Academy of Sciences 116, 17900-17905.

Barras, C., 2019. Ancient worm fossil rolls back origins of animal life. Nature 573, 15.

Chang, S., Zhang, L., Clausen, S., Bottjer, D.J., Feng, Q., 2019. The Ediacaran-Cambrian rise of siliceous sponges and development of modern oceanic ecosystems. Precambrian Research 333, 105438.

Dahl, T.W., Connelly, J.N., Li, D., Kouchinsky, A., Gill, B.C., Porter, S., Maloof, A.C., Bizzarro, M., 2019. Atmosphere–ocean oxygen and productivity dynamics during early animal radiations. Proceedings of the National Academy of Sciences 116, 19352-19361.

Demoulin, C.F., Lara, Y.J., Cornet, L., François, C., Baurain, D., Wilmotte, A., Javaux, E.J., 2019. Cyanobacteria evolution: Insight from the fossil record. Free Radical Biology and Medicine 140, 206-223.

Ding, W., Dong, L., Sun, Y., Ma, H., Xu, Y., Yang, R., Peng, Y., Zhou, C., Shen, B., 2019. Early animal evolution and highly oxygenated seafloor niches hosted by microbial mats. Scientific Reports 9, 13628.

Evans, S.D., Gehling, J.G., Droser, M.L., 2019. Slime travelers: Early evidence of animal mobility and feeding in an organic mat world. Geobiology 17, 490-509.

Gould, S.B., Garg, S.G., Handrich, M., Nelson-Sathi, S., Gruenheit, N., Tielens, A.G.M., Martin, W.F., 2019. Adaptation to life on land at high O2 via transition from ferredoxin-to NADH-dependent redox balance. Proceedings of the Royal Society B: Biological Sciences 286, 20191491.

Graham, H.V., Herrera, F., Jaramillo, C., Wing, S.L., Freeman, K.H., 2019. Canopy structure in Late Cretaceous and Paleocene forests as reconstructed from carbon isotope analyses of fossil leaves. Geology 47, 977-981.

Hohl, S.V., Jiang, S.-Y., Wei, H.-Z., Pi, D.-H., Liu, Q., Viehmann, S., Galer, S.J.G., 2019. Cd isotopes trace periodic (bio)geochemical metal cycling at the verge of the Cambrian animal evolution. Geochimica et Cosmochimica Acta 263, 195-214.


Kröger, B., Franeck, F., Rasmussen, C.M.Ø., 2019. The evolutionary dynamics of the early Palaeozoic marine biodiversity accumulation. Proceedings of the Royal Society B: Biological Sciences 286, 20191634.

Lindgren, J., Nilsson, D.-E., Sjövall, P., Jarenmark, M., Ito, S., Wakamatsu, K., Kear, B.P., Schultz, B.P., Sylvestersen, R.L., Madsen, H., LaFountain, J.R., Alwmark, C., Eriksson, M.E., Hall, S.A., Lindgren, P., Rodríguez-Meizoso, I., Ahlberg, P., 2019. Fossil insect eyes shed light on trilobite optics and the arthropod pigment screen. Nature 573, 122-125.

Nelson, L.L., Smith, E.F., 2019. Tubey or not tubey: Death beds of Ediacaran macrofossils or microbially induced sedimentary structures? Geology 47, 909-913.

Servais, T., Cascales-Miñana, B., Cleal, C.J., Gerrienne, P., Harper, D.A.T., Neumann, M., 2019. Revisiting the Great Ordovician Diversification of land plants: Recent data and perspectives. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109280.

ORIGINS OF LIFE/MICROBIAL GENOMICS

Alleon, J., Summons, R.E., 2019. Organic geochemical approaches to understanding early life. Free Radical Biology and Medicine 140, 103-112.

Castañeda, A.D., Li, Z., Joo, T., Benham, K., Burcar, B.T., Krishnamurthy, R., Liotta, C.L., Ng, N.L., Orlando, T.M., 2019. Prebiotic phosphorylation of uridine using diamidophosphate in aerosols. Scientific Reports 9, 13527.


Das, T., Ghule, S., Vanka, K., 2019. Insights into the origin of life: Did it begin from HCN and H2O? ACS Central Science 5, 1532-1540.

Guglielmini, J., Woo, A.C., Krupovic, M., Forterre, P., Gaia, M., 2019. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes. Proceedings of the National Academy of Sciences 116, 19585.

Hehenberger, E., Gast, R.J., Keeling, P.J., 2019. A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis. Proceedings of the National Academy of Sciences 116, 17934-17942.

Hess, S., Eme, L., Roger, A.J., Simpson, A.G.B., 2019. A natural toroidal microswimmer with a rotary eukaryotic flagellum. Nature Microbiology 4, 1620–1626.

Ilardo, M., Bose, R., Meringer, M., Rasulev, B., Grefenstette, N., Stephenson, J., Freeland, S., Gillams, R.J., Butch, C.J., Cleaves, H.J., 2019. Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets. Scientific Reports 9, 12468.

Kjeldsen, K.U., Schreiber, L., Thorup, C.A., Boesen, T., Bjerg, J.T., Yang, T., Dueholm, M.S., Larsen, S., Risgaard-Petersen, N., Nierychlo, M., Schmid, M., Bøggild, A., van de Vossenberg, J., Geelhoed, J.S., Meysman, F.J.R., Wagner, M., Nielsen, P.H., Nielsen, L.P., Schramm, A., 2019. On the evolution and physiology of cable bacteria. Proceedings of the National Academy of Sciences 116, 19116-19125.

Meisner, J., Zhu, X., Martínez, T.J., 2019. Computational discovery of the origins of life. ACS Central Science 5, 1493-1495.

Novoa, E.M., Jungreis, I., Jaillon, O., Kellis, M., 2019. Elucidation of codon usage signatures across the domains of life. Molecular Biology and Evolution 36, 2328-2339.

Šponer, J.E., Šponer, J., Di Mauro, E., 2019. Structural and energetic compatibility: The driving principles of molecular evolution. Astrobiology 19, 1117-1122.

Takagi, H., Kimoto, K., Fujiki, T., Saito, H., Schmidt, C., Kucera, M., Moriya, K., 2019. Characterizing photosymbiosis in modern planktonic foraminifera. Biogeosciences 16, 3377-3396.

HOMINID EVOLUTION

Bennett, E.A., Crevecoeur, I., Viola, B., Derevianko, A.P., Shunkov, M.V., Grange, T., Maureille, B., Geigl, E.-M., 2019. Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals. Science Advances 5, eaaw3950.

Callaway, E., 2019. First portrait of mysterious Denisovans drawn from DNA. Nature 573, 475-476.

Haile-Selassie, Y., Melillo, S.M., Vazzana, A., Benazzi, S., Ryan, T.M., 2019. A 3.8-million-year-old hominin cranium from Woranso-Mille, Ethiopia. Nature 573, 214-219.

Morley, M.W., Goldberg, P., Uliyanov, V.A., Kozlikin, M.B., Shunkov, M.V., Derevianko, A.P., Jacobs, Z., Roberts, R.G., 2019. Hominin and animal activities in the

microstratigraphic record from Denisova Cave (Altai Mountains, Russia). Scientific Reports 9, 13785.

Mounier, A., Mirazón Lahr, M., 2019. Deciphering African late middle Pleistocene hominin diversity and the origin of our species. Nature Communications 10, 3406.

Narasimhan, V.M., Patterson, N., Moorjani, P., Rohland, N., Bernardos, R., Mallick, S., Lazaridis, I., Nakatsuka, N., Olalde, I., Lipson, M., Kim, A.M., Olivieri, L.M., Coppa, A., Vidale, M., Mallory, J., Moiseyev, V., Kitov, E., Monge, J., Adamski, N., Alex, N., Broomandkhoshbacht, N., Candilio, F., Callan, K., Cheronet, O., Culleton, B.J., Ferry, M., Fernandes, D., Freilich, S., Gamarra, B., Gaudio, D., Hajdinjak, M., Harney, É., Harper, T.K., Keating, D., Lawson, A.M., Mah, M., Mandl, K., Michel, M., Novak, M., Oppenheimer, J., Rai, N., Sirak, K., Slon, V., Stewardson, K., Zalzala, F., Zhang, Z., Akhatov, G., Bagashev, A.N., Bagnera, A., Baitanayev, B., Bendezu-Sarmiento, J., Bissembaev, A.A., Bonora, G.L., Chargynov, T.T., Chikisheva, T., Dashkovskiy, P.K., Derevianko, A., Dobeš, M., Douka, K., Dubova, N., Duisengali, M.N., Enshin, D., Epimakhov, A., Fribus, A.V., Fuller, D., Goryachev, A., Gromov, A., Grushin, S.P., Hanks, B., Judd, M., Kazizov, E., Khokhlov, A., Krygin, A.P., Kupriyanova, E., Kuznetsov, P., Luiselli, D., Maksudov, F., Mamedov, A.M., Mamirov, T.B., Meiklejohn, C., Merrett, D.C., Micheli, R., Mochalov, O., Mustafokulov, S., Nayak, A., Pettener, D., Potts, R., Razhev, D., Rykun, M., Sarno, S., Savenkova, T.M., Sikhymbaeva, K., Slepchenko, S.M., Soltobaev, O.A., Stepanova, N., Svyatko, S., Tabaldiev, K., Teschler-Nicola, M., Tishkin, A.A., Tkachev, V.V., Vasilyev, S., Velemínský, P., Voyakin, D., Yermolayeva, A., Zahir, M., Zubkov, V.S., Zubova, A., Shinde, V.S., Lalueza-Fox, C., Meyer, M., Anthony, D., Boivin, N., Thangaraj, K., Kennett, D.J., Frachetti, M., Pinhasi, R., Reich, D., 2019. The formation of human populations in South and Central Asia. Science 365, eaat7487.

Price, M., 2019. Stunning skull shakes human family tree. Science 365, 850.

Saylor, B.Z., Gibert, L., Deino, A., Alene, M., Levin, N.E., Melillo, S.M., Peaple, M.D., Feakins, S.J., Bourel, B., Barboni, D., Novello, A., Sylvestre, F., Mertzman, S.A., Haile-Selassie, Y., 2019. Age and context of mid-Pliocene hominin cranium from Woranso-Mille, Ethiopia. Nature 573, 220-224.

Schaefer, N.K., Shapiro, B., 2019. New middle chapter in the story of human evolution. Science 365, 981-982.

Spoor, F., 2019. Elusive cranium of early hominin found. Nature 573, 200-202.

Fluid Inclusions

Álvaro, J.J., González-Acebrón, L., 2019. Sublacustrine hydrothermal seeps and silicification of microbial bioherms in the Ediacaran Oued Dar'a caldera, Anti-Atlas, Morocco. Sedimentology 66, 2048-2071.

Bai, D., Yang, M., Lei, Z., Zhang, Y., 2020. Effect of tectonic evolution on hydrocarbon charging time: A case study from Lower Shihezi Formation (Guadalupian), the Hangjinqi area, northern Ordos, China. Journal of Petroleum Science and Engineering 184, 106465.



Liang, J., Chen, J.-w., Zhang, Y.-g., Ou, G.-x., Zhang, P.-h., Yuan, Y., 2019. New evidence of Silurian hydrocarbon accumulation is discovered by fluid inclusion analysis in the South Yellow Sea Basin. China Geology 2, 110-111.

Liu, L.-h., Wang, C.-l., Zhao, X.-m., 2019. First report of TSR origin minerals filled in anhydrite dissolved pores in southeastern Ordos Basin. China Geology 2, 245-247.

Xu, W., Hu, S., Li, N., Wei, X., Gao, J., Zhao, Z., Li, X., Liu, J., Zhang, Y., Song, W., 2019. Characteristics and exploration directions of inner gas source from the middle assemblage of Ordovician in Ordos Basin. Acta Petrolei Sinica 40, 900-913.

Zhang, W., Williams-Jones, A.E., Leng, C.-B., Zhang, X.-C., Chen, W.T., Qin, C.-J., Su, W.-C., Yan, J.-H., 2019. The origin of CH4-rich fluids in reduced porphyry–skarn Cu–Mo–Au systems. Ore Geology Reviews 114, 103135.

General Interest

de Santana, C.D., Crampton, W.G.R., Dillman, C.B., Frederico, R.G., Sabaj, M.H., Covain, R., Ready, J., Zuanon, J., de Oliveira, R.R., Mendes-Júnior, R.N., Bastos, D.A., Teixeira, T.F., Mol, J., Ohara, W., Castro, N.C.e., Peixoto, L.A., Nagamachi, C., Sousa, L., Montag, L.F.A., Ribeiro, F., Waddell, J.C., Piorsky, N.M., Vari, R.P., Wosiacki, W.B., 2019. Unexpected species diversity in electric eels with a description of the strongest living bioelectricity generator. Nature Communications 10, 4000.

Geology

Berg, R.D., Solomon, E.A., Teng, F.-Z., 2019. The role of marine sediment diagenesis in the modern oceanic magnesium cycle. Nature Communications 10, 4371.


Wang, W., Liu, C., Zhang, D., Liu, W., Chen, L., Liu, W., 2019. Radioactive genesis of hydrogen gas under geological conditions: An experimental study. Acta Geologica Sinica - English Edition 93, 1125-1134.

Yu, K., Qiu, L., Cao, Y., Sun, P., Qu, C., Yang, Y., 2019. Hydrothermal origin of early Permian saddle dolomites in the Junggar Basin, NW China. Journal of Asian Earth Sciences 184, 103990.

BOLIDE IMPACTS/CRATER GEOCHEMISTRY

Hand, E., 2019. World's oldest impact crater dated in Australian outback. Science 365, 852-853.

Hydrates

Fang, B., Ning, F., Ou, W., Wang, D., Zhang, Z., Yu, Y., Lu, H., Wu, J., Vlugt, T.J.H., 2019. The dynamic behavior of gas hydrate dissociation by heating in tight sandy reservoirs: A molecular dynamics simulation study. Fuel 258, 116106.

Gambelli, A.M., Castellani, B., Nicolini, A., Rossi, F., 2019. Gas hydrate formation as a strategy for CH4/CO2 separation: Experimental study on gaseous mixtures produced via Sabatier reaction. Journal of Natural Gas Science and Engineering 71, 102985.

Li, D., Ren, S., Xu, Y., Rui, H., 2019. Experimental study on kinetic behaviors of natural gas hydrate production via continuous simulated seawater injection. Energy & Fuels 33, 8222-8230.

Portnov, A., Cook, A.E., Sawyer, D.E., Yang, C., Hillman, J.I.T., Waite, W.F., 2019. Clustered BSRs: Evidence for gas hydrate-bearing turbidite complexes in folded regions, example from the Perdido Fold Belt, northern Gulf of Mexico. Earth and Planetary Science Letters 528, 115843.

Portnov, A., Santra, M., Cook, A.E., Sawyer, D.E., 2020. The Jackalope gas hydrate system in the northeastern Gulf of Mexico. Marine and Petroleum Geology 111, 261-278.

Xiong, P., Lu, H., Xie, X., Zhang, G., Fu, S., Jiang, L., Zhang, P., 2020. Geochemical responses and implications for gas hydrate accumulation: Case study from site SHC in Shenhu Area within northern South China Sea. Marine and Petroleum Geology 111, 650-661.

Isotope Geochemistry

Chapman, T.W., Cui, Y., Schubert, B.A., 2019. Stable carbon isotopes of fossil plant lipids support moderately high pCO2 in the early Paleogene. ACS Earth and Space Chemistry 3, 1966-1973.

Coppola, A.I., Seidel, M., Ward, N.D., Viviroli, D., Nascimento, G.S., Haghipour, N., Revels, B.N., Abiven, S., Jones, M.W., Richey, J.E., Eglinton, T.I., Dittmar, T., Schmidt, M.W.I., 2019. Marked isotopic variability within and between the Amazon River and marine dissolved black carbon pools. Nature Communications 10, 4018.

Curtin, L., D'Andrea, W.J., Balascio, N., Pugsley, G., de Wet, G., Bradley, R., 2019. Holocene and Last Interglacial climate of the Faroe Islands from sedimentary plant wax hydrogen and carbon isotopes. Quaternary Science Reviews 223, 105930.

D’Arcy, F., Boucher, É., De Moor, J.M., Hélie, J.-F., Piggott, R., Stix, J., 2019. Carbon and sulfur isotopes in tree rings as a proxy for volcanic degassing. Geology 47, 825-828.

Fowler, A.P.G., Liu, Q.-l., Huang, Y., Tan, C., Volk, M.W.R., Shanks, W.C.P., Seyfried, W., 2019. Pyrite δ34S and Δ33S constraints on sulfur cycling at sublacustrine hydrothermal vents in Yellowstone Lake, Wyoming, USA. Geochimica et Cosmochimica Acta 265, 148-162.



Jeltsch-Thömmes, A., Joos, F., 2019. The response to pulse-like perturbations in atmospheric carbon and carbon isotopes. Climate of the Past Discussions 2019, 1-36.

Kobayashi, K., Makabe, A., Yano, M., Oshiki, M., Kindaichi, T., Casciotti, K.L., Okabe, S., 2019. Dual nitrogen and oxygen isotope fractionation during anaerobic ammonium oxidation by anammox bacteria. The ISME Journal 13, 2426-2436.


Liu, H., Liu, Z., Zhao, C., Liu, W., 2019. n-Alkyl lipid concentrations and distributions in aquatic plants and their individual δD variations. Science China Earth Sciences 62, 1441-1452.

Liu, J., An, Z., Wu, H., Yu, Y., 2019. Comparison of n-alkane concentrations and δD values between leaves and roots in modern plants on the Chinese Loess Plateau. Organic Geochemistry 138, 103913.

Lukens, W.E., Eze, P., Schubert, B.A., 2019. The effect of diagenesis on carbon isotope values of fossil wood. Geology 47, 987-991.

Pahlevan, K., Schaefer, L., Hirschmann, M.M., 2019. Hydrogen isotopic evidence for early oxidation of silicate Earth. Earth and Planetary Science Letters 526, 115770.

Ren, L., Hu, W., Hou, J., Li, L., Yue, S., Sun, Y., Wang, Z., Li, X., Pavuluri, C.M., Hou, S., Liu, C.-Q., Kawamura, K., Ellam, R.M., Fu, P., 2019. Compound-specific stable carbon isotope ratios of terrestrial biomarkers in urban aerosols from Beijing, China. ACS Earth and Space Chemistry 3, 1896-1904.

Sim, M.S., 2019. Effect of sulfate limitation on sulfur isotope fractionation in batch cultures of sulfate reducing bacteria. Geosciences Journal 23, 687-694.

Tang, S., Zhou, Y., Yao, X., Feng, X., Li, Z., Wu, G., Zhu, G., 2019. The mercury isotope signatures of coalbed gas and oil-type gas: Implications for the origins of the gases. Applied Geochemistry 109, 104415.

Tuerena, R.E., Ganeshram, R.S., Humphreys, M.P., Browning, T.J., Bouman, H., Piotrowski, A.P., 2019. Isotopic fractionation of carbon during uptake by phytoplankton across the South Atlantic subtropical convergence. Biogeosciences 16, 3621-3635.

Wilkes, E.B., Pearson, A., 2019. A general model for carbon isotopes in red-lineage phytoplankton: Interplay between unidirectional processes and fractionation by RubisCO. Geochimica et Cosmochimica Acta 265, 163-181.

Mathematical Geochemistry/Phase Behavior

Li, T., Li, J., Zhang, H., Sun, K., Xiao, J., 2019. DFT study on the dibenzothiophene pyrolysis mechanism in petroleum. Energy & Fuels 33, 8876-8895.

Meyra, A.G., Ferrara, C.G., 2019. Study of nanoconfined mixtures of decane and water: Structure and dynamic. Fluid Phase Equilibria 502, 112279.

Perez Claro, Y.A., Schoeggl, F.F., Taylor, S.D., Yarranton, H.W., 2019. Phase behavior of mixtures of bitumen and n-butane. Energy & Fuels 33, 8530-8543.

Ruiz-Morales, Y., Miranda-Olvera, A.D., Portales-Martínez, B., Domínguez, J.M., 2019. Determination of 13C NMR chemical shift structural ranges for polycyclic aromatic hydrocarbons (PAHs) and PAHs in asphaltenes: An experimental and theoretical density functional theory study. Energy & Fuels 33, 7950-7970.

Zhang, J., Pei, G., Zhang, L., 2019. Molecular dynamics simulation of methane gas flow in nanopores. Petroleum 5, 252-259.

Microbiology/Extremophiles

Finke, N., Simister, R.L., O’Neil, A.H., Nomosatryo, S., Henny, C., MacLean, L.C., Canfield, D.E., Konhauser, K., Lalonde, S.V., Fowle, D.A., Crowe, S.A., 2019. Mesophilic microorganisms build terrestrial mats analogous to Precambrian microbial jungles. Nature Communications 10, 4323.

Grant, S.R., Church, M.J., Ferrón, S., Laws, E.A., Rappé, M.S., 2019. Elemental composition, phosphorous uptake, and characteristics of growth of a SAR11 strain in batch and continuous culture. mSystems 4, e00218-00218.

Hamilton-Brehm, S.D., Stewart, L.E., Zavarin, M., Caldwell, M., Lawson, P.A., Onstott, T.C., Grzymski, J., Neveux, I., Sherwood Lollar, B., Russell, C.E., Moser, D.P., 2019. Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a novel fumarate-fermenting microorganism from a deep fractured carbonate aquifer of the US Great Basin. Frontiers in Microbiology 10, 2224. doi: 2210.3389/fmicb.2019.02224.

Kato, S., Itoh, T., Yuki, M., Nagamori, M., Ohnishi, M., Uematsu, K., Suzuki, K., Takashina, T., Ohkuma, M., 2019. Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring. The ISME Journal 13, 2465-2474.

Manoharan, L., Kozlowski, J.A., Murdoch, R.W., Löffler, F.E., Sousa, F.L., Schleper, C., 2019. Metagenomes from coastal marine sediments give insights into the ecological role and cellular features of Loki- and Thorarchaeota. mBio 10, e02039-02019.

Severino, R., Froufe, H.J.C., Barroso, C., Albuquerque, L., Lobo-da-Cunha, A., da Costa, M.S., Egas, C., 2019. High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria. MicrobiologyOpen 8, e00840.

Sorokin, D.Y., Yakimov, M., Messina, E., Merkel, A.Y., Bale, N.J., Sinninghe Damsté, J.S., 2019. Natronolimnobius sulfurireducens sp. nov. and Halalkaliarchaeum desulfuricum gen. nov., sp. nov., the first sulfur-respiring alkaliphilic haloarchaea from hypersaline alkaline lakes. International Journal of Systematic and Evolutionary Microbiology 69, 2662-2673.

Sun, X., Kop, L.F.M., Lau, M.C.Y., Frank, J., Jayakumar, A., Lücker, S., Ward, B.B., 2019. Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones. The ISME Journal 13, 2391-2402.

Thorell, K., Meier-Kolthoff, J.P., Sjöling, Å., Martín-Rodríguez, A.J., 2019. Whole-genome sequencing redefines Shewanella taxonomy. Frontiers in Microbiology 10, 1861. doi: 1810.3389/fmicb.2019.01861.

MICROBIAL ECOSYSTEMS

Böhnke, S., Perner, M., 2019. Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments. The ISME Journal 13, 2475-2488.

Cario, A., Oliver, G.C., Rogers, K.L., 2019. Exploring the deep marine biosphere: Challenges, innovations, and opportunities. Frontiers in Earth Science 7, 225. doi: 210.3389/feart.2019.00225.

Gao, P., Li, Y., Tan, L., Guo, F., Ma, T., 2019. Composition of bacterial and archaeal communities in an alkali-surfactant-polyacrylamide-flooded oil reservoir and the responses of microcosms to nutrients. Frontiers in Microbiology 10, 2197. doi: 2110.3389/fmicb.2019.02197.

Gionchetta, G., Romaní, A.M., Oliva, F., Artigas, J., 2019. Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances. Scientific Reports 9, 13506.

Lincy, J., Manohar, C., 2019. High-throughput screening of sediment bacterial communities from Oxygen Minimum Zones of the northern Indian Ocean. Biogeosciences Discussions 2019, 1-28.


McGonigle, J.M., Bernau, J.A., Bowen, B.B., Brazelton, W.J., 2019. Robust archaeal and bacterial communities inhabit shallow subsurface sediments of the Bonneville Salt Flats. mSphere 4, e00378-00319.

Nema, P., Paul, D., Karmalkar, N.R., Shouche, Y.S., 2019. Bacterial diversity in the metal-rich terrestrial deep subsurface sediments of Krishna Godavari Basin, India. Geomicrobiology Journal 36, 917-932.

Pereira, O., Hochart, C., Auguet, J.C., Debroas, D., Galand, P.E., 2019. Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. MicrobiologyOpen 8, e00852.



Shurigin, V., Hakobyan, A., Panosyan, H., Egamberdieva, D., Davranov, K., Birkeland, N.-K., 2019. A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups. MicrobiologyOpen 8, e00850.

Thakur, M.P., van der Putten, W.H., Cobben, M.M.P., van Kleunen, M., Geisen, S., 2019. Microbial invasions in terrestrial ecosystems. Nature Reviews Microbiology 17, 621-631.

van Elden, S., Meeuwig, J.J., Hobbs, R.J., Hemmi, J.M., 2019. Offshore oil and gas platforms as novel ecosystems: A global perspective. Frontiers in Marine Science 6, 548. doi: 510.3389/fmars.2019.00548.


Zhang, S., Song, W., Wemheuer, B., Reveillaud, J., Webster, N., Thomas, T., 2019. Comparative genomics reveals ecological and evolutionary insights into sponge-associated Thaumarchaeota. mSystems 4, e00288-00219.



PETROLEUM DEGRADERS

Chettri, B., Singha, N.A., Mukherjee, A., Rai, A.N., Chattopadhyay, D., Singh, A.K., 2019. Hydrocarbon degradation potential and competitive persistence of hydrocarbonoclastic bacterium Acinetobacter pittii strain ABC. Archives of Microbiology 201, 1129-1140.




Paleoclimatology/Paleoceanography

Adiatma, Y.D., Saltzman, M.R., Young, S.A., Griffith, E.M., Kozik, N.P., Edwards, C.T., Leslie, S.A., Bancroft, A.M., 2019. Did early land plants produce a stepwise change in atmospheric oxygen during the Late Ordovician (Sandbian ~458 Ma)? Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109341.



Da, J., Zhang, Y.G., Li, G., Meng, X., Ji, J., 2019. Low CO2 levels of the entire Pleistocene epoch. Nature Communications 10, 4342.

Dietze, E., Mangelsdorf, K., Andreev, A., Karger, C., Schreuder, L.T., Hopmans, E.C., Rach, O., Sachse, D., Wennrich, V., Herzschuh, U., 2019. Relationships between low-temperature fires, climate and vegetation during the last 430 kyrs in northeastern Siberia reconstructed from monosaccharide anhydrides in Lake El’gygytgyn sediments. Climate of the Past Discussions 2019, 1-29.


Kleinen, T., Mikolajewicz, U., Brovkin, V., 2019. Terrestrial methane emissions from Last Glacial Maximum to preindustrial. Climate of the Past Discussions 2019, 1-32.

Krencker, F.-N., Lindström, S., Bodin, S., 2019. A major sea-level drop briefly precedes the Toarcian oceanic anoxic event: implication for Early Jurassic climate and carbon cycle. Scientific Reports 9, 12518.

Liu, H., Zartman, R.E., Ireland, T.R., Sun, W.-d., 2019. Global atmospheric oxygen variations recorded by Th/U systematics of igneous rocks. Proceedings of the National Academy of Sciences 116, 18854-18859.

Methner, K., Lenz, O., Riegel, W., Wilde, V., Mulch, A., 2019. Paleoenvironmental response of midlatitudinal wetlands to Paleocene–early Eocene climate change (Schöningen lignite deposits, Germany). Climate of the Past 15, 1741-1755.

Pattan, J.N., Parthiban, G., Amonkar, A., 2019. Productivity controls on the redox variation in the southeastern Arabian Sea sediments during the past 18 kyr. Quaternary International 523, 1-9.

Rodrigues, B., Silva, R.L., Reolid, M., Mendonça Filho, J.G., Duarte, L.V., 2019. Sedimentary organic matter and δ13CKerogen variation on the southern Iberian palaeomargin (Betic Cordillera, SE Spain) during the latest Pliensbachian–Early Toarcian. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109342.

Rose, C.V., Webb, S.M., Newville, M., Lanzirotti, A., Richardson, J.A., Tosca, N.J., Catalano, J.G., Bradley, A.S., Fike, D.A., 2019. Insights into past ocean proxies from micron-scale mapping of sulfur species in carbonates. Geology 47, 833-837.

Steinthorsdottir, M., Vajda, V., Pole, M., Holdgate, G., 2019. Moderate levels of Eocene pCO2 indicated by Southern Hemisphere fossil plant stomata. Geology 47, 914-918.

Sun, W., Zhang, E., Chang, J., Shulmeister, J., Bird, M.I., Zhao, C., Jiang, Q., Shen, J., 2019. Microbial membrane tetraether lipid-inferred paleohydrology and paleotemperature of Lake Chenghai during the Pleistocene-Holocene transition. Climate of the Past Discussions 2019, 1-29.

Wei, B., Jia, G., Hefter, J., Kang, M., Park, E., Mollenhauer, G., 2019. Comparison of the U37K ' ',

LDI, TEX 86H and RI-OH temperature proxies in the northern shelf of the South China Sea.

Biogeosciences Discussions 2019, 1-26.


Zhang, X., Joachimski, M.M., Over, D.J., Ma, K., Huang, C., Gong, Y., 2019. Late Devonian carbon isotope chemostratigraphy: A new record from the offshore facies of South China. Global and Planetary Change 182, 103024.

Zhu, J., Poulsen, C.J., Tierney, J.E., 2019. Simulation of Eocene extreme warmth and high climate sensitivity through cloud feedbacks. Science Advances 5, eaax1874.

EXTINCTION EVENTS

Bowman, C.N., Young, S.A., Kaljo, D., Eriksson, M.E., Them, T.R., II, Hints, O., Martma, T., Owens, J.D., 2019. Linking the progressive expansion of reducing conditions to a stepwise mass extinction event in the late Silurian oceans. Geology 47, 968-972.

Foster, W.J., Lehrmann, D.J., Yu, M., Martindale, R.C., 2019. Facies selectivity of benthic invertebrates in a Permian/Triassic boundary microbialite succession: Implications for the “microbialite refuge” hypothesis. Geobiology 17, 523-535.

Gulick, S.P.S., Bralower, T.J., Ormö, J., Hall, B., Grice, K., Schaefer, B., Lyons, S., Freeman, K.H., Morgan, J.V., Artemieva, N., Kaskes, P., de Graaff, S.J., Whalen, M.T., Collins, G.S., Tikoo, S.M., Verhagen, C., Christeson, G.L., Claeys, P., Coolen, M.J.L., Goderis, S., Goto, K., Grieve, R.A.F., McCall, N., Osinski, G.R., Rae, A.S.P., Riller, U., Smit, J., Vajda, V., Wittmann, A., 2019. The first day of the Cenozoic. Proceedings of the National Academy of Sciences 116, 19342-19351.

Schmitz, B., Farley, K.A., Goderis, S., Heck, P.R., Bergström, S.M., Boschi, S., Claeys, P., Debaille, V., Dronov, A., van Ginneken, M., Harper, D.A.T., Iqbal, F., Friberg, J., Liao, S., Martin, E., Meier, M.M.M., Peucker-Ehrenbrink, B., Soens, B., Wieler, R., Terfelt, F., 2019. An extraterrestrial trigger for the mid-Ordovician ice age: Dust from the breakup of the L-chondrite parent body. Science Advances 5, eaax4184.

Tóth, A.B., Lyons, S.K., Barr, W.A., Behrensmeyer, A.K., Blois, J.L., Bobe, R., Davis, M., Du, A., Eronen, J.T., Faith, J.T., Fraser, D., Gotelli, N.J., Graves, G.R., Jukar, A.M., Miller, J.H., Pineda-Munoz, S., Soul, L.C., Villaseñor, A., Alroy, J., 2019. Reorganization of surviving mammal communities after the end-Pleistocene megafaunal extinction. Science 365, 1305-1308.

Xie, T., Zhang, Q., Hu, S., Zhou, C., Huang, J., Wen, W., 2019. The Mesozoic maximum of 87Sr/86Sr ratio: a critical turning point after the end-Permian mass extinction. Carbonates and Evaporites 34, 1021-1029.

Petroleum Systems

EXPLORATION

Ahmed, M.A., Hegab, O.A., Awadalla, A.S., Farag, A.E., Hassan, S., 2019. Hydrocarbon generation, in-source conversion of oil to gas and expulsion: Petroleum system modeling of the Duwi Formation, Gulf of Suez, Egypt. Natural Resources Research 28, 1547-1573.


Chen, J.-w., Xu, M., Lei, B.-h., Liang, J., Zhang, Y.-g., Wu, S.-y., Shi, J., Yuan, Y., Wang, J.-q., Zhang, Y.-x., Li, G., Wang, W.-j., 2019. Prospective prediction and exploration

situation of marine Mesozoic-Paleozoic oil and gas in the South Yellow Sea. China Geology 2, 67-84.

Curry, D.J., 2019. Future directions in basin and petroleum systems modeling: A survey of the community. American Association of Petroleum Geologists Bulletin 103, 2285-2293.

Lei, Z.-y., Zhang, L., Su, M., Luo, S.-b., Qian, X., Zhang, B.-d., 2019. Types, characteristics and implication for hydrocarbon exploration of the Middle Miocene deep-water sediments in Beikang Basin, southern South China Sea. China Geology 2, 85-93.


Shiraishi, K., Yamada, Y., Nibe, T., 2019. Thermogenic petroleum potential of the Nankai Subduction Zone, offshore SW Japan. Journal of Petroleum Geology 42, 417-434.

Spacapan, J.B., D'Odorico, A., Palma, O., Galland, O., Rojas Vera, E., Ruiz, R., Leanza, H.A., Medialdea, A., Manceda, R., 2020. Igneous petroleum systems in the Malargüe fold and thrust belt, Río Grande Valley area, Neuquén Basin, Argentina. Marine and Petroleum Geology 111, 309-331.

Wu, D.-t., Ramaniraka, J.I., Xu, F.-m., Shao, J.-b., Zhou, Y.-h., Zhao, Y.-d., Ralison, B., 2019. Characteristics and potential analysis of Madagascar hydrocarbon-bearing basins. China Geology 2, 56-66.

Zhou, Y., Chen, Q., Wu, K., Wang, X., Liu, Y., 2019. The basin and range systems and their evolution of the northwestern margin of Junggar Basin, China: Implications for the hydrocarbon accumulation. Energy Exploration & Exploitation 37, 1577-1598.

Zhu, G., Zhang, Z., Zhou, X., Li, T., Han, J., Sun, C., 2019. The complexity, secondary geochemical process, genetic mechanism and distribution prediction of deep marine oil and gas in the Tarim Basin, China. Earth-Science Reviews 198, 102930.

GENERATION & EXPULSION

Drozd, R.J., 2019. Adventures in pyrolysis II, modeling pyrolysis peaks of petroleum source rocks. Journal of Analytical and Applied Pyrolysis 142, 104385.

Gardiner, D., Schofield, N., Finlay, A., Mark, N., Holt, L., Grove, C., Forster, C., Moore, J., 2019. Modeling petroleum expulsion in sedimentary basins: The importance of igneous intrusion timing and basement composition. Geology 47, 904-908.

He, K., Zhang, S., Mi, J., Fang, Y., Zhang, W., 2019. Carbon and hydrogen isotope fractionation for methane from non-isothermal pyrolysis of oil in anhydrous and hydrothermal conditions. Energy Exploration & Exploitation 37, 1558-1576.


Ma, W., Hou, L., Luo, X., Tao, S., Guan, P., Liu, J., Lin, S., 2020. Role of bitumen and NSOs during the decomposition process of a lacustrine Type-II kerogen in semi-open pyrolysis system. Fuel 259, 116211.

Serovaiskii, A.Y., Kolesnikov, A.Y., Kutcherov, V.G., 2019. Formation of iron hydride and iron carbide from hydrocarbon systems at ultra-high thermobaric conditions. Geochemistry International 57, 1008-1014.

Wei, Z., Wang, Y., Wang, G., Ma, X., He, W., Zhang, T., Yu, X., Zou, Y.-R., 2019. Isotopic composition of abiogenic gas produced in closed-system Fischer-Tropsch synthesis: Implications for the origins of the deep Songliao Basin gases in China. Geofluids 2019, 2823803.

Xu, L., Shi, Y., Chen, X., Wan, C., Wang, J., 2019. Kinetic analysis of hydrocarbon generation based on saline lacustrine source rock and kerogen samples in the western Qaidam Basin, China. Carbonates and Evaporites 34, 1045-1053.

Yan, K., Zuo, Y., Yang, M., Zhou, Y., Zhang, Y., Wang, C., Song, R., Feng, R., Feng, Y., 2019. Kerogen pyrolysis experiment and hydrocarbon generation kinetics in the Dongpu depression, Bohai Bay Basin, China. Energy & Fuels 33, 8511-8521.

OIL & GAS



Gainullina, L.R., Tutubalina, V.P., 2019. Oxidative methods for the study of the structural group composition of organosulfur compounds. Chemistry and Technology of Fuels and Oils 55, 272-279.



Killops, S.D., Nytoft, H.P., di Primio, R., 2019. Biodegradative production and destruction of norhopanes – An example from residual oil in a Paleogene paleomigration conduit on the Utsira High, Norwegian North Sea. Organic Geochemistry 138, 103906.

Li, S., Wang, X.-C., Li, C.-F., Wilde, S.A., Zhang, Y., Golding, S.D., Liu, K., Zhang, Y., 2019. Direct rubidium-strontium dating of hydrocarbon charge using small authigenic illitic clay aliquots from the Silurian bituminous sandstone in the Tarim Basin, NW China. Scientific Reports 9, 12565.

Liang, Y., Shan, X., Makeen, Y.M., Abdullah, W.H., Hao, G., Tong, L., Lawal, M., Zhao, R., Ayinla, H.A., 2019. Geochemical characteristics of oil from Oligocene Lower Ganchaigou Formation oil sand in northern Qaidam Basin, China. Natural Resources Research 28, 1521-1546.

Mohammed, S., Opuwari, M., Titinchi, S., Bata, T., Abubakar, M.B., 2019. Evaluation of source rock potential and hydrocarbon composition of oil sand and associated clay deposits from the Eastern Dahomey Basin, Nigeria. Journal of African Earth Sciences 160, 103603.

Onojake, M.C., Abrakasa, S., 2019. Distribution of methylhopanes in some Niger Delta oils. Arabian Journal of Geosciences 12, 584.

Petersen, H.I., Hillock, P., Milner, S., Pendlebury, M., Scarlett, D., 2019. Monitoring gas distribution and origin in the Culzean Field, UK Central North Sea, using data from a continuous isotope logging tool and isotube and test samples. Journal of Petroleum Geology 42, 435-449.

Tang, S., Zhou, Y., Yao, X., Feng, X., Li, Z., Wu, G., Guangyou, Z., 2019. The mercury isotope signatures of coalbed gas and oil-type gas: Implications for the origins of the gases. Applied Geochemistry 109, 104415.

Wang, Q., Huang, H., Li, Z., Li, Z., 2019. Novel thermal maturity parameters derived from alkylbiphenyls and alkyldiphenylmethanes. Energy & Fuels 33, 8491-8502.

Wang, Y., Chen, J., Pang, X., Zhang, K., Shen, W., Chen, Z., Zhang, G., Luo, G., 2019. Analysis of Ordovician hydrocarbon migration in the Halahatang area, Tarim Basin, NW China. Carbonates and Evaporites 34, 1055-1075.

Yao, J., Xiao, Z., Liu, G., Han, M., 2019. Source of crude oil in Chang-8 member of Wuqi oil-field, Ordos Basin, China. Petroleum Science and Technology 37, 2288-2294.

Zhu, Z., Li, M., Tang, Y., Qi, L., Leng, J., Liu, X., Xiao, H., 2019. Identification of phenyldibenzothiophenes in coals and the effects of thermal maturity on their distributions based on geochemical data and theoretical calculations. Organic Geochemistry 138, 103910.

SOURCE ROCKS

Chen, R., Yuan, K., Zhang, Z.-y., Xu, Q.-f., 2019. Sedimentary environment of organic-rich shale in the Upper Permian Longtan Formation in Qinglong area, western Guizhou, China. China Geology 2, 108-109.

Goodarzi, F., Gentzis, T., Dewing, K., 2019. Influence of igneous intrusions on the thermal maturity of organic matter in the Sverdrup Basin, Arctic Canada. International Journal of Coal Geology 213, 103280.

Goryl, M., Banasik, K., Smolarek-Lach, J., Marynowski, L., 2019. Utility of Raman spectroscopy in estimates of the thermal maturity of Ediacaran organic matter: An example from the East European Craton. Geochemistry 79, 467-474.

Guo, P., Liu, C., Gibert, L., Huang, L., Zhang, D., Dai, J., 2020. How to find high-quality petroleum source rocks in saline lacustrine basins: A case study from the Cenozoic Qaidam Basin, NW China. Marine and Petroleum Geology 111, 603-623.

Guo, Z., Liu, W., Liu, C., Tian, J., Zeng, X., Cui, H., 2019. Biomarker characteristics of hydrocarbon source rocks in saline lacustrine basin: a case study of Paleogene–Neogene strata in the Western Qaidam Basin, western China. Carbonates and Evaporites 34, 679-698.

Hao, J., Zhong, N., Luo, Q., Liu, D., Wu, J., Liu, A., 2019. Raman spectroscopy of graptolite periderm and its potential as an organic maturity indicator for the Lower Paleozoic in southwestern China. International Journal of Coal Geology 213, 103278.

Henry, D.G., Jarvis, I., Gillmore, G., Stephenson, M., 2019. Raman spectroscopy as a tool to determine the thermal maturity of organic matter: Application to sedimentary, metamorphic and structural geology. Earth-Science Reviews 198, 102936.

Jiang, L., George, S.C., 2019. Biomarker signatures of Upper Cretaceous Latrobe Group petroleum source rocks, Gippsland Basin, Australia: Distribution and geological significance of aromatic hydrocarbons. Organic Geochemistry 138, 103905.

Li, Q., Wu, S., Xia, D., You, X., Zhang, H., Lu, H., 2020. Major and trace element geochemistry of the lacustrine organic-rich shales from the Upper Triassic Chang 7 Member in the southwestern Ordos Basin, China: Implications for paleoenvironment and organic matter accumulation. Marine and Petroleum Geology 111, 852-867.

Li, Y., Sun, P., Liu, Z., Wang, J., Li, Y., Zhang, M., 2019. Lake level controls on oil shale distribution in the Lucaogou Formation, Wujiawan area, Junggar Basin, northwest China. Energy & Fuels 33, 8383-8393.

Liang, F., Zhang, Q., Xiong, X., Cui, H., Liang, P., Ma, C., 2019. Sedimentary evolution model of Upper Ordovician Wufeng-Lower Silurian Longmaxi organic-rich shale in the Sichuan Basin and its surrounding area. Acta Sedimentologica Sinica 37, 847-857.

Liu, Y., Wu, B., Gong, Q., Cao, H., 2019. Geochemical characteristics of the lower Silurian Longmaxi Formation on the Yangtze Platform, South China: Implications for depositional environment and accumulation of organic matters. Journal of Asian Earth Sciences 184, 104003.

Makled, W.A., El Ashwah, A.A.E., Lotfy, M.M., Hegazey, R.M., 2020. Anatomy of the organic carbon related to the Miocene syn-rift dysoxia of the Rudeis Formation based on foraminiferal indicators and palynofacies analysis in the Gulf of Suez, Egypt. Marine and Petroleum Geology 111, 695-719.

Rauball, J.F., Sachsenhofer, R.F., Bechtel, A., Coric, S., Gratzer, R., 2019. The Oligocene–Miocene Menilite Formation in the Ukrainian Carpathians: A world-class source rock. Journal of Petroleum Geology 42, 393-415.

Rizzi, M., Fyhn, M.B.W., Schovsbo, N.H., Korte, C., Hovikoski, J., Olivarius, M., Thomsen, T.B., Keulen, N., Thuy, N.T.T., Hoang, B.H., Dung, B.V., Toan, D.M., Abatzis, I., Nielsen, L.H., 2020. Hinterland setting and composition of an Oligocene deep rift-lake sequence, Gulf of Tonkin, Vietnam: Implications for petroleum source rock deposition. Marine and Petroleum Geology 111, 496-509.

Wang, M.-j., Xiao, G.-l., Yang, C.-q., Yang, Y.-q., Chen, X., Huang, L., 2019. Characteristics and evaluation of Mesozoic source rocks in the southeastern East China Sea continental shelf. China Geology 2, 133-141.


Wang, Y., Cao, J., Li, X., Zhang, J., Wang, Y., 2019. Cretaceous and Paleogene saline lacustrine source rocks discovered in the southern Junggar Basin, NW China. Journal of Asian Earth Sciences 185, 104019.


Xue, C., Zhong, J., Hou, M., Li, F., Peng, C., 2019. Sedimentary facies distribution and the characteristics of transitional shale in the upper Palaeozoic in northeast Ordos basin, China. Arabian Journal of Geosciences 12, 530.

Yin, J., Guo, L., Meng, J., Hao, F., Chen, X., Cao, Y., Zou, H., 2019. Environmental reconstruction and formation mechanisms for lacustrine source rocks of the third member of the Shahejie Formation in the Raoyang Sag, Bohai Bay Basin, eastern China. Australian Journal of Earth Sciences 66, 1145-1162.

Zhang, G., Wang, D., Zeng, Q., Yang, H., Li, Z., Zhao, Z., Guo, S., 2019. Characteristics of coal-measure source rock and gas accumulation belts in marine-continental transitional facies fault basins: A case study of the Oligocene deposits in the Qiongdongnan Basin located in the northern region of the South China Sea. Energy Exploration & Exploitation 37, 1752-1778.



Zhu, X., Chen, J., Li, W., Pei, L., Liu, K., Chen, X., Zhang, T., 2020. Hydrocarbon generation potential of Paleogene coals and organic rich mudstones in Xihu sag, East China Sea Shelf basin, offshore eastern China. Journal of Petroleum Science and Engineering 184, 106450.

UNCONVENTIONALS

Abouelresh, M., Babalola, L., Bokhari, A., Omer, M., Koithan, T., Boyde, D., 2020. Sedimentology, geochemistry and reservoir potential of the organic-rich Qusaiba Shale, Tabuk Basin, NW Saudi Arabia. Marine and Petroleum Geology 111, 240-260.


Duan, Y.T., Li, X., Ranjith, P.G., Wu, Y.F., 2020. An investigation of the evolution of the internal structures and failure modes of Longmaxi shale using novel X-ray microscopy. Journal of Petroleum Science and Engineering 184, 106479.

Fan, W., Sun, H., Yao, J., Fan, D., Yang, Y., 2019. An upscaled transport model for shale gas considering multiple mechanisms and heterogeneity based on homogenization theory. Journal of Petroleum Science and Engineering 183, 106392.



Hu, S., Li, S., Xia, L., Lv, Q., Cao, J., 2020. On the internal oil migration in shale systems and implications for shale oil accumulation: A combined petrological and geochemical investigation in the Eocene Nanxiang Basin, China. Journal of Petroleum Science and Engineering 184, 106493.

Hu, X., Deng, H., Lu, C., Tian, Y., Jin, Z., 2019. Characterization of CO2/CH4 competitive adsorption in various clay minerals in relation to shale gas recovery from molecular simulation. Energy & Fuels 33, 8202-8214.

Ji, L., Lin, M., Jiang, W., Cao, G., Zhou, J., Luo, C., 2019. Investigation into the apparent permeability and gas-bearing property in typical organic pores in shale rocks. Marine and Petroleum Geology 110, 871-885.

Jiang, H., Daigle, H., 2019. Effects of fluids removal and thermal maturation on permeability and pore structure of organic-rich shale: Results from pyrolysis experiments. Journal of Petroleum Science and Engineering 183, 106453.

Khalid, P., Qureshi, J., Din, Z.U., Ullah, S., Sami, J., 2019. Effect of kerogen and TOC on seismic characterization of Lower Cretaceous shale gas plays in Lower Indus Basin, Pakistan. Journal of the Geological Society of India 94, 319-327.

Kurison, C., Kuleli, H.S., Mubarak, A.H., 2019. Unlocking well productivity drivers in Eagle Ford and Utica unconventional resources through data analytics. Journal of Natural Gas Science and Engineering 71, 102976.

Li, X., Jiang, Z., Jiang, S., Li, Z., Song, Y., Jiang, H., Qiu, H., Cao, X., Miao, Y., 2020. Various controlling factors of matrix-related pores from differing depositional shales of the Yangtze Block in south China: Insight from organic matter isolation and fractal analysis. Marine and Petroleum Geology 111, 720-734.

Liang, F., Zhang, Q., Cui, H., Meng, Q., Ma, C., Liang, P., Guo, W., 2019. Controlling factors of organic nanopore development: A case study on marine shale in the middle and

upper Yangtze region, South China. Acta Geologica Sinica - English Edition 93, 1047-1059.

Liu, Y., Hou, J., 2019. Investigation on the potential relationships between geophysical properties and CH4 adsorption in a typical shale gas reservoir. Energy & Fuels 33, 8354-8362.

Luo, S., Chen, X., Liu, A., Li, H., Sun, C., 2019. Characteristics and geological significance of canister desorption gas from the Lower Cambrian Shuijingtuo Formation shale in Yichang area, Middle Yangtze region. Acta Petrolei Sinica 40, 941-955.

Nie, H., Jin, Z., Sun, C., He, Z., Liu, G., Liu, Q., 2019. Organic matter types of the Wufeng and Longmaxi formations in the Sichuan Basin, South China: Implications for the formation of organic matter pores. Energy & Fuels 33, 8076-8100.



Xin, C., Chen, L., Guo, X., Wang, C., 2019. Geochemical characteristics of shale gas in the Silurian Longmaxi Formation, Jiaoshiba area, southeast Sichuan Basin, China. Energy & Fuels 33, 8045-8054.




Zhang, J., Xu, H., Zhou, Z., Ren, P., Guo, J., Wang, Q., 2019. Geological characteristics of shale gas reservoir in Yichang area, western Hubei. Acta Petrolei Sinica 40, 887-899.

Zhang, S., Liu, H., Liu, Y., Wang, Y., Wang, M., Bao, Y., Hu, Q., Li, Z., Zhang, S., Yao, S., Wang, Y., Xiong, W., Liu, P., Fang, Z., 2020. Main controls and geological sweet spot types in Paleogene shale oil rich areas of the Jiyang Depression, Bohai Bay basin, China. Marine and Petroleum Geology 111, 576-587.

Zhao, Y., Wang, C., Zhang, Y., Liu, Q., 2019. Experimental study of adsorption effects on shale permeability. Natural Resources Research 28, 1575-1586.

Precambrian Geochemistry

Liu, P., Harman, C.E., Kasting, J.F., Hu, Y., Wang, J., 2019. Can organic haze and O2 plumes explain patterns of sulfur mass-independent fractionation during the Archean? Earth and Planetary Science Letters 526, 115767.

Magalhães, N., Farquhar, J., Bybee, G., Penniston-Dorland, S., Rumble III, D., Kinnaird, J., McCreesh, M., 2019. Multiple sulfur isotopes reveal a possible non-crustal source of sulfur for the Bushveld Province, southern Africa. Geology 47, 982-986.

Mettam, C., Zerkle, A.L., Claire, M.W., Prave, A.R., Poulton, S.W., Junium, C.K., 2019. Anaerobic nitrogen cycling on a Neoarchaean ocean margin. Earth and Planetary Science Letters 527, 115800.


Pitarello, M.Z., Santos, T.J.S.d., Ancelmi, M.F., 2019. Syn-to post-depositional processes related to high grade metamorphic BIFs: Geochemical and geochronological evidences from a Paleo to Neoarchean (3.5–2.6 Ga) terrane in NE Brazil. Journal of South American Earth Sciences 96, 102312.

Shields, G.A., Mills, B.J.W., Zhu, M., Raub, T.D., Daines, S.J., Lenton, T.M., 2019. Unique Neoproterozoic carbon isotope excursions sustained by coupled evaporite dissolution and pyrite burial. Nature Geoscience 12, 823-827.

Sindhuja, C.S., Khelen, A.C., Manikyamba, C., 2019. Geochemistry of Archean–Proterozoic shales, Dharwar Craton, India: Implications on depositional environment. Geological Journal 54, 2759-2778.


ORGANICS/MICROFOSSILS/MICROBIAL EVOLUTION


Chen, H., Lin, X., Cheng, X., Yang, S., Zhang, F., Wu, L., Ding, W., Li, Y., Hu, B., Huang, W., Chen, Y., 2019. The Late Neoproterozoic sedimentary sequences in the Yutang section southwest Tarim Basin and their tectonic implications and hydrocarbon perspective: Insight from basinology. Precambrian Research 333, 105432.




Liu, X., Li, S., Zhang, J., Li, X., Zhao, S., Dai, L., Wang, G., 2019. Meso-Neoproterozoic strata and target source rocks in the North China Craton: A review. Precambrian Research 334, 105458.

Rasmussen, B., Muhling, J.R., 2019. Evidence for widespread oil migration in the 1.88 Ga Gunflint Formation, Ontario, Canada. Geology 47, 899-903.

Rule, R.G., Pratt, B.R., 2019. The pseudofossil Horodyskia: Flocs and flakes on microbial mats in a shallow Mesoproterozoic sea (Appekunny Formation, Belt Supergroup, western North America). Precambrian Research 333, 105439.

Wang, G., Li, S., Li, X., Zhao, W., Zhao, S., Suo, Y., Liu, X., Somerville, I., Liu, Y., Zhou, J., Wang, Z., 2019. Destruction effect on Meso-Neoproterozoic oil-gas traps derived from Meso-Cenozoic deformation in the North China Craton. Precambrian Research 333, 105427.

Zhu, G.-y., Li, T.-t., Zhao, K., Zhang, Z.-y., Chen, W.-y., Yan, H.-h., Zhang, K.-j., Chi, L.-x., 2019. Excellent source rocks discovered in the Cryogenian interglacial deposits in South China: Geology, geochemistry, and hydrocarbon potential. Precambrian Research 333, 105455.

PALEOCLIMATOLOGY/PALEOCEANOGRAPHY

Hodgskiss, M.S.W., Crockford, P.W., Peng, Y., Wing, B.A., Horner, T.J., 2019. A productivity collapse to end Earth’s Great Oxidation. Proceedings of the National Academy of Sciences 116, 17207-17212.

Hoffman, P.F., Lamothe, K.G., 2019. Seawater-buffered diagenesis, destruction of carbon isotope excursions, and the composition of DIC in Neoproterozoic oceans. Proceedings of the National Academy of Sciences 116, 18874-18879.

Shang, M., Tang, D., Shi, X., Zhou, L., Zhou, X., Song, H., Jiang, G., 2019. A pulse of oxygen increase in the early Mesoproterozoic ocean at ca. 1.57–1.56 Ga. Earth and Planetary Science Letters 527, 115797.

Thibon, F., Blichert-Toft, J., Albarede, F., Foden, J., Tsikos, H., 2019. A critical evaluation of copper isotopes in Precambrian Iron Formations as a paleoceanographic proxy. Geochimica et Cosmochimica Acta 264, 130-140.

CRUSTAL EVOLUTION

Capitanio, F.A., Nebel, O., Cawood, P.A., Weinberg, R.F., Chowdhury, P., 2019. Reconciling thermal regimes and tectonics of the early Earth. Geology 47, 923-927.

Gerya, T., 2019. Geodynamics of the early Earth: Quest for the missing paradigm. Geology 47, 1006-1007.

Production/Engineering Geochemistry




ASPHALTENES

Bassir, S.M., Madani, M., 2019. A new model for predicting asphaltene precipitation of diluted crude oil by implementing LSSVM-CSA algorithm. Petroleum Science and Technology 37, 2252-2259.


Cheshkova, T.V., Sergun, V.P., Kovalenko, E.Y., Gerasimova, N.N., Sagachenko, T.A., Min, R.S., 2019. Resins and asphaltenes of light and heavy oils: Their composition and structure. Energy & Fuels 33, 7971-7982.

Evdokimov, I.N., 2019. Colloidal asphaltenes—non-extinct “dinosaurs” in native petroleum. Energy & Fuels 33, 8440-8447.


Gray, M.R., Yarranton, H.W., 2019. Quantitative modeling of formation of asphaltene nanoaggregates. Energy & Fuels 33, 8566-8575.

Li, C., Zhu, H., Yang, F., Liu, H., Wang, F., Sun, G., Yao, B., 2019. Effect of asphaltene polarity on wax precipitation and deposition characteristics of waxy oils. Energy & Fuels 33, 7225-7233.

Morozov, E.V., Yushmanov, P.V., Martyanov, O.N., 2019. Temperature-triggered rearrangement of asphaltene aggregates as revealed by pulsed-field gradient NMR. Energy & Fuels 33, 6934-6945.

Ok, S., Mahmoodinia, M., Rajasekaran, N., Sabti, M.A., Lervik, A., van Erp, T.S., Cabriolu, R., 2019. Molecular structure and solubility determination of asphaltenes. Energy & Fuels 33, 8259-8270.

Ruiz-Morales, Y., Miranda-Olvera, A.D., Portales-Martínez, B., Domínguez, J.M., 2019. Determination of 13C NMR chemical shift structural ranges for polycyclic aromatic hydrocarbons (PAHs) and PAHs in asphaltenes: An experimental and theoretical density functional theory study. Energy & Fuels 33, 7950-7970.

Shikhov, I., Thomas, D.S., Arns, C.H., 2019. On the optimum aging time: Magnetic resonance study of asphaltene adsorption dynamics in sandstone rock. Energy & Fuels 33, 8184-8201.

Valyaeva, O.V., Ryabinkina, N.N., Bushnev, D.A., 2019. Composition of the thermolysis products of asphaltenes from natural bitumen of the Voya deposit in the Timan–Pechora Province. Petroleum Chemistry 59, 956-960.

Vanani, M.B., Daneshfar, R., Khodapanah, E., 2019. A novel MLP approach for estimating asphaltene content of crude oil. Petroleum Science and Technology 37, 2238-2245.

INTERFACES/EOR



Druetta, P., Picchioni, F., 2019. Branched polymers and nanoparticles flooding as separate processes for enhanced oil recovery. Fuel 257, 115996.

Feyzullayev, A.A., Lerche, I., 2019. Organic matter in rock–water systems of petroliferous basins: interrelationships (a case study: South Caspian Basin). Oil & Gas Science and Technology – Revue d’IFP Energies nouvelles 74, 74.



Koleini, M.M., Badizad, M.H., Kargozarfard, Z., Ayatollahi, S., 2019. Interactions between rock/brine and oil/brine interfaces within thin brine film wetting carbonates: A molecular dynamics simulation study. Energy & Fuels 33, 7983-7992.

Li, Z., Kang, W., Bai, B., Wu, H., Gou, C., Yuan, Y., Xu, D., Lu, Y., Hou, J., 2019. Fabrication and mechanism study of the fast spontaneous emulsification of crude oil with anionic/cationic surfactants as an enhanced oil recovery (EOR) method for low-permeability reservoirs. Energy & Fuels 33, 8279-8288.

Machale, J., Majumder, S.K., Ghosh, P., Sen, T.K., 2019. Development of a novel biosurfactant for enhanced oil recovery and its influence on the rheological properties of polymer. Fuel 257, 116067.

Moosavi, S.R., Wood, D.A., Ahmadi, M.A., Choubineh, A., 2019. ANN-based prediction of laboratory-scale performance of CO2-foam flooding for improving oil recovery. Natural Resources Research 28, 1619-1637.

Zeng, L., Chen, Y., Hossain, M.M., Saeedi, A., Xie, Q., 2019. Wettability alteration induced water uptake in shale oil reservoirs: A geochemical interpretation for oil-brine-OM interaction during hydraulic fracturing. International Journal of Coal Geology 213, 103277.

Zeng, L., Chen, Y., Lu, Y., Lau, H.C., Hossain, M.M., Saeedi, A., Xie, Q., 2019. Interpreting water uptake by shale with ion exchange, surface complexation, and disjoining pressure. Energy & Fuels 33, 8250-8258.

Zhong, X., Li, C., Pu, H., Zhou, Y., Zhao, J.X., 2019. Increased nonionic surfactant efficiency in oil recovery by integrating with hydrophilic silica nanoparticle. Energy & Fuels 33, 8522-8529.

Zou, J., Liao, X., Chen, Z., Zhao, X., Mu, L., Chu, H., Dong, P., Guan, C., 2019. Integrated PVT and coreflooding studies of carbonated water injection in tight oil reservoirs: A case study. Energy & Fuels 33, 8852-8863.

HEAVY OIL PRODUCTION

Baek, K.H., Argüelles-Vivas, F.J., Abeykoon, G.A., Okuno, R., Weerasooriya, U.P., 2019. Application of ultrashort hydrophobe surfactants with cosolvent characters for heavy oil recovery. Energy & Fuels 33, 8241-8249.

Mozhdehei, A., Hosseinpour, N., Bahramian, A., 2019. Dimethylcyclohexylamine switchable solvent interactions with asphaltenes toward viscosity reduction and in situ upgrading of heavy oils. Energy & Fuels 33, 8403-8412.

Recent Sediments

Aepfler, R.F., Bühring, S.I., Elvert, M., 2019. Substrate characteristic bacterial fatty acid production based on amino acid assimilation and transformation in marine sediments. FEMS Microbiology Ecology 95, fiz131.

Chávez-Lara, C.M., Holtvoeth, J., Roy, P.D., Pancost, R.D., 2019. Lipid biomarkers in lacustrine sediments of subtropical northeastern Mexico and inferred ecosystem changes during the late Pleistocene and Holocene. Palaeogeography, Palaeoclimatology, Palaeoecology 535, 109343.

Chen, L., Luo, M., Dale, A.W., Rashid, H., Lin, G., Chen, D., 2019. Reconstructing organic matter sources and rain rates in the southern West Pacific Warm Pool during the transition from the deglaciation period to early Holocene. Chemical Geology 529, 119291.

Coffinet, S., Meador, T.B., Mühlena, L., Becker, K.W., Schröder, J., Zhu, Q.-Z., Lipp, J.S., Heuer, V.B., Crump, M.P., Hinrichs, K.-U., 2019. Structural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs). Biogeosciences Discussions 2019, 1-17.

De Schepper, S., Ray, J.L., Skaar, K.S., Sadatzki, H., Ijaz, U.Z., Stein, R., Larsen, A., 2019. The potential of sedimentary ancient DNA for reconstructing past sea ice evolution. The ISME Journal 13, 2566-2577.

Dearing Crampton-Flood, E., Peterse, F., Sinninghe Damsté, J.S., 2019. Production of branched tetraethers in the marine realm: Svalbard fjord sediments revisited. Organic Geochemistry 138, 103907.

Gar’kusha, D.N., Fedorov, Y.A., Tambieva, N.S., Andreev, Y.A., Mikhailenko, O.A., 2019. Methane in water and bottom sediments of Lake Baikal. Water Resources 46, 726-737.

He, H., Liu, Z., Chen, C., Wei, Y., Bao, Q., Sun, H., Hu, Y., Yan, H., 2019. Influence of the biological carbon pump effect on the sources and deposition of organic matter in Fuxian Lake, a deep oligotrophic lake in southwest China. Acta Geochimica 38, 613-626.

Huguet, C., Kim, J.H., González-Arango, C., Ramírez-Valencia, V., Kang, S., Gal, J.K., Shin, K.H., 2019. Sources of organic matter in two contrasting tropical coastal environments: The Caribbean Sea and the eastern Pacific. Journal of South American Earth Sciences 96, 102349.

Ma, J., Xu, X., Yu, C., Liu, H., Wang, G., Li, Z., Xu, B., Shi, R., 2020. Molecular biomarkers reveal co-metabolism effect of organic detritus in eutrophic lacustrine sediments. Science of The Total Environment 698, 134328.

Matys, E.D., Mackey, T., Grettenberger, C., Mueller, E., Jungblut, A., Sumner, D.Y., Hawes, I., Summons, R.E., 2019. Environmental controls on bacteriohopanepolyol profiles of benthic microbial mats from Lake Fryxell, Antarctica. Geobiology 17, 551-563.

Pederson, C.L., Klaus, J.S., Swart, P.K., McNeill, D.F., 2019. Deposition and early diagenesis of microbial mud in the Florida Everglades. Sedimentology 66, 1989-2010.

Scheingross, J.S., Hovius, N., Dellinger, M., Hilton, R.G., Repasch, M., Sachse, D., Gröcke, D.R., Vieth-Hillebrand, A., Turowski, J.M., 2019. Preservation of organic carbon during active fluvial transport and particle abrasion. Geology 47, 958-962.

Sun, W., Zhang, E., Chen, R., Shen, J., 2019. Lacustrine carbon cycling since the last interglaciation in northeast China: Evidence from n-alkanes in the sediments of Lake Xingkai. Quaternary International 523, 101-108.

Wang, K.J., O'Donnell, J.A., Longo, W.M., Amaral-Zettler, L., Li, G., Yao, Y., Huang, Y., 2019. Group I alkenones and Isochrysidales in the world’s largest maar lakes and their potential paleoclimate applications. Organic Geochemistry 138, 103924.

Wang, X., Bayon, G., Kim, J.-H., Lee, D.-H., Kim, D., Guéguen, B., Rouget, M.-L., Barrat, J.-A., Toffin, L., Feng, D., 2019. Trace element systematics in cold seep carbonates and associated lipid compounds. Chemical Geology 528, 119277.

ATMOSPHERIC GEOCHEMISTRY

Barati, F., Yao, Q., Asa-Awuku, A.A., 2019. Insight into the role of water-soluble organic solvents for the cloud condensation nuclei activation of cholesterol. ACS Earth and Space Chemistry 3, 1697-1705.

Fulgham, S.R., Brophy, P., Link, M., Ortega, J., Pollack, I., Farmer, D.K., 2019. Seasonal flux measurements over a Colorado pine forest demonstrate a persistent source of organic acids. ACS Earth and Space Chemistry 3, 2017-2032.


HYDROSPHERE GEOCHEMISTRY


Cornejo-Castillo, F.M., Zehr, J.P., 2019. Hopanoid lipids may facilitate aerobic nitrogen fixation in the ocean. Proceedings of the National Academy of Sciences 116, 18269-18271.

Davis, C.E., Blackbird, S., Wolff, G., Woodward, M., Mahaffey, C., 2019. Seasonal organic matter dynamics in a temperate shelf sea. Progress in Oceanography 177, 101925.

Durham, B.P., Boysen, A.K., Carlson, L.T., Groussman, R.D., Heal, K.R., Cain, K.R., Morales, R.L., Coesel, S.N., Morris, R.M., Ingalls, A.E., Armbrust, E.V., 2019. Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nature Microbiology 4, 1706-1715.

Holland, A.T., Williamson, C.J., Sgouridis, F., Tedstone, A.J., McCutcheon, J., Cook, J.M., Poniecka, E., Yallop, M.L., Tranter, M., Anesio, A.M., The Black & Bloom Group, 2019.

Dissolved organic nutrients dominate melting surface ice of the Dark Zone (Greenland Ice Sheet). Biogeosciences 16, 3283-3296.

Ikenoue, T., Kimoto, K., Okazaki, Y., Sato, M., Honda, M.C., Takahashi, K., Harada, N., Fujiki, T., 2019. Phaeodaria: An important carrier of particulate organic carbon in the mesopelagic twilight zone of the North Pacific Ocean. Global Biogeochemical Cycles 33, 1146-1160.


Li, Y., Sun, L.-L., Sun, Y.-Y., Cha, Q.-Q., Li, C.-Y., Zhao, D.-L., Song, X.-Y., Wang, M., McMinn, A., Chen, X.-L., Zhang, Y.-Z., Qin, Q.-L., 2019. Extracellular enzyme activity and its implications for organic matter cycling in northern Chinese marginal seas. Frontiers in Microbiology 10, 2137. doi: 2110.3389/fmicb.2019.02137.

Macreadie, P.I., Anton, A., Raven, J.A., Beaumont, N., Connolly, R.M., Friess, D.A., Kelleway, J.J., Kennedy, H., Kuwae, T., Lavery, P.S., Lovelock, C.E., Smale, D.A., Apostolaki, E.T., Atwood, T.B., Baldock, J., Bianchi, T.S., Chmura, G.L., Eyre, B.D., Fourqurean, J.W., Hall-Spencer, J.M., Huxham, M., Hendriks, I.E., Krause-Jensen, D., Laffoley, D., Luisetti, T., Marbà, N., Masque, P., McGlathery, K.J., Megonigal, J.P., Murdiyarso, D., Russell, B.D., Santos, R., Serrano, O., Silliman, B.R., Watanabe, K., Duarte, C.M., 2019. The future of Blue Carbon science. Nature Communications 10, 3998.

Maiorano, P., Marino, M., De Lange, G.J., 2019. Dynamic surface-water alterations during sapropel S1 preserved in high-resolution shallow-water sediments of Taranto Gulf, central Mediterranean. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109340.

Meister, P., Liu, B., Khalili, A., Böttcher, M.E., Jørgensen, B.B., 2019. Factors controlling the carbon isotope composition of dissolved inorganic carbon and methane in marine porewater: An evaluation by reaction-transport modelling. Journal of Marine Systems 200, 103227.



SOIL GEOCHEMISTRY

Li, T., Song, F., Zhang, J., Liu, S., Xing, B., Bai, Y., 2020. Pyrolysis characteristics of soil humic substances using TG-FTIR-MS combined with kinetic models. Science of The Total Environment 698, 134237.

Musadji, N.Y., Lemée, L., Caner, L., Porel, G., Poinot, P., Geffroy-Rodier, C., 2020. Spectral characteristics of soil dissolved organic matter: Long-term effects of exogenous organic matter on soil organic matter and spatial-temporal changes. Chemosphere 240, 124808.

Roth, V.-N., Lange, M., Simon, C., Hertkorn, N., Bucher, S., Goodall, T., Griffiths, R.I., Mellado-Vázquez, P.G., Mommer, L., Oram, N.J., Weigelt, A., Dittmar, T., Gleixner, G., 2019. Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nature Geoscience 12, 755-761.

van der Voort, T.S., Mannu, U., Hagedorn, F., McIntyre, C., Walthert, L., Schleppi, P., Haghipour, N., Eglinton, T.I., 2019. Dynamics of deep soil carbon – insights from 14C time series across a climatic gradient. Biogeosciences 16, 3233-3246.


Zheng, F., Chen, Y., Tang, X., Su, J., Zhu, Y., Zhang, C., 2019. Changes in archaeal ether lipid composition in response to agriculture alternation in ancient and modern paddy soils. Organic Geochemistry 138, 103912.

Remote Sensing-Hydrocarbon Seepage


Smrzka, D., Zwicker, J., Misch, D., Walkner, C., Gier, S., Monien, P., Bohrmann, G., Peckmann, J., 2019. Oil seepage and carbonate formation: A case study from the southern Gulf of Mexico. Sedimentology 66, 2318-2353.

Abstracts


http://www.sciencedirect.com/science/article/pii/S1875510019302549

This study aims to experimentally investigate the potential of solubility trapping mechanism in increasing CO2 storage during EGR by CO2 injection and sequestration in conventional natural gas reservoirs. A laboratory core flooding process was carried out to simulate EGR on a sandstone core at 0, 5, 10 wt% NaCl formation water salinity at 1300 psig, 50 °C and 0.3 ml/min injection rate. The results show that CO2 storage capacity was improved significantly when solubility trapping was considered. Lower connate water salinities (0 and 5 wt%) showed higher CO2 solubility from IFT measurements. With 10% connate water salinity, the highest accumulation of the CO2 in the reservoir was realised with about 63% of the total CO2 injected stored; an indication of improved storage capacity. Therefore, solubility trapping can potentially increase the CO2 storage capacity of the gas reservoir by serving as a secondary trapping mechanism in addition to the primary structural and stratigraphic trapping and improving CH4 recovery.

Abouelresh, M., Babalola, L., Bokhari, A., Omer, M., Koithan, T., Boyde, D., 2020. Sedimentology, geochemistry and reservoir potential of the organic-rich Qusaiba Shale, Tabuk Basin, NW Saudi Arabia. Marine and Petroleum Geology 111, 240-260.


The Qusaiba Shale Formation of the Qalibah Group is the most prolific source rock for the Paleozoic petroleum system in Saudi Arabia and is recently considered as a potential unconventional shale gas reservoir. Detailed sedimentological, petrographical, and geochemical analyses were undertaken on an ~31 m thick outcrop of this organic-rich shale exposed in the northwest of Tayma City, NW of Saudi Arabia to provide a better understanding of the vertical and lateral lithofacies variations and the effects of such variations on reservoir properties.

X-ray diffraction analysis reveals that clay minerals (average: 50%) and quartz (average: 28%) dominate the bulk mineralogical composition while K-feldspar, plagioclase, and pyrite occur as common to minor components in the analyzed samples. An integration of the sedimentological description, petrography and mineralogical composition allows the subdivision of the investigated outcrop section into six lithofacies. These are: Laminated organic-rich shale, Graptolitic concretion, Massive organic-rich shale, Organic-lean shale, Siltstone-shale interbedded, and Cross-stratified siltstone/sandstone lithofacies. TOC content in the laminated and massive organic-rich shale lithofacies ranges between 0.5 and 6.1 wt% (average 2.52 wt%) then it decreases upward (0.04–0.35 wt%, average 0.18 wt%) in the overlying organic-lean shale and siltstone lithofacies. Trace elements (Cu, Mo, As, Ni, Co, U and V) show positive excursions in the lowermost 20 m of the organic-rich, dark-grey shale interval and display abrupt depletions at the contact with overlying organic-lean shale. The enrichment factors of these trace elements are characterized by similar distribution patterns as their measured concentrations. Like the elements, these factors also exhibit a significant depletion at the contact between the organic-rich shale and the overlying organic-lean shale. Out of all the redox indices, V/(V + Cr), V/(V + Ni), Th/U and [Mo]s/TOC were found to best distinguish between the organic-rich and the overlying organic-lean intervals.

The laminated organic-rich shale lithofacies indicate deposition of hemipelagic sediments by a relatively low energy quiet anoxic bottom water, most likely in a sulfidic conditions that were associated with a strongly restricted bottom water mass circulation at the time of its deposition. This restricted hydrographic condition was likely enhanced in the study area due to the paleotopography that was created by the deglaciation of the Early Silurian time. The TOC richness, common occurrence of pyrite and high enrichment of redox elements Mo, U and V in the organic-rich shale intervals support the existence of anoxic bottom water at the time of deposition. The abrupt decrease of the TOC and the redox sensitive elements and their associated indices from the underlying organic-rich lithofacies to the overlying organic-lean shale lithofacies is likely due to a gradual increase in oxygen level. This improved bottom water oxygenation condition might have led to a reduction in organic productivity and limited organic matter preservation in the organic-lean shale lithofacies. The graptolitic concretion lithofacies found in the sequence, refers to an in-situ, syngenetic to early diagenetic origin formed close to the sediment-water layer when there was little or no deposition or at periods characterized by low sedimentation rates. The siltstone - fine sandstone lithofacies in the topmost part of the studied section, is interpreted to indicate the dominance of high energy and highly oxygenated shallow bottom water conditions during deposition, probably in a middle to inner shelf depositional settings.

The kerogen in QS is a mixture of type III (gas prone) and type IV (inert kerogen), Tmax values with an average of 430 °C, and VRo values (average 0.58) calculated from the Tmax, assigned the studied section as immature. Qualitative evaluation of porosity allows the identification of three different types of porosity including inorganic porosity, organic porosity and natural fracture porosity. Although the ductile clay minerals are the most abundant minerals in the lower part of the studied QS (average 56%), the brittle minerals (Quartz, Feldspar, and Pyrite) form an average of 42% and exhibit a uniform distribution of brittleness in the organic-rich interval.

Adiatma, Y.D., Saltzman, M.R., Young, S.A., Griffith, E.M., Kozik, N.P., Edwards, C.T., Leslie, S.A., Bancroft, A.M., 2019. Did early land plants produce a stepwise change in atmospheric oxygen during the Late Ordovician (Sandbian ~458 Ma)? Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109341.


A stepwise change in atmospheric oxygen (O2) levels during the Ordovician has been attributed to the emergence of land plants. This phenomenon is tied to a major baseline shift in the stable carbon isotope (δ13C) curve and inferred increase in nutrient delivery and enhanced primary productivity in nearshore settings, which led to high organic carbon burial. The timing and magnitude of this baseline shift, however, is still elusive in part because of the lack of high-resolution δ13C data that span this period. Much of the existing Ordovician δ13C literature is focused on isotopic excursions with less emphasis on identifying long-term shifts in baseline (pre- and post-excursion) values.

This study presents new high resolution δ13C data from stratigraphic sections at Germany Valley (West Virginia) and Union Furnace (Pennsylvania) in the Central Appalachian Basin. These sections span the entire Sandbian Stage and continue into the lower Katian Stage. The δ13C data from both sections are characterized by relative stability carbon isotope values (mean = −0.61‰) in the lower Sandbian, followed by a + 1.2‰ shift in the upper Sandbian (mean = +0.62‰). Herein, we propose that the positive shift represents a long-term global shift in baseline δ13C values of dissolved inorganic carbon. The timing of this positive shift coinciding with the diversification of early land plants (i.e., bryophytes) supports earlier models that suggested enhanced organic carbon burial rates served as a mechanism for the stepwise oxygenation of the atmosphere during the Late Ordovician.

Aepfler, R.F., Bühring, S.I., Elvert, M., 2019. Substrate characteristic bacterial fatty acid production based on amino acid assimilation and transformation in marine sediments. FEMS Microbiology Ecology 95, fiz131.

https://doi.org/10.1093/femsec/fiz131

Polar lipid-derived fatty acids (PLFAs) and their stable carbon isotopes are frequently combined to characterize microbial populations involved in the degradation of organic matter, offering a link to biogeochemical processes and carbon sources used. However, PLFA patterns derive from multiple species and may be influenced by substrate types. Here, we investigated such dependencies by monitoring the transformation of position-specifically 13C-labeled amino acids (AAs) in coastal marine sediments dominated by heterotrophic bacteria. Alanine was assimilated into straight-chain FAs, while valine and leucine incorporation led to the characteristic production of even- and odd-numbered iso-series FAs. This suggests that identical microbial communities adjust lipid biosynthesis according to substrate availability. Transformation into precursor molecules for FA biosynthesis was manifested in increased 13C recoveries of the corresponding volatiles acetate, isobutyrate and isovalerate of up to 39.1%, much higher than for PLFAs (<0.9%). A significant fraction of 13C was found in dissolved inorganic carbon (up to 37.9%), while less was recovered in total organic carbon (up to 17.3%). We observed a clear discrimination against the carboxyl C, whereby C2 and C3 positions were preferentially incorporated into PLFAs. Therefore, position-specific labeling is an appropriate tool for reconstructing the metabolic fate of protein-derived AAs in marine environments.

Ahmed, M.A., Hegab, O.A., Awadalla, A.S., Farag, A.E., Hassan, S., 2019. Hydrocarbon generation, in-source conversion of oil to gas and expulsion: Petroleum system modeling of the Duwi Formation, Gulf of Suez, Egypt. Natural Resources Research 28, 1547-1573.

https://doi.org/10.1007/s11053-019-09458-9

A multiple forward 1D modeling approach on four wells in the Abu Rudeis-Sidri oil field has been performed in accordance with the plate tectonics and crustal development of the Gulf of Suez, Egypt. The current work intends to simulate the hydrocarbon generating capability, in-source conversion of oil to gas, expulsion and adsorption (retention) of marine sulfur-rich Duwi kerogen. The integration of log responses and organic geochemistry indicate mature organic-rich intervals that have been confirmed by the 1D model. The rifting phases and its associated thermal cooling have a prominent contribution on the thermal maturation, particularly the Mio-Pliocene event. The elevated basal heat flow associated with the lithosphere thinning due to different rifting phases accelerates the thermal maturation of the high sulfur content of Duwi organic-rich interval. The pre-rift sequences are thermal insulators in contrast to the post-rift sequences of evaporites that can cool the underlying strata. Hydrocarbon generation, gas secondary cracking and expulsion are influenced by the post-rift thermal subsidence (the first and second phases). The kerogen has attained a thermal maturity level to generate liquid hydrocarbon since the Messinian (~ 5.8 Ma) and thermogenic gas secondary cracking since Zanclean (~ 3.57 Ma). The hydrocarbon generation (Early Pliocene) is related to the combination of basin burial (accompanied the first phase post-rift thermal subsidence) and the rift renewal through the Pliocene (Messinian Time Event). The gas generation is related to the second phase post-rift thermal subsidence that is accompanied by the deposition of the Post-Zeit Formation. Most of the hydrocarbons attained peak bulk generation during Pliocene (5.8 Ma), which dominated until expulsion commenced (2.52 Ma). The expulsion onset (Late Pliocene) attained subsequent to gas generation and after rift structural trap formation in Late Oligocene–Early Miocene. The expulsion onset (2.52 Ma) related mainly due to a high transformation ratio of kerogen, compaction and partly because of higher initial values of TOC (4.8%) as compared with its present-day values (3.2%). Applying the sensitivity analysis inferred that the source rock properties (HI and TOC) are not assigned as a controlling factor in the maturation process. The eroded thickness has small influence on the maturation process. In contrast, the excellent correlation (Pearson correlation coefficient = 1) supports that heat flow superimposed on the burial-related maturation.

Ali, I., Suhail, M., Aboul-Enein, H.Y., 2019. Advances in chiral multidimensional liquid chromatography. TrAC Trends in Analytical Chemistry 120, 115634.


It is well known that the chiral separation is different but very important in separation science. Increase in number of chiral centers makes the chiral separations more difficult. In this respect multidimensional chromatography is gaining importance in chiral separations. There is a great demand of multidimensional chromatography in the chiral separations. The present article describes the separation and identification various racemates using multidimensional chromatography i.e. high performance liquid chromatography, gas chromatography, super critical fluid chromatography, thin layer chromatography. Besides, the efforts were made to discuss the importance of chiral separations, multidimensional chromatography, future perspectives and challenges. Certainly, this article will be useful for the researchers, academicians, government authorities and industrial persons.

Alleon, J., Summons, R.E., 2019. Organic geochemical approaches to understanding early life. Free Radical Biology and Medicine 140, 103-112.


Here we discuss the early geological record of preserved organic carbon and the criteria that must be applied to distinguish biological from non-biological origins. Sedimentary graphite, irrespective of its isotopic composition, does not constitute a reliable biosignature because the rocks in which it is found are generally metamorphosed to the point where convincing signs of life have been erased. Rather, multiple lines of evidence,

including sedimentary textures, microfossils, large accumulations of organic matter and isotopic data for co-existing carbon, nitrogen and sulfur are required before biological origin can be convincingly demonstrated.

Alvarez, H.M., Herrero, O.M., Silva, R.A., Hernández, M.A., Lanfranconi, M.P., Villalba, M.S., 2019. Insights into the metabolism of oleaginous Rhodococcus spp. Applied and Environmental Microbiology 85, e00498-19.

http://aem.asm.org/content/85/18/e00498-19.abstract

Some species belonging to the Rhodococcus genus, such as Rhodococcus opacus, R. jostii, and R. wratislaviensis, are known to be oleaginous microorganisms, since they are able to accumulate triacylglycerols (TAG) at more than 20% of their weight (dry weight). Oleaginous rhodococci are promising microbial cell factories for the production of lipids to be used as fuels and chemicals. Cells could be engineered to create strains capable of producing high quantities of oils from industrial wastes and a variety of high-value lipids. The comprehensive understanding of carbon metabolism and its regulation will contribute to the design of a reliable process for bacterial oil production. Bacterial oleagenicity requires an integral configuration of metabolism and regulatory processes rather than the sole existence of an efficient lipid biosynthesis pathway. In recent years, several studies have been focused on basic aspects of TAG biosynthesis and accumulation using R. opacus PD630 and R. jostii RHA1 strains as models of oleaginous bacteria. The combination of results obtained in these studies allows us to propose a metabolic landscape for oleaginous rhodococci. In this context, this article provides a comprehensive and integrative view of different metabolic and regulatory attributes and innovations that explain the extraordinary ability of these bacteria to synthesize and accumulate TAG. We hope that the accessibility to such information in an integrated way will help researchers to rationally select new targets for further studies in the field.


https://doi.org/10.1111/sed.12568

This paper presents a case study of the sublacustrine precipitation of hydrothermal silica ± TiO2 in the Ediacaran Mançour Group of the Saghro inlier, Anti‐Atlas, Morocco. Lacustrine carbonates containing stromatolitic mats and bioherms occur in ephemeral ponds developed within the Oued Da'ra caldera. Its syn‐eruptive infill consists of pyroclastites, ashflow tuffs, and subsidiary lava flows and sills, whereas inter‐eruptive deposition is mainly represented by slope‐related debris‐flow breccias and landslides, alluvial fans and fluvial channels. Carbonate production took place in a mosaic of differentially subsiding, fault‐bounded intra‐caldera blocks controlled by episodic collapse‐induced drowning, pyroclastic blanketing and migration of alluvial/fluvial environments. After microbial carbonate production, the carbonates recorded several early‐diagenetic processes, punctuated by polyphase fissuring (controlling secondary permeability) locally linked to hydrothermal influx. Three generations of carbonate cements are recognisable: (i) fibrous, botryoidal and blocky/drusy mosaics of calcite; (ii) idiotopic mosaics of dolomite caused by flushing of hypersaline Mg‐rich brines; and (iii) euhedral to drusy calcite via dedolomitization. The δ13C and δ18O values from carbonate cements broadly become successively isotopically lighter, as a result of meteoric and hydrothermal influence, and were probably overprinted by the Panafrican‐3 phase that affected the top of the Mançour Group. Two mechanisms of silicification are involved: (i) early‐diagenetic occlusion of interparticle pores at the sediment/water interface of pyroclastic substrates and reefal core and flanks; and (ii) hydrothermal precipitation of silica ± TiO2 lining fissures and vuggy porosity encased in the host rock. Silica conduits cross‐cutting lacustrine mats and bioherms exhibit high potential of preservation in collapsed volcanic calderas. Primary fluid inclusions of hydrothermal silica contain brine relics with NaCl/CaCl2 ratios of 2·1 to 4·4, representing minimum entrapment temperatures of about 142 to 204°C, and abiotic hydrocarbons (heavy alkanes) related to serpentinization of the volcanic and volcanosedimentary basement of the Oued Dar'a caldera.

Amonette, J.E., Zhong, L., Darrah, T.H., Grove, B.S., Cole, D.R., 2019. Noble and major gases released from rock core materials as intrinsic tracers for detecting carbon dioxide leakage – Laboratory evaluation. International Journal of Greenhouse Gas Control 89, 76-88.


Acidification of pore water in geological formations by carbon dioxide (CO2) results in the release of trapped gases, the detection of which can potentially be used to signal leakage of CO2 from storage reservoirs at carbon sequestration sites. In a set of laboratory tests, core materials from a stratigraphic borehole at the proposed FutureGen 2.0 carbon storage site (Jacksonville, IL, USA) were reacted with phosphoric acid to simulate contact with aqueous CO2. Gas released by the reaction was collected and analysed for the composition of the major and noble gases (including isotopes). These experiments yielded several promising tracer candidates for intrinsic monitoring of CO2 leakage at the proposed FutureGen 2.0 site. The most robust signals are the CH4 and 4He released by carbonates in the dolomite and siltstone formations that comprise the proposed primary containment zone. Xenon released from the primary-containment zone also showed promise as a tracer, but a more robust analysis requires a different experimental set up. A general enrichment of CH4, N2 and light noble-gas isotopes with respect to Ar abundance was observed and is consistent with the addition of major gases (CO2, CH4, and to a lesser extent, N2) released by decomposition of carbonate mineral phases and/or organic matter in the dolomite and siltstone formations. No useful signal was obtained from the sandstone formation (representing the proposed injection zone) due to its very low yield of gas when acidified.


https://doi.org/10.1134/S0965544119090020

It has been shown that deep biodegradation of the components of oils with the change in the molecular composition of aliphatic, naphthenic, and aromatic hydrocarbons (HCs) occurs upon the biodegradation of Ashal’chinskoe crude petroleum by indigenous soil microflora under laboratory conditions. It has been found that alkanes and tri- and tetracyclic aromatic HCs are present in the oils of the biodegraded petroleum not only in the molecular form but also in the form of structural fragments linked through ether or sulfide bridges in the composition of complex high-molecular-weight entities. The composition of O- and S-linked compounds of the aforementioned types is different in the oils of the petroleum subjected to biodegradation.

Ayuso-Fernández, I., Rencoret, J., Gutiérrez, A., Ruiz-Dueñas, F.J., Martínez, A.T., 2019. Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants. Proceedings of the National Academy of Sciences 116, 17900-17905.

https://doi.org/10.1073/pnas.1905040116

Significance: We analyze the evolution of ligninolytic peroxidases from wood-rotting fungi using conifer and angiosperm lignin as representatives of 2 steps of lignin evolution. By enzyme resurrection, we show that during fungal evolution, these enzymes improved their activity and switched their degradative preferences with the rise of a surface tryptophan conferring on them the ability to oxidize nonphenolic lignin. We calibrated the peroxidase phylogeny and determined that this residue appeared coincident with angiosperm diversification, characterized by the synthesis of a more complex and less phenolic lignin due to the general incorporation of a new unit in its structure. This way, we show that fungal evolution followed that of lignin synthesis, pointing to a coevolution between fungal saprotrophs and their plant hosts.

Abstract: A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (k2app and k3app) showed a progressive increase during peroxidase evolution (up to 50-fold higher values for the rate-limiting k3app). The above agreed with 2-dimensional NMR analyses during steady-state treatments of hardwood lignin, showing that its degradation (estimated from the normalized aromatic signals of lignin units compared

with a control) and syringyl-to-guaiacyl ratio increased with the enzyme evolutionary distance from the first peroxidase ancestor. More interestingly, the stopped-flow estimations of electron transfer rates also showed how the most recent peroxidase ancestors that already incorporated the exposed tryptophan into their molecular structure (as well as the extant lignin peroxidase) were comparatively more efficient at oxidizing hardwood (angiosperm) lignin, while the most ancestral “tryptophanless” enzymes were more efficient at abstracting electrons from softwood (conifer) lignin. A time calibration of the ancestry of Polyporales peroxidases localized the appearance of the first peroxidase with a solvent-exposed catalytic tryptophan to 194 ± 70 Mya, coincident with the diversification of angiosperm plants characterized by the appearance of dimethoxylated syringyl lignin units.

Baca, M., Desmet, G., Ottevaere, H., De Malsche, W., 2019. Achieving a peak capacity of 1800 using an 8 m long pillar array column. Analytical Chemistry 91, 10932-10936.

https://doi.org/10.1021/acs.analchem.9b02236

In the present study, the peak capacity potential of ultralong porous cylindrical pillar array columns is investigated. Coupling 4 columns of 2 m long allows for working near the minimal separation impedance of small molecules under retained conditions at a maximal pressure load of 250 bar. Minimal plate heights of H = 5.0 μm, H = 6.3 μm, and H = 7.7 μm were obtained for uracil (unretained), butyrophenone (k = 0.85), and valerophenone (k = 1.94), respectively, corresponding to a number of theoretical plates of N = 1.6 × 106, N = 1.2 × 106, and N = 1.0 × 106. The optimal linear velocities were 0.60 mm/s for a retained compound and 0.74 mm/s for an unretained compound. Based on a mixture of 9 compounds, the peak capacity nc was determined as a function of gradient time (tG). Peak capacities (tG-based) of 1103 and 1815 were obtained when applying 650 min and 2050 min gradients (tG/t0 = 4.5 and 14, respectively, with tG as the gradient time and t0 as the void time). These values are much higher than earlier reported peak capacity values for small molecules.

Baek, K.H., Argüelles-Vivas, F.J., Abeykoon, G.A., Okuno, R., Weerasooriya, U.P., 2019. Application of ultrashort hydrophobe surfactants with cosolvent characters for heavy oil recovery. Energy & Fuels 33, 8241-8249.

https://doi.org/10.1021/acs.energyfuels.9b01716

A new class of ultrashort hydrophobe surfactants with cosolvent characters was investigated as a sole additive to conventional polymer flooding for heavy oil recovery. No alkali was used for emulsification. The surfactants were composed of a short hydrophobe (phenol in this research) extended by propylene oxide (PO) and ethylene oxide (EO) units to achieve a sufficient level of surface activity and aqueous stability: phenol-xPO-yEO. Results are presented for the selection of ultrashort hydrophobe surfactants, aqueous stability, emulsion phase behavior, and oil displacement through a glass-bead pack at 368 K. Results show that 2 wt % phenol-4PO-20EO was able to reduce the interfacial tension between oil and NaCl brine to 0.39 dyn/cm, in comparison to 11 dyn/cm with no surfactant, at 368 K. Water flooding, 40 cp polymer flooding, and surfactant-improved polymer flooding were conducted for displacement of 276 cp heavy oil through a glass-bead pack that represents the clean-sand facies of a heavy oil reservoir in Alberta, Canada. The oil recovery after 2.0 pore volumes of injection (PVI) was 84% with the surfactant-improved polymer flooding, which was 54 and 22% greater than the water flooding and the polymer flooding, respectively. Results suggest a new opportunity of enhanced heavy oil recovery by adding a slug of one nonionic surfactant with cosolvent characters to conventional polymer flooding.



A giant gas field has been discovered in the Lower Shihezi Formation in the Hangjinqi area, northern Ordos Basin, China. Coal seams and mudstone in the Taiyuan and Shanxi Formation are considered as source rocks

and sandstone in the Lower Shihezi Formation is treated as reservoirs for gas. The charging time in the sandstone reservoirs was studied based on the homogenization temperature of aqueous inclusions, thermal and burial history simulation and K-Ar dating of authigenic illite. Two episodes of gas charging in the northern part and one episode in the southern part were delineated in the reservoirs of the Hangjinqi area, evidenced by microscopic observation of the occurrence of fluid inclusions and the analysis of salinity in aqueous inclusions. In the southern part of the study area gas charging occurred between circa 171-162 Ma, whereas in the northern part gas charging was between 158-144 Ma and 120-109 Ma, respectively. The gas charging events appeared to be influenced by the tectonic evolution of northern Ordos Basin. Paleo topography caused reduction in thickness of source rocks northwards, and contributed to differences in hydrocarbon generation potential and thermal evolution between the northern and the southern part of the study area. Therefore, gas charging occurred in the southern part prior to that in the northern part. Furthermore, tilting occurred in Middle Jurassic and provided the driver and pathways for gas, leading to a first charging event in the northern part of the study area.

Barati, F., Yao, Q., Asa-Awuku, A.A., 2019. Insight into the role of water-soluble organic solvents for the cloud condensation nuclei activation of cholesterol. ACS Earth and Space Chemistry 3, 1697-1705.

https://doi.org/10.1021/acsearthspacechem.9b00161

Organic aerosol is ubiquitous, and partially soluble organic particles can uptake water, form droplets, and act as cloud condensation nuclei (CCN). Cholesterol is a well-known organic aerosol. Cholesterol is insoluble in water (<0.002 g in 100 mL of H2O at 293 K) but readily dissolves in organic solvents. In this study, we examine the ability of cholesterol generated in 7.2%, 10.4%, and 18.9% (by volume) dilutions of three water-soluble organic solvents (ethanol, 2-propanol, and acetone) to act as CCN. The measured apparent particle hygroscopicity, κ, can vary over 2 orders of magnitude, from ∼0.001 to 0.1. We use statistical analysis of variance (ANOVA) to quantify experimental design factors, not explicitly addressed in traditional theory, that modify κ-values. Results show that (i) particle sizes (electrical mobility and aerodynamic diameters) are important for apparent hygroscopicity κ-values and that (ii) atomized aerosol formed in the presence of organic solvents modifies particle size and droplet surface tension at the air–water interface and promotes droplet formation. As the volume of water (dilution) in the atomized solution increases, the organic solvent decreases and κ decreases. Increases in organic solvent concentration decrease droplet surface tension and change aerosol shape. Thus, the apparent κ is corrected with surface tension and shape factor data. The results imply that miscible atmospheric organic solvents that readily adsorb and solvate in water enhance the droplet forming potential of cholesterol and may thus extend to other atmospheric water-insoluble organic particles.

Barberis, E., Manfredi, M., Marengo, E., Zilberstein, G., Zilberstein, S., Kossolapov, A., Righetti, P.G., 2019. Leonardo's Donna Nuda unveiled. Journal of Proteomics 207, 103450.


The painting “Donna Nuda” by Leonardo was acquired by Catherine II (the Great) from the R. Walpole collection, Houghton Hall, England, in 1779 for the Hermitage in St. Petersburg. By exploiting the EVA film technology (ethylene vinyl acetate polymer embedded with strong cation and anion exchangers and with C8 and/or C18 resins) we have explored the surface of the painting in order to ascertain the techniques used in its drawing. Five EVA films were affixed on the body and on the landscape for 60 min. Upon elution from the recovered films, the harvested material was analyzed by gas-chromatography/mass spectrometry as well as by liquid chromatography/mass spectrometry. “Tempera grassa” (consisting of linseed oil admixed with egg yolk) was used in the entire painting. The surface was then protected by a layer of conifer resin. It is hypothesized that access to the layer underneath the protective layer was obtained via micro-cracks on the conifer resin itself. Rosemary oil was used as diluent to slow down the drying process and so to perform the glazing technique, thus obtaining the “aerial perspective” in correspondence of the landscape. To our reckoning, this is the first time in which a Leonardo painting is analyzed in depth but also in which his artistic technique is deciphered via modern techniques for exploring Cultural Heritage. The EVA film technology might be used for ascertaining the authenticity of paintings and uncover frauds. Significance statement Leonardo da Vinci was the most famous

Italian polymath of the Renaissance and one of the most important innovators of his time. He was the author of several important artworks such as “La Gioconda”, but he also painted the “Donna Nuda” conserved at the Hermitage Museum. Although some attempts permitted the identification of part of the materials used by Leonardo, to date no analytical investigations were able to fully characterize and decipher the recipes. We explored the surface of the “Donna Nuda” painting through a non-invasive approach that uses a functionalized film to adsorb nano-scopic amounts of materials that were then analyzed by mass spectrometry. This method has the potential to revolutionize the approaches used to analyze cultural heritage.

Barras, C., 2019. Ancient worm fossil rolls back origins of animal life. Nature 573, 15.

https://www.nature.com/articles/d41586-019-02556-x

Half-a-billion-year-old creature challenges theory that animals burst onto the scene in an abrupt event known as the Cambrian explosion.

More than half a billion years ago, a strange, worm-like creature died as it crawled across the muddy sea floor. Both the organism and the trail it left lay undisturbed for so long that they fossilized. Now, they are helping to revise our understanding of when and how animals evolved.

The fossil, which formed some time between 551 million and 539 million years ago, in the Ediacaran period, joins a growing body of evidence that challenges the idea that animal life on Earth burst onto the scene in an event known as the Cambrian explosion, which began about 539 million years ago.

“It is just pushing things further and further back into the Ediacaran,” says Rachel Wood, a geoscientist at the University of Edinburgh, UK. The Cambrian explosion no longer appears to be such an abrupt event in the history of life on Earth, she says. An analysis of the fossil, along with a few dozen similar specimens found in the same rock sequence in southern China, is published in Nature1.

“What’s extraordinary about this paper is it’s three home runs in the same five-page manuscript,” says Simon Darroch, a palaeontologist at Vanderbilt University in Nashville, Tennessee. First, it’s exceptionally rare to find a dead animal preserved at the end of a trail it made when alive, he says. Second, the fossil dates to a crucial moment in the evolution of animal life.

And third: “It’s such a bizarre-looking organism,” says Darroch. The creature, which has been named Yilingia spiciformis and was up to 27 centimetres long, seems to be a biologically complex animal with a distinct front and rear end. “We don’t really have many of those from the Ediacaran,” he says.

Ancient organisms. The rock record has already revealed that the Ediacaran seas were rich in life, but many Ediacaran fossils have strange anatomical features that are unlike those seen in modern animals. Because of this, palaeontologists have struggled to relate the Ediacaran organisms to the creatures of the Cambrian period. This bolstered the idea that the Cambrian explosion represented the dramatic first appearance of familiar animals.

But opinions have begun to shift in the past few years. Some Ediacaran organisms have been recognized as animals despite their peculiar anatomy, which suggests that animal life began millions of years before the Cambrian explosion.

Yilingia spiciformis fits into that picture and pushes the idea further. With a segmented body that is symmetrical down its length, it has an anatomy that is more obviously similar to that of Cambrian animals, says Shuhai Xiao, a palaeontologist at Virginia Tech in Blacksburg and a co-author of the study.

What’s more, the trail demonstrates that Y. spiciformis could crawl over the sea floor like a modern animal. Palaeontologists have found only few pieces of evidence that the strange organisms of the Ediacaran were similarly mobile. Collectively, Xiao’s team’s findings mean that Y. spiciformis looked and behaved like a Cambrian animal — despite living up to 12 million years before what is usually considered the start of the Cambrian explosion.

“In the past, palaeontologists emphasized the differences between the Ediacaran and Cambrian,” says Xiao. “But when you think about it, life had to continue through the boundary. Some lineages had to survive.”

Seeking descendants. Exactly which animal lineage Y. spiciformis belonged to is unclear. The researchers suggest it might be a relative of insects and crustaceans such as shrimp and lobsters, because it seems to have leg-like structures. If further analysis shows that those structures are actually an artefact of the fossilization process, the animal might instead be some sort of primitive segmented worm.

“There’s a third possibility,” says Xiao: it could be an ancestor to both groups. The idea that segmented worms and shrimp-like creatures all evolved from a single group of segmented animals dates back to the nineteenth century, but it’s controversial because most researchers now think that shrimp-like animals are more closely related to nematode worms and other creatures that grow by shedding an exoskeleton.

Xiao thinks the evolution of segments could have been a key event in the history of animal life. Segmented animals might be able to evolve more or fewer segments without fatally disrupting their biology. So, he reasons, once a single group of segmented animals evolved, it might have had great potential to diversify into a whole range of lineages adapted to new niches, explaining why animal life flourished a few million years after Y. spiciformis appeared.

But Doug Erwin, a palaeobiologist at the Smithsonian National Museum of Natural History in Washington DC, isn’t convinced by the idea: he thinks segmentation probably arose several times in animal evolution. Partly as a consequence, he thinks Y. spiciformis could even belong to a completely different branch of the animal evolutionary tree, which has since gone extinct.

Bassir, S.M., Madani, M., 2019. A new model for predicting asphaltene precipitation of diluted crude oil by implementing LSSVM-CSA algorithm. Petroleum Science and Technology 37, 2252-2259.

https://doi.org/10.1080/10916466.2019.1632896

One of the severe problems in all the oil production stages from the pore walls of the reservoir rocks to the wellhead, transfer pipelines, and production units of a large portion of the world?s hydrocarbon reservoirs, is asphaltene precipitation and deposition from crude oil on solid surfaces. In this article, least squares support vector machine optimized by coupled simulated annealing is employed for estimation of the amount of asphaltene precipitated weight percent of diluted crude oil with paraffin based on titration tests data from a recently published article. The results indicated that there is an excellent correlation between predicted and experimental values with an average absolute relative deviation percent, mean square error, and a determination coefficient of 0.0727%, 0.0242, and 0.9972, respectively. The developed predicting model can be applied to estimate the amount of asphaltene precipitated when the crude oil is diluted with paraffin and to eschew experimental titration test that is tedious and time-consuming.

Bechtel, A., Widera, M., Woszczyk, M., 2019. Composition of lipids from the First Lusatian lignite seam of the Konin Basin (Poland): Relationships with vegetation, climate and carbon cycling during the mid-Miocene Climatic Optimum. Organic Geochemistry 138, 103908.


Samples of detrital lignite have been collected for detailed organic geochemical and carbon isotope analyses from the First Lusatian lignite seam at the Adamów, Jóźwin IIB and Tomisławice opencast mines, deposited after the last peak of the Mid-Miocene Climatic Optimum. Carbon isotopic compositions of biomarkers from Polish lignite are reported for the first time. The aim of the study is to improve the chemotaxonomic value of biomarkers by relating the results to existing paleobotanical data, and to gain information about the influencing factors on δ13C of lignite and lipids. Furthermore, biomarker and isotopic proxies are tested for their applicability in paleoclimate studies.

The molecular composition of the extracted lipids is highly variable, including leaf-wax n-alkanes in the C23 to C31 range, diterpenoids, hopanoids, and angiosperm-derived triterpenoids, as well as saturated fatty acids, long-chain n-alkanols and n-alkan-2-ones. The relative abundances of mid-chain (C23, C25) n-alkanes and their 1–2‰ higher δ13C values compared to long-chain n-alkanes (C29, C31) argue for a minor contribution of macrophytes (graminoids, etc.) to peat formation, enhanced during periods of raised water level. The presence of ferruginol and dehydroferruginol testifies the contribution of Taxodiaceae. The abundances of pimarane-type diterpenoids and the presence of non-aromatic abietane-derivatives argue for the contribution of Pinaceae. Based on the presence of lupeol and lupane-type triterpenoids, an input of Betulaceae can be concluded. The contribution of further angiosperms cannot be specified based on the composition of pentacyclic triterpenoids. However, the results indicate mixed vegetation, and are in agreement with paleobotanical data highlighting abundant conifers of the Taxodiaceae/Cupressaceae and Pinaceae families, as well as angiosperms of various families (e.g., Nyssa, Quercus, Fagus), including Betulaceae (e.g., Alnus, Betula, Corylus). Based on the relationship between the carbon preference index of n-alkanes and mean annual air temperatures, obtained from a global database of peatlands, an average temperature of 24.5 °C is obtained. This value is significantly higher as estimated from paleobotanical data (15.7–19.7 °C), probably due to the influence of changes in vegetation on carbon preference index.

The relative abundances of diterpenoids versus di- plus angiosperm-derived triterpenoids in detrital lignite samples revealed variable contributions of gymnosperms and angiosperms during the middle Miocene. Consistent with these results, a positive relationship exists between the di-/(di- + tri-) terpenoid biomarker ratios and δ13C of lignite samples, indicating the dominating role of varying gymnosperm/angiosperm contributions on the carbon isotopic composition of lignite. The C-isotope data of long-chain n-alkanes, diterpenoids, and angiosperm-derived triterpenoids co-vary within the profiles, arguing for an overall control of changes in δ13C of atmospheric CO2 on δ13C of plant lipids. Fluctuations in δ13C of individual compounds may also be related to changes in carbon cycling within the peat, humidity and air temperature. The influence of local variations in ambient CO2 (e.g., the canopy effect) cannot be excluded.

Benford, J., 2019. Looking for lurkers: Co-orbiters as SETI observables. The Astronomical Journal 158, 150.

http://dx.doi.org/10.3847/1538-3881/ab3e35

A recently discovered group of nearby co-orbital objects is an attractive location for extraterrestrial intelligence (ETI) to locate a probe to observe Earth while not being easily seen. These near-Earth objects provide an ideal way to watch our world from a secure natural object. That provides resources an ETI might need: materials, a firm anchor, and concealment. These have been little studied by astronomy and not at all by the Search for Extraterrestrial Intelligence (SETI) or planetary radar observations. I describe the objects found thus far and propose both passive and active observations of them as possible sites for extraterrestrial (ET) probes.

Bennett, E.A., Crevecoeur, I., Viola, B., Derevianko, A.P., Shunkov, M.V., Grange, T., Maureille, B., Geigl, E.-M., 2019. Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals. Science Advances 5, eaaw3950.

http://advances.sciencemag.org/content/5/9/eaaw3950.abstract

A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.

Berg, R.D., Solomon, E.A., Teng, F.-Z., 2019. The role of marine sediment diagenesis in the modern oceanic magnesium cycle. Nature Communications 10, 4371.

https://doi.org/10.1038/s41467-019-12322-2

The oceanic magnesium cycle is largely controlled by continental weathering and marine authigenic mineral formation, which are intimately linked to long-term climate. Uncertainties in the magnesium cycle propagate into other chemical budgets, and into interpretations of paleo-oceanographic reconstructions of seawater δ26Mg and Mg/Ca ratios. Here, we produce a detailed global map of the flux of dissolved magnesium from the ocean into deeper marine sediments (greater than ∼1 meter below seafloor), and quantify the global flux and associated isotopic fractionation. We find that this flux accounts for 15–20% of the output of magnesium from the ocean, with a flux-weighted fractionation factor of ∼0.9994 acting to increase the magnesium isotopic ratio in the ocean. Our analysis provides the best constraints to date on the sources and sinks that define the oceanic magnesium cycle, including new constraints on the output flux of magnesium and isotopic fractionation during low-temperature ridge flank hydrothermal circulation.

Betts, B.H., Warmflash, D., Fraze, R.E., Friedman, L., Vorobyova, E., Lilburn, T.G., Smith, A., Rettberg, P., Jönsson, K.I., Ciftcioglu, N., Fox, G.E., Svitek, T., Kirschvinck, J.L., Moeller, R., Wassmann, M., Berger, T., 2019. Phobos LIFE (Living Interplanetary Flight Experiment). Astrobiology 19, 1177-1185.

https://doi.org/10.1089/ast.2018.1904

The Planetary Society's Phobos Living Interplanetary Flight Experiment (Phobos LIFE) flew in the sample return capsule of the Russian Federal Space Agency's Phobos Grunt mission and was to have been a test of one aspect of the hypothesis that life can move between nearby planets within ejected rocks. Although the Phobos Grunt mission failed, we present here the scientific and engineering design and motivation of the Phobos LIFE experiment to assist with the scientific and engineering design of similar future experiments. Phobos LIFE flew selected organisms in a simulated meteoroid. The 34-month voyage would have been the first such test to occur in the high-radiation environment outside the protection of Earth's magnetosphere for more than a few days. The patented Phobos LIFE “biomodule” is an 88 g cylinder consisting of a titanium outer shell, several types of redundant seals, and 31 individual Delrin sample containers. Phobos LIFE contained 10 different organisms, representing all three domains of life, and one soil sample. The organisms are all very well characterized, most with sequenced genomes. Most are extremophiles, and most have flown in low Earth orbit. Upon return from space, the health and characteristics of organisms were to have been compared with controls that remained on Earth and have not yet been opened.



The Central Canyon sandstones, located in the Ledong–Lingshui Depression, Qiongdongnan Basin, South China Sea, are the main reservoirs of the deep-water area. The present study aimed to examine the diagenetic processes and reservoir quality of these sandstones. Using an integrated approach of examination of casting thin sections, X-ray diffraction, porosity and permeability measurements, scanning electron microscopy, carbon and oxygen stable isotope analyses, fluid inclusion analyses and electron microprobe analysis, we analysed the diagenetic features of the sandstones and the reservoir quality of the LD30-1 and LS17-2 sandstones, respectively. The results showed that the sandstones consist of lithic arkoses and sublitharenites, the main pore systems consist of primary intergranular pores and secondary pores, and the main cements consist of authigenic quartz, clay minerals, and carbonates. By combining the analyses of burial history and hydrocarbon charging history, we discovered that the LD30-1 sandstone reservoirs and the LS17-2 sandstone reservoirs are quite different. A significant negative shift in δ13C and δ18O (ranging from −4.88‰ to −2.27‰ and from −11.83‰ to −5.96‰, respectively) is evident in the carbonate cements of the LD30-1 sandstones, and oxidation of organic matter had an important role in the occurrence of the carbonate cements. However, relatively high and

concentrated δ13C and δ18O values in the LS17-2 sandstones, ranging from −1.76‰ to −0.48‰ and −5.04‰ to −2.95‰, respectively, are closer to the original isotopic compositions. Based on casting thin sections, the abundance of quartz overgrowths in the LD30-1 sandstones is higher than that in the LS17-2 sandstones. The development of each clay mineral in the LD30-1 and LS17-2 sandstones is quite different. The LS17-2 sandstones have higher reservoir quality than the LD30-1 sandstones. Early hydrocarbon charge is an important factor causing the differences of diagenetic minerals and reservoir quality between the LS17-2 sandstones and the LD30-1 sandstones.



Reduction of Ecuadorian asphaltenes by lithium in liquid ammonia (Birch conditions) yields asphaltene salts that can be protonated by tert-butyl alcohol to yield deflocculated hydroasphaltene. Studies were carried out using asphaltenes from both low- and high-viscosity oils. The dimensions of the hydroasphaltenes were determined by atomic force microscopy. Relative to the starting asphaltene, the nominal asphaltene aggregate height of the low-viscosity asphaltene 1 was reduced from 1.3 to 0.7 nm, indicating that the asphaltene was fully exfoliated. The height of the high-viscosity asphaltene 2 was reduced from 4 to 2 nm. 13C nuclear magnetic resonance of the Birch-reduced asphaltenes shows a reduction in aromaticity from 49 to 46%, indicating that a low level of hydrogen was added to the aromatic core during the Birch reduction.

Blanco-Zubiaguirre, L., Olivares, M., Castro, K., Carrero, J.A., García-Benito, C., García-Serrano, J.Á., Pérez-Pérez, J., Pérez-Arantegui, J., 2019. Wine markers in archeological potteries: detection by GC-MS at ultratrace levels. Analytical and Bioanalytical Chemistry 411, 6711-6722.

https://doi.org/10.1007/s00216-019-02044-1

The detection of organic residues that remain absorbed into the pores of ceramic artifacts constitutes a source of information regarding their management. Taking into account the poor conservation state of the potteries and the low amount of the organic tracers together with the main drawbacks to get the relevant information concerning different aspects of past societies, the detection of organic biomarkers is still an analytical challenge. In this work, an improved analytical methodology to maximize the recovery of organic markers related to wine in archeological ceramics is presented. The developed method consists on the extraction of wine-related organic compounds including tartaric acid, malic acid, fumaric acid, succinic acid, citric acid, and syringic acid by means of ultrasonic probe-assisted extraction (UPAE) followed by a preconcentration step by mixed-mode strong anion exchange and reversed-phase solid-phase extraction (SPE) and a derivatization step prior to analysis by means of gas chromatography-mass spectrometry (GC-MS). Finally, the method was applied to real archeological ceramic fragments (two dolia), suspected to have been used to store wine, together with organic residues found inside two amphorae from Zaragoza (Spain).

Blázquez, S., González, D., García-Sáez, A., Antiñolo, M., Bergeat, A., Caralp, F., Mereau, R., Canosa, A., Ballesteros, B., Albaladejo, J., Jiménez, E., 2019. Experimental and theoretical investigation on the OH + CH3C(O)CH3 reaction at interstellar temperatures (T = 11.7–64.4 K). ACS Earth and Space Chemistry 3, 1873-1883.


The rate coefficient, k(T), for the gas-phase reaction between OH radicals and acetone CH3C(O)CH3, has been measured using the pulsed CRESU (French acronym for Reaction Kinetics in a Uniform Supersonic Flow) technique (T = 11.7–64.4 K). The temperature dependence of k(T = 10–300 K) has also been computed using a RRKM-Master equation analysis after partial revision of the potential energy surface. In agreement with previous studies we found that the reaction proceeds via initial formation of two prereactive complexes both leading to H2O + CH3C(O)CH2 by H-abstraction tunneling. The experimental k(T) was found to increase as

temperature was lowered. The measured values have been found to be several orders of magnitude higher than k(300 K). This trend is reproduced by calculations, with an especially good agreement with experiments below 25 K. The effect of total gas density on k(T) has been explored. Experimentally, no pressure dependence of k(20 K) and k(64 K) was observed, while k(50 K) at the largest gas density 4.47 × 1017 cm–3 is twice higher than the average values found at lower densities. The computed k(T) is also reported for 103 cm–3 of He (representative of the interstellar medium). The predicted rate coefficients at 10 K surround the experimental value which appears to be very close to that of the low pressure regime prevailing in the interstellar medium. For gas-phase model chemistry of interstellar molecular clouds, we suggest using the calculated value of 1.8 × 10–10 cm3 molecule–1 s–1 at 10 K, and the reaction products are water and CH3C(O)CH2 radicals.

Böhnke, S., Perner, M., 2019. Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments. The ISME Journal 13, 2475-2488.

https://doi.org/10.1038/s41396-019-0439-3

Almost all the inorganic carbon on Earth is converted into biomass via the Calvin–Benson–Bassham (CBB) cycle. Here, the central carboxylation reaction is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which can be found in numerous primary producers including plants, algae, cyanobacteria, and many autotrophic bacteria. Although RubisCO possesses a crucial role in global biomass production, it is not a perfect catalyst. Therefore, research interest persists on accessing the full potential of yet unexplored RubisCOs. We recently developed an activity-based screen suited to seek active recombinant RubisCOs from the environment—independent of the native host’s culturability. Here, we applied this screen to twenty pre-selected genomic fosmid clones from six cultured proteobacteria to demonstrate that a broad range of phylogenetically distinct RubisCOs can be targeted. We then screened 12,500 metagenomic fosmid clones from six distinct hydrothermal vents and identified forty active RubisCOs. Additional sequence-based screening uncovered eight further RubisCOs, which could then also be detected by a modified version of the screen. Seven were active form III RubisCOs from yet uncultured Archaea. This indicates the potential of the activity-based screen to detect RubisCO enzymes even from organisms that would not be expected to be targeted.

Bowman, C.N., Young, S.A., Kaljo, D., Eriksson, M.E., Them, T.R., II, Hints, O., Martma, T., Owens, J.D., 2019. Linking the progressive expansion of reducing conditions to a stepwise mass extinction event in the late Silurian oceans. Geology 47, 968-972.

https://doi.org/10.1130/G46571.1

The late Ludlow Lau Event was a severe biotic crisis in the Silurian, characterized by resurgent microbial facies and faunal turnover rates otherwise only documented during the “big five” mass extinctions. This asynchronous late Silurian marine extinction event preceded an associated positive carbon isotope excursion (CIE), the Lau CIE, although a mechanism for this temporal offset remains poorly constrained. Here, we report thallium isotope data from locally reducing late Ludlow strata within the Baltic Basin to document the earliest onset of global marine deoxygenation. The initial expansion of anoxia coincided with the onset of the extinction and therefore preceded the Lau CIE. Additionally, sulfur isotope data record a large positive excursion parallel to the Lau CIE, interpreted to indicate an increase in pyrite burial associated with the widely documented CIE. This suggests a possible global expansion of euxinia (anoxic and sulfidic water column) following deoxygenation. These data are the most direct proxy evidence of paleoredox conditions linking the known extinction to the Lau CIE through the progressive expansion of anoxia, and most likely euxinia, across portions of the late Silurian oceans.

Brenan, J.M., Mungall, J.E., Bennett, N.R., 2019. Abundance of highly siderophile elements in lunar basalts controlled by iron sulfide melt. Nature Geoscience 12, 701-706.

https://doi.org/10.1038/s41561-019-0426-3

The Moon accreted meteoritic material towards the end of Solar System formation. Quantification of this late accretion requires an estimation of the abundance of highly siderophile, or iron-loving, elements in the lunar mantle. As lunar mantle samples are not available, estimates are derived from lunar basalt compositions, but the melting phase relations needed to derive the mantle composition are poorly constrained. Here we present sulfur solubility measurements from laboratory experiments, combined with thermodynamic calculations, which show that the lunar basalt source is likely to be saturated in a sulfur-poor, iron-rich sulfide melt that concentrates some highly siderophile elements more than others. We found that the observed range in the ratios of highly siderophile elements in primitive lunar basalts is much smaller than expected from residual sulfide control alone. Instead, the elemental ratios are consistent with mixing between primary sulfide-saturated melts and minute (<1%) amounts of lunar regolith that contain impact debris. Although the composition of some samples suggests a highly depleted lunar mantle, the exact level of depletion is unclear, because mixing trajectories overlap at the inferred level of regolith contamination. We conclude that the composition of the lunar mantle is veiled by regolith contamination of the lunar basalts. If so, highly siderophile element abundances in lunar mantle-derived materials cannot be used to determine the mass of material accreted late onto the Moon.

Caesar, L.K., Nogo, S., Naphen, C.N., Cech, N.B., 2019. Simplify: A mass spectrometry metabolomics approach to identify additives and synergists from complex mixtures. Analytical Chemistry 91, 11297-11305.


In fields ranging from environmental toxicology to drug discovery, it is critical to identify how multiple chemical compounds interact to perturb biological systems. Isolation-based approaches fail to incorporate multiconstituent interactions, such as synergy. We have developed an approach called “Simplify”, which identifies mixture constituents that interact to achieve biological effects. Simplify combines biological and mass spectrometric data sets and uses an “activity index” to predict mixture interactions. Using the plant Salvia miltiorrhiza as a case study, we employed Simplify to identify four individual constituents that contribute to antimicrobial activity, three additives and one synergist. Our study is the first to enable identification of unknown synergists prior to isolating them, demonstrating the ability of the Simplify workflow to predict key contributors to the biological effect of a complex mixture. While utilized for natural products discovery in this study, this approach is expected to prove useful across multiple disciplines that rely on mixture analysis.

Callaway, E., 2019. First portrait of mysterious Denisovans drawn from DNA. Nature 573, 475-476.

https://www.nature.com/articles/d41586-019-02820-0

Scientists analysed chemical changes to the ancient humans’ DNA to reveal broad, Neanderthal-like facial features.

For the first time, scientists analysing the DNA of Denisovans — an extinct group of hominins that was discovered around a decade ago — have offered a glimpse of what they might have looked like.

Ever since archaeologists uncovered the first fragmented Denisovan remains in a Siberian cave, researchers have scoured the globe for clues to how the mysterious hominins looked. Denisova Cave has yielded a few more small fossils, mostly teeth. A jawbone from the Tibetan Plateau added detail this year, as did information on a missing finger bone that moved between labs in Russia, California and Paris. But none of these fossils is large or complete enough to reconstruct many anatomical details.

Now, computational biologists have produced a rough sketch of Denisovan anatomy based on epigenetic changes — chemical modifications to DNA that can alter gene activity. Their approach reveals that Denisovans were similar in appearance to Neanderthals but had some subtle differences, such as a wider jaw and skull1.

“It does help to paint a clearer picture of how they might have looked. Just the idea that it’s possible to use the DNA to predict morphology so well is very impressive,” says Bence Viola, a palaeoanthropologist at the University of Toronto in Canada who has analysed Denisovan remains, but was not involved in this research.

Mapping methylation. Epigenetic modifications to DNA have a profound influence on development, disease and most biological traits throughout life. They can help to determine differences between cells with otherwise identical genomes. One of the best-studied epigenetic changes is the addition to a DNA base of a methyl chemical group — made up of one carbon atom and three hydrogens — which often quells the activity of a gene.

The methyl group degrades after death, so cannot be spotted in ancient DNA. But a team co-led by Liran Carmel, a computational biologist at the Hebrew University of Jerusalem, discovered a way to identify parts of ancient DNA that had once been methylated, by analysing patterns of chemical damage that accrues to the DNA over time. In 2014, Carmel’s team mapped methylation patterns across the genomes of Neanderthals and Denisovans, and identified a limb-development gene for which these patterns differed between the extinct groups and modern humans2.

In the latest study, Carmel and computational biologist David Gokhman, also at the Hebrew University of Jerusalem, led a team that identified thousands more regions of the genome in which the methylation patterns of Denisovans and Neanderthals were distinct from those of modern humans. They compared these with databases of epigenetic modifications in human tissue — where the impacts on gene expression are known — and produced a list of hundreds of genes for which expression levels probably differed between archaic groups and modern humans.

To connect this list to anatomical traits that would affect the Denisovans’ appearance, the researchers looked at another database, which catalogues the physical effects of genetic mutations in people with rare conditions. Carmel and Gokhman reasoned that the reduced gene expression caused by DNA methylation was roughly analogous to the effects of the disease-causing mutations.

Neanderthal comparison. Before applying their method to Denisovans, Carmel and Gokhman’s team first tested whether it could successfully predict the anatomy of Neanderthals, which is known from hundreds of fossils.

The predictions about physical appearance made using this approach are qualitative and relative, Carmel explains. “I can tell you that fingers are longer, but I cannot tell you they are longer by 2 millimetres,” he says.

The team found 33 Neanderthal traits that could potentially be predicted from methylation patterns. The results accurately predicted 29 of those traits, for instance that the species had broader faces and flatter heads than modern humans. But it wrongly indicated that the indentations between fused skull bones, known as sutures, were wider in humans.

The researchers then turned the technique to Denisovans. They predicted that these hominins shared many traits with Neanderthals, such as their low foreheads and wide rib cages, but identified some differences, including wider jaws and skulls. Although it is impossible to know how accurate their picture is, some of the predictions are supported by evidence from Denisovan remains.

The best-characterized Denisovan feature in the fossil record is gigantic molar teeth. Although the researchers weren’t able to predict this — because molar size was not in the database they used — they did determine that Denisovans had long dental arches, a potential adaptation for big teeth.

The 160,000-year-old lower jawbone from the Tibetan Plateau matched Gokhman and Carmel’s predictions for 3 out of 4 traits. And a piece of skull from Denisova Cave that Viola has presented at meetings (but not yet described in a paper) suggests the group had wide heads — which matches the epigenetic reconstruction. However, a reconstruction of the Denisovan fingertip, published this month3, suggested theirs was slender like humans’ — unlike the thick Neanderthal-like fingers in the prediction.

“I think the big picture is correct, but with the individual traits, there is a lot of leeway,” says Viola. Although he is impressed by the predictions, he is unsure sure how they will help determine what Denisovans actually looked like. Potential Denisovan bones are so rare that most are already tested for DNA or protein — currently the only way to link remains to the extinct group.

This is an “absolutely valid approach”, says Manolis Kellis, a computational biologist at the Massachusetts Institute of Technology in Cambridge who works with epigenetic data. The authors do a good job of accounting for uncertainties that feed into their predictions, he adds. “The resulting findings are quite robust.”

In the future, scientists might use epigenetics to reconstruct the anatomy of hominins known from fragmentary fossils or perhaps even DNA from dirt, says Pontus Skoglund, a population geneticist at the Francis Crick Institute in London. But he thinks the approach could be most useful in predicting traits, such as behaviour, that don’t leave an impression in the fossil record.

References1. Gokhman, D. et al. Cell https://doi.org/10.1016/j.cell.2019.08.035 (2019).2. Gokhman, D. et al. Science 344, 523–527 (2014).3. Bennett, E. A. et al. Sci. Adv. 5, eaaw3950 (2019).


https://doi.org/10.1111/1755-6724.13865

Nanoscale pore characteristics of the Upper Permian Longtan transitional mudrocks and their equivalent strata Wujiaping Formation marine mudrocks in and around the eastern Sichuan Basin was investigated using field emission scanning electron microscopy (FE-SEM) and low-pressure N2 adsorption experiments. The results indicate that the Upper Permian mudrock is at a mature stage with total organic carbon (TOC) values ranging between 0.47% and 12.3%. The Longtan mudrocks mainly contain vitrinite, and their mineral composition is primarily clay. In contrast, the Wujiaping mudrocks are dominated by sapropelinite and solid bitumen, and their mineral compositions are mainly quartz and a notably high amount of pyrite. The FE-SEM reveals that clay mineral pores and microcracks are the common pore types in the Longtan mudrocks. The specific surface area and pore volume depend on the clay content but are negatively correlated with the TOC. The generation of nanometer pores in the Longtan mudrocks is caused by high clay mineral contents. Meanwhile, the Wujiaping mudrock mainly contains OM pores, and the pore parameters are positively correlated with the TOC. The OM pore development exhibits remarkable differences in the Longtan and Wujiaping mudrocks, which might be related to their sedimentary facies and maceral fractions. Vitrinite and inertinite appear as discrete particles in these mudrocks and cannot generate pores during thermal maturation. Sapropelinite often contains many secondary pores, and solid bitumen with large particles, usually with several pores, is not the major contributor to the pore system of the investigated mudrock.

Capitanio, F.A., Nebel, O., Cawood, P.A., Weinberg, R.F., Chowdhury, P., 2019. Reconciling thermal regimes and tectonics of the early Earth. Geology 47, 923-927.

https://doi.org/10.1130/G46239.1

Thermomechanical models of mantle convection and melting in an inferred hotter Archean Earth show the emergence of pressure-temperature (P-T) regimes that resemble present-day plate tectonic environments yet developed within a non–plate tectonics regime. The models’ P-T gradients are compatible with those inferred from evolving tonalite-trondhjemite-granodiorite series rocks and the paired metamorphic belt record, supporting the feasibility of divergent and convergent tectonics within a mobilized, yet laterally continuous, lithospheric lid. “Hot” P-T gradients of 10–20 °C km–1 form along asymmetric lithospheric drips, then migrate to areas of deep lithospheric downwelling within ∼300–500 m.y., where they are overprinted by high-pressure warm and, later, cold geothermal signatures, up to ∼8 °C km–1. Comparisons with the crustal production and reworking record suggest that this regime emerged in the Hadean.

Cario, A., Oliver, G.C., Rogers, K.L., 2019. Exploring the deep marine biosphere: Challenges, innovations, and opportunities. Frontiers in Earth Science 7, 225. doi: 10.3389/feart.2019.00225.

https://www.frontiersin.org/article/10.3389/feart.2019.00225

The deep marine biosphere is one of the largest, and yet least explored, microbial habitats on the planet. Quantifying the extent, diversity, and activity of subsurface microbial communities is a crucial part of understanding their role in global biogeochemical cycles. Even though deep biosphere habitats can vary widely in chemistry, temperature, turnover rates, and energy sources, all subsurface microbes inherently experience high pressures. While not all subsurface microbes require elevated pressures, for many high pressures are essential to their cellular function and metabolism. Thus, when targeting this elusive portion of the biosphere, it is critical to maintain in situ pressure while sampling and cultivating subsurface microorganisms. In this perspective paper we highlight the sampling and cultivation technologies available to study these communities under in situ conditions. Maintaining elevated pressures throughout sampling, transfer, cultivation, and isolation is challenging, and more often than not samples are decompressed at some point during sample handling, potentially leading to biases in both community diversity and isolate physiology. The development of devices that maintain in situ pressures during sampling and allow for sample transfer without decompression have begun to address this challenge (like the PUSH – Pressurized Underwater Sample Handler). Such vessels can be used for both retrieval and enrichment of deep subsurface samples, as well as high-pressure growth and physiology experiments, thus expanding possibilities for deep biosphere exploration. Finally, we discuss the significant need to develop and share high-pressure facilities across the deep biosphere community, in order to expand the opportunities to discover novel piezophiles from the deep subsurface.

Casey, J.A., Goin, D.E., Rudolph, K.E., Schwartz, B.S., Mercer, D., Elser, H., Eisen, E.A., Morello-Frosch, R., 2019. Unconventional natural gas development and adverse birth outcomes in Pennsylvania: The potential mediating role of antenatal anxiety and depression. Environmental Research 177, 108598.


Background: Studies have reported associations between unconventional natural gas development (UNGD) and adverse birth outcomes. None have evaluated potential mediating mechanisms.

Objectives: To evaluate associations between (1) UNGD and antenatal anxiety and depression and (2) antenatal anxiety and depression and preterm birth (<37 weeks gestation) and reduced term birth weight, (3) stochastic direct and indirect effects of UNGD on preterm birth and term birth weight operating through antenatal anxiety and depression, and (4) effect modification by family-level socioeconomic status.

Methods: This retrospective cohort study included mothers without prevalent anxiety or depression at time of conception, who delivered at Geisinger in Pennsylvania between January 2009–January 2013. We assembled phase-specific UNGD activity data from public sources. Mothers were categorized as exposed (quartile 4) or unexposed (quartiles 1–3) based on average daily inverse distance-squared UNGD activity metric between conception and the week prior to anxiety or depression (cases) or the pregnancy-average daily metric (non-cases). We estimated associations with a doubly robust estimator (targeted minimum loss-based estimation) and adjusted for potential individual- and community-level confounding variables.

Results: Analyses included 8,371 births to 7,715 mothers, 12.2% of whom had antenatal anxiety or depression. We found 4.3 additional cases of antenatal anxiety or depression per 100 women (95% CI: 1.5, 7.0) under the scenario where all mothers lived in the highest quartile of UNGD activity versus quartiles 1–3. The risk difference appeared larger among mothers receiving Medical Assistance (indicator of low family income) compared to those who did not, 5.6 (95% CI: 0.5, 10.6) versus 2.9 (95% CI: -0.7, 6.5) additional cases of antenatal anxiety or depression per 100 women. We found no relationship between antenatal anxiety or depression and adverse birth outcomes and no mediation effect either overall or when stratifying by Medical Assistance.

Conclusion: We observed a relationship between UNGD activity and antenatal anxiety and depression, which did not mediate the overall association between UNGD activity and adverse birth outcomes.

Castañeda, A.D., Li, Z., Joo, T., Benham, K., Burcar, B.T., Krishnamurthy, R., Liotta, C.L., Ng, N.L., Orlando, T.M., 2019. Prebiotic phosphorylation of uridine using diamidophosphate in aerosols. Scientific Reports 9, 13527.

https://doi.org/10.1038/s41598-019-49947-8

One of the most challenging fundamental problems in establishing prebiotically plausible routes for phosphorylation reactions using phosphate is that they are thermodynamically unfavorable in aqueous conditions. Diamidophosphate (DAP), a potentially prebiotically relevant compound, was shown to phosphorylate nucleosides in aqueous medium, albeit at a very slow rate (days/weeks). Here, we demonstrate that performing these reactions within an aerosol environment, a suitable model for the early Earth ocean-air interface, yields higher reaction rates when compared to bulk solution, thus overcoming these rate limitations. As a proof-of-concept, we demonstrate the effective conversion (~6.5–10%) of uridine to uridine-2′,3′-cyclophosphate in less than 1 h. These results suggest that aerosol environments are a possible scenario in which prebiotic phosphorylation could have occurred despite unfavorable rates in bulk solution.

Chan, M.A., Hinman, N.W., Potter-McIntyre, S.L., Schubert, K.E., Gillams, R.J., Awramik, S.M., Boston, P.J., Bower, D.M., Des Marais, D.J., Farmer, J.D., Jia, T.Z., King, P.L., Hazen, R.M., Léveillé, R.J., Papineau, D., Rempfert, K.R., Sánchez-Román, M., Spear, J.R., Southam, G., Stern, J.C., Cleaves, H.J., 2019. Deciphering biosignatures in planetary contexts. Astrobiology 19, 1075-1102.

https://doi.org/10.1089/ast.2018.1903

Microbial life permeates Earth's critical zone and has likely inhabited nearly all our planet's surface and near subsurface since before the beginning of the sedimentary rock record. Given the vast time that Earth has been teeming with life, do astrobiologists truly understand what geological features untouched by biological processes would look like? In the search for extraterrestrial life in the Universe, it is critical to determine what constitutes a biosignature across multiple scales, and how this compares with ?abiosignatures? formed by nonliving processes. Developing standards for abiotic and biotic characteristics would provide quantitative metrics for comparison across different data types and observational time frames. The evidence for life detection falls into three categories of biosignatures: (1) substances, such as elemental abundances, isotopes, molecules, allotropes, enantiomers, minerals, and their associated properties; (2) objects that are physical features such as mats, fossils including trace-fossils and microbialites (stromatolites), and concretions; and (3) patterns, such as physical three-dimensional or conceptual n-dimensional relationships of physical or chemical phenomena, including patterns of intermolecular abundances of organic homologues, and patterns of stable isotopic abundances between and within compounds. Five key challenges that warrant future exploration by the astrobiology community include the following: (1) examining phenomena at the ?right? spatial scales because biosignatures may elude us if not examined with the appropriate instrumentation or modeling approach at that specific scale; (2) identifying the precise context across multiple spatial and temporal scales to understand how tangible biosignatures may or may not be preserved; (3) increasing capability to mine big data sets to reveal relationships, for example, how Earth's mineral diversity may have evolved in conjunction with life; (4) leveraging cyberinfrastructure for data management of biosignature types, characteristics, and classifications; and (5) using three-dimensional to n-D representations of biotic and abiotic models overlain on multiple overlapping spatial and temporal relationships to provide new insights.

Chang, S., Zhang, L., Clausen, S., Bottjer, D.J., Feng, Q., 2019. The Ediacaran-Cambrian rise of siliceous sponges and development of modern oceanic ecosystems. Precambrian Research 333, 105438.


The lack of unequivocal sponge fossils before the Cambrian despite their probable deep origin during the Cryogenian period has been a conundrum to geologists. Their impact on the dramatic evolution of ecosystems and the seawater silica cycle during the Ediacaran-Cambrian (E-C) transition is also speculative. In this study, abundant sponge spicules and spicule-like structures that probably represent original sponge fossils were recovered from four sections of the E-C boundary interval in the Yangtze Gorges, South China. The

paleontological and geochemical data presented herein provides evidence for a continuous distribution of relatively abundant sponge spicules, some even forming spiculites, as well as the earliest biogenic deposition of silica by metazoans in the Ediacaran-Cambrian boundary interval. These results further confirm that a biological takeover of oceanic dissolved Si co-occurred with the evolution of silica biomineralization in the E-C interval, resulting in the widespread deposition of biogenic chert. Hydrothermal input in spicule-bearing cherts is also observed. Such hydrothermal activity might have favored the blooming of sponges through significant nutrient supply. These results provide the first conjunction of geochemical and paleontological proxies in support of previous models considering that sponges, by ventilation, filtration and oxygenation of seawater, were important ecosystem engineers of the E-C bioradiation event and of the related establishment of modern-type ecosystems.



The atmospheric CO2 concentration (pCO2) affects the carbon isotope composition (δ13C) of plant tissue produced during photosynthesis. This observation has led to the suggestion that changes in the δ13C value of bulk terrestrial organic matter (TOM) can be used to reconstruct pCO2 on geologic time scales. It is possible, however, for bulk TOM to be affected by differential degradation that may affect the δ13C value post-deposition and, therefore, bias estimates of pCO2. Long-chain n-alkanes are commonly preserved in the fossil record and represent compound-specific biomarkers of higher order land plants, suggesting that their δ13C values may provide a less biased estimate of pCO2 than bulk TOM. Here, we report new pCO2 estimates determined from published δ13C data on long-chain, odd-numbered n-alkanes extracted from early Paleogene samples. During the early Paleogene, n-C27, n-C29, and n-C31 showed significantly higher net carbon isotope discrimination (Δ) compared to modern values (p < 0.001), consistent with moderately high CO2 levels (average early Paleogene pCO2 = 462 + 349/–162 ppm); n-C33 showed no significant change in discrimination compared to modern values (p = 0.754). Sensitivity analysis shows that independent knowledge on changes in plant taxa and mean annual precipitation can help improve the precision of our pCO2 reconstruction. These results support background pCO2 less than ∼3 times pre-industrial levels in the 10 million years leading up to the early Eocene climate optimum.

Chávez-Lara, C.M., Holtvoeth, J., Roy, P.D., Pancost, R.D., 2019. Lipid biomarkers in lacustrine sediments of subtropical northeastern Mexico and inferred ecosystem changes during the late Pleistocene and Holocene. Palaeogeography, Palaeoclimatology, Palaeoecology 535, 109343.


Evolution of ecosystems in the northeastern Mexico since the Last Glacial Maximum (LGM) and through the Holocene are yet to be fully characterised, creating a gap in our understanding of the ecological response to climate change in this water scarce region. Here we explore the response of lacustrine and surrounding terrestrial habitats of this region to hydrological changes of the late Pleistocene and especially the Holocene. Biomarker-based proxy data from the El Potosi Basin indicates dynamic and variable input of organic matter (OM) into the basin, with sources being the surrounding vegetation, bacterial biomass and aquatic microfauna. Changes in these inputs reveal distinct stages of ecosystem development over the last 20,000 years. Overall low lipid abundances (as a proportion of TOC) from 20 to 19 cal kyr BP, mainly from aquatic/in-situ microbial biomass and degraded terrestrial OM, are attributed to relatively low runoff. Increasing lipid proportions during the deglaciation, from 19 to 15 cal kyr BP, were mostly derived from terrestrial sources like woodland vegetation, soil and wetland vegetation, and we attribute them to more rainfall and runoff. Subsequently, the wetland biomarkers disappeared, and woodland input began to dominate the OM assemblage from 15 to 11.7 cal kyr BP. During the early- and mid-Holocene, after about 11.7 cal kyr BP, putative woodland and grass inputs decreased and the dominant vegetation appeared to shift to subtropical desert shrub, which could have been due to increasing regional aridity. The onset of the dry late Holocene was characterised by gradual environmental transition and ecosystem adaption, especially from 4.2 to 2.8 cal kyr BP. The terrestrial

vegetation comprised increasing proportions of C4 grasses, documented by changes in leaf wax carbon isotopic compositions, and potentially more open-vegetation, while the in-lake bacterial production increased. With increasing desertification from 2.8 cal kyr BP, the terrestrial productivity decreased substantially, the lake became shallower/ephemeral, and the surrounding soils became more alkaline. Changes of the limnic habitat from algal towards microbial communities occurred ~300 years after the onset of terrestrial habitat changes. During the last millennium, the C3 components of the vegetation again dominated. This implies an enhanced moisture supply, possibly from agricultural activities. Overall, this work reveals the marked sensitivity of northeastern Mexico ecosystems to the climatic shifts that occurred since the LGM, and this perhaps indicates their vulnerability to future global warming.

Chen, B., Stuart, F.M., Xu, S., Gyӧre, D., Liu, C., 2019. Evolution of coal-bed methane in Southeast Qinshui Basin, China: Insights from stable and noble gas isotopes. Chemical Geology 529, 119298.

http://www.sciencedirect.com/science/article/pii/S000925411930405X

The late Carboniferous-early Permian coal seams of the Qinshui Basin in Shanxi Province are the most prolific producer of coalbed methane (CBM) in China. Methane formed in the late Triassic during deep burial and reheating in late Jurassic-early Cretaceous driven by magmatic underplating. Basin inversion brought the coal seams to 400–700 m from the surface in the mid-late Cenozoic. Here we present results of a study aimed at understanding the origin of the methane, and how it was affected by Cenozoic exhumation of the basin. Methane from a 12 km traverse perpendicular to the basin margin in the southeast part of the basin have stable isotope compositions (δ13C = −30.2 to −35.2‰, and δD = −155 to −194‰) indicating a thermogenic origin with limited biogenic input. They are, however, lighter than expected based on coal maturity, and C1/(C2 + C3) (>1000) are significantly higher than typical thermogenic methane (<50). This is due to diffusive fractionation during commercial gas extraction. He-Ne-Ar isotopes are a mixture of crustal-radiogenic gas with air-derived noble gases. 4He concentrations (0.52 to 33.25 ppmv) and 4He/40Ar⁎ ratios (0.06–1.74) are unusually low. He-Ne-Ar concentrations are consistent with the open system Rayleigh fractionation of noble gases derived from air-saturated water with 4He/40Ar⁎ = 1 during gas extraction. The low 4He/40Ar⁎, compared with average crust (5) or local production (13) values, implies that >90% of the radiogenic 4He produced in the coals has been lost prior to equilibrium between gas and water phase in the reservoir. This likely occurred in response to gas loss process during rapid exhumation in Cenozoic, showing that the He and Ar content of natural gases is a sensitive indicator of gas loss event caused by recent basin inversion. The event may have led to the loss of up to 44% of the methane from the coal seams. This study demonstrates the importance of basin inversion on gas preservation in shallow CBM, and shows that, in contrast to δ13CCH4, the light noble gases are essential for tracing such a process.

Chen, H., Lin, X., Cheng, X., Yang, S., Zhang, F., Wu, L., Ding, W., Li, Y., Hu, B., Huang, W., Chen, Y., 2019. The Late Neoproterozoic sedimentary sequences in the Yutang section southwest Tarim Basin and their tectonic implications and hydrocarbon perspective: Insight from basinology. Precambrian Research 333, 105432.


The Late Neoproterozoic sedimentary sequences in the Tarim Basin are pivotal for understanding basin evolution and related tectonic setting, and evaluating the hydrocarbon perspective. In this study, tectonostratigraphic investigation has been conducted on the Late Neoproterozoic succession in the Yutang area, including strata of the Kexili, Yutang, Kuerkake and Kezisuhumu formations, along the Xinjiang-Tibet Highway ~90 km southwest of the Yecheng at the southwest Tarim Basin. The results indicate that the sediments represent a fluvial/alluvial-lacustrine-shallow marine tectonostratigraphic sequence complex upward the section, which is comparable with the deposition of sedimentary basin obeying evolution path from syn-rifting, late-rifting, transitional to post-rifting stage. These results lead to an interpretation of evolution from rift basin to passive margin or cratonic basin for the southwest Tarim Basin during the Late Neoproterozoic. Of these strata, the lacustrine dark shales of the late-rifting stage and the dolomites of the post-rifting stage can server as high-quality source rocks and reservoirs, respectively.

Chen, J.-w., Xu, M., Lei, B.-h., Liang, J., Zhang, Y.-g., Wu, S.-y., Shi, J., Yuan, Y., Wang, J.-q., Zhang, Y.-x., Li, G., Wang, W.-j., 2019. Prospective prediction and exploration situation of marine Mesozoic-Paleozoic oil and gas in the South Yellow Sea. China Geology 2, 67-84.


The South Yellow Sea Basin is a large sedimentary basin superimposed by the Mesozoic-Paleozoic marine sedimentary basin and the Mesozoic-Cenozoic terrestrial sedimentary basin, where no oil and gas fields have been discovered after exploration for 58 years. After the failure of oil and gas exploration in terrestrial basins, the exploration target of the South Yellow Sea Basin turned to the marine Mesozoic-Paleozoic strata. After more than ten years’ investigation and research, a lot of achievements have been obtained. The latest exploration obtained effective seismic reflection data of deep marine facies by the application of seismic exploration technology characterized by high coverage, abundant low-frequency components and strong energy source for the deep South Yellow Sea Basin. In addition, some wells drilled the Middle-Upper Paleozoic strata, with obvious oil and gas shows discovered in some horizons. The recent petroleum geological research on the South Yellow Sea Basin shows that the structure zoning of the marine residual basin has been redetermined, the basin structure has been defined, and 3 seismic reflection marker layers are traceable and correlatable in the residual thick Middle-Paleozoic strata below the continental Meso-Cenozoic strata in the South Yellow Sea Basin. Based on these, the seismic sequence of the marine sedimentary strata was established. According to the avaliable oil and gas exploration and research, the marine Mesozoic-Paleozoic oil and gas prospects of the South Yellow Sea were predicted as follows. (1) The South Yellow Sea Basin has the same sedimentary formation and evolution history during the sedimentary period of the Middle-Paleozoic marine basin with the Sichuan Basin. (2) There are 3 regional high-quality source rocks. (3) The carbonate and clastic reservoirs are developed in the Mesozoic-Paleozoic strata. (4) The three source-reservoir-cap assemblages are relatively intact. (5) The Laoshan Uplift is a prospect area for the Lower Paleozoic oil and gas, and the Wunansha Uplift is one for the marine Upper Paleozoic oil and gas. (6) The Gaoshi stable zone in the Laoshan Uplift is a favorable zone. (7) The marine Mesozoic-Paleozoic strata in the South Yellow Sea Basin has the geological conditions required to form large oil and gas fields, with remarkable oil and gas resources prospect. An urgent problem to be addressed now within the South Yellow Sea Basin is to drill parametric wells for the Lower Paleozoic strata as the target, to establish the complete stratigraphic sequence since the Paleozoic period, to obtain resource evaluation parameters, and to realize the strategic discovery and achieve breakthrough in oil and gas exploration understanding. ©2019 China Geology Editorial Office.

Chen, L., Luo, M., Dale, A.W., Rashid, H., Lin, G., Chen, D., 2019. Reconstructing organic matter sources and rain rates in the southern West Pacific Warm Pool during the transition from the deglaciation period to early Holocene. Chemical Geology 529, 119291.


Transient features in the organic carbon content of deep-sea sediment cores resulting from changes in the flux and/or quality of sedimentary organic matter are not uncommon. We examined the geochemical characteristics of sediments retrieved with a gravity corer from the northwestern Solomon Sea (3908 m water depth), southern West Pacific Warm Pool (WPWP). δ13C and δ15N of sedimentary organic matter, together with TOC/TN data suggest that the organic material is characterized by a mixture of marine and terrestrial origins with a higher contribution from marine algae. The data were analyzed with an inverse non-steady-state reaction-transport model to examine the variability and magnitude of particulate organic carbon (POC) flux to the seafloor during the transition between the deglaciation period and early Holocene. Measured POC content and porewater NO3

−, NH4

+, DIC and SO42− concentrations were used to constrain the model. Hindcast results revealed that POC flux

decreased from 75 to 37.5 μg cm−2 yr−1 during the deglaciation–early Holocene transition. The rate of POC degradation in the present setting is slightly lower compared to that in the pre-Holocene setting. The synchronous decline in the relative contribution of terrestrial organic matter input and rapid sea level rise during this transition suggest that sea level, rather than surface productivity, is the dominant factor controlling the POC deposition flux in the Solomon Sea. This is conceivable because the sampling site is proximal to high-relief islands with high rainfall, a well-developed submarine canyon system and narrow and steep continental margins. Consequently, we suggest that deep-water basins in proximity to similar high-relief mountainous

islands in the tropical Pacific may represent important sinks for terrestrial organic material, especially during sea level lowstands.

Chen, R., Yuan, K., Zhang, Z.-y., Xu, Q.-f., 2019. Sedimentary environment of organic-rich shale in the Upper Permian Longtan Formation in Qinglong area, western Guizhou, China. China Geology 2, 108-109.


1. Objective. The Qinglong area is located in the Eastern Yunnan-Western Guizhou uplift tectonic belt, west of the Zishui fault zone and north of the Youjiang basin. There are many sets of organic-rich shale in Longtan Formation in Qinglong area. Many predecessors did a great deal of research on the geological features of Permian coal fields in Western Guizhou (Mei MX et al., 2004; Dou XZ et al., 2012), but lack of the research on sedimentary background and distribution characteristics of organic-rich shale in Longtan Formation. Therefore, this study focuses on the analysis of the sedimentary environment of the Upper Permian Longtan Formation in Qinglong area.

2. Methods. The distribution characteristics and sedimentary environment of shale are the important basis for shale gas exploration (Zhai GY et al., 2018). Based on the analysis of sedimentary facies of typical profiles and wells, the sedimentary facies were analyzed and six sections (wells) in Qinglong and its surrounding area have been contrasted according to rock type, mudstone color and biodistribution. The sedimentary environment of Qinglong area in the late Permian is discussed.

3. Results. According to the lateral comparison, the depositional thickness of the Upper Permian Longtan Formation in the northern part of Qinglong County is the thickest, and in the central part is the thinnest. The sedimentation thickness of the Longtan Formation increases from south to north. The Longtan Formation in Qinglong and its peripheral area can be divided into three sequences and five system fields (Fig. 1).

Sequence I developed transgressive systems tract and highstand system tract (Fig. 1). There are one or more biogenic limestone layers in the transgressive system tract. The biological fossils in sequence I shows that sedimentary facies were tidal flat and lagoon facies. In the high system tract, there are mostly mudstone and siltstone with one or more sets of coal seam, showing the deepening of water bodies. In Qinglong area, the sedimentary facies of Sequence I were mainly shunt bay, swamp, tidal flat and lagoon facies (Fig. 2a). During this period, the Qinglong area was still in a relatively deep-water environment.

In sequence II, the transgressive system tract and the highstand system tract are developed. The northern part of Qinglong was the delta front facies with deltas developed, and gradually transformed into the former delta facies and the tidal flat-lagoon facies (Fig. 2b). During this period, the water was shallower from south to north. The delta appearing in the north shows that the source may come from the north.

Sequence III developed transgressive system tract. The wells in the northern area are mainly composed of siltstone and thin-bedded mudstone. In the southern area, sequence III developed siltstone, mudstone, coal seam and argillaceous limestone, the layers of Limestone are more than the northern area. The sedimentary facies of northwestern Qinglong convert to shunt bay of the delta plain (Fig. 2c). The southwestern Qinglong remained deep water basin but compare to sequence II the depth of water was much shallower.

4. Conclusion. The Longtan Formation of the Upper Permian in the Qinglong area can be divided into three second-order sequences and five system tracts. The early depositional environment was dominated by tidal flats and lagoon facies, and by the middle of the Longtan Formation, deltas began to appear from the northwest. In late period of Longtan Formation, delta further expands and the depth of water in northern part further lighten. The number and thickness of shale layers in the southwestward direction gradually decreases. The sedimentary environment was mainly delta-carbonate mild-sloped platform-slope-deepwater basin.

Chen, Y., Montero, L., Schmitz, O.J., 2019. Advance in on-line two-dimensional liquid chromatography modulation technology. TrAC Trends in Analytical Chemistry 120, 115647.


For some years now, multidimensional chromatography has been the focus of development in liquid chromatography in order to comprehensively analyze increasingly complex samples. It becomes clear that the molecular composition in biological samples is much more complex than previously assumed. Thus, the manifold variations of multidimensional chromatography allow a deeper understanding of the processes in nature. This review introduces the most important and creative modulators for the realization of two-dimensional liquid chromatography and discusses their advantages and disadvantages. One critical point in 2D-LC is, that the fractions from the 1D are often eluted in an incompatible or non-optimal injection solvent for the 2D, which causes in no or low retention of analytes, loss of separation power or increasing peak broadening in the 2D. Therefore, in this review the modulators are considered with regard to their ability to combine orthogonal separation mechanisms.



Methanogenic crude oil degradation is a significant process in subsurface environments and degradation of crude oil n-alkanes has been well documented. However, little is known about the biodegradability of the resulting heavy oil. In this study, a methanogenic consortium enriched from Shengli oilfield could generate 1.3–1.9 mmol CH4/g of heavy oil at a rate of 2.9–8.8 μmol CH4/g of oil/day. Four SARA fractions (saturates, aromatics, resins and asphaltenes) of oils experienced a loss in linear aliphatic structures. n-Alkylcyclohexanes, methyl-n-alkylcyclohexane, n-alkyldecalin, n-alkylbenzenes, n-alkyltoluenes and n-alkylxylenes with alkyl side chains longer than 14 carbons were degraded over 50% compared to the undegraded oil. In addition, the extent of degradation of these hydrocarbons increased with increasing carbon length. Correspondingly, n-fatty acids and naphthenic acids with 1–3 naphthenic rings accumulated over time. 16S rRNA gene analysis revealed that aceticlastic Methanosarcina and Methanothrix dominated in the archaeal domain, and bacterial members related to Dehalococcoidia and Soehngenia were consistently present in the successive transfer cultures. However, neither assA/masD-like genes nor alkyl-substituted succinate metabolites were detected, indicating an alternative degradation pathway rather than addition to fumarate. This study provides novel insights into methanogenic degradation of long-chain alkyl substituted hydrocarbons in heavy oil, which also extend our understanding of anaerobic degradation of crude oil in subsurface sedimentary environments.

Cheshkova, T.V., Sergun, V.P., Kovalenko, E.Y., Gerasimova, N.N., Sagachenko, T.A., Min, R.S., 2019. Resins and asphaltenes of light and heavy oils: Their composition and structure. Energy & Fuels 33, 7971-7982.


The complex of physicochemical methods of analysis (elemental analysis, cryoscopy in benzene, IR and 1H NMR spectroscopies, structural group analysis, gas chromatography–mass spectrometry, and selective chemical cleavage of sulfide and ether bonds) is used to comparatively characterize resins and asphaltenes of light and heavy oils. Attention is paid to the study of their structural group composition and the composition of moieties bound in molecules of resin–asphaltene substances (RAS) through ether and sulfide bridges, as well as the composition of compounds occluded by asphaltene molecules and nitrogen bases of resins. It is found that resins and asphaltenes of the heavy oil are characterized by higher average molecular masses and large overall sizes of mean molecules, due to the increased content of aromatic cycles in the naphthenic–aromatic system. The similar sets of linear and branched alkanes, alkylcyclopentanes, alkylcyclohexanes, steranes, mono- and disubstituted alkylbenzenes, and dibenzothiophenes identified in occluded compounds and products of chemolysis of resins and asphaltenes under study suggest the presence of most of these compounds as structural fragments in RAS molecules of light and heavy crude oils under study. Alkyl-substituted quinolines and benzoquinolines are identified in the nitrogen bases of resins. The feature of the light oil is the presence of “sulfur-bound” alkenes and polycycloalkenes in the structure of its asphaltenes. The findings expand our

understanding of the structure of petroleum resins and asphaltenes. They can be used to simulate their structure in developing new controlled methods for processing hydrocarbon feedstock.

Chettri, B., Singha, N.A., Mukherjee, A., Rai, A.N., Chattopadhyay, D., Singh, A.K., 2019. Hydrocarbon degradation potential and competitive persistence of hydrocarbonoclastic bacterium Acinetobacter pittii strain ABC. Archives of Microbiology 201, 1129-1140.

https://doi.org/10.1007/s00203-019-01687-z

Acinetobacter pittii strain ABC was isolated from oily sludge sediments and characterized with regard to utilization/degradation of hydrocarbons and competitive persistence in hydrocarbon-amended media. The isolate grew in both aliphatic- and aromatic hydrocarbon-amended Bushnell–Haas medium (BHM). When incubated in 1% (v/v) Assam crude oil-amended BHM for 5 and 10 days, this strain was able to degrade 88% and 99.8% of the n-hexane extractable crude oil components, respectively. The isolate showed appreciable emulsification index (E24 65.26 ± 1.2%), hydrophobicity (60.88 ± 3.5%) and produced lipopeptide biosurfactant (0.57 g L−1). The isolate was able to tolerate heavy metal salts at concentrations reported in crude oil-polluted sediments from Assam. A 16S rDNA DGGE-based screening showed the persistence of A. pittii strain ABC in hydrocarbon-amended microcosms co-inoculated with other hydrocarbonoclastic bacterial strains (Pseudomonas aeruginosa AKS1, Bacillus sp. AKS2, Arthrobacter sp. BC1, and Novosphingobium panipatense P5:ABC), each isolated from the same oily sludge sediment. These findings indicate A. pittii strain ABC as a potential agent for the bioremediation of crude oil-polluted environment.

Coffinet, S., Meador, T.B., Mühlena, L., Becker, K.W., Schröder, J., Zhu, Q.-Z., Lipp, J.S., Heuer, V.B., Crump, M.P., Hinrichs, K.-U., 2019. Structural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs). Biogeosciences Discussions 2019, 1-17.

https://www.biogeosciences-discuss.net/bg-2019-332/

Butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs) are membrane lipids recently discovered in sedimentary environments and in the methanogenic archaeon Methanomassiliicoccus luminyensis. They possess an unusual structure, which challenges fundamental assumptions in lipid biochemistry. Indeed, they bear a butanetriol or a pentanetriol backbone instead of a glycerol at one end of their core structure. In this study, we unambiguously located the additional methyl group of the BDGT compound on the C3 carbon of the lipid backbone via high-field two-dimensional NMR experiments. We further systematically explored the abundance, distribution and isotopic composition of BDGTs and PDGTs as both intact polar and core lipid forms in marine sediments collected in contrasting environments of the Mediterranean Sea and Black Sea. In addition, relatively 13C-depleted BDGTs from the Rhone delta and from the Black Sea are in agreement with a probable methanogenic source for these lipids. In line with this interpretation, high proportions of intact polar BDGTs and PDGTs were detected in the deeper methane-laden sedimentary layers. However, relatively 13C enriched BDGTs and contrasting headgroup distribution patterns of BDGTs and PDGTs in sediments of the Eastern Mediterranean Sea imply that additional archaeal groups also produce these unique lipids.


https://doi.org/10.1038/s41467-019-11543-9

Riverine dissolved organic carbon (DOC) contains charcoal byproducts, termed black carbon (BC). To determine the significance of BC as a sink of atmospheric CO2 and reconcile budgets, the sources and fate of this large, slow-cycling and elusive carbon pool must be constrained. The Amazon River is a significant part of global BC cycling because it exports an order of magnitude more DOC, and thus dissolved BC (DBC), than any other river. We report spatially resolved DBC quantity and radiocarbon (Δ14C) measurements, paired with

molecular-level characterization of dissolved organic matter from the Amazon River and tributaries during low discharge. The proportion of BC-like polycyclic aromatic structures decreases downstream, but marked spatial variability in abundance and Δ14C values of DBC molecular markers imply dynamic sources and cycling in a manner that is incongruent with bulk DOC. We estimate a flux from the Amazon River of 1.9–2.7 Tg DBC yr−1 that is composed of predominately young DBC, suggesting that loss processes of modern DBC are important.

Corami, F., Rosso, B., Bravo, B., Gambaro, A., Barbante, C., 2020. A novel method for purification, quantitative analysis and characterization of microplastic fibers using Micro-FTIR. Chemosphere 238, 124564.


Microplastics pose a worldwide risk for the environment. Microplastic fibers, which are released during the household washing of synthetic fabrics, are a substantial percentage of microplastics in rivers and in oceans. A novel quantification and simultaneous identification of fiber polymers via Micro-FTIR (Fourier Transform Infrared Spectroscopy) was developed. Washing simulations with commercially available household products were performed and effluents were filtered either on GF/F filters (0.7 μm) or on Anodisc filter (0.2 μm), to gather even the smallest fibers. Furthermore, a novel purification procedure of effluents was developed. Subsequently, filters were analyzed also with the scanning electronic microscope (SEM) to confirm the width and length of fibers. This novel method is robust and replicable and it allows better quantification of fibers released and identification of fiber polymers with optimal matches (averagely 80%).

Cornejo-Castillo, F.M., Zehr, J.P., 2019. Hopanoid lipids may facilitate aerobic nitrogen fixation in the ocean. Proceedings of the National Academy of Sciences 116, 18269-18271.


Cyanobacterial diazotrophs are considered to be the most important source of fixed N2 in the open ocean. Biological N2 fixation is catalyzed by the extremely O2-sensitive nitrogenase enzyme. In cyanobacteria without specialized N2-fixing cells (heterocysts), mechanisms such as decoupling photosynthesis from N2 fixation in space or time are involved in protecting nitrogenase from the intracellular O2 evolved by photosynthesis. However, it is not known how cyanobacterial cells limit O2 diffusion across their membranes to protect nitrogenase in ambient O2-saturated surface ocean waters. Here, we explored all known genomes of the major marine cyanobacterial lineages for the presence of hopanoid synthesis genes, since hopanoids are a class of lipids that might act as an O2 diffusion barrier. We found that, whereas all non−heterocyst-forming cyanobacterial diazotrophs had hopanoid synthesis genes, none of the marine Synechococcus, Prochlorococcus (non−N2-fixing), and marine heterocyst-forming (N2-fixing) cyanobacteria did. Finally, we conclude that hopanoid-enriched membranes are a conserved trait in non−heterocyst-forming cyanobacterial diazotrophs that might lower the permeability to extracellular O2. This membrane property coupled with high respiration rates to decrease intracellular O2 concentration may therefore explain how non−heterocyst-forming cyanobacterial diazotrophs can fix N2 in the fully oxic surface ocean.



Significance: How did the first cells on Earth arise? In a minimal cell, a membrane separates proteins and RNA from the surrounding aqueous environment. Cell-like membranes spontaneously assemble from simple prebiotic surfactants called fatty acids. However, fatty acid membranes are unstable in solutions containing salts that were likely present in environments of the early Earth. We find that amino acids, the building blocks of proteins, bind to fatty acid membranes and stabilize them against salts. Moreover, enhanced stabilization persists after dilution as would occur when a dehydrated pool refills with water—a likely setting for the

emergence of cells. In addition to explaining how the first membranes were stabilized, our findings answer how key components of the first cells colocalized.

Abstract: The membranes of the first protocells on the early Earth were likely self-assembled from fatty acids. A major challenge in understanding how protocells could have arisen and withstood changes in their environment is that fatty acid membranes are unstable in solutions containing high concentrations of salt (such as would have been prevalent in early oceans) or divalent cations (which would have been required for RNA catalysis). To test whether the inclusion of amino acids addresses this problem, we coupled direct techniques of cryoelectron microscopy and fluorescence microscopy with techniques of NMR spectroscopy, centrifuge filtration assays, and turbidity measurements. We find that a set of unmodified, prebiotic amino acids binds to prebiotic fatty acid membranes and that a subset stabilizes membranes in the presence of salt and Mg2+. Furthermore, we find that final concentrations of the amino acids need not be high to cause these effects; membrane stabilization persists after dilution as would have occurred during the rehydration of dried or partially dried pools. In addition to providing a means to stabilize protocell membranes, our results address the challenge of explaining how proteins could have become colocalized with membranes. Amino acids are the building blocks of proteins, and our results are consistent with a positive feedback loop in which amino acids bound to self-assembled fatty acid membranes, resulting in membrane stabilization and leading to more binding in turn. High local concentrations of molecular building blocks at the surface of fatty acid membranes may have aided the eventual formation of proteins.

Cotruvo, J.A., 2019. The chemistry of lanthanides in biology: Recent discoveries, emerging principles, and technological applications. ACS Central Science 5, 1496-1506.

https://doi.org/10.1021/acscentsci.9b00642

The essential biological role of rare earth elements lay hidden until the discovery in 2011 that lanthanides are specifically incorporated into a bacterial methanol dehydrogenase. Only recently has this observation gone from a curiosity to a major research area, with the appreciation for the widespread nature of lanthanide-utilizing organisms in the environment and the discovery of other lanthanide-binding proteins and systems for selective uptake. While seemingly exotic at first glance, biological utilization of lanthanides is very logical from a chemical perspective. The early lanthanides (La, Ce, Pr, Nd) primarily used by biology are abundant in the environment, perform similar chemistry to other biologically useful metals and do so more efficiently due to higher Lewis acidity, and possess sufficiently distinct coordination chemistry to allow for selective uptake, trafficking, and incorporation into enzymes. Indeed, recent advances in the field illustrate clear analogies with the biological coordination chemistry of other metals, particularly CaII and FeIII, but with unique twists—including cooperative metal binding to magnify the effects of small ionic radius differences—enabling selectivity. This Outlook summarizes the recent developments in this young but rapidly expanding field and looks forward to potential future discoveries, emphasizing continuity with principles of bioinorganic chemistry established by studies of other metals. We also highlight how a more thorough understanding of the central chemical question—selective lanthanide recognition in biology—may impact the challenging problems of sensing, capture, recycling, and separations of rare earths.

Curry, D.J., 2019. Future directions in basin and petroleum systems modeling: A survey of the community. American Association of Petroleum Geologists Bulletin 103, 2285-2293.

http://archives.datapages.com/data/bulletns/2019/10oct/BLTN17152/bltn17152.html

In the last 30 yr, basin and petroleum system modeling (BPSM) has evolved into a large and diverse field encompassing a broad range of scientific disciplines. As BPSM is applied to an increasingly wide range of problems, what are, or should be, the future directions in the evolution of BPSM comes into question.

To address this question, a survey was conducted at the AAPG Hedberg Research Conference on “The Future of Basin and Petroleum Systems Modeling,” held in Santa Barbara, California, April 3–8, 2016. To capture the full range of thoughts, participants were asked to list in priority order what they think are the three most important future directions in BPSM. The responses were collated into six general categories for analysis. The

categorization process involved some qualitative judgements because some areas spanned several of the general areas.

The results show that the most frequently cited directions are related to BPSM workflows, organizations, and processes. This category includes how modelers are used in an organization, how projects are executed, and how the results are interpreted and integrated.

Migration modeling (primary and secondary) is the most frequently cited technical need. The results indicate that migration processes are not well understood and there are still substantial differences of thought about the processes involved and the best ways to model them.

Some subjects, such as uncertainty and unconventionals, were mentioned in several of the general categories, whereas other subjects, such as increased functionality in the models, were only seldom mentioned.



The Last Interglacial period (LIG) is Earth's most recent globally warm period and is analogous in some ways to projected future global warming. However, questions remain regarding the state of the climate during the LIG in the North Atlantic, a region that is extremely sensitive to changes in oceanic and atmospheric circulation. Here, we present hydrogen and carbon isotope (δD and δ13C) records from a suite of plant wax biomarkers preserved in Holocene and LIG lacustrine sediments from the North Atlantic Faroe Islands and interpret them as qualitative proxies for temperature and hydroclimate variability. These data are used to directly compare LIG and Holocene climate using the same proxy approaches from the same terrestrial location. Measuring multiple isotopes on multiple types of waxes elucidates the sources of homologous plant waxes. We deduce that the δD values of long-chain n-alkanes (C27–C33) and mid-chain n-alkanes (C23–C25) in these sedimentary archives reflect leaf water and lake water δD values, respectively, while the δD values for both long-chain (C28–C30) and mid-chain n-alkanoic acids (C24–C26) primarily represent lake water δD values. Plant wax-inferred δD values of precipitation during the early Holocene (10,100 to 8,200  cal  yr BP) are ∼35‰ more positive than late Holocene values, and decline over the Holocene. δD-inferred hydrologic change and δ13C -inferred plant water use efficiency both indicate that the Faroe Islands became drier throughout the Holocene. Comparison with measurements from LIG plant waxes indicates that late LIG in the Faroe Islands was hydrologically similar to the early-to mid-Holocene (8,200 to 4,000  cal  yr BP), with enriched precipitation isotopes and reduced evapotranspiration indicating a warmer, wetter environment.

D’Arcy, F., Boucher, É., De Moor, J.M., Hélie, J.-F., Piggott, R., Stix, J., 2019. Carbon and sulfur isotopes in tree rings as a proxy for volcanic degassing. Geology 47, 825-828.

https://doi.org/10.1130/G46323.1

Trees are useful archives of past atmospheric conditions. They have most commonly been used to infer large-scale changes in climate, industrial pollution, and the magnitude and frequency of geological hazards. While geochemical changes in tree rings have been linked to localized anthropogenic smelter pollution, their potential to track geochemical changes in volcanic degassing has not yet been fully realized. Here, we applied a new proxy using sulfur and carbon isotopes in tree rings to examine fluctuations in gas emission at Turrialba volcano, Costa Rica. Since 2009, Turrialba has emitted a persistent gas plume and increasingly frequent explosions and ash eruptions as activity has accelerated. We collected cores from a species of alder tree, Alnus acuminata, at several locations surrounding the volcano. Biannual isotopic analysis of rings demonstrated a notable δ34S shift of –5.2‰ and a similarly sharp δ13C shift of +1.3‰ in trees downwind of the plume following the onset of strong degassing in 2009. We propose that these shifts in the isotopic values of the tree correspond to those of the volcanic SO2 and CO2, and in the case of the δ13C, an additional fractionation caused by leaf

impairment from exposure to volcanic SO2. This new proxy can be applied to other volcanoes as a novel method of obtaining a temporal record of degassing, a crucial tool for volcano monitoring.

Da, J., Zhang, Y.G., Li, G., Meng, X., Ji, J., 2019. Low CO2 levels of the entire Pleistocene epoch. Nature Communications 10, 4342.

https://doi.org/10.1038/s41467-019-12357-5

Quantifying ancient atmospheric pCO2 provides valuable insights into the interplay between greenhouse gases and global climate. Beyond the 800-ky history uncovered by ice cores, discrepancies in both the trend and magnitude of pCO2 changes remain among different proxy-derived results. The traditional paleosol pCO2 paleobarometer suffers from largely unconstrained soil-respired CO2 concentration (S(z)). Using finely disseminated carbonates precipitated in paleosols from the Chinese Loess Plateau, here we identified that their S(z) can be quantitatively constrained by soil magnetic susceptibility. Based on this approach, we reconstructed pCO2 during 2.6–0.9 Ma, which documents overall low pCO2 levels (<300 ppm) comparable with ice core records, indicating that the Earth system has operated under late Pleistocene pCO2 levels for an extended period. The pCO2 levels do not show statistically significant differences across the mid-Pleistocene Transition (ca. 1.2–0.8 Ma), suggesting that CO2 is probably not the driver of this important climate change event.

Da Pieve, F., 2019. Physicochemical properties and complexity of amino acids beyond our biosphere: Analysis of the isoleucine group from meteorites. ACS Earth and Space Chemistry 3, 1955-1965.


Understanding the physicochemical properties of biomolecules and how these properties drive the emergence of complexity in the assembly/condensation of such systems is important for understanding a variety of reactions taking place in astrophysical environments, in particular those where polymerization processes occur on mineral surfaces or solid organic matter form in cold-chemistry processes. Here, a computational study of the structural and electronic properties of the gas and condensed phases of the isoleucine group of amino acids, found with large enantiomeric excess in Antarctic meteorites, is presented. An analysis of a statistical complexity measure related to their electronic properties, of the degree of chirality, and of the H-bond patterns is also reported. The results, based on Density Functional Theory, Many Body Perturbation Theory, and Møller–Plesset perturbation theory, show that a) the condensed amino acids keep reminiscence of structural and electronic properties of the gas phase molecules, b) the proteinogenic l-isoleucine gains in complexity and chirality upon condensation, contrary to its diastereomer, which is absent in living systems, and c) the complexity based on electronic properties can contrast with the notion of structural/geometrical complexity. The findings suggest that future scoring strategies of organic molecules should rely on both structural/geometrical molecular complexity and on the electronic properties, which in different states of matter are determined by other degrees of freedom (configurational or chiral) to a different extent, as well as on information storage capability of self-assembly configurations constrained by an atomistic chemistry perspective.

Dahl, T.W., Connelly, J.N., Li, D., Kouchinsky, A., Gill, B.C., Porter, S., Maloof, A.C., Bizzarro, M., 2019. Atmosphere–ocean oxygen and productivity dynamics during early animal radiations. Proceedings of the National Academy of Sciences 116, 19352-19361.


Significance: We have discovered 2 major oceanic anoxic events (OAEs) in the early Cambrian at the time when animals markedly diversified. We present a multiproxy constraint on the global biogeochemical cycles to show that these events, in contrast to most younger OAEs, could have been driven by declining atmospheric O2 levels, plausibly set off by the appearance of bioturbating animals. Pulses of animal appearances may have occurred at different times on different continents, but the last pulse occurred after the OAEs and at a time when we predict higher marine productivity and O2 levels in the surface oceans suggesting energy supply into the marine food chain was maximal.

Abstract: The proliferation of large, motile animals 540 to 520 Ma has been linked to both rising and declining O2 levels on Earth. To explore this conundrum, we reconstruct the global extent of seafloor oxygenation at approximately submillion-year resolution based on uranium isotope compositions of 187 marine carbonates samples from China, Siberia, and Morocco, and simulate O2 levels in the atmosphere and surface oceans using a mass balance model constrained by carbon, sulfur, and strontium isotopes in the same sedimentary successions. Our results point to a dynamically viable and highly variable state of atmosphere–ocean oxygenation with 2 massive expansions of seafloor anoxia in the aftermath of a prolonged interval of declining atmospheric pO2 levels. Although animals began diversifying beforehand, there were relatively few new appearances during these dramatic fluctuations in seafloor oxygenation. When O2 levels again rose, it occurred in concert with predicted high rates of photosynthetic production, both of which may have fueled more energy to predators and their armored prey in the evolving marine ecosystem.

Danso, D., Chow, J., Streit, W.R., 2019. Plastics: Environmental and biotechnological perspectives on microbial degradation. Applied and Environmental Microbiology 85, e01095-19.

http://aem.asm.org/content/85/19/e01095-19.abstract

Plastics are widely used in the global economy, and each year, at least 350 to 400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health. Therefore, recent microbial research has addressed the question of if and to what extent microorganisms can degrade plastics in the environment. This review summarizes current knowledge on microbial plastic degradation. Enzymes available act mainly on the high-molecular-weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). Unfortunately, the best PUR- and PET-active enzymes and microorganisms known still have moderate turnover rates. While many reports describing microbial communities degrading chemical additives have been published, no enzymes acting on the high-molecular-weight polymers polystyrene, polyamide, polyvinylchloride, polypropylene, ether-based polyurethane, and polyethylene are known. Together, these polymers comprise more than 80% of annual plastic production. Thus, further research is needed to significantly increase the diversity of enzymes and microorganisms acting on these polymers. This can be achieved by tapping into the global metagenomes of noncultivated microorganisms and dark matter proteins. Only then can novel biocatalysts and organisms be delivered that allow rapid degradation, recycling, or value-added use of the vast majority of most human-made polymers.

Das, T., Ghule, S., Vanka, K., 2019. Insights into the origin of life: Did it begin from HCN and H2O? ACS Central Science 5, 1532-1540.


The seminal Urey–Miller experiments showed that molecules crucial to life such as HCN could have formed in the reducing atmosphere of the Hadean Earth and then dissolved in the oceans. Subsequent proponents of the “RNA World” hypothesis have shown aqueous HCN to be the starting point for the formation of the precursors of RNA and proteins. However, the conditions of early Earth suggest that aqueous HCN would have had to react under a significant number of constraints. Therefore, given the limiting conditions, could RNA and protein precursors still have formed from aqueous HCN? If so, what mechanistic routes would have been followed? The current computational study, with the aid of the ab initio nanoreactor (AINR), a powerful new tool in computational chemistry, addresses these crucial questions. Gratifyingly, not only do the results from the AINR approach show that aqueous HCN could indeed have been the source of RNA and protein precursors, but they also indicate that just the interaction of HCN with water would have sufficed to begin a series of reactions leading to the precursors. The current work therefore provides important missing links in the story of prebiotic chemistry and charts the road from aqueous HCN to the precursors of RNA and proteins.

Davies, M.B., Kokaia, G., 2019. Stellar encounters with giant molecular clouds. Monthly Notices of the Royal Astronomical Society 489, 5165–5180.

https://doi.org/10.1093/mnras/stz813

Giant molecular clouds (GMCs) are believed to affect the biospheres of planets as their host star passes through them. We simulate the trajectories of stars and GMCs in the Galaxy and determine how often stars pass through GMCs. We find a strong decreasing dependence with Galactocentric radius, and with the velocity perpendicular to the Galactic plane, Vz. The XY-component of the kinematic heating of stars was shown to not affect the GMC hit rate, unlike the Z-dependence (Vz) implies that stars hit fewer GMCs as they age. GMCs are locations of star formation, therefore we also determine how often stars pass near supernovae. For the supernovae the decrease with Vzis steeper as how fast the star passes through the GMC determines the probability of a supernova encounter. We then integrate a set of Sun-like trajectories to see the implications for the Sun. We find that the Sun hits 1.6 ± 1.3 GMCs per Gyr which results in 1.5 ± 1.1 or (with correction for clustering) 0.8 ± 0.6 supernova closer than 10 pc per Gyr. The different the supernova frequencies are from whether one considers multiple supernova per GMC crossing (few Myr) as separate events. We then discuss the effect of the GMC hits on the Oort cloud, and the Earth’s climate due to accretion, we also discuss the records of distant supernova. Finally, we determine Galactic Habitable Zone using our model. For the thin disk we find it to lie between 5.8-8.7 kpc and for the thick disk to lie between 4.5-7.7 kpc.

Davis, C.E., Blackbird, S., Wolff, G., Woodward, M., Mahaffey, C., 2019. Seasonal organic matter dynamics in a temperate shelf sea. Progress in Oceanography 177, 101925.

https://www.sciencedirect.com/science/article/pii/S0079661117302136

Organic matter (OM) plays an important role in productive shelf seas and their contribution to global carbon (C) and nutrient cycles. We investigated dissolved and particulate OM (DOM and POM, respectively) dynamics over a seasonal cycle in the Celtic Sea. The quantity of OC was largest during the spring bloom and lowest in autumn. DOM was always C rich relative to the POM pool and the Redfield ratio (106C:16N:P). There was clear decoupling between C, N and P and the response of OM composition to different seasons and nutrient statuses of the microbial community. The C:P stoichiometry was much more variable than the C:N stoichiometry, which was near constant. Downward OC fluxes were dominated by POM during bloom events and DOM during the stratified summer. In terms of partitioning, 92–96% of OC was in the DOM pool throughout sampling, which given its high C:N (12.4–17) suggests it was an efficient vehicle for potential off-shelf export of C during winter mixing.

Davis, L.G., Madsen, D.B., Becerra-Valdivia, L., Higham, T., Sisson, D.A., Skinner, S.M., Stueber, D., Nyers, A.J., Keen-Zebert, A., Neudorf, C., Cheyney, M., Izuho, M., Iizuka, F., Burns, S.R., Epps, C.W., Willis, S.C., Buvit, I., 2019. Late Upper Paleolithic occupation at Cooper’s Ferry, Idaho, USA, ~16,000 years ago. Science 365, 891-897.

http://science.sciencemag.org/content/365/6456/891.abstract

Abstract: Radiocarbon dating of the earliest occupational phases at the Cooper’s Ferry site in western Idaho indicates that people repeatedly occupied the Columbia River basin, starting between 16,560 and 15,280 calibrated years before the present (cal yr B.P.). Artifacts from these early occupations indicate the use of unfluted stemmed projectile point technologies before the appearance of the Clovis Paleoindian tradition and support early cultural connections with northeastern Asian Upper Paleolithic archaeological traditions. The Cooper’s Ferry site was initially occupied during a time that predates the opening of an ice-free corridor (≤14,800 cal yr B.P.), which supports the hypothesis that initial human migration into the Americas occurred via a Pacific coastal route.

Editor's summary: The early occupation of America. The Cooper's Ferry archaeological site in western North America has provided evidence for the pattern and time course of the early peopling of the Americas. Davis et al. describe new evidence of human activity from this site, including stemmed projectile points. Radiocarbon dating and Bayesian analysis indicate an age between 16,560 and 15,280 years before present. Humans therefore arrived in the Americas before an inland ice-free corridor had opened, so a Pacific coastal route was

the probable entry route. The stemmed projectile points closely resemble those found in Upper Paleolithic Japan, also supporting the hypothesis of a coastal route.


https://www.frontiersin.org/article/10.3389/fmicb.2019.02046

Candida parapsilosis is the most frequent cause of catheter-related candidemia among non-Candida albicans species. This may be related to intrinsic capabilities as adhering and forming a biofilm on abiotic surfaces such as on medical devices. As previously demonstrated, patients infected with high biofilm-producing C. parapsilosis isolates had a greater mortality risk compared to patients infected with low biofilm-producing C. parapsilosis isolates. We developed the BIOF–HILO assay, a MALDI–TOF mass spectrometry (MS)-based assay, which compares mass spectra obtained from attached and suspended isolate cells during the early (i.e., 3-h) adhesion phase of in vitro biofilm formation. The composite correlation index (CCI) analysis was used to discriminate between mass spectra differences of the two cell types, classifying all 50 C. parapsilosis clinical isolates, included in the study, after only 3-h of testing, in high or low biofilm producers. All high (n = 25) or low (n = 25) biofilm producers had, according to CCI mass spectra comparison values, higher or lower than one CCI ratios, which were obtained by dividing the CCIsuspended cells by the CCIattached cells. In conclusion, the BIOF–HILO assay allows a rapid categorization of C. parapsilosis clinical isolates in high or low biofilm producers. This information, if timely provided to physicians, may improve treatment outcomes in patients with C. parapsilosis candidemia.

de Santana, C.D., Crampton, W.G.R., Dillman, C.B., Frederico, R.G., Sabaj, M.H., Covain, R., Ready, J., Zuanon, J., de Oliveira, R.R., Mendes-Júnior, R.N., Bastos, D.A., Teixeira, T.F., Mol, J., Ohara, W., Castro, N.C.e., Peixoto, L.A., Nagamachi, C., Sousa, L., Montag, L.F.A., Ribeiro, F., Waddell, J.C., Piorsky, N.M., Vari, R.P., Wosiacki, W.B., 2019. Unexpected species diversity in electric eels with a description of the strongest living bioelectricity generator. Nature Communications 10, 4000.

https://doi.org/10.1038/s41467-019-11690-z

Is there only one electric eel species? For two and a half centuries since its description by Linnaeus, Electrophorus electricus has captivated humankind by its capacity to generate strong electric discharges. Despite the importance of Electrophorus in multiple fields of science, the possibility of additional species-level diversity in the genus, which could also reveal a hidden variety of substances and bioelectrogenic functions, has hitherto not been explored. Here, based on overwhelming patterns of genetic, morphological, and ecological data, we reject the hypothesis of a single species broadly distributed throughout Greater Amazonia. Our analyses readily identify three major lineages that diverged during the Miocene and Pliocene—two of which warrant recognition as new species. For one of the new species, we recorded a discharge of 860 V, well above 650 V previously cited for Electrophorus, making it the strongest living bioelectricity generator.

De Schepper, S., Ray, J.L., Skaar, K.S., Sadatzki, H., Ijaz, U.Z., Stein, R., Larsen, A., 2019. The potential of sedimentary ancient DNA for reconstructing past sea ice evolution. The ISME Journal 13, 2566-2577.

https://doi.org/10.1038/s41396-019-0457-1

Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA), as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions. Although use of sedimentary aDNA in paleoceanographic and paleoclimatic studies is still in its infancy, we use here metabarcoding and single-species quantitative DNA detection methods to document the sea ice conditions in a Greenland Sea marine sediment

core. Metabarcoding has allowed identifying biodiversity changes in the geological record back to almost ~100,000 years ago that were related to changing sea ice conditions. Detailed bioinformatic analyses on the metabarcoding data revealed several sea-ice-associated taxa, most of which previously unknown from the fossil record. Finally, we quantitatively traced one known sea ice dinoflagellate in the sediment core. We show that aDNA can be recovered from deep-ocean sediments with generally oxic bottom waters and that past sea ice conditions can be documented beyond instrumental time scales. Our results corroborate sea ice reconstructions made by traditional tools, and thus demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.

Dearing Crampton-Flood, E., Peterse, F., Sinninghe Damsté, J.S., 2019. Production of branched tetraethers in the marine realm: Svalbard fjord sediments revisited. Organic Geochemistry 138, 103907.


Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids thought to be predominantly produced on land. They are used as a terrestrial paleothermometer based on an empirical relation between their molecular composition and air temperature in surface soils worldwide. The proxy has been applied in continental margin sediments based on the assumption that all brGDGTs originate from land and are transported to marine sediments predominantly by rivers. However, this assumption has been challenged by the discovery of in situ brGDGT production in the coastal marine environment. To better understand marine brGDGT production, we examined newly collected marine surface sediments from the Krossfjorden and Kongsfjorden in Svalbard with a chromatography method to separate previously co-eluting 5- and 6-methylated brGDGT isomers. ‘Living’ intact polar lipid (IPL)-derived and ‘fossil’ core lipid (CL) brGDGTs were also studied for a subset of fjord sediments. The relative proportion of cyclopentane moieties in tetramethylated brGDGTs, used as indicator for brGDGT production in coastal marine settings, is much higher in the fjord sediments (#ringstetra = 0.65–0.93 for CL and 0.24–0.79 for IPL-derived brGDGTs) compared to those in nearby soils (#ringstetra = 0.00–0.37), and confirms the predominantly marine source of the brGDGTs in the fjord. Surprisingly, however, IPL-derived brGDGTs have a substantially lower #ringstetra (up to 0.52 offset) compared to that of CL-brGDGTs in the same sediment. This suggests that brGDGTs are produced in situ in different distributions throughout the year, of which the CL distribution in the sediment is an integrated signal. The offset in #ringstetra between IPL-derived and CL brGDGTs varies between 0.15 and 0.52 and increases towards the open ocean, possibly linking brGDGT production to the natural salinity gradient and associated microbial community changes.



Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.



The use of total acid number (TAN) to measure the acidity of crude oil samples is a common practice. Daily practice in petroleum refineries shows that oil with a TAN less than 0.5 mg KOH g−1 can usually have unexpected corrosive behavior. Although naphthenic corrosion has been studied for many years, its process is not entirely understood. Therefore, this study investigated the influence of linear, cyclic and aromatic NAs molecules, evaluating the effect of their concentrations, molar weight (Mw), structural and electronic properties on the corrosion rate of AISI 1020 steel samples at 320 °C. The type and extension of corrosion were determined by surface characterization of the sample using optical microscopy (LM), atomic force microscopy (AFM), and scanning electron microscopy (SEM). The results showed that even when TAN was below the detection limit, the corrosion rate (CR) value was significant (CR < 0.19 mm year−1) and considered high for the industry. For concentrations of benzoic (BENA) and stearic (STA) acids higher than 5000 ppm, the corrosion rate varied proportionally with the TAN. Also, there was an inverse proportional correlation between molecular weight (Mw), the number of aromatic rings and NAs corrosiveness. In general, NAs standards containing a lower molar volume were found to cause a higher corrosion rate. SEM micrographs revealed changes in the surface area of all samples exposed to linear, cyclic and aromatic NAs, indicating the formation of a protective layer under the surface of the carbon steel specimen. AFM imaging showed drastic changes in the topographic profile and phase images characterized by the formation of valleys and peaks, as well as variations in the mechanical properties of the surface of the AISI 1020 steel sample. Results obtained in this study confirm the influence of the electronic-structural properties of the molecules of organic acids on the naphthenic corrosion.



Force spectroscopy is used to investigate crude oil/brine/rock interactions at reservoir temperatures and pressures, up to 120 °C and 10 MPa, for the first time. A newly-developed, high pressure, high temperature atomic force microscope (HP/HT-AFM) is used in combination with newly-designed, crude-oil functionalized AFM probes compatible with these conditions. Our results show that both temperature and pressure have significant impact on adhesion forces, demonstrating the necessity of testing in this environment to obtain results that accurately reflect interactions at reservoir conditions. The HP/HT-AFM design introduced here also allows changing many other variables such as brine composition, dissolved gases, injection fluid additives, the type of crude oil, as well as the type of mineral surface. Consequently, the system introduced here has the capability to investigate interfacial interactions at reservoir conditions with unprecedented specificity, providing the basis for the development of optimized and tailored oil recovery techniques.

Dietze, E., Mangelsdorf, K., Andreev, A., Karger, C., Schreuder, L.T., Hopmans, E.C., Rach, O., Sachse, D., Wennrich, V., Herzschuh, U., 2019. Relationships between low-temperature fires, climate and vegetation during the last 430 kyrs in northeastern Siberia reconstructed from monosaccharide anhydrides in Lake El’gygytgyn sediments. Climate of the Past Discussions 2019, 1-29.

https://www.clim-past-discuss.net/cp-2019-103/

Landscapes in high northern latitudes are assumed to be highly sensitive to future global change, but the rates and long-term trajectories of changes are rather uncertain. In the boreal zone, fires are an important factor in climate–vegetation–interactions and biogeochemical cycles. Fire regimes are characterized by small, frequent, low-intensity fires within summergreen boreal forests dominated by larch, whereas evergreen boreal forests dominated by spruce and pine burn large areas less frequently, but at higher intensities. Here, we explore the potential of the monosaccharide anhydrides (MA) levoglucosan, mannosan, and galactosan to serve as proxies of low-intensity biomass burning in glacial-to-interglacial lake sediments from the high northern latitudes. We use sediments from Lake El’gygytgyn (cores PG 1351 and ICDP 5011-1), located in the far north-east of Russia, and study glacial and interglacial samples of the last 430 kyrs (marine isotope stages 5e, 6, 7e, 8, 11c, 12) that had different climate and biome configurations. Combined with pollen and non-pollen palynomorph

records from the same samples, we assess past relationships between fire, climate, and vegetation on orbital to centennial time scales. We find that MAs were well-preserved in up to 430 kyrs old sediments with higher influxes from low-intensity biomass burning in interglacials compared to glacials. MA influxes significantly increase when summergreen boreal forest spreads closer to the lake, whereas they decrease when tundra-steppe environments and, especially, Sphagnum peatlands spread. This suggests that low-temperature fires are a typical property of Siberian larch forest on long timescales. The results also suggest that low-intensity fires would be reduced by vegetation shifts towards very dry environments due to reduced biomass availability, as well as by shifts towards peatlands, which limits fuel dryness. In addition, we observed very low MA ratios, which we interpret as high contributions of galactosan and mannosan from other than currently monitored biomass sources, such as the moss-lichen mats in the understorey of the summergreen boreal forest. Overall, sedimentary MAs can provide a powerful proxy for fire regime reconstructions and extend our knowledge on long-term fire–climate–vegetation feedbacks in the high northern latitudes.



Along the western edge of the Bohemian Massif, SE Germany, graphitic carbon occurs in metabasic rocks plus calcsilicates, metabiolites, and paragneisses (graphite I), in pegmatites (graphite II) and in mineralized structure zones (semigraphite and impsonite) The current studies unveiled these graphitic carbon compounds are strikingly different with regard to their age and temperature of formation: Graphite I (≥324 Ma, 570 to 625 °C), graphite II (317 ± 3 Ma, >400 °C), semi-graphite (305 ± Ma, 225 to 400 °C), impsonite (<298 ± 4 Ma, 100 to 363 °C). Semi-graphite takes a special position among these graphitic carbon compounds because it links the different carbon modifications with regard to its age of formation, its structural position and its S- and C isotopes that point to a mantle and crustal influence on its formation in contrast to graphite (graphite I: crustal, graphite II: mantle) and impsonite (mantle). Semi-graphite precipitated in a fault zone which evolved from a zone of strong felsic mobilization in metabasic rocks spawning KNa feldspar-quartz pegmatoids/aploids. During conversion of a pre-existing zone of felsic mobilization into a brittle shearzone not only carbonaceous matter but also Ni-, Pb-, Cu-, Zn-, As-, Fe-, Hg- and Mo sulfides were concentrated. The semi-graphite-bearing mineralized zone is located near rare element pegmatites hosting graphite flakes. The C-bearing systems are useful pathfinders to locate structurebound mineral deposits hosting U or base metals in the Variscan orogen.

The structurebound metalliferous semi-graphite mineralization in metabasic rocks can be taken as a reference type of dual-source hydrocarbon immigration into fault zones, syn- to postkinematically relative to the fault movement. The model can be applied to host rocks undergoing retrograde medium- to very-low-grade stage dynamo-metamorphic conditions.

To elucidate the complex history of the various types of graphite and metamorphosed bitumen a multidisciplinary approach has been taken involving petrographic and geological field mapping combined with drill core examination, petrographic and ore microscopy supplemented by electron microprobe, X-ray diffraction and scanning electron microscopy with EDX, micro-Raman spectroscopy in addition to classical coal petrographic studies, and inorganic geochemistry of major and minor elements and isotope (carbon and sulfur) chemical analysis followed up by a statistical treatment of the various chemical datasets.


https://doi.org/10.1038/s41467-019-12214-5

Tibetan permafrost largely formed during the late Pleistocene glacial period and shrank in the Holocene Thermal Maximum period. Quantifying the impacts of paleoclimatic extremes on soil carbon stock can shed light on the vulnerability of permafrost carbon in the future. Here, we synthesize data from 1114 sites across the

Tibetan permafrost region to report that paleoclimate is more important than modern climate in shaping current permafrost carbon distribution, and its importance increases with soil depth, mainly through forming the soilʼs physiochemical properties. We derive a new estimate of modern soil carbon stock to 3 m depth by including the paleoclimate effects, and find that the stock (36.6 +2.3 −2.4 PgC) is triple that predicted by ecosystem models (11.5 ± 4.2 s.e.m PgC), which use pre-industrial climate to initialize the soil carbon pool. The discrepancy highlights the urgent need to incorporate paleoclimate information into model initialization for simulating permafrost soil carbon stocks.

Ding, W., Dong, L., Sun, Y., Ma, H., Xu, Y., Yang, R., Peng, Y., Zhou, C., Shen, B., 2019. Early animal evolution and highly oxygenated seafloor niches hosted by microbial mats. Scientific Reports 9, 13628.

https://doi.org/10.1038/s41598-019-49993-2

The earliest unambiguous evidence for animals is represented by various trace fossils in the latest Ediacaran Period (550–541 Ma), suggesting that the earliest animals lived on or even penetrated into the seafloor. Yet, the O2 fugacity at the sediment-water interface (SWI) for the earliest animal proliferation is poorly defined. The preferential colonization of seafloor as a first step in animal evolution is also unusual. In order to understand the environmental background, we employed a new proxy, carbonate associated ferrous iron (Fecarb), to quantify the seafloor oxygenation. Fecarb of the latest Ediacaran Shibantan limestone in South China, which yields abundant animal traces, ranges from 2.27 to 85.43 ppm, corresponding to the seafloor O2 fugacity of 162 μmol/L to 297 μmol/L. These values are significantly higher than the oxygen saturation in seawater at the contemporary atmospheric pO2 levels. The highly oxygenated seafloor might be attributed to O2 production of the microbial mats. Despite the moderate atmospheric pO2 level, microbial mats possibly provided highly oxygenated niches for the evolution of benthic metazoans. Our model suggests that the O2 barrier could be locally overcome in the mat ground, questioning the long-held belief that atmospheric oxygenation was the key control of animal evolution.


http://www.sciencedirect.com/science/article/pii/S0025326X19306915

Polycyclic aromatic hydrocarbons (PAH) are a group of ubiquitous environmental pollutants among which some compounds show carcinogenic properties. The emission of PAH from anthropogenic and natural sources to the aquatic environment demands monitoring. In this study, ten different surface water samples were collected and analyzed for 48 different PAH compounds by gas chromatography-atmospheric-pressure-laser-ionization coupled to mass spectrometry (GC-APLI-MS) after liquid-liquid extraction. Results varied from 9.22 ng/L for fluoranthene in harbor water to 0.01 ng/L for 4-methylchrysene in Rhine river water. Overall low PAH concentrations were found in the samples. Toxic equivalent (TEQ) calculations were used to assess the potential environmental impact of the analyzed compounds. The results showed higher concentrations and TEQ for the samples from harbors in comparison to riverine and estuarine sampling locations. Suspected target analysis indicated the occurrence of alkylated PAH in the surface water samples.

Drozd, R.J., 2019. Adventures in pyrolysis II, modeling pyrolysis peaks of petroleum source rocks. Journal of Analytical and Applied Pyrolysis 142, 104385.


Programmed pyrolysis is an integral part petroleum source rock evaluation. The analysis is used to determine the potential of a source rock to generate further petroleum, and with other geochemical measurements, how much it may have generated in the past. An important part of the overall evaluation is an estimate of the source rock thermal maturity. Unfortunately, the addition of any extraneous, non-native hydrocarbons can negatively impact the yield of the samples, and more important, the thermal maturity determination. These extraneous hydrocarbons can be petroleum previously generated and retained within the source rock, fluids that migrated in

the subsurface into the rocks, or organic material added during the drilling process. The objective of this study was to determine if mathematical methods could be used to remove these extraneous contributions from the true source rock yields, and arrive at a better determination of thermal maturity.

Eighteen samples were studies using the standard pyrolysis method applied in the geochemical services industry. Two aliquots of each sample were analyzed: one as-received and a second after solvent extraction solvents to remove soluble organic matter but not kerogen. The pyrograms typically associate with the conversion of native organic matter in the rock were considered as the sum of up to three underlying components which could be recovered by non-linear least squares methods. Four distribution functions were used to model the pyrograms: classical Gaussian distribution, the Cauchy function, the Logistic function and the Weibull distribution. In addition to the ability of each model to match the measured data, each was evaluated for ease of use. All models reproduced the total pyrolysis yields of the test samples, and generated Tmax values with agreed within 2 °C.

• The Gaussian model was marginally better at fitting the measurements than the Logistic or Weibull models, and distinctly better than the Cauchy model. Based upon experience, the Gaussian model was the most forgiving in the choice of initial parameters.

• The Cauchy model performed the poorest at fitting the measurements and had the largest differences between extracted and unextracted Tmax values. The deviations from the measured values were most pronounced at high and low temperatures due the longer tail of the Cauchy function.

• The Logistic model has marginally lower ability to fit the measured data than the Gaussian model, and similar to the Weibull model. However, the Logistic model was more sensitive to the choice of initial values than the Gaussian model, but less sensitive than the Weibull model.

• The Weibull model was marginally poorer at fitting the measurements than the Gaussian model and similar to the Logistic model. It did less well at fitting the four component model for the more complex samples. It was most sensitive to the accurate choices for the initial conditions to insure convergence. For some samples sequential manual choices for these parameters was needed before the Gauss-Newton method could be employed.

Druetta, P., Picchioni, F., 2019. Branched polymers and nanoparticles flooding as separate processes for enhanced oil recovery. Fuel 257, 115996.


Since it was first theorized more than half-century ago, nanotechnology has proven to be the perfect boost for existing technologies and the oil industry has made use of this avant-garde discipline to upsurge the productivity of mature oilfields. With respect to polymer flooding, recent research has stressed the importance of the (macro)molecules’ architecture on the physical properties. This paper presents the numerical simulation of these two agents in standard, not combined, oil recovery processes. The polymer solution viscosity is calculated considering the polymer’s architecture, its degradation and the salinity. The nanoparticles affect the carrier-phase viscosity and the rock formation wettability, which modifies the oil mobility. Results evidenced the improved capabilities of branched (i.e. star/comb) polymers with respect to traditional linear ones. The modified architecture improves not only the rheological but also the viscoelastic properties, which ultimately increases the microscopic sweeping efficiency. Nanoparticles increase slightly the carrier phase viscosity, but their main recovery mechanism is their adsorption onto the rock and subsequent wettability modification, reducing the residual oil saturation. Furthermore, it is also important to properly characterize both the particles’ average size and also their aggregation rate, since these affect the recovery efficiency. Simulations show the importance of a good characterization of oil recovery agents and their effect on the phases’ physical properties as well as the potential of nanoparticles to act as a boost of traditional enhanced recovery processes.

Duan, Y.T., Li, X., Ranjith, P.G., Wu, Y.F., 2020. An investigation of the evolution of the internal structures and failure modes of Longmaxi shale using novel X-ray microscopy. Journal of Petroleum Science and Engineering 184, 106479.


An accurate description of the evolution of the internal structure of shale during loading and fracturing is important to understand the failure mechanisms that are related to shale-gas migration. The aim of this work was to investigate and characterize the void evolution and failure of Longmaxi shale quantitatively under uniaxial tests, and analyze the relationship between the distribution of the meso-scale (voxel-scale) minerals and the failure mode. Novel X-ray microscopy combined with an in-situ microtest device was used and three groups of shale specimens were tested under uniaxial conditions with different scanning stresses. Some three-dimensional stereograms of different loading forces and an entire force–displacement curve were obtained for each in-situ test. Based on the results, an evolution of the void distribution was characterized and divided into four stages: weakened damage, linear, damage evolution and stable development, and accelerated damage development. The degree of development of the final cracks was distinguished by the crack volume, equivalent aperture width and connectivity rate. The structure evolution and failure mode of shale were described quantitatively by the void changes and the crack characteristics. Three phenomena of intergranular fracture, transgranular fracture and arrest cracks were observed at a meso-scale to explain the effect of mineral distribution on the crack pattern. These quantitative results can provide a guide for the design in shale fracturing engineering and some references for numerical analysis.

Ducklow, H., Plank, T., 2019. Volcano-stimulated marine photosynthesis. Science 365, 978-979.


Marine phytoplankton, microscopic unicellular algae, are responsible for about half of the photosynthesis on Earth (1). Photosynthesis, on land and sea, maintains atmospheric oxygen and CO2 levels, governing the habitability of the planet. This ocean photosynthesis (called primary production) is supported by opposing physical oceanographic mechanisms. Vertical stability, or buoyancy, of the ocean surface layer maintains the photosynthesizing biomass in the solar-irradiated euphotic zone, whereas vertical mixing or upwelling supplies deepwater nutrients, such as nitrogen, phosphorus, and silicon, which are required for phytoplankton growth. On page 1040 of this issue, Wilson et al. (2) report a heretofore unknown mechanism that enhances primary production of organic matter off Hawai'i. They found that lava discharged into the ocean by the erupting Kīlauea volcano created a plume of increased nutrient concentrations, enhanced phytoplankton growth, increased plankton abundance, and altered plankton species composition. Any of these responses could alter the local carbon cycle.

The fertility of volcanic soils is well established (3), and iron in airborne volcanic ash can fertilize the ocean many hundreds of kilometers downstream (4)—a process of global importance because iron is the limiting nutrient for plankton growth over vast regions of the open sea. But the role of lava in marine ecosystems was not previously suspected, and effects on ocean organisms had not been investigated (5). Because lava from Kīlauea, a highly active volcano in Hawai'i, contains no fixed nitrogen species (6), Wilson et al. hypothesized that the fertilization effect of the lava was indirect, caused by the upwelling of buoyant deep seawater heated by the lava and carrying high concentrations of nitrate. The stable isotope composition of nitrogen and oxygen in the “new” nitrate was consistent with a deepwater source and was distinct from nitrogen derived from biological nitrogen fixation and from groundwater. Using a computational model, the authors demonstrated phytoplankton growth enhancement and community compositional shifts induced by lava entry, consistent with observations.

The study of Wilson et al. raises questions about the response of the plankton ecosystem to nutrient enrichment across the subtropical North Pacific Ocean, the largest ecosystem on Earth. The response of ecosystems to ongoing external perturbations is a critically important problem to understand in an era of global change. How far can we push ecosystems before they break? Abrupt state changes may occur from which ecosystems cannot recover, even if the external perturbations return to normal (7, 8). State changes are felt over the lifetime of the affected organisms: a few days or weeks in the case of phytoplankton or decades to centuries for penguins and whales (8). The shifts observed in this study were transient, probably because the eruption ceased after a few

weeks. As the authors suggest, the nutrient enrichment caused by lava discharge to the ocean is a natural experiment addressing the physical-ecological stimulus-response process. Other, similar natural experiments include the passage of hurricanes (9) and turbulent eddies (10). In their normal unperturbed state, subtropical ocean ecosystems are dominated by the actions of the smallest primary producers, called picoplankton (Prochlorococcus and Synechococcus cyanobacteria that are less than 1 µm in diameter). In response to lava enrichment, these were overtaken by a larger-celled community dominated by diatoms (another type of phytoplankton). Shifts to diatoms are important because they enhance carbon export to deep ocean storage (10). The sequestration of atmospheric CO2 in the deep sea is a major factor that regulates Earth's climate.

Another globally important ecosystem transition in the subtropical ocean is from the picoplankton community to one dominated by the large, bloom-forming Trichodesmium species. These phytoplankton fix elemental atmospheric nitrogen (N2) that is dissolved in seawater into organic tissue. Because their nitrogen supply is virtually infinite, their growth is limited by phosphate and iron, both abundant in volcanic lava and dust. Trichodesmium and related species are important in the ocean carbon cycle because they have the potential to sequester more CO2 than non–nitrogen-fixing organisms, such as diatoms, that take up dissolved nitrate and inorganic carbon (11). Wilson et al. originally hypothesized that the phosphate and iron in lava would stimulate Trichodesmium. But this was not the case, probably because the iron and phosphate precipitated, becoming unavailable for biological uptake. Another limiting nutrient had to be found.

What are the wider implications of lavaplankton interactions? The 2018 eruption was one of the largest at Kīlauea in the past 200 years, but Kīlauea is just one volcano. There have been 16 new subaerial volcanic eruptions so far in 2019, two of which occurred in or near the ocean (12). Just one, Piton de la Fournaise, is in the tropics and surrounded by nutrient-depleted waters, making fertilization likely. Piton de la Fournaise has erupted nine times in the past decade, quite similar to Kīlauea. Indeed, the tropics are studded with active volcanic islands, including those of the Marianas, Antilles, and Tonga, as well as fully submarine volcanoes. Submarine eruptions, such as the 2012 eruption of the Havre volcano north of New Zealand, may drive even greater upwelling (13) and primary production than lava sea entries. Although there have been just 70 submarine eruptions recorded since 1755, they are likely to be underreported because they often occur in remote regions and are undetected.

It is generally assumed that volcanic eruptions supply CO2 to the atmosphere. However, the offsetting biological carbon export to the deep sea discovered by Wilson et al. is ∼10 million kg CO2 per day, the same magnitude as Kīlauea eruptive carbon emissions [estimated from the Kīlauea sulfur emission in (14), using the C/S ratio of 0.3 in (15)]. Perhaps phytoplankton blooms mediate the global warming effects of volcanic eruptions.

References and Notes1. C. B. Field, M. J. Behrenfeld, J. T. Randerson, P. Falkowski, Science 281, 237 (1998).2. S. T. Wilson et al., Science 365, 1040 (2019).3. P. A. Sanchez, C. A. Palm, S. W. Buol, Geoderma 114, 157 (2003).4. S. Duggen et al., Biogeosciences 7, 827 (2010).5. F. J. Sansone, J. A. Resing J. Geophys. Res. 100, 13555 (1995).6. Y. Li, H. Keppler, Geochim. Cosmochim. Acta 129, 13 (2014).7. M. Scheffer, S. Carpenter, J. A. Foley, C. Folke, B. Walker, Nature 413, 591 (2001).8. B. T. Bestelmeyer et al., Ecosphere 2, 129 (2011).9. S. M. Babin, J. A. Carton, T. D. Dickey, J. D. Wiggert, J. Geophys. Res. Oceans 109, C03043 (2004).10. C. R. Benitez-Nelson et al., Science 316, 1017 (2007).11. D. M. Karl, R. M. Letelier, Mar. Ecol. Prog. Ser. 364, 257 (2008).12. “What was erupting in the year…?”; http://volcano.si.edu/faq/index.cfm?question=eruptionsbyyear&checkyear=2019.13. M. Manga et al., Earth Planet. Sci. Lett. 489, 49 (2018).14. C. A. Neal et al., Science 363, 367 (2019).15. T. M. Gerlach, E. J. Graeber, Nature 313, 273 (1985).

Durham, B.P., Boysen, A.K., Carlson, L.T., Groussman, R.D., Heal, K.R., Cain, K.R., Morales, R.L., Coesel, S.N., Morris, R.M., Ingalls, A.E., Armbrust, E.V., 2019. Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nature Microbiology 4, 1706-1715.

https://doi.org/10.1038/s41564-019-0507-5

In the surface ocean, phytoplankton transform inorganic substrates into organic matter that fuels the activity of heterotrophic microorganisms, creating intricate metabolic networks that determine the extent of carbon recycling and storage in the ocean. Yet, the diversity of organic molecules and interacting organisms has hindered detection of specific relationships that mediate this large flux of energy and matter. Here, we show that a tightly coupled microbial network based on organic sulfur compounds (sulfonates) exists among key lineages of eukaryotic phytoplankton producers and heterotrophic bacterial consumers in the North Pacific Subtropical Gyre. We find that cultured eukaryotic phytoplankton taxa produce sulfonates, often at millimolar internal concentrations. These same phytoplankton-derived sulfonates support growth requirements of an open-ocean isolate of the SAR11 clade, the most abundant group of marine heterotrophic bacteria. Expression of putative sulfonate biosynthesis genes and sulfonate abundances in natural plankton communities over the diel cycle link sulfonate production to light availability. Contemporaneous expression of sulfonate catabolism genes in heterotrophic bacteria highlights active cycling of sulfonates in situ. Our study provides evidence that sulfonates serve as an ecologically important currency for nutrient and energy exchange between microbial autotrophs and heterotrophs, highlighting the importance of organic sulfur compounds in regulating ecosystem function.

Eble, C.F., Greb, S.F., Williams, D.A., Hower, J.C., O’Keefe, J.M.K., 2019. Palynology, organic petrology and geochemistry of the Bell coal bed in Western Kentucky, Eastern Interior (Illinois) Basin, USA. International Journal of Coal Geology 213, 103264.


The Bell coal bed is one of the stratigraphically oldest coals (Atokan, Duckmantian) in the Illinois Basin that has been commercially mined and occurs near the Morrowan-Atokan boundary, which was a time of significant lithologic change in the basin. The Bell coal occurs as a series of discontinuous pods, in contrast to younger (Asturian) coals in the basin that are thicker and more extensive in occurrence. Thirty-two samples of coal and carbonaceous shale, collected from surface mine, outcrop, and drill core locations were analyzed geochemically, petrographically and palynologically to ascertain the origin of the Bell coal bed in western Kentucky.

The Bell coal exhibits a great deal of variability in thickness and composition, both temporally and spatially. Based on ash yields, the Bell coal consists of intercalated layers of coal (≤25% ash), impure coal (>25 to <50% ash) and carbonaceous shale (≥50% ash). Sulfur contents vary significantly, from 0.2% to 10.0%. Petrographically, the Bell coal is mainly a high vitrinite coal (>80%, mmf), with telovitrinite occurring more frequently than detrovitrinite and gelovitrinite. Certain layers, however, contain elevated amounts of liptinite and inertinite. Among the inertinite macerals, examples of both fire (e.g., fusinite) and degradation (e.g., macrinite) origin are evident. Samples with elevated amounts of inertinite are commonly, though not exclusively, high in ash, indicating that some of the inertinite may be of allochthonous origin.

Palynologically, the Bell coal is dominated by arborescent lycopod spores (avg. >70%), occurring primarily as Lycospora, with some samples containing increased proportions of spores and pollen from other Pennsylvanian plant groups. Samples with more heterogenous palynofloras commonly have elevated ash yields, indicating that some portion of the assemblages may be also of allochthonous origin.

Collectively, the Bell coal is interpreted to have formed from a series of small, disconnected paleomires that were planar and topogenous with paleotopography having an influence on peat development. A planar, topogenous origin helps to explain the highly variable ash yields and sulfur contents. Accumulating peat, principally from arborescent lycopod source material, was mainly well-preserved, but punctuated with intervals marked by sediment influx, the development of more heterogeneous palynofloras and degradation and oxidation of the surficial peat by both biologic (decay) and abiotic (fire) processes.

Editorial, 2019. The path of biomolecular mass spectrometry into open research. Nature Communications 10, 4029.

https://doi.org/10.1038/s41467-019-12150-4

Originally designed for measuring isotope abundances and elemental masses, mass spectrometry is becoming a mainstay across life sciences. As electrospray ionization of biomolecules turns 30 and the Orbitrap mass analyzer 20, we take this opportunity to highlight the role of both inventions in stirring mass spectrometry from physics into biology and discuss the advances and challenges that may impact the future applications of biomolecular mass spectrometry.



Molecular networking (MN) allows one to organize tandem mass spectrometry (MS/MS) data by spectral similarities. Cosine-score used as a metric to calculate the distance between two spectra is based on peak lists containing fragments and neutral losses from MS/MS spectra. Until now, the workflow excluded the generation of the molecular network from electron ionization (EI) MS data as no selection of the putative parent ion is achieved when performing classical gas chromatography (GC)-EI-MS analysis. In order to fill this gap, new functionalities on MetGem 1.2.2 software (https://github.com/metgem/metgem/releases) have been implemented, and results from a large EI-MS database and GC-EI-MS analysis will be exemplified.

Evans, S.D., Gehling, J.G., Droser, M.L., 2019. Slime travelers: Early evidence of animal mobility and feeding in an organic mat world. Geobiology 17, 490-509.

https://doi.org/10.1111/gbi.12351

Mobility represents a key innovation in the evolution of complex animal life. The ability to move allows for the exploration of new food sources, escapes from unfavorable environmental conditions, enhanced ability to exchange genetic material, and is one of the major reasons for the diversity and success of animal life today. The oldest widely accepted trace fossils of animal mobility are found in Ediacaran‐aged rocks (635–539 Ma). The earliest definitive evidence for movement associated with exploitation of resources for feeding occurs in the White Sea assemblage of the Ediacara Biota—macroscopic, soft‐bodied fossils of Ediacaran age. Here, we evaluate potential support for mobility in dickinsoniomorphs, presenting new data regarding abundant Dickinsonia and associated trace fossils from the Ediacara Member, South Australia. Results quantitatively demonstrate that Dickinsonia was capable of mobility on relatively short, ecological timescales. This organism was bilaterally symmetrical, likely moved via muscular peristalsis, and left trace fossils due to active removal of the organic mat related to feeding. Analogous structures associated with Yorgia indicate that it was also mobile and fed in a similar manner. Morphological evidence suggests that two other modular taxa, Andiva and Spriggina, were able to move but did not feed in a manner that impacted the organic mat. Together, these data suggest that mobility was present in multiple disparate bilaterally symmetrical Ediacaran taxa.

Evdokimov, I.N., 2019. Colloidal asphaltenes—non-extinct “dinosaurs” in native petroleum. Energy & Fuels 33, 8440-8447.


One of the important paradigms of fundamental petroleum geochemistry has been (and still is) that native asphaltenes in present day crude oils originated in the respective source rocks and are representative of the molecular composition in ancient organic deposits. The survival of “prehistoric” molecular species is enabled by shielding them in complex macromolecular structures of asphaltene nanocolloidal particles. In addition, the maturity of petroleum expelled from the source may define the structures of asphaltene colloidal aggregates, as indicated by recent advances in colloid science. On the other hand, in applied asphaltene research, the above

paradigm is most often ignored, while its revitalization may improve our understanding of asphaltene behavior in native crude oils and, in particular, may provide a new criterion for potential instability of some crude oils with respect to asphaltene precipitation and deposition.

Falcinelli, S., Vecchiocattivi, F., Pirani, F., Alagia, M., Schio, L., Richter, R., Stranges, S., Zhaunerchyk, V., Balucani, N., Rosi, M., 2019. The fragmentation dynamics of simple organic molecules of astrochemical interest interacting with VUV photons. ACS Earth and Space Chemistry 3, 1862-1872.


An experimental investigation on the fragmentation dynamics following the double photoionization of simple organic molecules of astrochemical interest, propylene oxide and N-methylformamide molecules, induced by VUV photons has been reported. Experiments used linearly polarized light in the 18–37 eV (propylene oxide) and 26–45 eV (N-methylformamide) photon energy range at the ELETTRA Synchrotron Facility of Trieste (Italy), coupling ion imaging and electron–ion–ion coincidence techniques with time-of-flight mass spectrometry. In the case of propylene oxide, six different two-body fragmentation processes have been recorded with the formation of CH2

+/C2H4O+, CH3+/C2H3O+, O+/C3H6

+, OH+/C3H5+, C2H3

+/CH3O+, C2H4+/CH2O+

ion pairs. On the other hand, the double photoionization of N-methylformamide occurs producing two main fragmentation reactions, forming CH3

+ + CH2NO+ and H+ + C2H4NO+. The relative cross sections and the threshold energies for all fragmentation channels are recorded as a function of the photon energy. Furthermore, in the case of the double photoionization of propylene oxide, the measure of the kinetic energy released distribution for the CH3

+/C2H3O+ final ions with their angular distributions allowed the identification of a bimodal behavior indicating the possible formation of two different stable isomers of C2H3O+: acetyl and oxiranyl cations. The obtained results are important to clarify the physical chemistry of the elementary processes induced by the interaction of ionizing radiations with simple organic molecules of astrochemical interest: propylene oxide and N-methylformamide.

Fan, W., Sun, H., Yao, J., Fan, D., Yang, Y., 2019. An upscaled transport model for shale gas considering multiple mechanisms and heterogeneity based on homogenization theory. Journal of Petroleum Science and Engineering 183, 106392.


Because of the complex pore structure and multiple types of gas storage, the traditional Darcy permeability model is not valid for describing shale gas flow. In this paper, an upscaled transport model is established based on homogenization theory to consider multiple transport mechanisms and the heterogeneity of shale samples. This new transport model is employed to successfully explain pressure decay experimental data. The results show that absorbed gas cannot be ignored in pressure decay experiment and the pressure difference decreases rapidly when the absorbed gas is not considered. Then several critical conclusions have been drawn as follows. The permeability anisotropy for stochastic distribution model can be ignored and the effective permeability will be underestimated by double porosity model if surface diffusion dominates gas flow in shale reservoir. In addition, shale gas transport is dominated by Knudsen diffusion when the pore pressure is below 2 MPa and the contribution of surface diffusion increases as the pore pressure increases. The macroscopic effective permeability of the whole domain is dominated by the permeability of the connected phase; meanwhile, it can be influenced by the permeability of the disconnected phase. When the pore pressure is below 3.52 MPa, the effective permeability increases as the organic matter content (TOC) decreases. However, the effective permeability increases as the TOC increases when the pore pressure is above 3.52 MPa, which is different from traditionally believed when the relationship between the TOC and gas absorption capacity of the shale matrix is not considered. The effective permeability particularly increases at a high pore pressure as the Langmuir volume increases. In addition, the effective permeability increases as the Langmuir pressure decreases; however, this becomes apparent when the pore pressure is smaller.

Fang, B., Ning, F., Ou, W., Wang, D., Zhang, Z., Yu, Y., Lu, H., Wu, J., Vlugt, T.J.H., 2019. The dynamic behavior of gas hydrate dissociation by heating in tight sandy reservoirs: A molecular dynamics simulation study. Fuel 258, 116106.


Knowledge on the kinetics of gas hydrate dissociation in microporous sediments is very important for developing safe and efficient approaches to gas recovery from natural gas hydrate (NGH) deposits. Herein, molecular dynamics (MD) simulations are used to study the dissociation kinetics in microporous sediments. The hydrate phase occupies a confined sandy nanopore formed by two hydroxylated silica surfaces with a buffering water layer between the hydrate and silica phase, meanwhile, this system is in contact with the bulk phase outside the pore. The hydrates in this sediment system dissociate layer-by-layer in a shrinking core manner. The released methane molecules aggregate and eventually evolve into nanobubbles, most of which are spherical cap-shaped on the hydroxylated silica surfaces. At high initial temperatures, a faster decomposition of the hydrate phase is observed, however, fewer methane molecules migrate to the bulk phase from the pore phase. These phenomena may occur because more methane molecules are released from the hydrate phase and facilitate the formation of nanobubbles with large heat injection; these nanobubbles can stably adsorb on the surface of silica and capture the surrounding methane molecules, thereby decreasing the number of methane molecules in the water phase. In addition, the injection speed of heat flow should be significantly increased at high dissociation temperatures when using the thermal stimulation method to extract gas from hydrates in tight sediments. This study provides molecular level insight into the kinetic mechanism of hydrate dissociation and theoretical guidance for gas production by thermal injection from sediments with low permeabilities.


https://doi.org/10.1007/s00253-019-10024-9

Rammed earth has been enjoying a renaissance as sustainable construction material with cement stabilized rammed earth (CSRE). At the same time, it is important to convert CSRE to be a stronger, durable, and environment-friendly building material. Bacterial application is established to improve cementitious materials; however, bioaugmentation is not widely acceptable by engineering communities. Hence, the present study is an attempt applying biostimulation approach to develop CSRE as sustainable construction material. Results showed that biostimulation improved the compressive strength of CSRE by 29.6% and resulted in 27.7% lower water absorption compared to control. The process leading to biocementation in improving CSRE was characterized by Fourier transform infrared spectroscopy, X-ray diffraction, and scanning electron microscope-energy dispersive spectrometer. Further, Illumina MiSeq sequencing was used to investigate changes in bacterial community structures after biostimulation that identified majority of ureolytic bacteria dominated by phylum Firmicutes and genus Sporosarcina playing role in biocementation. The results open a way applying biological principle that will be acceptable to a wide range of civil engineers.



To investigate supercritical methane adsorption on shale and its controlling factors, high-pressure (up to 20 MPa) methane adsorption experiments were performed on overmature Niutitang shales from the Upper Yangtze area in China. Combining field emission scanning electron microscopy, low-pressure N2 adsorption (LP-N2-GA), and CO2 adsorption (LP-CO2-GA), the pore structure and fractal characteristics were studied. According to the LP-N2-GA and Frenkel–Halsey–Hill (FHH) model, pore surface and spatial structure are characterized by the fractal heterogeneity with corresponding fractal dimensions D1 (2.32–2.69) and D2 (2.49–2.82). The measured supercritical methane excess adsorption isotherms show three stages: (i) a sharp increase under 6 MPa, (ii) a slow increase until reaching the maximum (Vexm = 1.06–4.60 cm3/g) at the pressure of Pm (7.53–

10.41 MPa), and (iii) a decline at various rates over the Pm. The rates of decline in excess adsorption at high pressures vary (0.031–0.074 cm3/g/MPa) and positively correlate with the total organic carbon (TOC) content, pore volume, and specific surface area (SSA) of micropores and fractal dimension D1, whereas the Pm possesses weakly negative relationships with these factors. The excess adsorption data can be accurately fitted by the supercritical Langmuir-based adsorption model with the maximum absolute adsorption capacities (VL) ranging from 2.88 to 6.57 cm3/g. Misinterpreting the low-pressure (0–10 MPa) experimental excess adsorption data as the absolute adsorption values to fit the adsorption isotherms, the actual adsorption capacity will be underestimated with the errors ranging from 18.44 to 45.34% for the calculated VL, and an underestimation will exist in extrapolated in situ adsorbed gas content. TOC still plays an important role in promoting methane adsorption capacity even for the overmature shales. Meanwhile, the methane adsorption capacity is positively correlated with the SSA, micropore volume, and fractal dimension D1, and microporosity is the governing factor on adsorbed gas occurrence.

Feyzullayev, A.A., Lerche, I., 2019. Organic matter in rock–water systems of petroliferous basins: interrelationships (a case study: South Caspian Basin). Oil & Gas Science and Technology – Revue d’IFP Energies nouvelles 74, 74.

https://doi.org/10.2516/ogst/2019046

Generalizations and analyses are given of the data accumulated to date on the content of Organic Matter (OM) in formation waters of various stratigraphic complexes, as well as of mud volcanoes, and the correlation with OM in South Caspian Basin (SCB) sedimentary rocks. Results are based on about 300 analyses of formation waters and waters of mud volcanoes, as well as on more than 400 analyses of the content of OM in rocks (outcrops and wells from both onshore and offshore petroleum fields of the SCB). The stratigraphic interval covers the period from the Lower Pliocene to the Jurassic, and the depth interval from 73 m to 6043 m. In these intervals, the values of Dissolved Organic Matter (DOM) in reservoir waters vary from 4.1 mg/L to 271.2 mg/L, averaging (219 analyses) 48.9 mg/L. A good correlation has been established between the values of DOM and OM in rocks. Paleogene and Jurassic rocks have the highest correlations. DOM varies with depth with an increase in value from a depth of about 3.3 km, likely due to catagenetic transformation of OM into hydrocarbons in the rock–water system. The highest values of DOM are for waters with mineralization less than 50 g/L. Mud volcano waters are characterized by low levels of DOM and low mineralization, likely due to the condensate nature. The results of the studies show that underground water, as one of the components of a single rock–water system of the Earth’s sedimentary cover, together with the rocks, participates in the processes of hydrocarbon generation and migration.


https://doi.org/10.1038/s41467-019-11541-x

Development of Archean paleosols and patterns of Precambrian rock weathering suggest colonization of continents by subaerial microbial mats long before evolution of land plants in the Phanerozoic Eon. Modern analogues for such mats, however, have not been reported, and possible biogeochemical roles of these mats in the past remain largely conceptual. We show that photosynthetic, subaerial microbial mats from Indonesia grow on mafic bedrocks at ambient temperatures and form distinct layers with features similar to Precambrian mats and paleosols. Such subaerial mats could have supported a substantial aerobic biosphere, including nitrification and methanotrophy, and promoted methane emissions and oxidative weathering under ostensibly anoxic Precambrian atmospheres. High C-turnover rates and cell abundances would have made these mats prime locations for early microbial diversification. Growth of landmass in the late Archean to early Proterozoic Eons could have reorganized biogeochemical cycles between land and sea impacting atmospheric chemistry and climate.

Foster, W.J., Lehrmann, D.J., Yu, M., Martindale, R.C., 2019. Facies selectivity of benthic invertebrates in a Permian/Triassic boundary microbialite succession: Implications for the “microbialite refuge” hypothesis. Geobiology 17, 523-535.


Thrombolite and stromatolite habitats are becoming increasingly recognized as important refuges for invertebrates during Phanerozoic Oceanic Anoxic Events (OAEs); it is posited that oxygenic photosynthesis by cyanobacteria in these microbialites provided a refuge from anoxic conditions (i.e., the “microbialite refuge” hypothesis). Here, we test this hypothesis by investigating the distribution of ~34, 500 benthic invertebrate fossils found in ~100 samples from a microbialite succession that developed following the latest Permian mass extinction event on the Great Bank of Guizhou (South China), representing microbial (stromatolites and thrombolites) and non‐microbial facies. The stromatolites were the least taxonomically diverse facies, and the thrombolites also recorded significantly lower diversities when compared to the non‐microbial facies. Based on the distribution and ornamentation of the bioclasts within the thrombolites and stromatolites, the bioclasts are inferred to have been transported and concentrated in the non‐microbial fabrics, that is, cavities around the microbial framework. Therefore, many of the identified metazoans from the post‐extinction microbialites are not observed to have been living within a microbial mat. Furthermore, the lifestyle of many of the taxa identified from the microbialites was not suited for, or even amenable to, life within a benthic microbial mat. The high diversity of oxygen‐dependent metazoans in the non‐microbial facies on the Great Bank of Guizhou, and inferences from geochemical records, suggests that the microbialites and benthic communities developed in oxygenated environments, which disproves that the microbes were the source of the oxygenation. Instead, we posit that microbialite successions represent a taphonomic window for exceptional preservation of the biota, similar to a Konzentrat‐Lagerstätte, which has allowed for diverse fossil assemblages to be preserved during intervals of poor preservation.

Fowler, A.P.G., Liu, Q.-l., Huang, Y., Tan, C., Volk, M.W.R., Shanks, W.C.P., Seyfried, W., 2019. Pyrite δ34S and Δ33S constraints on sulfur cycling at sublacustrine hydrothermal vents in Yellowstone Lake, Wyoming, USA. Geochimica et Cosmochimica Acta 265, 148-162.


Sulfur isotope values (δ34S and Δ33S) of pyrite in sediment from steam-heated hydrothermal vents on the floor of Yellowstone Lake (WY) were measured using secondary ionization mass spectrometry (SIMS). The high resolution of the SIMS data place important constraints on sulfur cycling processes at/near the vent fluid-lake water interface. Pyrite with a distinct mantle-basalt (δ34S = 0‰) isotope composition (δ34S = +0.5 to +3.1‰) replaces pyrrhotite during incipient stages of alteration at moderately high temperature. Disseminated cubic pyrite (δ34S = +2.0 to +5.3‰) occurs in zones where more extensive oxidation is likely. Framboidal pyrite with δ34S values ranging from –5.2 to +4.1‰ and Δ33S up to +0.30‰ suggest formation from low-temperature microbial sulfate reduction in sediments near but not directly in the vent fluid up-flow zone. The co-occurrence of pyrite with S isotope values characteristic of distinct formation processes, coupled with notable intra-crystal S isotope variations, suggests the venting locus is dynamic in time and space.

Freiburghaus, K., Largiadèr, C.R., Stettler, C., Fiedler, G.M., Bally, L., Bovet, C., 2019. Metabolomics by UHPLC–MS: benefits provided by complementary use of Q-TOF and QQQ for pathway profiling. Metabolomics 15, 120.

https://doi.org/10.1007/s11306-019-1585-3

Introduction: Non-targeted metabolic profiling using high-resolution mass spectrometry (HRMS) is a standard approach for pathway identification despite technical limitations.

Objectives: To assess the performance of combining targeted quadrupole (QQQ) analysis with HRMS for in-depth pathway profiling.

Methods: Serum of exercising patients with type 1 diabetes (T1D) was profiled using targeted and non-targeted assays.

Results: Non-targeted analysis yielded a broad unbiased metabolic profile, targeted analysis increased coverage of purine metabolism (twofold) and TCA cycle (three metabolites).

Conclusion: Our screening strategy combined the benefits of the unbiased full-scan HRMS acquisition with the deeper insight into specific pathways by large-scale QQQ analysis.

Fulgham, S.R., Brophy, P., Link, M., Ortega, J., Pollack, I., Farmer, D.K., 2019. Seasonal flux measurements over a Colorado pine forest demonstrate a persistent source of organic acids. ACS Earth and Space Chemistry 3, 2017-2032.


Forests can be both sources and sinks of volatile organic compounds to the atmosphere. The role that forests play in controlling organic acid concentrations remains poorly understood with multiple model-measurement comparisons reporting missing sources of formic acid. We conducted seasonal measurements of concentrations and eddy covariance fluxes of oxidized volatile organic compounds over a ponderosa pine forest in Colorado in 2016. Diel concentration profiles show mid-day maxima, consistent with previous studies. We observed persistent but variable upward fluxes of formic, propionic, methacrylic, and butyric acids from the pine forest during all seasons. Formic acid concentrations and fluxes were ∼10 times higher than the other organic acids with daytime exchange velocities on the order of 4–6 cm s–1. The other organic acids had similar exchange velocities as formic acid in the warmer seasons and much smaller exchange velocities in the colder seasons. The upward fluxes for all organic acids increased exponentially with temperature. The observed net upward flux demonstrated that dry deposition was smaller than ecosystem sources of the organic acids. Primary emissions from soil and pine trees were small, in contrast to estimates of in-canopy chemistry. Our study points to an underestimated ecosystem source of organic acids (e.g., in-canopy chemistry of large or multifunctional terpenoids), an overestimated dry deposition sink (potentially due to the arid environment), and/or an unresolved sink of organic acids in the upper boundary layer. Forests are potentially large sources of atmospheric organic acids in warmer seasons but further investigation into dry deposition mechanisms and in-canopy chemistry is warranted.

Gainullina, L.R., Tutubalina, V.P., 2019. Oxidative methods for the study of the structural group composition of organosulfur compounds. Chemistry and Technology of Fuels and Oils 55, 272-279.

https://doi.org/10.1007/s10553-019-01030-8

The composition of the organosulfur compounds of the oil fraction of Arlan oil was studied using a method involving the two-step oxidation of these compounds with 30% hydrogen peroxide in the presence of an acid catalyst at 80° and 100°C. Vacuum distillation of the organosulfur compounds into narrow fractions showed that the sulfoxides obtained by oxidation of the organic sulfur compounds of the oil fraction are thiamono-, thiabi-, and thiatricycloalkanes, aliphatic sulfides, and alkylcycloalkyl sulfides. No aromatic compounds were detected in the sulfoxides. Sulfones in the narrow fractions are mainly represented by thiaindanes, alkylcyclano- and alkylbicyclanobenzthiophenes with long alkyl substituents containing from 10 to 15 carbon atoms. Translated from Khimiya i Tekhnologiya Topliv i Masel, No. 3, pp. 40 — 44, May — June, 2019.



Separation of the components of gas mixtures is a critical problem. We considered the possibility of using the hydrate formation process to separate species contained in gas mixtures. We applied this strategy to mixtures of CH4/CO2 produced through the Sabatier process. Both species tend to form hydrates, but through different conditions. The results reported here show that, depending on the methanation efficiency, three different hydrate formation results are possible. If the efficiency is in the range from 0.00 to 0.69, the formation mainly involves CO2. For values ranging from 0.90 to 1.00, the opposite occurs and methane can be stored as solid form. For efficiency values ranging from 0.70 to 0.89, the formation conditions of both species are very similar and therefore the method cannot give rise to CH4/CO2 separation.



Anaerobic biodegradation of crude oil is one of the main mechanisms for the formation of heavy oil and gas (referred to as crude oil degradation gas). With the Linfanjia area in the Jiyang Depression of the Bohai Bay Basin in eastern China taken as an example, we conducted a biodegradation simulation experiment on the conventional crude oil of well Y141-1 using cultured anaerobic microbial flora. The causes and characteristics of crude oil alteration and natural gas formation were studied by combining oil and gas geochemistry and carbon isotope data. The theoretical analysis and experimental results show that the saturated hydrocarbon content of crude oil is significantly reduced with the progress of anaerobic biodegradation, while the contents of aromatic compounds, resins, and asphaltenes remain relatively high. Crude oil components, such as n-alkanes and isoparaffins, undergo different degrees of biodegradation. The values of pristane (Pr)/phytane (Ph) and ∑C21–/∑C22+ are significantly reduced, while the values of Pr/n-C17, Ph/n-C18, the carbon-preference index, the odd-over-even predominance, and 25-norhopane/hopane are relatively high. Biodegradation causes crude oil to continuously thicken to form heavy oil. Moreover, methane and carbon dioxide gas are produced as crude oil is degraded by anaerobic microorganisms; for example, the average production per gram of crude oil reaches 3 mmol of methane during 250 days of biodegradation. Both the carbon isotope values of methane (all less than −45‰) and carbon isotope values of carbon dioxide (all greater than 2‰) tend to become heavier, which are typical characteristics of crude oil degradation gas. Therefore, anaerobic biodegradation of crude oil can not only generate heavy oil but also produce a considerable amount of crude oil degradation gas that is mainly composed of methane. Data provide evidence for the large-scale methanogenic biodegradation of crude oil under anaerobic conditions during the geological period. Crude oil degradation gas and crude oil release gas together form the main sources of shallow gas reservoirs and at least 60% of the crude oil degradation gas in shallow gas reservoirs. The homologous symbiotic relationship and coupling distribution characteristics of heavy oil reservoirs and shallow gas reservoirs can provide a theoretical basis for the efficient joint exploration of both types of reservoirs.



The microbial communities in alkali-surfactant-polyacrylamide-flooded (ASP-flooded) oil reservoirs have rarely been investigated compared to those in water-flooded oil reservoirs. Here, the bacterial and archaeal communities in an ASP-flooded reservoir and the adjacent water-flooded block, and responses of the microbial communities in microcosms to nutrients were investigated by 16S rRNA gene sequencing and cultivation. Compared with the water-flooded block, both the bacterial and archaeal communities inhabiting the ASP-flooded block had lower Sobs indices (91:232 and 34:55, respectively), lower Shannon indices (1.296:2.256 and 0.845:1.627, respectively) and higher Simpson indices (0.391:0.248 and 0.678:0.315, respectively). Halomonas (58.4–82.1%) and Anoxynatronum (14.5–18.2%) predominated in the ASP-flooded production wells, and were less than 0.05% in the bacterial communities of the adjacent water-flooded production wells, which were dominated by Pseudomonas and Thauera. Methanobacterium accounted for 65.0–94.5% of the archaeal

communities inhabiting the ASP-flooded production wells, and Methanosaeta (36.7–94.5%) dominated the adjacent water-flooded production wells. After nutrients stimulation, the quantity of cultivable microorganisms increased from 103/mL to 107/mL. Community analysis indicated that the relative abundances of some species that belonged to Halomonas and Pseudomonas obviously increased, yet there were no oil emulsification or dispersion and changes of surface tension of the water-oil mixture. In addition, 6 alkali-tolerating strains showing 98% similarity of 16S rRNA genes with those of Halomonas alkalicola and Halomonas desiderata and 2 strains with 99% similarity with Pseudomonas stutzeri gene were isolated from the nutrients stimulated brines. In summary, this study indicated that Halomonas, Anoxynatronum, and Methanobacterium were dominant populations in the ASP-flooded reservoir, the extreme environment decreased microbial diversity, and restricted microbial growth and metabolisms.

Gao, Y., Wang, W., He, C., Fang, Z., Zhang, Y., Shi, Q., 2019. Fractionation and molecular characterization of natural organic matter (NOM) by solid-phase extraction followed by FT-ICR MS and ion mobility MS. Analytical and Bioanalytical Chemistry 411, 6343-6352.

https://doi.org/10.1007/s00216-019-01943-7

Electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has been widely used for the characterization of dissolved organic matter (DOM) extracted by solid-phase extraction (SPE) from various environmental waters. It is known that common SPE generally has a relatively low recovery and the non-polar and weakly polar components are less likely to be ionized due to ionization discrimination. However, the molecular selectivity during SPE is not clear so far. In this study, the Suwannee River natural organic matter (SRNOM) was fractionated by multi-step SPE with different solvents and the fractions were characterized by negative ESI FT-ICR MS and trapped ion mobility spectrometry-mass spectrometry (IMS-MS). The sequential solvent elution increased the extraction recovery of DOM in water by SPE and enabled the characterization of a weakly polar component, which cannot be detected in common SPE separation. The weakly polar component accounts for 5.7% in TOC for the SRNOM, which has complex but different molecular composition with methanol- and/or water-eluted fractions. Lipid-like compounds were enriched in this fraction. Compared with the polar molecules directly eluted by one-step SPE from the SRNOM, the weakly polar fractions exhibit larger molecular size. The results are helpful for understanding of the molecular composition of SRNOM, as well as other environmental waters. In addition, the study demonstrates that the combination of FT-ICR MS and IMS-MS has potential to characterize the chemical composition of a complex mixture, like DOM, to a new depth.

Gar’kusha, D.N., Fedorov, Y.A., Tambieva, N.S., Andreev, Y.A., Mikhailenko, O.A., 2019. Methane in water and bottom sediments of Lake Baikal. Water Resources 46, 726-737.

https://doi.org/10.1134/S0097807819050063

The distribution of methane concentration measured in 2014 and 2015 in different parts of Lake Baikal has been analyzed. In the period of expedition studies, methane concentration in lake water and bottom sediments varied from <0.1 to 13.9 µL/dm3 (on the average, 0.7 µL/dm3) and from <0.01 to 3.69 µg/g dry residue (on the average, 0.34 µg/g). The maximal concentrations of methane in water and bottom sediments of the lake were typical of the northern area, which receives waters of the Upper Angara and Kichera, and at some stations on a profile running along the mouth area of the Selenga R., as well as stations in the zone of underwater discharge of wastewater from Baikal’sk City and the Baikal Pulp and Paper Plant (BPPP), which was closed down in 2013. The presence of higher or lower methane concentrations in the examined upper horizons of Lake Baikal deposits is due to the differences in the level of anthropogenic impact; variations in sedimentation conditions, which determine the grain-size distribution and the concentration of organic matter, and, as a consequence, the rate of methanogenesis.

García-Descalzo, L., Parro, V., García-Villadangos, M., Cockell, S.C., Moissl-Eichinger, C., Perras, A., Rettberg, P., Beblo-Vranesevic, K., Bohmeier, M., Rabbow, E., Westall, F., Gaboyer, F., Amils, R., Malki, M., Marteinsson, V., Vannier, P., Ehrenfreund, P., Monaghan, E., Riedo, A., Cabezas, P., Walter, N., Gómez, G.F., 2019.

Microbial markers profile in anaerobic Mars analogue environments using the LDChip (Life Detector Chip) antibody microarray core of the SOLID (Signs of Life Detector) platform. Microorganisms 7, 365.

https://www.mdpi.com/2076-2607/7/9/365

One of the main objectives for astrobiology is to unravel and explore the habitability of environments beyond Earth, paying special attention to Mars. If the combined environmental stress factors on Mars are compatible with life or if they were less harsh in the past, to investigate the traces of past or present life is critical to understand its potential habitability. Essential for this research is the characterization of Mars analogue environments on Earth through the development of techniques for biomarker detection in them. Biosensing techniques based on fluorescence sandwich microarray immunoassays (FSMI) have shown to be a powerful tool to detect biosignatures and depict the microbial profiles of different environments. In this study, we described the microbial biomarker profile of five anoxic Mars analogues sites using the Life Detector Chip (LDChip), an antibody microarray for multiple microbial marker detection. Furthermore, we contributed to new targets by developing a new 26-polyclonal antibodies microarray using crude extracts from anaerobic sampling sites, halophilic microorganisms, and anaerobic isolates obtained in the framework of the European Mars Analogues for Space Exploration (MASE) project. The new subset of antibodies was characterized and implemented into a microarray platform (MASE-Chip) for microbial marker searching in salty and anaerobic environments.

Gardiner, D., Schofield, N., Finlay, A., Mark, N., Holt, L., Grove, C., Forster, C., Moore, J., 2019. Modeling petroleum expulsion in sedimentary basins: The importance of igneous intrusion timing and basement composition. Geology 47, 904-908.

https://doi.org/10.1130/G46578.1

The concept of a critical moment in a petroleum system (the time of highest probability of entrapment and preservation of oil and gas) has underlain petroleum exploration for over 25 years. However, one area where understanding the critical moment is challenging is the Faroe-Shetland Basin (FSB; offshore UK). Isotopic dating of oils suggests that petroleum generation began between ca. 68 and 90 Ma; however, most basin models invoke an earlier generation beginning in the mid-Cretaceous at ca. 100 Ma, predating deposition of Paleocene and Eocene reservoirs. This time discrepancy has previously been explained by remigration from intermediary accumulations (“motel” hypothesis) and/or overpressure retardation of kerogen maturation. The FSB is characterized by a thick Cretaceous stratigraphic package (up to 5 km) that includes a large net thickness (up to 2 km) of Paleogene igneous material. In our model, separating sedimentary and igneous material and adding the igneous material at the correct time between ca. 58 and 55 Ma shallows the modeled burial depth of the Upper Jurassic source rocks during the Cretaceous sufficiently to delay maturation by 17 m.y. in comparison to results of previous studies. Additionally, previous studies have invoked crustal radiogenic heat production (RHP) based on the Phanerozoic crust averaging ∼2.8 µW/m3 in the North Sea (300 km to the east). However, the FSB basement is composed of significantly older, colder Neoarchean orthogneisses (ca. 2.7–2.9 Ga), reducing RHP by up to 50% to ∼1.6 µW/m3 (σ = 0.74). For the first time, our model unifies geological, geochronological, and geochemical observations, delaying the onset of petroleum expulsion by up to 40 m.y. in comparison to previous models.



A method of sequential liquid–solid extraction (leaching) has been developed to extract the V, Ni, and S compounds present in asphaltenes (n-C7) according to their molecular weight distribution. For the high-molecular-weight (HMW) compounds, two new families of compounds were extracted, labeled as HMW1 and HMW2, where the latter was smaller than HMW1, and together represented approximately 85% of the asphaltene mass according to the mass balance obtained after the extractions. The compounds associated with HMW1 were asphaltenes that were insoluble in hot dimethylformamide (DMF), while the compounds

associated with HMW2 were soluble in DMF but insoluble in the second leaching step based on hot acetone. The third family of obtained compounds was the medium-molecular-weight (MMW) compounds, which were soluble in hot acetone but insoluble in acetonitrile (ACN). The last fraction to be obtained was the low-molecular-weight compounds, which were soluble in ACN. The results reported here represent a new method that allows the extraction of different types of aggregated asphaltenes according to their molecular weights. With respect to the temperature and number of extraction steps, it was observed that an increase in both parameters increased the extraction efficiency.

Gerya, T., 2019. Geodynamics of the early Earth: Quest for the missing paradigm. Geology 47, 1006-1007.

https://doi.org/10.1130/focus102019.1

In contrast to modern-day plate tectonics, geodynamics of the early Earth presents a unique challenge, as currently there is no consensus on a global paradigm concerning the mantle dynamics and lithosphere tectonics in the Precambrian (Benn et al., 2006; Gerya, 2014). This challenge is mainly due to the severe objective restrictions of obtaining geological and/or geophysical observations constraining Earth’s surface and interior dynamics back in geological time (Fig. 1).

The subject of geodynamics can be schematically represented by the time-depth diagram (see Fig. 1) covering the entire Earth’s history and interior. In theory, the entire diagram should be “covered” by data points characterizing the physical-chemical state of Earth at different depths, for different moments in geological time. However, in practice, observations are only available along two axes: (1) geophysical data for Earth’s internal structure at all ranges of depths, but only for the very short present-day time, and (2) the geological record preserved in rocks formed over a broad range of geological times, but only at a very shallow depth range. As a result, the importance of well-constrained geological and geophysical data, and thoroughly studied present-day geodynamic regime (modern-style plate tectonics) is almost unavoidably exaggerated and “stretched” toward the Precambrian Earth. This “plate tectonics trap” can only be avoided by further calibrating our geological intuition on the basis of numerical geodynamic modeling that integrates available geological, geochemical, petrological, and geochronological records (Gerya, 2014).

An emerging holistic view of the evolution of early Earth geodynamics (e.g., Gerya, 2014; Sobolev and Brown, 2019) can be summarized as follows (Fig. 1):

Â· Hadean-Archean squishy-lid tectonics before ca. 3 Ga was characterized by mantle temperatures ∼200–250 °C higher than present-day values, and was dominated by widespread plume-induced processes under conditions of an internally deformable (squishy) Venus-like global lid (e.g., Van Kranendonk, 2010; Gerya et al., 2015; Harris and Bédard, 2014; Rozel et al., 2017). In this pre–plate tectonics regime, both proto-oceanic and proto-continental lithospheres were formed by tectonomagmatic differentiation processes (e.g., Sizova et al., 2015). These lithospheres were rheologically weak due to the high Moho temperature and melt percolation from hot, partially molten, sublithospheric mantle (Sizova et al., 2015). The lid evolution was driven by episodic regional-scale tectonomagmatic activity combining (Sizova et al., 2015; Fischer and Gerya, 2016a) (1) a longer (80–100 m.y.) and relatively quiet ‘growth phase’ which is marked by growth of crust and lithosphere, followed by (2) a short (∼20 m.y.) and catastrophic ‘removal phase’, where unstable parts of the crust and mantle lithosphere are removed by eclogitic dripping and delamination. Plume- and impact-induced retreating subduction and delamination contributed to the episodic regional-scale lid recycling (Gerya et al., 2015; O’Neill et al., 2017).

Â· During Archean-Proterozoic transitional tectonics between 3 Ga and 1 Ga, squishy-lid tectonics gradually evolved toward a plate tectonics regime (e.g., Fischer and Gerya, 2016b; Chowdhury et al., 2017; Sobolev and Brown, 2019). Numerical models suggest that the transitional tectonics occurred at mantle temperatures ∼100–200 °C higher than present-day values, and was triggered by stabilization of rheologically strong plates (e.g., Sizova et al., 2010, 2014; Fischer and Gerya, 2016b). Plume-induced subduction was likely very common in the beginning, and triggered the onset of this transitional plate-tectonic–like regime (Gerya et al., 2015). Elements of squishy-lid (plume-lid) tectonics were also locally present (Fischer and Gerya, 2016b). Delamination of the mantle lithosphere in long-lived ultra-hot accretionary orogens controlled silicification and rising of the

continents due to recycling of mafic lower crust (Perchuk et al., 2018; Chowdhury et al., 2017). The episodic (short-lived), rapidly retreating subduction was associated with massive decompression melting of the mantle resulting in formation of oceanic plateau basalts (Perchuk et al., 2019).

Â· The establishment of modern-style plate tectonics at ca. 1–0.5 Ga was attained by a combination of (Bercovici and Ricard, 2014; Gerya, 2014; Gerya et al., 2015; Sobolev and Brown, 2019) (1) further cooling of the mantle to temperatures ∼50–100 °C higher than present-day values, (2) emergence of a global mosaic of rigid plates divided by localized, long-lived, week boundaries, (3) rise of the continents, and (4) growing intensity of surface erosion, providing weak sediments that lubricated subduction trenches. Widespread development of modern-style (cold) continental collision started during the Neoproterozoic (Sizova et al., 2014) and created favorable conditions for the generation of ultrahigh-pressure metamorphic complexes. The transition to modern-style plate tectonics followed a long period of reduced tectonomagmatic activity—the boring billion (years) (Sobolev and Brown, 2019). The unprecedented scale of surface erosion following the snowball Earth glaciations possibly initiated the modern-style plate tectonics, and triggered the Cambrian explosion of life on Earth (e.g., Stern, 2016; Sobolev and Brown, 2019).

Further progress in deciphering Precambrian geodynamics clearly requires cross-disciplinary efforts, with a special emphasis placed upon numerical models that are thoroughly compared to the available limited observational record. The paper by Capitanio et al. (2019, p. 923 in this issue of Geology) follows this coupled modeling-observation–based approach by focusing on the thermal regimes of Hadean-Archean geodynamics that are recorded in oldest magmatic and metamorphic rocks.

Our understanding of the period of Earth’s earliest history (ca. 4.5–3.0 Ga) is strongly biased and relies on very limited observational data from respective preserved continental terrains (e.g., Kamber, 2015). Geothermobarometric estimates for mineral assemblages formed in these terranes recognized widespread variations in metamorphic gradients (from cold to hot), as far back as ca. 3.7 Ga. These gradients become pronounced and grouped into a bimodal distribution from Neoarchean time onward, <2.8 Ga (Brown and Johnson, 2018). Because this paired association of thermal gradients is a distinct characteristic of modern-style plate tectonics, it has been suggested that its appearance marks the establishment of plate-tectonics–like behavior of the lithosphere since the Neorchean (Brown and Johnson, 2018). Capitanio et al. challenge this interpretation by using numerical models of mantle convection and melting performed under Archean mantle temperature conditions. Based on these relatively simple models, they were able to show that different tectonic modes can coexist and alternate (both spatially and temporally) within a single, global, non–plate tectonics regime of mantle circulation. The authors document the development of two tectonomagmatic domains: (1) the vertical tectonics domain in which lithospheric generation and recycling occurs at sites of localized vertical drips, and (2) the horizontal tectonics domain, in which the coupling of mantle and stiffened lithospheric proto-plates results in large-scale lateral motion, and the proto-plates’ recycling back into the mantle along inclined planes.

The horizontal tectonics domain replicates several key features of plate tectonics, including stable divergent and convergent zones, long-lived environments for calc-alkaline magmatic activity inboard of zones of dipping lithospheric recycling, and paired metamorphic belts with contrasting pressure-temperature (P-T) gradients. On the other hand, this domain differs significantly from modern-style plate tectonics in that it does not form strongly localized plate margins and a globally linked plate-mosaic system (cf., Bercovici and Ricard, 2014; Cawood et al., 2018). The P-T gradients obtained by Capitanio et al. compare well with the P-T estimates made for tonalite-trondhjemite-granodiorite (TTG) series rocks and the paired metamorphic belt record, thereby supporting the feasibility of their formation within a mobilized, yet laterally continuous (i.e., non–plate tectonic), lithospheric lid. Comparisons of the numerical modeling results with the crustal production and reworking record led Capitanio et al. to conclude that the suggested mobilized lid regime had emerged in the Hadean. This regime also bears similarities with the squishy-lid regime predicted by more-complex tectonomagmatic numerical models (Sizova et al., 2015; Fischer and Gerya, 2016a; Rozel et al., 2017).

The relatively simple models of Capitanio et al. replicate fundamental P-T regimes preserved in the Archean rock record through non–plate tectonic processes. This result clearly warns against exaggeration of the roles of modern-style subduction and plate tectonics for early Earth geodynamics, and calls for further thorough

development of the self-consistent Precambrian geodynamics paradigm without falling into the “plate tectonics trap.”

Giese, C.-C., Ten Kate, I.L., Plümper, O., King, H.E., Lenting, C., Liu, Y., Tielens, A.G.G.M., 2019. The evolution of polycyclic aromatic hydrocarbons under simulated inner asteroid conditions. Meteoritics & Planetary Science 54, 1930-1950.

https://doi.org/10.1111/maps.13359

Large polycyclic aromatic hydrocarbons (PAHs) are an important component of the interstellar medium. PAHs have been identified in the soluble and insoluble matter of carbonaceous chondrites (CCs). Here, we study the evolution of PAHs under conditions relevant to the interiors of asteroids and compare our results to PAHs observed in CCs. We have performed long-term and short-term hydrothermal experiments, in which we exposed PAH-mineral mixture analogs of meteorites to temperature conditions representative of those predicted for asteroids interiors. Our results show that small PAHs with melting points within the aqueous alteration temperature of CCs form carbonaceous spherules in the presence of water. In this work, we describe the microstructure and morphology of these spherules. We discuss the similarities and differences compared to globules isolated from CCs.

Gionchetta, G., Romaní, A.M., Oliva, F., Artigas, J., 2019. Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances. Scientific Reports 9, 13506.

https://doi.org/10.1038/s41598-019-49832-4

Stream microbes that occur in the Mediterranean Basin have been shown to possess heightened sensitivity to intensified water stress attributed to climate change. Here, we investigate the effects of long-term drought (150 days), storms and rewetting (7 days) on the diversity and composition of archaea, bacteria and fungi inhabiting intermittent streambed sediment (surface and hyporheic) and buried leaves. Hydrological alterations modified the archaeal community composition more than the bacterial community composition, whereas fungi were the least affected. Throughout the experiment, archaeal communities colonizing sediments showed greater phylogenetic distances compared to those of bacteria and fungi, suggesting considerable adaptation to severe hydrological disturbances. The increase in the class abundances, such as those of Thermoplasmata within archaea and of Actinobacteria and Bacilli within bacteria, revealed signs of transitioning to a drought-favoured and soil-like community composition. Strikingly, we found that in comparison to the drying phase, water return (as sporadic storms and rewetting) led to larger shifts in the surface microbial community composition and diversity. In addition, microhabitat characteristics, such as the greater capacity of the hyporheic zone to maintain/conserve moisture, tended to modulate the ability of certain microbes (e.g., bacteria) to cope with severe hydrological disturbances.

Glasser, W.G., 2019. About making lignin great again—some lessons from the past. Frontiers in Chemistry 7, 565. doi: 10.3389/fchem.2019.00565.

https://www.frontiersin.org/article/10.3389/fchem.2019.00565

Lignin, the second most abundant biopolymer on the planet, serves land-plants as bonding agent in juvenile cell tissues and as stiffening (modulus-building) agent in mature cell walls. The chemical structure analysis of cell wall lignins from two partially delignified wood species representing between 6 and 65% of total wood lignin has revealed that cell wall-bound lignins are virtually invariable in terms of inter-unit linkages, and resemble the native state. Variability is recognized as the result of isolation procedure. In native state, lignin has a low glass-to-rubber transition temperature and is part of a block copolymer with non-crystalline polysaccharides. This molecular architecture determines all of lignin's properties, foremost of all its failure to undergo interfacial failure by separation from (semi-) crystalline cellulose under a wide range of environmental conditions. This seemingly unexpected compatibility (on the nano-level) between a carbohydrate component and the highly aromatic lignin represents a lesson by nature that human technology is only now beginning to mimic. Since the

isolation of lignin from lignocellulosic biomass (i.e., by pulping or biorefining) necessitates significant molecular alteration of lignin, isolated lignins are highly variable in structure and reflect the isolation method. While numerous procedures exist for converting isolated (carbon-rich) lignins into well-defined commodity chemicals by various liquefaction techniques (such as pyrolysis, hydrogenolysis, etc.), the use of lignin in man-made thermosetting and thermoplastic structural materials appears to offer greatest value. The well-recognized variabilities of isolated lignins can in large part be remedied by targeted chemical modification, and by adopting nature's principles of functionalization leading to inter-molecular compatibility. Lignins isolated from large-scale industrial delignification processes operating under invariable isolation conditions produce polymers of virtually invariable character. This makes lignin from pulp mills a potentially valuable biopolymeric resource. The restoration of molecular character resembling that in native plants is illustrated in this review via the demonstrated (and in part commercially-implemented) use of pulp lignins in bio-degradable (or compostable) polymeric materials.

Gleißner, P., 2019. The Earth–Moon late-accretion conundrum. Nature Geoscience 12, 683-684.

https://doi.org/10.1038/s41561-019-0445-0

The distribution of iron-loving elements between the mantles of the Moon and Earth may differ from established belief, suggest two studies that determine the hafnium–tungsten ratio and sulfide–silicate melt partitioning of elements in the lunar mantle.

The mantles of the Moon and Earth have many compositional and isotopic similarities. Nevertheless, the abundances of elements that preferentially partition into metal, termed siderophile elements, are notably different between them. It has been proposed that the lunar mantle hosts substantially fewer highly siderophile elements (HSEs) than the terrestrial mantle1. In addition, the isotopic abundance of tungsten 182W, a decay product of the short-lived hafnium isotope 182Hf, is slightly higher in the lunar mantle than in the terrestrial mantle2. The similarities in stable isotopes are now mostly in line with giant-impact models of the Moon’s formation3,4. There are, however, multiple hypotheses to explain the differences in the abundances of HSEs, including less impactor retention on the Moon5 and the stochastic nature of planetary accretion6. In this issue of Nature Geoscience, Thiemens et al.7 and Brenan et al.8 together suggest that the siderophile-element composition of the lunar mantle is less constrained than previously thought.

Lunar basalts (Fig. 1) contain about 100-times less HSEs than their terrestrial counterparts1. With the current understanding of sulfide-undersaturated lunar mantle melting and basalt formation, sub-nanogram HSE concentrations in the mantle source of lunar basalts were proposed1, around 40-times lower than in the Earth’s mantle9. This Earth–Moon difference is interpreted to reflect disproportionate late accretion of primitive matter after core formation, with an estimated mass of 1.5 × 1019 kg being added to the Moon (0.02% of its mass) versus about 2 × 1022 kg to the Earth (0.5% of its mass)1,6,9. The inferred additions of impactor material constrain the Earth and Moon to having had indistinguishable abundances of 182W before late accretion. This is inconsistent, however, with recent models of Moon formation by a giant impact, which predict a significant difference in 182W abundance2,10,11. Knowledge of the Hf/W ratio of a given planetary reservoir is a prerequisite for interpretation of 182W variations in terms of differences in formation time. This is not trivial, however, because of the different geochemical behaviour of W and Hf during planetary-differentiation processes.

Thiemens et al. analyse the Hf and W mass fractions in lunar samples with high precision, revealing that although the Hf/W ratio varies between different rock types, that of lunar basalts can be explained by the composition of their respective mantle source and subsequent fractionation processes. They quantify the fractionation processes and narrow down the bulk silicate Moon’s Hf/W ratio to a range of 30 to 50. This result is important, because such a high Hf/W ratio would result in strong radiogenic ingrowth of 182W from decay of 182Hf within its short lifetime, until 60 million years after Solar System formation. Previous assessments proposed lower Hf/W ratios, closer to that found for the bulk silicate Earth.

Among the different possibilities to explain the Hf/W ratio and 182W abundance of the bulk silicate Moon, Thiemens et al. advocate a scenario of early lunar core formation and conclude that the 182W excess in lunar rocks can be explained by the decay of now extinct 182Hf in the lunar mantle. This explanation is novel because it implies that lunar core formation was the predominant control on the Hf/W ratio, and thus on the W isotopic

composition of the silicate Moon. However, the extent of equilibration between metal and silicate during the Moon-forming impact and its effect on Hf/W and the W isotopic composition are not well constrained10,11. From this point of view, the isotopic evolution and the influence of late accretion on the 182W abundance of the lunar mantle remain ambiguous.

In contrast to W, HSEs partition almost completely into metal during core formation. Therefore, the HSE abundances in the lunar mantle should provide more definite estimates of the mass of late-accreted matter. Assessing the Moon’s HSE inventory from basalt compositions, however, requires knowledge of phase relations during partial melting of the mantle. In this regard, the abundance and speciation of the moderately siderophile and volatile element sulfur in the lunar mantle is important. Residual sulfide phases would retain significant quantities of HSEs and diminish the utility of lunar basalts as a measure of late accretion12.

Brenan et al. report experiments on the solubility of sulfur in silicate melts and the sulfide–silicate melt partitioning of HSEs for a model lunar basalt composition. They find that at the reduced conditions of the lunar interior, the basalt source is likely to be saturated in a sulfide melt phase. Since sulfide retains some HSEs more than others, lunar basalts should have significant fractionations between different HSEs. Because these fractionations are not observed, Brenan et al. suggest that most lunar basalts may be contaminated with minute amounts of unfractionated HSEs from impactor material in the lunar megaregolith. Thus, the true HSE content of the lunar mantle could be veiled by residual sulfide and contamination with impactor debris. The mantle could therefore host a larger range of HSE abundances, which in principle now includes mass fractions of late accretion as high as predicted from moderately siderophile and volatile elements13.

Thiemens et al. and Brenan et al. differ in their appraisal of the processes that exert the dominant control on siderophile-element abundances in the lunar mantle and the resulting implications for the evolution of the Earth–Moon system. Thiemens et al. argue that lunar differentiation is the main control and imply that late accretion might be insignificant, whereas the results of Brenan et al. suggest that late accretion onto the Moon could have been more substantial than we thought.

References1. Day, J. M. D. & Walker, R. J. Earth Planet. Sci. Lett. 423, 114–124 (2015).2. Kruijer, T. S. & Kleine, T. Earth Planet. Sci. Lett. 475, 15–24 (2017).3. Canup, R. M. Science 338, 1052–1055 (2012).4. Hosono, N., Karato, S.-I., Makino, J. & Saitoh, T. R. Nat. Geosci. 12, 418–423 (2019).5. Zhu, M.-H. et al. Nature 571, 226–229 (2019).6. Bottke, W. F., Walker, R. J., Day, J. M. D., Nesvorny, D. & Elkins-Tanton, L. Science 330, 1527–1530

(2010).7. Thiemens, M. M., Sprung, P., Fonseca, R. O. C., Leitzke, F. P. & Münker, C. Nat. Geosci.

https://doi.org/10.1038/s41561-019-0398-3 (2019).8. Brenan, J. M., Mungall, J. E. & Bennett, N. R. Nat. Geosci. https://doi.org/10.1038/s41561-019-0426-3

(2019).9. Becker, H. et al. Geochim. Cosmochim. Acta 70, 4528–4550 (2006).10. Fischer, R. A. & Nimmo, F. Earth Planet. Sci. Lett. 499, 257–265 (2018).11. Walker, R. J. et al. Chem. Geol. 411, 125–142 (2015).12. Day, J. M. D. Am. Mineral. 103, 1734–1740 (2018).13. Hauri, E. H., Saal, A. E., Rutherford, M. J. & Van Orman, J. A. Earth Planet. Sci. Lett. 409, 252–264

(2015).

Goodarzi, F., Gentzis, T., Dewing, K., 2019. Influence of igneous intrusions on the thermal maturity of organic matter in the Sverdrup Basin, Arctic Canada. International Journal of Coal Geology 213, 103280.


The influence of igneous intrusions on the trend of thermal maturity with depth in two drillholes, one on Ellesmere Island and the other on Ellef Ringnes Island, Arctic Canada, was assessed using vitrinite and solid bitumen reflectance, Rock-Eval pyrolysis/TOC, and gas composition analysis in order to assess the impact of igneous intrusions on the hydrocarbon system in the area. Thick sequences of Permo-Pennsylvanian strata in

Sabine Peninsula, Melville Island, were intruded by two igneous intrusions in the Panarctic Chads Creek B-64 (influenced by one intrusion) and the Panarctic Drake Point D-68 (influenced by two intrusions). Sedimentary strata in Chads Creek B-64 were intruded by a 120 m-thick diabase sill (with temperature of ~1100 °C) of unknown age. This resulted in increased reflectance of vitrinite from 0.90% to 1.65% and of pyrobitumen from 2.90% to almost 5.80% near the sill contact at depth of 3600 m. Solid bitumen outside of the thermal aureole zones and having reflectance values <1.50% followed the extrapolated trend for solid bitumen present in the country rocks. In Panarctic Drake Point D-68, the intrusives are granodiorite sills of 45 m and 75 m thickness and were emplaced during the Upper Jurassic (152 Ma) and Lower Cretaceous (131 Ma). The intrusion temperature was 800 °C. The Vitrinite Rr prior to sill emplacement was <1.0% outside the aureole and increased to approximately 2.0% near the intrusive zone. The rocks were well-lithified prior to sill emplacement. Solid bitumen underwent carbonization after being exposed to a temperature of at least 800 °C. Solid bitumen reflectance also showed a sudden increase from a minimum of 1.50% outside the aureole to approximately 7.0% near the sill contact, a 5× increase as compared to an increase of 2× for vitrinite. This indicates that solid bitumen is a very sensitive indicator of temperature variation, more sensitive than vitrinite. Solid bitumen reflectance prior to the sill emplacement can only be inferred from the solid bitumen below the lower, younger sill because of poor control on solid bitumen in the interval just above the upper, older sill. Reflectance trends above and below the sills appear to be symmetrical despite the superimposition of the effects of one sill on the other. The metamorphic effects of the sill, as determined vertically by the reflectance trend, can be observed for a distance of up to seven times its thickness. The upper, older sill is approximately 45 m thick and the thermal aureole zone above it has a width of 330 m. The thickness of the aureole below the sill is difficult to establish because it has been obliterated by the effect of the lower, younger sill. The thickness of the lower sill is 75 m. An additional factor that influenced solid bitumen reflectance in this case may have been the thickness of the sill, which, in turn, affects the cooling time of the intrusive body. The granodiorite sills are approximately 45–75 m thick and the diabase sill is almost 120 m.



The Vaca Muerta Shale in Argentina is the first major commercial shale oil/gas play outside of North America. High-resolution 2D/3D imaging of shale rocks for the purpose of establishing their mineralogy, total, and connected porosities has become more and more sophisticated. In this paper, nanoscale-resolution focused ion beam (FIB)–scanning electron microscopy (SEM) nano-tomography was used to obtain images of pore structures within two organic-rich regions of interest (ROIs), selected based on correlative SEM and automated mineralogy maps. Advanced machine learning classification tools were used to segment the images and assign porosities and other components. Pore size distribution and pore connectivity analyzes revealed that about 95% of all the pores, present within the two ROIs, had a diameter of less than approximately 75 nm, and that most of these pores were poorly connected. In a similar fashion, the flow rate distribution analysis showed that pores with diameters of about 150–330 nm contributed to over 50% of the flow capacity of the connected pore systems. These results suggest that although most of the pores typically found in shales have pore diameter smaller than about 100 nm, most of the hydrocarbon production may be carried by a relatively small number of larger connected pores with pore diameter greater than about 150 nm. This study implies that a large portion of the organic-hosted pores (with diameter typically smaller than about 100 nm) may not provide permeable flow pathways for the oil and/or gas migration, and hence may have very little contribution to the hydrocarbon production.



Raman spectroscopy was used as a supplementary method to characterise the thermal maturity of Ediacaran organic matter (OM) from the East European Craton. Because this method is based on organic particles measurement, it appears to be a good supplementary method in addition to the acquisition of biomarker data, which is based on extractable organic matter and may be affected by potential contamination. Raman spectroscopy seems to be particularly useful for lower Palaeozoic rocks, which do not contain vitrinite. Here, we compared C31 22S/(S + R) homohopane ratio results (obtained using gas chromatography – mass spectrometry), with various Raman parameters including: G_STA, Gmax position, Dmax/Gmax, FWHMG, RAR, D_STA, and PDmax. Close correlations were observed between C31 22S/(S + R) and G_STA, Gmax position, Dmax/Gmax, and FWHMG, reaching values of R2 = 0.5‒0.6, whereas no correlation existed between homohopane ratio and the RAR, D_STA, and PDmax parameters. Raman spectroscopy results divided Ediacaran samples into two distinctive groups: (i) immature (Russian, Lithuanian, and Belarusian), characterised by relatively higher values of G_STA, Dmax/Gmax, and FWHMG and relatively lower values of PGmax, and (ii) mature (Polish and Ukrainian), with relatively lower values of G_STA, Dmax/Gmax, and FWHMG and relatively higher values of PGmax. Within each group no statistically confirmed differences were found. However, significant discrepancies were observed between the hopane ratio and Raman parameters in Lithuanian samples, in relation to other samples from the group (i). Values of the C31 22S/(S + R) ratio for Lithuanian samples are close to those for the group (ii) and significantly higher than those for the group (i). However, all Raman parameters are the same as those of the rest samples from the group (i), indicating the immature character of OM from Lithuanian rocks. We interpret this discrepancy as representing contamination of the cores with drilling fluids, resulting in increased values for the C31 22S/(S + R) ratio. In this case, Raman spectroscopy is a useful tool for detecting extract contamination and appears to be an effective and decisive method in the case of rocks suspected of contamination.

Gould, S.B., Garg, S.G., Handrich, M., Nelson-Sathi, S., Gruenheit, N., Tielens, A.G.M., Martin, W.F., 2019. Adaptation to life on land at high O2 via transition from ferredoxin-to NADH-dependent redox balance. Proceedings of the Royal Society B: Biological Sciences 286, 20191491.

https://doi.org/10.1098/rspb.2019.1491

Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H2 as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function—redox balance—served by two electron-transfers in the NADH- and O2-dependent respiratory chains of mitochondria. Although they possess O2-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O2. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O2 levels (21% v/v), Chlamydomonas reinhardtii expresses them with diurnal regulation. High O2 environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O2 environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O2-insensitive two-electron carrier NADH.


https://doi.org/10.1130/G46152.1

While modern forests have their origin in the diversification and expansion of angiosperms in the Late Cretaceous and early Cenozoic, it is unclear whether the rise of closed-canopy tropical rainforests preceded or followed the end-Cretaceous extinction. The “canopy effect” is a strong vertical gradient in the carbon isotope (δ13C) composition of leaves in modern closed-canopy forests that could serve as a proxy signature for canopy structure in ancient forests. To test this, we report measurements of the carbon isotope composition of nearly

200 fossil angiosperm leaves from two localities in the Paleocene Cerrejón Formation and one locality in the Maastrichtian Guaduas Formation of Colombia. Leaves from one Cerrejón fossil assemblage deposited in a small fluvial channel exhibited a 6.3‰ range in δ13C, consistent with a closed-canopy forest. Carbon isotope values from lacustrine sediments in the Cerrejón Formation had a range of 3.3‰, consistent with vegetation along a lake edge. An even-narrower range of δ13C values (2.7‰) was observed for a leaf assemblage recovered from the Cretaceous Guaduas Formation, and suggests vegetation with an open canopy structure. Carbon isotope fractionation by Late Cretaceous and early Paleogene leaves was in all cases similar to that by modern relatives, consistent with estimates of low atmospheric CO2 during this time period. This study confirms other lines of evidence suggesting that closed-canopy forests in tropical South America existed by the late Paleocene, and fails to find isotopic evidence for a closed-canopy forest in the Cretaceous.

Grant, S.R., Church, M.J., Ferrón, S., Laws, E.A., Rappé, M.S., 2019. Elemental composition, phosphorous uptake, and characteristics of growth of a SAR11 strain in batch and continuous culture. mSystems 4, e00218-18.

http://msystems.asm.org/content/4/4/e00218-18.abstract

Abstract: In this study, a strain of SAR11 subgroup IIIa (termed HIMB114) was grown in seawater-based batch and continuous culture in order to quantify cellular features and metabolism relevant to SAR11 ecology. We report some of the first direct measurements of cellular elemental quotas for nitrogen (N) and phosphorus (P) for SAR11, grown in batch culture: 1.4 ± 0.9 fg N and 0.44 ± 0.01 fg P, respectively, that were consistent with the small size of HIMB114 cells (average volume of 0.09 μm3). However, the mean carbon (C) cellular quota of 50 ± 47 fg C was anomalously high, but variable. The rates of phosphate (PO4

3−) uptake measured from both batch and continuous cultures were exceptionally slow: in chemostats growing at 0.3 day−1, HIMB114 took up 1.1 ± 0.3 amol P cell−1 day−1, suggesting that <30% of the cellular P requirement of HIMB114 was met by PO4

3− assimilation. The mean rate of leucine incorporation, a measure of bacterial production, during late-log-phase growth of batch HIMB114 cultures was 0.042 ± 0.02 amol Leu cell−1 h−1. While only weakly correlated with changes in specific growth rates, the onset of stationary phase resulted in decreases in cell-specific leucine incorporation that were proportional to changes in growth rate. The rates of cellular production, respiratory oxygen consumption, and changes in total organic C concentrations constrained cellular growth efficiencies to 13% ± 4%. Hence, despite a small genome and diminutively sized cells, SAR11 strain HIMB114 appears to grow at efficiencies similar to those of naturally occurring bacterioplankton communities.

Importance: While SAR11 bacteria contribute a significant fraction to the total picoplankton biomass in the ocean and likely are major players in organic C and nutrient cycling, the cellular characteristics and metabolic features of most lineages have either only been hypothesized from genomes or otherwise not measured in controlled laboratory experimentation. The dearth of data on even the most basic characteristics for what is arguably the most abundant heterotroph in seawater has limited the specific consideration of SAR11 in ocean ecosystem modeling efforts. In this study, we provide measures of cellular P, N, and C, aerobic respiration, and bacterial production for a SAR11 strain growing in natural seawater medium that can be used to directly relate these features of SAR11 to biogeochemical cycling in the oceans. Through the development of a chemostat system to measure nutrient uptake during steady-state growth, we have also documented inorganic P uptake rates that allude to the importance of organic phosphorous to meet cellular P demands, even in the presence of nonlimiting PO4

3− concentrations.

Gray, M.R., Yarranton, H.W., 2019. Quantitative modeling of formation of asphaltene nanoaggregates. Energy & Fuels 33, 8566-8575.


Association of asphaltene molecules to form aggregates is a defining property of this fraction of petroleum, which has impacts on all aspects of production and refining. Association has been detected over a very wide range of concentrations, but the quantitative modeling of this aggregation of molecules has mainly been restricted to fitting relatively high-asphaltene concentration data from vapor-pressure osmometry. This paper examines the capability of the termination/propagation model for association to represent low-concentration behavior. The addition of an additional strongly associating fraction to the model is necessary to obtain dimer

formation over the observed range of concentrations. Unfortunately, the data required to fit such a model with confidence are lacking. Data from ultracentrifugation of asphaltene aggregates can also be fitted to a termination/propagation model. Transient measurements of ultracentrifuge concentration profiles have the potential to enable more comprehensive models of association behavior, especially when applied to subfractions with known aggregation behavior.

Griffero, L., Alcántara-Durán, J., Alonso, C., Rodríguez-Gallego, L., Moreno-González, D., García-Reyes, J.F., Molina-Díaz, A., Pérez-Parada, A., 2019. Basin-scale monitoring and risk assessment of emerging contaminants in South American Atlantic coastal lagoons. Science of The Total Environment 697, 134058.


Emerging contaminants (ECs) such as pharmaceuticals, personal care products, drugs of abuse and polar pesticides are under particular attention due to their high consumption, frequent detection in the environment and reported ecotoxicological risk. This study investigates the occurrence and distribution of multiclass of ECs in surface waters at basin scale of two Atlantic coastal lagoons of Uruguay, South America. For this purpose, a target screening approach covering up to 362 compounds was employed using nanoflow liquid chromatography – high resolution mass spectrometry (nanoLC/HRMS). 53 compounds were identified including five banned pesticides in the European Union: atrazine, carbendazim, chlorpyrifos ethyl, diazinon, and ethion. Pharmaceuticals, hormones and drugs of abuse showed maximum detection frequencies and concentrations downstream cities. The highest occurrence of pesticides was found in lagoons and streams with neighboring agricultural activity. ECs were also found in coastal sea. Environmental risk assessment revealed that the hormones 17α-ethinylestradiol and 17-β-estradiol showed the highest risk to aquatic organisms in these basins. This study represents the first basin- scale monitoring of ECs in superficial waters encompassing streams, lagoons, and coastal seas in Uruguay, South America.

Gros, J., Schmidt, M., Dale, A.W., Linke, P., Vielstädte, L., Bigalke, N., Haeckel, M., Wallmann, K., Sommer, S., 2019. Simulating and quantifying multiple natural subsea CO2 seeps at Panarea Island (Aeolian Islands, Italy) as a proxy for potential leakage from subseabed carbon storage sites. Environmental Science & Technology 53, 10258-10268.

https://doi.org/10.1021/acs.est.9b02131

Carbon dioxide (CO2) capture and storage (CCS) has been discussed as a potentially significant mitigation option for the ongoing climate warming. Natural CO2 release sites serve as natural laboratories to study subsea CO2 leakage in order to identify suitable analytical methods and numerical models to develop best-practice procedures for the monitoring of subseabed storage sites. We present a new model of bubble (plume) dynamics, advection-dispersion of dissolved CO2, and carbonate chemistry. The focus is on a medium-sized CO2 release from 294 identified small point sources around Panarea Island (South-East Tyrrhenian Sea, Aeolian Islands, Italy) in water depths of about 40–50 m. This study evaluates how multiple CO2 seep sites generate a temporally variable plume of dissolved CO2. The model also allows the overall flow rate of CO2 to be estimated based on field measurements of pH. Simulations indicate a release of ∼6900 t y–1 of CO2 for the investigated area and highlight an important role of seeps located at >20 m water depth in the carbon budget of the Panarea offshore gas release system. This new transport-reaction model provides a framework for understanding potential future leaks from CO2 storage sites.

Guglielmini, J., Woo, A.C., Krupovic, M., Forterre, P., Gaia, M., 2019. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes. Proceedings of the National Academy of Sciences 116, 19585.


Significance: The viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage regularly draw the attention of the scientific community for their surprising features, from the gigantism of some viruses’

particles to their genome content. They shook the very definition of viruses and shed new light on the debate over their nature and putative role in the evolution of the cellular domains. Their origin(s) and evolution remain to be elucidated, however. Our phylogenetic analyses reveal the evolutionary relationships between the NCLDV families and their origin from a common ancestor, from which they diversified before the origin of modern eukaryotes. Our results also point to their likely role in the emergence of multiple DNA-dependent RNA polymerases in proto-eukaryotes.

Abstract: Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects of intense debate. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of 2 superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were transferred between 2 clades of NCLDVs and proto-eukaryotes, giving rise to 2 of the 3 eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.

Guillemant, J., Albrieux, F., Lacoue-Nègre, M., Pereira de Oliveira, L., Joly, J.-F., Duponchel, L., 2019. Chemometric exploration of APPI(+)-FT-ICR MS data sets for a comprehensive study of aromatic sulfur compounds in gas oils. Analytical Chemistry 91, 11785-11793.


Because of the ever-increasing depletion rate of conventional oil resources, it is essential to design processes for heavy oil recovery from petroleum reservoirs. Heavy oils contain high quantities of large molecules, such as asphaltenes, giving rise to high viscosities during production. Solvent extraction processes are capable candidates for heavy oil recovery; however, the separation of conventional solvents is energy-intensive. Therefore, a solvent with not only a high capacity for heavy oil dissolution but also an easy and environmentally friendly separation is in demand. In this work, the N,N-dimethylcyclohexylamine switchable hydrophilicity solvent (SHS) was employed for viscosity reduction and upgrading of heavy oils. Optimum weight ratios of the SHS were added to three different dead heavy oil samples with 11.33 to 17.54 °API and a corresponding room-temperature viscosity of more than 4287.0 to 3365.4 cp. To shed light on the interactions of the SHS with asphaltenes, the solvent was also added to heavy oil model solutions of asphaltenes in toluene. The solutions containing the solvent and the recovered oil were exposed to pressurized CO2 in the presence of deionized water to switch the hydrophilicity of the solvent to water-miscible and separate the recovered oil. The thus-obtained aqueous solution was then warmed up to 65 °C in the presence of N2 gas bubbling through the liquid to switch the solvent hydrophilicity to water-immiscible form and recover the SHS. Results indicate that more than 52 wt % of the oils are recovered at the optimum solvent-to-oil ratio (SOR). The heavier the oil, the higher the optimum SOR is, resulting in the viscosity reductions of more than 70%. Dynamic light scattering shows that the size of asphaltene aggregates becomes smaller and considerably uniform by the SHS, indicating weakening of the asphaltene self-association interactions. Dynamic interfacial tension measurements calibrate the amount of impurity in the recovered SHS.

Gulick, S.P.S., Bralower, T.J., Ormö, J., Hall, B., Grice, K., Schaefer, B., Lyons, S., Freeman, K.H., Morgan, J.V., Artemieva, N., Kaskes, P., de Graaff, S.J., Whalen, M.T., Collins, G.S., Tikoo, S.M., Verhagen, C., Christeson, G.L., Claeys, P., Coolen, M.J.L., Goderis, S., Goto, K., Grieve, R.A.F., McCall, N., Osinski, G.R., Rae, A.S.P., Riller, U., Smit, J., Vajda, V., Wittmann, A., 2019. The first day of the Cenozoic. Proceedings of the National Academy of Sciences 116, 19342-19351.


Significance: Chicxulub impact crater cores from the peak ring include ∼130 m of impact melt rock and breccia deposited on the first day of the Cenozoic. Within minutes of the impact, fluidized basement rocks formed a ring of hills, which were rapidly covered by ∼40 m of impact melt and breccia. Within an hour, ocean waters flooded the deep crater through a northeast embayment, depositing another 90 m of breccia. Within a day, a tsunami deposited material from distant shorelines, including charcoal. Charcoal and absence of sulfur-rich target rocks support the importance of impact-generated fires and release of sulfate aerosols for global cooling and darkness postimpact.

Abstract: Highly expanded Cretaceous–Paleogene (K-Pg) boundary section from the Chicxulub peak ring, recovered by International Ocean Discovery Program (IODP)–International Continental Scientific Drilling Program (ICDP) Expedition 364, provides an unprecedented window into the immediate aftermath of the impact. Site M0077 includes ∼130 m of impact melt rock and suevite deposited the first day of the Cenozoic covered by <1 m of micrite-rich carbonate deposited over subsequent weeks to years. We present an interpreted series of events based on analyses of these drill cores. Within minutes of the impact, centrally uplifted basement rock collapsed outward to form a peak ring capped in melt rock. Within tens of minutes, the peak ring was covered in ∼40 m of brecciated impact melt rock and coarse-grained suevite, including clasts possibly generated by melt–water interactions during ocean resurge. Within an hour, resurge crested the peak ring, depositing a 10-m-thick layer of suevite with increased particle roundness and sorting. Within hours, the full resurge deposit formed through settling and seiches, resulting in an 80-m-thick fining-upward, sorted suevite in the flooded crater. Within a day, the reflected rim-wave tsunami reached the crater, depositing a cross-bedded sand-to-fine gravel layer enriched in polycyclic aromatic hydrocarbons overlain by charcoal fragments. Generation of a deep crater open to the ocean allowed rapid flooding and sediment accumulation rates among the highest known in the geologic record. The high-resolution section provides insight into the impact environmental effects, including charcoal as evidence for impact-induced wildfires and a paucity of sulfur-rich evaporites from the target supporting rapid global cooling and darkness as extinction mechanisms.

Guo, P., Liu, C., Gibert, L., Huang, L., Zhang, D., Dai, J., 2020. How to find high-quality petroleum source rocks in saline lacustrine basins: A case study from the Cenozoic Qaidam Basin, NW China. Marine and Petroleum Geology 111, 603-623.


Despite having made significant contributions to global hydrocarbon occurrences, source rocks in saline lacustrine basins show great mineralogical and organic geochemical heterogeneity and the controlling mechanism is weakly studied. Here, we use the Cenozoic Qaidam Basin as an example to compare the organic and inorganic parameters of fine-grained sediments in different lacustrine facies and to figure out the characterization and distribution of effective petroleum source rocks in saline lacustrine systems. Organic-inorganic database of six selected boreholes show that in the bench-margin (high-gradient) lacustrine system, fine-grained sediments in sublittoral brackish-mesosaline zones containing low chlorides (<2000 ppm) and high carbonates (25–50%) show low total organic carbon (TOC) contents (0.4–1.0%) and high chloroform extracts (0.05–0.2%); centripetally sediments in penesaline profundal zones averagely have higher chlorides (2000–15000 ppm), lower carbonates (15–35%), higher TOC contents (0.6–1.2%), and higher extracts (0.05–0.3%). These two facies can both develop valid petroleum source rocks. In the ramp-margin (low-gradient) lacustrine system, dark fine-grained sediments in penesaline centers with low carbonate (15–25%) and high chloride contents (2000–15000 ppm) show high TOC contents (0.8–2.0%) but extremely low hydrogen indexes (<100 mg HC/g TOC) (little extracts), only developing as valid gas/or biogas source rocks. Supersaline fine-grained sediments in both lacustrine systems develop invalid source rocks. Lateral superimposition maps show that fine-grained sediments with high hydrocarbon generation potential generally contain averagely 25–50% carbonates. Therefore, brackish-penesaline water salinity and bench-type basement are two necessary conditions to develop high-quality petroleum source rocks in saline lacustrine systems and average carbonate content can be a general good mineralogical indicator.

Guo, Q., Fink, R., Littke, R., Zieger, L., 2019. Methane sorption behaviour of coals altered by igneous intrusion, South Sumatra Basin. International Journal of Coal Geology 214, 103250.


A detailed understanding on how igneous intrusions alter coal properties is important for predicting coalbed methane generation and storage behavior. Twelve coal samples were collected from an area influenced by an andesitic igneous sill in the South Sumatra Basin, Indonesia to investigate the changes in coal properties, water uptake and high-pressure methane sorption behavior under dry and moist condition. Vitrinite reflectance is at about 0.55% for the unaltered samples and ranges from 1.4 to 5.2% for the igneous-affected coals. Those coals affected by the intrusion show higher aromaticity and a lower contribution of carbonyl/carboxyl functional groups as revealed by ATR-FTIR analysis. Water uptake is dramatically decreased in intrusion-altered coals, the water uptake being controlled both by abundance of oxygen-containing functional groups and pore properties within the coal matrix. The results show that methane sorption capacity of selected coals is mainly controlled by micropore volume, where sorption takes place. Intrusion altered and unaltered coals show a similar competitive sorption behavior between water and methane that can be described by a volumetric displacement where on average 1.5 water molecules displace a single methane molecule. Therefore, the significantly larger uptake of water in unaltered coals results in a stronger loss of methane sorption capacity compared to thermally metamorphosed coals.

Guo, Z., Liu, W., Liu, C., Tian, J., Zeng, X., Cui, H., 2019. Biomarker characteristics of hydrocarbon source rocks in saline lacustrine basin: a case study of Paleogene–Neogene strata in the Western Qaidam Basin, western China. Carbonates and Evaporites 34, 679-698.

https://doi.org/10.1007/s13146-018-0466-6

During the Paleogene–Neogene, the Qaidam Basin was a saline lacustrine basin so the biomarkers of hydrocarbon source rocks exhibited unique characteristics under the salinization conditions. Saturated hydrocarbons extracted from a large number of source-rock samples were analyzed using gas chromatography and mass spectrometry. The results showed that n-alkanes in the source rocks were evenly distributed between even and odd carbon numbers, isoprenoid alkenes were predominantly phytanes, and ratios of pristane to phytane (Pr/Ph) were low, mostly in the range from 0.2 to 0.8. Terpanes typically showed high contents of C35 homohopane and gammacerane. Overall, the ratios of gammacerane to C30 hopane (gammacerane/C30 hopane) and C35–C34 homohopane (C35/C34 homohopane) exhibited a positive correlation. Differing concentrations of oleanane were detected. The relative content of C27 and C29 steranes in the hydrocarbon source rocks varied from 25 to 75%, and the relative content of C28 sterane in a considerable number of samples was higher than 30%. C27–C29 steranes generally showed an asymmetric V-shaped distribution, and the distribution of sterane/hopane and Pr/Ph ratios showed negative correlations. The salinity and reducibility indexes of the southern area of the Western Qaidam Basin were significantly higher than those of the northern area of the basin during the Oligocene–Miocene. Source rocks in the northern area were formed in a low-salinity and weakly reductive environment with type II2–III kerogen, whereas the hydrocarbon source rocks in the southern area formed in a high salinity and strongly reductive environment. The sedimentary water salinity and reducibility of the different areas were reduced in the following order: Hongliuquan, Yuejin, Shizigou, and Wunan–Lvcaotan. The best source rocks in this basin were developed in the Hongliuquan, Yuejin, and Shizigou areas with type II1–II2 kerogen. This study lays a foundation for further understanding the geochemical distribution of the hydrocarbon source rocks and crude oil in addition to the characteristics of the oil source in Paleogene and Neogene.

Haile-Selassie, Y., Melillo, S.M., Vazzana, A., Benazzi, S., Ryan, T.M., 2019. A 3.8-million-year-old hominin cranium from Woranso-Mille, Ethiopia. Nature 573, 214-219.

https://doi.org/10.1038/s41586-019-1513-8

The cranial morphology of the earliest known hominins in the genus Australopithecus remains unclear. The oldest species in this genus (Australopithecus anamensis, specimens of which have been dated to 4.2–3.9 million years ago) is known primarily from jaws and teeth, whereas younger species (dated to 3.5–2.0 million years ago) are typically represented by multiple skulls. Here we describe a nearly complete hominin cranium from Woranso-Mille (Ethiopia) that we date to 3.8 million years ago. We assign this cranium to A. anamensis

on the basis of the taxonomically and phylogenetically informative morphology of the canine, maxilla and temporal bone. This specimen thus provides the first glimpse of the entire craniofacial morphology of the earliest known members of the genus Australopithecus. We further demonstrate that A. anamensis and Australopithecus afarensis differ more than previously recognized and that these two species overlapped for at least 100,000 years—contradicting the widely accepted hypothesis of anagenesis.

Hameau, A., Frölicher, T.L., Mignot, J., Joos, F., 2019. Is deoxygenation detectable before warming in the thermocline? Biogeosciences Discussions 2019, 1-32.


Multiple lines of evidence from observation- and model-based studies show that anthropogenic greenhouse gas emissions cause ocean warming and oxygen depletion, with adverse impacts on marine organisms and ecosystems. Temperature is considered as one of the main indicators of climate change, but, in the thermocline, anthropogenic changes in biogeochemical tracers such as oxygen may emerge from the bounds of natural variability before changes in temperature. Here, we compare the local time of emergence (ToE) of anthropogenic temperature and oxygen changes in the thermocline within an ensemble of Earth system model simulations from the fifth phase of the Coupled Model Intercomparison Project (CMIP5). Anthropogenic deoxygenation emerges from natural internal variability before warming in 35 ± 11 % of the global thermocline. Earlier emergence of oxygen than temperature change is simulated by all models in parts of the subtropical gyres of the Pacific and the Southern Ocean. Earlier detectable changes in oxygen than temperature are typically related to decreasing trends in ventilation. The supply of oxygen-rich surface waters to the thermocline is reduced as evidenced by an increase in apparent oxygen utilisation over the simulations. Concomitantly, the propagation of the warming signal is hindered by slowing ventilation, which delays the warming in the thermocline. As the magnitudes of internal variability and simulated temperature and oxygen changes, which determine ToE, vary considerably among models, we compute the local ToE relative to the global mean ToE within each model. This reduces the inter-model spread in the relative ToE compared to the traditionally evaluated absolute ToE. Our results underline the importance of an ocean biogeochemical observing system and that the detection of anthropogenic impacts becomes more likely when using multi-tracer observations.

Hamilton-Brehm, S.D., Stewart, L.E., Zavarin, M., Caldwell, M., Lawson, P.A., Onstott, T.C., Grzymski, J., Neveux, I., Sherwood Lollar, B., Russell, C.E., Moser, D.P., 2019. Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a novel fumarate-fermenting microorganism from a deep fractured carbonate aquifer of the US Great Basin. Frontiers in Microbiology 10, 2224. doi: 10.3389/fmicb.2019.02224.


Deep fractured rock ecosystems across most of North America have not been studied extensively. However, the US Great Basin, in particular the Nevada National Security Site (NNSS, formerly the Nevada Test Site), has hosted a number of influential subsurface investigations over the years. This investigation focuses on resident microbiota recovered from a hydrogeologically confined aquifer in fractured Paleozoic carbonate rocks at 863 – 923 meters below land surface. Analysis of the microorganisms living in this oligotrophic environment provides a perspective into microbial metabolic strategies required to endure prolonged hydrogeological isolation deep underground. Here we present a microbiological and physicochemical characterization of a deep continental carbonate ecosystem and describe a bacterial genus isolated from the ecosystem. Strain DRI-13T is a strictly anaerobic, moderately thermophilic, fumarate-respiring member of the phylum Firmicutes. This bacterium grows optimally at 55°C and pH 8.0, can tolerate a concentration of 100 mM NaCl, and appears to obligately metabolize fumarate to acetate and succinate. Culture-independent 16S rRNA gene sequencing indicates a global subsurface distribution, while the closest cultured relatives of DRI-13T are Pelotomaculum thermopropionicum (90.0% similarity) and Desulfotomaculum gibsoniae (88.0% similarity). The predominant fatty acid profile is iso-C15:0, C15:0, C16:0 and C14:0. The percentage of the straight-chain fatty acid C15:0 is a defining characteristic not present in the other closely related species. The genome is estimated to be 3,649,665 bp, composed of 87.3% coding regions with an overall average of 45.1% G + C content. Strain DRI-13T represents a novel genus of subsurface bacterium isolated from a previously uncharacterized rock-hosted

geothermal habitat. The characterization of the bacterium combined with the sequenced genome provides insights into metabolism strategies of the deep subsurface biosphere. Based on our characterization analysis we propose the name Thermoanaerosceptrum fracticalcis (DRI-13T = DSM 100382T = ATCC TSD-12T).

Hand, E., 2019. World's oldest impact crater dated in Australian outback. Science 365, 852-853.


Barlangi Rock, an ancient hill in the outback of Western Australia, is dimpled by the quarries of Aboriginal people who chiseled its fine-grained rocks into sharp tools. Now, geologists have added a much deeper layer of history to those rocks by showing they were forged 2.229 billion years ago, when an asteroid crashed into our planet. The finding makes Yarrabubba crater, the 70-kilometer-wide scar left by the collision, Earth's oldest.

The geologists who reported the date last week, here at the Goldschmidt geochemistry conference, also point out a conspicuous coincidence: The impact came at the tail end of a planetwide deep freeze known as Snowball Earth. They say the impact may have helped thaw Earth by vaporizing thick ice sheets and lofting steam into the stratosphere, creating a powerful greenhouse effect.

“It's intriguing to think what a moderate to large impact event could do in this time period,” says Timmons Erickson, a geochronologist at NASA's Johnson Space Center in Houston, Texas, who led the study. “The temporal coincidence is striking,” agrees Eva Stüeken, a geobiologist at the University of St. Andrews in the United Kingdom. But she and other researchers are skeptical that Yarrabubba—which is just one-third the size of the crater left by the dinosaur-killing impact 66 million years ago—could have had such a profound effect on the climate. Still, Stüeken says, paleoclimate studies should consider the possible role of such violent collisions. “It forces us to think more about these impacts and these potential feedbacks.”

Earth likes to cover its tracks. Erosion from wind and water, as well as the churn of plate tectonics, mean impact craters are scarcer the further one goes back in time—even though the cratered surfaces of the moon and Mars show impacts were actually more common in the tumultuous early solar system. Prior to the dating of Yarrabubba crater, the oldest known impact was the Vredefort Dome, a 2.02-billion-year-old feature in South Africa that, at 300 kilometers wide, is the world's largest.

Western Australia is a good place to look for old craters because it contains the Yilgarn Craton, one of Earth's oldest surviving pieces of crust. In 2001, a magnetic survey near Yarrabubba revealed circular features in the bedrock, although no crater rim can be seen at the surface. And when Francis Macdonald, a geologist at the University of California (UC), Santa Barbara, took a close look at rocks from the region, he found the signatures of an impact's shock: microscopic planar patterns in mineral crystals and shatter cones, horsetail fracture patterns up to 1 meter long. Some of the melted and recrystallized rocks from beneath the crater—including Barlangi Rock—had also survived. “We're looking at the roots of it,” Macdonald says. In a 2003 discovery paper, he and his colleagues named the crater after the local sheep shearing station. They knew the impact was ancient, but could not give it a firm date.

In 2014, Erickson saw an opportunity while on his way to field work elsewhere in Western Australia. He camped near Barlangi Rock and crisscrossed the hill with a sledgehammer, filling a backpack with a dozen chunks of rock. In a laboratory tub, he zapped the rocks with 100,000 volts of electricity, breaking them up into their component minerals without damaging delicate textures.

Next, Erickson had to sift for crystals suitable for dating. Like a gold prospector, he used pans to float off less dense quartz and feldspar, and he extracted other unwanted minerals with a magnet. Finally, with tweezers and a microscope, he picked out several hundred grains of zircon and monazite, each smaller than the width of a human hair. “You need a good podcast or music when you're doing that,” he says.

He wanted crystals with rims that had melted and recrystallized, an assurance that the impact had reset a clock in which small amounts of radioactive uranium, trapped within the crystal, decay into lead. He mounted some of the best crystals in epoxy, polished them down to a fresh face, and vaporized spots on the rims with an ion beam. A mass spectrometer measured the abundance of uranium and lead in the vapor; from the proportions and

the known half-life of the uranium, he and his colleagues could calculate an age. They ended up with a date of 2.229 billion years old, plus or minus 5 million years.

That puts the impact at a turbulent time in Earth's history. Life had existed for more than 1 billion years, but photosynthetic life—cyanobacteria living in shallow waters—was a recent evolutionary invention, one that triggered a sharp rise in atmospheric oxygen about 2.4 billion years ago. Previously, high levels of methane in the atmosphere had generated a greenhouse effect that warmed the planet. But many scientists think the methane was destroyed by chemical reactions with Earth's first ozone, produced when ultraviolet light from the sun struck the oxygen molecules. They suspect loss of methane sent Earth crashing into a set of severe and long-lived ice ages, even at low latitudes. Three or maybe four of these icy episodes took place between 2.45 billion and 2.22 billion years ago, which means Australia might have been covered in ice at the time of the Yarrabubba impact.

Scientists have assumed that volcanic eruptions ended the ice ages, by belching carbon dioxide and warming the planet. But Erickson and his colleagues speculate that Yarrabubba could have helped. They modeled the effect of a 7-kilometer-wide asteroid striking an ice sheet between 2 and 5 kilometers thick. They found the impact could have spread dust thousands of kilometers, darkening ice and enhancing its ability to absorb heat. It also would have sent half a trillion tons of steam into the stratosphere—orders of magnitude more water vapor than in today's stratosphere—where it would have trapped heat.

Andrey Bekker, a geologist at UC Riverside, doubts that the water vapor would have persisted for the centuries needed to thaw Earth. “I'm not convinced that by itself it could do this job,” he says. Christian Koeberl, an impact expert and the director general of the Natural History Museum in Vienna, shares those doubts, but says paleoclimate researchers need to model the effects explicitly.

If the Yarrabubba impact did thaw the planet, allowing life to reclaim icy continents and oceans, it wouldn't be the first example of life benefiting from a cosmic blow, Koeberl says. Although the public tends to associate impacts with extinctions, he notes that impacts 4 billion years ago could have jump-started life. Asteroids delivered phosphorus, a key nutrient, and the impacts also created the protected, energy-rich hydrothermal systems where some biologists believe life began. “Impacts can be bringers of life, impacts can be destroyers of life,” he says.

Hao, J., Zhong, N., Luo, Q., Liu, D., Wu, J., Liu, A., 2019. Raman spectroscopy of graptolite periderm and its potential as an organic maturity indicator for the Lower Paleozoic in southwestern China. International Journal of Coal Geology 213, 103278.


The determination of organic maturity for Lower Paleozoic sediments is challenging due to the lack of vitrinite. Many studies have been completed on the morphology and optical properties of graptolite periderm, but little is known about vibrational changes in its structure with increasing maturation (e.g., Raman spectroscopy). In this study, the vibrational structure of graptolite periderm was determined using the Raman spectrum. Raman spectra were obtained from natural samples with a wide range of organic maturity and from two artificially matured sample sets (E1 and AS-DD-LG).

As graptolite reflectance increases, the position of the disorder band shifts to lower wavenumbers and the graphite band becomes narrower. Due to these alterations, the width ratio (FWHM-D/FWHM-G), area ratio (AD/AG) and band separation (RBS) increase. Graptolite reflectance displays negative correlations with the maximum position of the D1 peak (WD) and the full width at half maximum of the G band (FWHM-G). These observations demonstrate that the structural order and aromatization in graptolite periderms increase as organic maturity increases. A positive correlation between RBS and graptolite reflectance is shown in this study. Based on the relationship between vitrinite reflectance and graptolite reflectance proposed by Luo et al. (2018), a conversion equation of the equivalent vitrinite reflectance on the basis of RBS values of graptolite periderm is proposed to assess the thermal maturity for the Lower Paleozoic.

He, H., Liu, Z., Chen, C., Wei, Y., Bao, Q., Sun, H., Hu, Y., Yan, H., 2019. Influence of the biological carbon pump effect on the sources and deposition of organic matter in Fuxian Lake, a deep oligotrophic lake in southwest China. Acta Geochimica 38, 613-626.

https://doi.org/10.1007/s11631-019-00359-5

Biological carbon pumping (BCP) is a key process in which dissolved inorganic carbon in terrestrial aquatic ecosystems is utilized by aquatic autotrophs for photosynthesis and transformed into autochthonous organic matter (AOC). However, the mechanisms underlying BCP and the amount of generated AOC deposited effectively, are still poorly understood. Therefore, we conducted a systematic study combining modern hydrochemical monitoring and a sediment trap experiment in Fuxian Lake (Yunnan, SW China), the second-deepest plateau, oligotrophic freshwater lake in China. Temperature, pH, EC (electrical conductivity), DO (dissolved O2), [HCO3

−], [Ca2+], SIc, partial CO2 (pCO2) pressure, and carbon isotopic compositions of HCO3−

(δ13CDIC) in water from Fuxian Lake all displayed distinct seasonal and vertical variations. This was especially apparent in an inverse correlation between pCO2 and DO, indicating that variations of hydrochemistry in the lake water were mainly controlled by the metabolism of the aquatic phototrophs. Furthermore, the lowest C/N ratios and highest δ13Corg were recorded in the trap sediments. Analyses of the C/N ratio demonstrated that the proportions of AOC ranged from 30% to 100% of all OC, indicating that AOC was an important contributor to sedimentary organic matter (OC). It was calculated that the AOC flux in Fuxian Lake was 20.43 t C km−2 in 2017. Therefore, AOC produced by carbonate weathering and aquatic photosynthesis could potentially be a significant carbon sink and may have an important contribution to solving the lack of carbon sinks in the global carbon cycle.

He, K., Zhang, S., Mi, J., Fang, Y., Zhang, W., 2019. Carbon and hydrogen isotope fractionation for methane from non-isothermal pyrolysis of oil in anhydrous and hydrothermal conditions. Energy Exploration & Exploitation 37, 1558-1576.

https://doi.org/10.1177/0144598719857189

In this study, to ascertain the carbon and hydrogen isotope fractionation of oil cracking gas (secondary gas) in hydrothermal conditions, non-isothermal pyrolysis of oil with and without water was carried out by a gold-tube system. By determination of the yields of individual gas products, it is found that the presence of water enhanced the yields of hydrocarbon gases. However, kinetic calculations indicate that Ea for the generation of methane and C2–5 in pyrolysis in hydrothermal conditions are essentially identical with those in anhydrous pyrolysis. The yields of carbon dioxide (CO2) and alkene gases in pyrolysis in hydrothermal conditions are evidently higher than those in anhydrous pyrolysis. It is reasonable that water–hydrocarbon reactions occurred and contributed to the generation of secondary gas in hydrothermal conditions. Meanwhile, the presence of water resulted in a slight depletion of 13C for methane and an evident depletion of 13C for CO2. Thermodynamic calculations suggest that water–hydrocarbon reactions in non-isothermal pyrolysis are dominated by free radical mechanism rather than ionic mechanism. Moreover, δ2H values of methane are apparently different in pyrolysis involving water with different δ2H. This result demonstrates that water provided hydrogen for hydrocarbon gas generation. Finally, we established mathematical models based on isotope fractionation to quantitatively determine the contribution of water–hydrocarbon reactions for gas generation in both experimental and geological conditions.

Hecht, E.E., Smaers, J.B., Dunn, W.J., Kent, M., Preuss, T.M., Gutman, D.A., 2019. Significant neuroanatomical variation among domestic dog breeds. The Journal of Neuroscience 39, 7748-7758.

http://www.jneurosci.org/content/early/2019/08/30/JNEUROSCI.0303-19.2019.abstract

Abstract: Humans have bred different lineages of domestic dogs for different tasks, like hunting, herding, guarding, or companionship. These behavioral differences must be the result of underlying neural differences, but surprisingly, this topic has gone largely unexplored. The current study examined whether and how selective breeding by humans has altered the gross organization of the brain in dogs. We assessed regional volumetric variation in MRI studies of 62 male and female dogs of 33 breeds. Notably, neuroanatomical variation is plainly

visible across breeds. This variation is distributed non-randomly across the brain. A whole-brain, data-driven independent components analysis established that specific regional sub-networks covary significantly with each other. Variation in these networks is not simply the result of variation in total brain size, total body size, or skull shape. Furthermore, the anatomy of these networks correlates significantly with different behavioral specialization(s) such as sight hunting, scent hunting, guarding, and companionship. Importantly, a phylogenetic analysis revealed that most change has occurred in the terminal branches of the dog phylogenetic tree, indicating strong, recent selection in individual breeds. Together, these results establish that brain anatomy varies significantly in dogs, likely due to human-applied selection for behavior.

Significance statement:: Dog breeds are known to vary in cognition, temperament, and behavior, but the neural origins of this variation are unknown. In an MRI-based analysis, we found that brain anatomy covaries significantly with behavioral specializations like sight hunting, scent hunting, guarding, and companionship. Neuroanatomical variation is not simply driven by brain size, body size, or skull shape, and is focused in specific networks of regions. Nearly all of the identified variation occurs in the terminal branches of the dog phylogenetic tree, indicating strong, recent selection in individual breeds. These results indicate that through selective breeding, humans have significantly altered the brains of different lineages of domestic dogs in different ways.

Hehenberger, E., Gast, R.J., Keeling, P.J., 2019. A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis. Proceedings of the National Academy of Sciences 116, 17934-17942.


Significance: Kleptoplasty is the process by which a heterotrophic predator eats an algal prey cell and then steals and temporarily retains the alga’s photosynthetic plastid organelle. Kleptoplasty is relatively common in nature, but also represents a key step in the early stages of integration of stable endosymbiotic organelles. We characterized a kleptoplastidic dinoflagellate at the genomic level and compared it with relatives that have fully integrated a closely related plastid, to better understand the tipping point between temporary and fully integrated plastids. We find that genetic integration of the plastid and host and host control over the plastid function occur early, before the plastid is fully fixed in the cell, allowing us to see the order of key events in plastid organelle origins.

Abstract: Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.

Henry, D.G., Jarvis, I., Gillmore, G., Stephenson, M., 2019. Raman spectroscopy as a tool to determine the thermal maturity of organic matter: Application to sedimentary, metamorphic and structural geology. Earth-Science Reviews 198, 102936.


Raman spectrometry is a rapid, non-destructive alternative to conventional tools employed to assess the thermal alteration of organic matter (OM). Raman may be used to determine vitrinite reflectance equivalent OM maturity values for petroleum exploration, to provide temperature data for metamorphic studies, and to determine the maximum temperatures reached in fault zones. To achieve the wider utilisation of Raman, the spectrum processing method, and the positions and nomenclature of Raman bands and parameters, all need to be standardized. We assess the most widely used Raman parameters as well as the best analytical practices that have been proposed. Raman band separation and G-band full-width at half-maximum are the best parameters to estimate the maturity for rocks following diagenesis–metagenesis. For metamorphic studies, the ratios of band areas after performing deconvolution are generally used. Further work is needed on the second-order region, as well as assessing the potential of using integrated areas on the whole spectrum, to increase the calibrated temperature range of Raman parameters. Applying Raman spectroscopy on faults has potential to be able to infer both temperature and deformation processes. We propose a unified terminology for OM Raman bands and parameters that should be adopted in the future. The popular method of fitting several functions to a spectrum is generally unnecessary, as Raman parameters determined from an un-deconvoluted spectrum can track the maturity of OM. To progress the Raman application as a geothermometer a standardized approach must be developed and tested by means of an interlaboratory calibration exercise using reference materials.

Hess, S., Eme, L., Roger, A.J., Simpson, A.G.B., 2019. A natural toroidal microswimmer with a rotary eukaryotic flagellum. Nature Microbiology 4, 1620–1626.

https://doi.org/10.1038/s41564-019-0478-6

We describe Idionectes vortex gen. nov., sp. nov., a unicellular microeukaryote that swims by continuous inversion of its surface, similar to a vortex ring. This previously unreported mode of motility approximates a hypothetical concept called the ‘toroidal swimmer’, in which a doughnut-shaped object rotates around its circular axis and travels in the opposite direction to its outer surface motion. During swimming, the flagellum of Idionectes rotates relative to its cell body, which is normally a hallmark of prokaryotic rather than eukaryotic flagella.

Hodgskiss, M.S.W., Crockford, P.W., Peng, Y., Wing, B.A., Horner, T.J., 2019. A productivity collapse to end Earth’s Great Oxidation. Proceedings of the National Academy of Sciences 116, 17207-17212.


Significance: The Great Oxidation Event (GOE) ca. 2,400 to 2,050 Ma caused the first significant accumulation of free oxygen in the atmosphere and potentially a dramatic growth of oxidant reservoirs on the Earth’s surface in a suggested “oxygen overshoot.” However, the termination of this event remains poorly understood. Here, we present geochemical data suggesting a drastic decline in gross primary productivity across the end-GOE transition, delineating a shift from “feast” to “famine” conditions characteristic of the next 1 billion y.

Abstract: It has been hypothesized that the overall size of—or efficiency of carbon export from—the biosphere decreased at the end of the Great Oxidation Event (GOE) (ca. 2,400 to 2,050 Ma). However, the timing, tempo, and trigger for this decrease remain poorly constrained. Here we test this hypothesis by studying the isotope geochemistry of sulfate minerals from the Belcher Group, in subarctic Canada. Using insights from sulfur and barium isotope measurements, combined with radiometric ages from bracketing strata, we infer that the sulfate minerals studied here record ambient sulfate in the immediate aftermath of the GOE (ca. 2,018 Ma). These sulfate minerals captured negative triple-oxygen isotope anomalies as low as ∼ −0.8‰. Such negative values occurring shortly after the GOE require a rapid reduction in primary productivity of >80%, although even larger reductions are plausible. Given that these data imply a collapse in primary productivity rather than export efficiency, the trigger for this shift in the Earth system must reflect a change in the availability of nutrients, such as phosphorus. Cumulatively, these data highlight that Earth’s GOE is a tale of feast and famine: A geologically unprecedented reduction in the size of the biosphere occurred across the end-GOE transition.

Hoffman, P.F., Lamothe, K.G., 2019. Seawater-buffered diagenesis, destruction of carbon isotope excursions, and the composition of DIC in Neoproterozoic oceans. Proceedings of the National Academy of Sciences 116, 18874-18879.


Significance: Carbonate sediments of Neoproterozoic age exhibit large secular excursions of carbon isotope composition outside the range of modern seawater dissolved inorganic carbon (DIC), but their origins are controversial. We show that in a Neoproterozoic carbonate platform in Namibia, such excursions disappear on the flanks of the platform, where compositions are more compatible with modern seawater. We attribute the observed spatial variation to early fluid-buffered alteration on the flanks of the platform, where seawater invaded the sediment in response to geothermal porewater convection. Accordingly, the isotope excursions in the platform interior are decoupled from open-ocean DIC, which remained close to the modern range. Our interpretation is testable and, if confirmed, has important ramifications for the origins of ancient carbon isotope excursions.

Abstract: Carbonate sediments of nonglacial Cryogenian (659 to 649 Ma) and early Ediacaran (635 to 590 Ma) age exhibit large positive and negative δ13Ccarb excursions in a shallow-water marine platform in northern Namibia. The same excursions are recorded in fringing deep-sea fans and in carbonate platforms on other paleocontinents. However, coeval carbonates in the upper foreslope of the Namibian platform, and to a lesser extent in the outermost platform, have relatively uniform δ13Ccarb compositions compatible with dissolved inorganic carbon (DIC) in the modern ocean. We attribute the uniform values to fluid-buffered diagenesis that occurred where seawater invaded the sediment in response to geothermal porewater convection. This attribution, which is testable with paired Ca and Mg isotopes, implies that large δ13Ccarb excursions observed in Neoproterozoic platforms, while sedimentary in origin, do not reflect the composition of ancient open-ocean DIC.



Cadmium (Cd) isotopes are an emerging proxy for biological controlled metal and nutrient cycling in the modern oceans, but its potential as a geochemical proxy in ancient environments is still uncertain yet. Sequential leaching experiments of organic matter (OM)-rich shales from the early Cambrian Niutitang Formation (Fm.) were performed in order to understand the cycling of bioessential metals short after the Cambrian animal evolution. Carbonate, OM, sulphide and silicate leachates of OM-rich shales show an overall Cd isotope variation of 6 ε112Cd/110Cd (ε112Cd) units, indicating preferential incorporation of light Cd isotopes in the order sulphide > OM > carbonate > silicate. Carbonate leachates not only show negative correlations of ε112Cd with bulk-rock total organic carbon (TOC) and δ13Corg but also show co-variations with redox-sensitive elements and bioessential metal concentrations, indicating a combined redox and primary productivity evolution of the early Cambrian Nanhua Basin on the Yangtze. Together with increased Cd/Zn ratios and decreasing total organic carbon (TOC) and redox-sensitive elements (RSE) concentrations in the upper Niutitang, this argues for an increase in essential metal availability for primary producers. Coinciding with the transition from a highly unstable ecosystem shortly after the Precambrian/Cambrian boundary to a more habitable environment increased nutrient uptake, oxygen availability and enhanced dissolved organic carbon (DOC) recycling match with the diversification of early metazoan fossil findings at the studied local. Our findings demonstrate that Cd isotopes in combination with trace metals can be used to infer changes in biogeochemical metal cycling in paleoenvironments and further allow establishing Cd isotope systematics as a reliable paleoproductivity proxy in the search for Earth’s earliest phototrophic life.

Holland, A.T., Williamson, C.J., Sgouridis, F., Tedstone, A.J., McCutcheon, J., Cook, J.M., Poniecka, E., Yallop, M.L., Tranter, M., Anesio, A.M., The Black & Bloom Group, 2019. Dissolved organic nutrients dominate melting surface ice of the Dark Zone (Greenland Ice Sheet). Biogeosciences 16, 3283-3296.

https://www.biogeosciences.net/16/3283/2019/

Glaciers and ice sheets host abundant and dynamic communities of microorganisms on the ice surface (supraglacial environments). Recently, it has been shown that Streptophyte glacier algae blooming on the surface ice of the south-western coast of the Greenland Ice Sheet are a significant contributor to the 15-year marked decrease in albedo. Currently, little is known about the constraints, such as nutrient availability, on this large-scale algal bloom. In this study, we investigate the relative abundances of dissolved inorganic and dissolved organic macronutrients (N and P) in these darkening surface ice environments. Three distinct ice surfaces, with low, medium and high visible impurity loadings, supraglacial stream water and cryoconite hole water, were sampled. Our results show a clear dominance of the organic phase in all ice surface samples containing low, medium and high visible impurity loadings, with 93 % of the total dissolved nitrogen and 67 % of the total dissolved phosphorus in the organic phase. Mean concentrations in low, medium and high visible impurity surface ice environments are 0.91, 0.62 and 1.0 µM for dissolved inorganic nitrogen (DIN), 5.1, 11 and 14 µM for dissolved organic nitrogen (DON), 0.03, 0.07 and 0.05 µM for dissolved inorganic phosphorus (DIP) and 0.10, 0.15 and 0.12 µM for dissolved organic phosphorus (DOP), respectively. DON concentrations in all three surface ice samples are significantly higher than DON concentrations in supraglacial streams and cryoconite hole water (0 and 0.7 µM, respectively). DOP concentrations are higher in all three surface ice samples compared to supraglacial streams and cryoconite hole water (0.07 µM for both). Dissolved organic carbon (DOC) concentrations increase with the amount of visible impurities present (low: 83 µM, medium: 173 µM and high: 242 µM) and are elevated compared to supraglacial streams and cryoconite hole water (30 and 50 µM, respectively). We speculate that the architecture of the weathering crust, which impacts on water flow paths and storage in the melting surface ice and/or the production of extracellular polymeric substances (EPS), containing both N and P in conjunction with C, is responsible for the temporary retention of DON and DOP in the melting surface ice. The unusual presence of measurable DIP and DIN, principally as NH4

+, in the melting surface ice environments suggests that factors other than macronutrient limitation are controlling the extent and magnitude of the glacier algae.

Houghton, J.L., Foustoukos, D.I., Fike, D.A., 2019. The effect of O2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila. Geobiology 17, 564-576.


Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur‐oxidizing micro‐organisms in particular. In this study, the thiosulfate‐oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04–1.9 mM) and high pressure (5–10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed‐system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O2 was 0.25 hr−1. This is comparable to the μmax (0.28 hr−1) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half‐saturation constant for O2 () estimated from this study was 0.2 mM (at a cell density of 105 cells/ml) and was robust at all pressures tested (0.4–10 MPa), consistent with piezotolerant behavior of this strain. The cell‐specific was determined to be 1.5 pmol O2/cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell‐specific and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).

Hu, S., Li, S., Xia, L., Lv, Q., Cao, J., 2020. On the internal oil migration in shale systems and implications for shale oil accumulation: A combined petrological and geochemical investigation in the Eocene Nanxiang Basin, China. Journal of Petroleum Science and Engineering 184, 106493.


Internal oil migration within shale systems is of significance to shale oil accumulation as indicating the retention, expulsion, and accumulation of shale oils. However, conventional geochemical proxies to study this internal oil migration are commonly overlapped, and thus the migration is still well understood. Here we conduct a case study using the methodology of combined petrology and geochemistry, rather than the geochemistry alone in previous studies which are mostly bulk and thus cannot reveal the complex migration in different scales including macro (millimeter), micro (micron), and nano. The study area is in the lacustrine Eocene Biyang sag, Nanxiang Basin of eastern China. Results show that three types can be identified according to the petrological characteristics of the internal oil migration. Their geochemistry was further clarified. In detail, according to the correlation between residual hydrocarbons (S1) and total organic carbon content (TOC): Type A, inward migrated oils from external sources within the shale system; Type B, weak expulsed oils to external space; and Type C, strong expulsed oils to external space. The amount of hydrocarbon expelled per unit rock mass (Qexpulsion) for migration types A, B and C are < 0, 0–1.5 mg/g rock, and >1.5 mg/g rock, respectively. They have good bulk and molecular geochemical responses. Typically, Type A samples have the highest saturates/aromatics and n-C19/ΣMP ratios, with Type C having the lowest ratios and Type B having intermediate values. Stable carbon-isotope compositions indicate the level of internal oil migration too. Our data suggest that combined petrological and geochemical methods can effectively characterize internal oil migration in shale oil systems. A good combination of source and reservoir in shale systems, i.e., interbedded or juxtaposed Type A and Type C sequences is favorable for shale oil accumulation. This is universal and obviously provides useful data for regional exploration.

Hu, X., Deng, H., Lu, C., Tian, Y., Jin, Z., 2019. Characterization of CO2/CH4 competitive adsorption in various clay minerals in relation to shale gas recovery from molecular simulation. Energy & Fuels 33, 8202-8214.


CO2 sequestration and enhanced gas recovery (CS-EGR) is a viable option with enormous potentials to produce shale gas. However, the microscopic competitive sorption behaviors of CH4 and CO2 in various clay minerals that are an important constituent of shale at actual formation conditions are still less clear. In this work, we study CO2/CH4 binary mixture competitive sorption in various clay minerals (montmorillonite, illite, and kaolinite) by using grand canonical Monte Carlo simulations. The effects of the clay mineral types and possible stratigraphic conditions, including temperature, pressure, CO2/CH4 molar fraction, and selectivity, are discussed in detail. The results demonstrate that the CO2 sorption capacity in the clay mineral follows an order of montmorillonite > illite > kaolinite. CO2 molecules are prone to be adsorbed on the surfaces of montmorillonite and illite nanopores with cation exchange than on the surface of the kaolinite nanopore without cation exchange. Moreover, cation exchange could distinctly increase the CO2/CH4 adsorption ratio so that the first layer of CH4 molecules can be displaced by CO2 molecules. The replacement ratio of CH4 is related to the type of adsorbent, which is independent of the original formation pressure. In addition, a case study is designed to quantify the enhanced gas recovery (EGR) and CO2–CH4 displacement efficiency. With a higher reservoir initial pressure when injecting CO2, the EGR of adsorbed CH4 gas could increase up to 28.97%. Our findings provide insights into gas mixture sorption in shale reservoirs and provide important guidelines for CS-EGR projects.


https://doi.org/10.1038/s41598-019-49495-1

Oil samples from the Bongor Basin, SW Chad have been geochemically characterized to investigate the biodegradation influence on alkylphenanthrenes. Concentrations of C0–3-alkylphenanthrenes (C0–3Ps) increase markedly after level 6 biodegradation due to the removal of other vulnerable components, decrease sharply after level 7 biodegradation and approach to absence at level 8. Phenanthrene appears to have higher ability to resist biodegradation than C1–3Ps at certain biodegradation levels (≤level 7) due to demethylation, which has been inferred as a possible reaction process during biodegradation of the aromatic hydrocarbons. The enrichment of

non-alkylated phenanthrene in biodegraded oils makes biodegradation assessment complicated on the basis of alkylphenanthrene distributions. Individual isomers in alkylphenanthrenes exhibit variable ability to resist biodegradation influence. While certain isomers do show higher ability to resist biodegradation than others, no uniform biodegradation sequence can be established. Meanwhile, the biodegradation susceptibility between hopanes and alkylphenanthrenes varies greatly in different samples. The biodegradation systematics of alkylphenanthrenes proves to be highly complex, which may be indicative of the multiple charges and mixing during biodegradation.



The low permeability of kerogen governs the storage and production of shale gas. The flexible kerogen constantly experiences mechanical deformation induced by reservoir environment and complex interplay with geofluids. However, the kerogen deformation associated with CH4/CO2 competitive sorption remains poorly understood. In this work, the effect of preloaded moisture on the deformation of kerogen with different organic types was investigated with molecular dynamics simulation. The kerogen deformation upon CH4/CO2 competitive sorption was quantified with the combination of grand canonical Monte Carlo simulations and poromechanics theory. The effects of various factors and their corresponding contributions were discussed in detail. The effects of kerogen deformation on CH4/CO2 diffusion were studied. Some implications for CO2 sequestration and enhanced gas recovery (CS-EGR) were proposed. Our results verify the theoretical feasibility of CS-EGR in shale gas reservoir. CO2 is observed to have a higher affinity with kerogen and a lower diffusion coefficient compared with CH4, facilitating it to replace CH4 and retain in the kerogen matrix. The rising CO2 composition can induce larger kerogen swelling, thus opening fluid flow pathways and increasing shale gas production. There are optimum moisture content and reservoir pressure corresponding to the maximum effective pore size in kerogen. It could be feasible to enhance the efficiency of CS-EGR by manipulating the reservoir moisture and CO2 injection timing. Thermal stimulation in deep shale reservoir may not be efficient for CS-EGR. CH4/CO2 competitive sorption can induce significant swelling of kerogen. The flexible nature of kerogen should be considered to improve the evaluation on both gas-in-place and CO2 storage capacity.

Huguet, C., Kim, J.H., González-Arango, C., Ramírez-Valencia, V., Kang, S., Gal, J.K., Shin, K.H., 2019. Sources of organic matter in two contrasting tropical coastal environments: The Caribbean Sea and the eastern Pacific. Journal of South American Earth Sciences 96, 102349.


In this study, we evaluate sources of organic matter (OM) in two contrasting tropical coastal environments in Colombia, using a combination of glycerol dialkyl glycerol tetraethers (GDGTs) and n-alkane lipid biomarkers. A clear difference between the less productive Caribbean Sea and the more productive eastern Pacific is observed, with higher terrestrial contributions into the eastern Pacific strongly associated with riverine inputs. Although higher land plant-derived n-alkanes can be transported as eolian dust, our results suggest mainly riverine sources for our samples. When looking at the branched GDGT compositions, in situ production could be identified in most Caribbean stations and some of the more coastal sites in the Pacific with #ringstetra index values of above 0.7. The remaining stations in the eastern Pacific display soil-eroded GDGTs inputs associated with river discharges and deposited in the proximity of the coast. Marine production as measured by short chain n-alkanes and crenarchaeol are also higher in the eastern Pacific. It appears that the terrestrial inputs would bring nutrients as well as OM fueling both auto- and heterotrophs making the eastern Pacific overall more productive. We also observe OM of petrogenic origin, albeit in a low amount, especially in coastal Caribbean sites located near main harbors. This study helps improve the understanding of the complex mixture of OM inputs, origins and transport mechanisms into Colombian coastal areas. The present work emphasizes the need to integrate climate, geological setting and hydrology to fully understand the carbon cycle at a regional scale.



Calcified microbial microfossils—often interpreted as cyanobacteria—were important components of Precambrian and Paleozoic limestones, but their paucity in modern marine environments complicates our ability to make conclusive interpretations about their taxonomic affinity and geologic significance. Freshwater spring‐associated limestones (e.g., travertine and tufa) serve as terrestrial analogs to investigate mineralization in and around aquatic biofilms on observable timescales. We document the diagenesis of calcite fabrics associated with the freshwater algae Oocardium stratum, an epiphytic colonial green algae (desmid) known for producing stalks of extracellular polymeric substances (EPS) and passively producing a bifurcating tubular calcite monocrystal. Bifurcating EPS stalks produced by Oocardium colonies can become calcified and preserved in ancient carbonate deposits. Calcified micritic EPS stalks have a filamentous morphology, show evidence of branching, and maintain uniformity in diameter thickness throughout the mm‐scale colony, much like the enigmatic calcimicrobe Epiphyton. We provide a mechanism by which calcification associated with a colonial semispherical micro‐organism produces microfossils that deceptively resemble filamentous forms. These findings have implications for the use of morphological traits when assigning taxonomic affinities to extinct microfossil groups and highlight the utility of calcifying freshwater modern environments to investigate microbial taphonomy.

Ikenoue, T., Kimoto, K., Okazaki, Y., Sato, M., Honda, M.C., Takahashi, K., Harada, N., Fujiki, T., 2019. Phaeodaria: An important carrier of particulate organic carbon in the mesopelagic twilight zone of the North Pacific Ocean. Global Biogeochemical Cycles 33, 1146-1160.

https://doi.org/10.1029/2019GB006258

Abstract Phaeodaria, which comprise one group of large, single-celled eukaryotic zooplankton, have been largely ignored by past marine biological studies because Phaeodaria and their delicate skeletons are liable to collapse. As a result, collection and quantification of specimens are difficult, and seasonal changes of phaeodarian abundance have not been thoroughly studied. The transport of biogenic elements by sinking phaeodarians has been estimated for only a few representative species. Sinking particles >1 mm in size and swimmers have traditionally been excluded when estimating sinking particle fluxes. The focus of this study is the large number of phaeodarians among the >1-mm sinking particles collected in the western North Pacific from June 2014 to July 2015. Careful sorting by microscopic examination and chemical analyses revealed that phaeodarians accounted for up to about 10% of the organic carbon in all sinking particles and accounted for a mean of 33% of the organic carbon in the >1-mm sinking particles. The high-standing stocks of phaeodarians at depths of 150?1,000 m in the mesopelagic twilight zone suggested that particles sinking from the euphotic zone as aggregates and fecal pellets can be efficiently exported to the deep sea by the ballasting effect of large phaeodarian particles rich in organic carbon.

Ilardo, M., Bose, R., Meringer, M., Rasulev, B., Grefenstette, N., Stephenson, J., Freeland, S., Gillams, R.J., Butch, C.J., Cleaves, H.J., 2019. Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets. Scientific Reports 9, 12468.

https://doi.org/10.1038/s41598-019-47574-x

Life uses a common set of 20 coded amino acids (CAAs) to construct proteins. This set was likely canonicalized during early evolution; before this, smaller amino acid sets were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically available. Many possible subsets of the modern CAAs or other presently uncoded amino acids could have comprised the earlier sets. We explore the hypothesis that the CAAs were selectively fixed due to their unique adaptive chemical properties, which facilitate folding, catalysis, and solubility of proteins, and gave adaptive value to organisms able to encode them. Specifically, we studied in silico hypothetical CAA sets of 3–19 amino acids comprised of 1913 structurally diverse α-amino acids, exploring the adaptive value of their combined physicochemical properties

relative to those of the modern CAA set. We find that even hypothetical sets containing modern CAA members are especially adaptive; it is difficult to find sets even among a large choice of alternatives that cover the chemical property space more amply. These results suggest that each time a CAA was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs.

Ilgrande, C., Mastroleo, F., Christiaens, M.E.R., Lindeboom, R.E.F., Prat, D., Van Hoey, O., Ambrozova, I., Coninx, I., Heylen, W., Pommerening-Roser, A., Spieck, E., Boon, N., Vlaeminck, S.E., Leys, N., Clauwaert, P., 2019. Reactivation of microbial strains and synthetic communities after a spaceflight to the International Space Station: Corroborating the feasibility of essential conversions in the MELiSSA loop. Astrobiology 19, 1167-1176.

https://doi.org/10.1089/ast.2018.1973

To sustain human deep space exploration or extra-terrestrial settlements where no resupply from the Earth or other planets is possible, technologies for in situ food production, water, air, and waste recovery need to be developed. The Micro-Ecological Life Support System Alternative (MELiSSA) is such a Regenerative Life Support System (RLSS) and it builds on several bacterial bioprocesses. However, alterations in gravity, temperature, and radiation associated with the space environment can affect survival and functionality of the microorganisms. In this study, representative strains of different carbon and nitrogen metabolisms with application in the MELiSSA were selected for launch and Low Earth Orbit (LEO) exposure. An edible photoautotrophic strain (Arthrospira sp. PCC 8005), a photoheterotrophic strain (Rhodospirillum rubrum S1H), a ureolytic heterotrophic strain (Cupriavidus pinatubonensis 1245), and combinations of C. pinatubonensis 1245 and autotrophic ammonia and nitrite oxidizing strains (Nitrosomonas europaea ATCC19718, Nitrosomonas ureae Nm10, and Nitrobacter winogradskyi Nb255) were sent to the International Space Station (ISS) for 7 days. There, the samples were exposed to 2.8 mGy, a dose 140 times higher than on the Earth, and a temperature of 22°C ± 1°C. On return to the Earth, the cultures were reactivated and their growth and activity were compared with terrestrial controls stored under refrigerated (5°C ± 2°C) or room temperature (22°C ± 1°C and 21°C ± 0°C) conditions. Overall, no difference was observed between terrestrial and ISS samples. Most cultures presented lower cell viability after the test, regardless of the type of exposure, indicating a harsher effect of the storage and sample preparation than the spaceflight itself. Postmission analysis revealed the successful survival and proliferation of all cultures except for Arthrospira, which suffered from the premission depressurization test. These observations validate the possibility of launching, storing, and reactivating bacteria with essential functionalities for microbial bioprocesses in RLSS.



In situ burning is often used as a response method for oil slicks in the marine environment. This process however forms viscous tar-like residues that either float on the surface or sink through the water column, introducing organic species into the water phase. The interaction of this burn residue with the water phase also introduces dissolved organics into the water column. In this study, we conducted laboratory-scale experiments to characterize and compare the organic species entering the water phase from the petrogenic (fresh oil) and pyrogenic (burnt oil) input during oil spills. The oil and water-soluble organics were characterized using ultra-high-resolution mass spectrometry (FTICR-MS). The results show that burning strongly increases concentrations of oil-related constituents entering the water phase, due to transformation reactions producing oxidized organic species with higher water solubility. The pyrogenic water-soluble organics also showed a higher percentage of unsaturated compounds relative to the petrogenic fraction. The effect of these highly unsaturated and oxygenated organic species on oil spill fate and their ecosystem impacts is currently unknown.

Jambrina-Enríquez, M., Herrera-Herrera, A.V., Rodríguez de Vera, C., Leierer, L., Connolly, R., Mallol, C., 2019. n-Alkyl nitriles and compound-specific carbon isotope analysis of lipid combustion residues from Neanderthal

and experimental hearths: Identifying sources of organic compounds and combustion temperatures. Quaternary Science Reviews 222, 105899.


Molecular and isotopic approaches offer the chance to identify combustion residues and substrate components of archaeological combustion features to infer past fire-related activities. Analysis of fatty acid methyl esters by gas chromatography-combustion-isotope ratio mass spectrometry have been successfully used to distinguish among different animal fat groups. However, plant oils from different tissues have not been widely investigated even though organic residues from leaf, root, and wood tissues are preserved in sediments from archaeological combustion structures. Our analyses of plant residues from controlled laboratory heating sequences and experimental hearths involving wood and animal residues, provide references to discern anatomical parts of fresh and charred plants and to differentiate contributions of terrestrial plants and animal sources in open air hearths. This information is compared with charred organic residues from combustion structures from three Middle Palaeolithic sites: El Salt (Spain), Abric del Pastor (Spain) and Crvena Stijena (Montenegro). The occurrence of n-alkyl nitriles in our samples corroborates their potential as combustion temperature biomarkers and the δ13C16:0 and δ13C18:0 values allow us differentiate between charred and fresh plant anatomical parts and between fresh plant oils and animal fats.



Measurements of carbon isotope variations in climate archives and isotope-enabled climate modelling foster the understanding of the carbon cycle. Perturbations in atmospheric CO2, and in its isotopic ratios (δ13C, ∆14C) are removed on different time scales and by partly different processes. We investigate these differences on timescales of up to 100,000 years in idealized pulse release experiments with the Bern3D-LPX Earth system model of intermediate complexity and by analytical solutions from a box model. Isotopic perturbations are initially removed much faster from the atmosphere than perturbations in CO2 as explained by aquatic carbonate chemistry. On longer time scales, the CO2 perturbation is removed by carbonate compensation and silicate rock weathering. In contrast, the δ13C perturbation is removed by the relentless flux of organic and calcium carbonate particles buried in sediments. The associated removal rate is significantly modified by spatial δ13C gradients within the ocean influencing the isotopic perturbation of the burial flux. Space-time variations in ocean δ13C perturbations are captured by three Principal Components and Empirical Orthogonal Functions. Analytical impulse response functions for atmospheric CO2 and δ13CO2 are provided. Our results show that changes in terrestrial carbon storage are unlikely the sole cause for the abrupt, centennial CO2 and δ13C variations recorded in ice during Heinrich Stadials HS1 and HS4 of the last glacial period. Ocean processes likely played a significant role. The δ113 offset between the penultimate and last glacial maximum reconstructed for the ocean and atmosphere is most likely caused by imbalances between weathering, volcanism and burial fluxes.

Ji, L., Lin, M., Jiang, W., Cao, G., Zhou, J., Luo, C., 2019. Investigation into the apparent permeability and gas-bearing property in typical organic pores in shale rocks. Marine and Petroleum Geology 110, 871-885.


Although substantial advances have been made in investigating the storage and transport properties of shale gas in past decades, understanding of the flow characteristics and gas-bearing property in organic pores remains limited. In this paper, organic pores in the organic matter (OM) of the marine Longmaxi Formation are classified into six types based on the morphology and sizes of nanoscale pores. The structures of the six types of typical organic pores under high temperature and pressure are investigated based on the digital core compressibility method introduced in this paper. The results show that the pore-size distribution and connectivity of organic pores under high temperature and pressure are considerably different from those under conventional conditions. The apparent permeability of OM with different proportions of macropores, mesopores, and micropores are analyzed. The results demonstrate that the permeability of OM with Type 1

organic pores has the largest changes after compaction, whereas OM with Type 5 organic pores has a relatively smaller change. The regularities of the absolute adsorption amount and the free gas amount of OM with typical organic pores are also investigated. The absolute adsorption amount of OM decreases with the proportion of macropores, whereas the amount of free gas of OM increases. Finally, a chart of the absolute adsorption amount and the free gas amount of OM at different depths is given, which is helpful for estimating the gas-bearing capacity of OM and preliminary understanding the quality of a shale reservoir.

Jiang, H., Daigle, H., 2019. Effects of fluids removal and thermal maturation on permeability and pore structure of organic-rich shale: Results from pyrolysis experiments. Journal of Petroleum Science and Engineering 183, 106453.


Laboratory measurements to determine petrophysical properties such as permeability are critical for shale reservoir characterization. Here we investigate effects of fluids removal and thermal maturation on permeability and pore structure of organic-rich shale. Mature and organic-rich shale samples were pyrolyzed at four temperature levels (110 °C, 250 °C, 450 °C, ≥ 600 °C), and performed nitrogen gas sorption and GRI (Gas Research Institute) permeability measurements after each heating level. Our results show that the measured porosity, permeability and pore structure are sensitive to the pyrolysis temperature. Surface area, N2 pore volume, GRI porosity and permeability increased as temperature increased, due to a combination of progressive loss of volatiles with increasing temperature and artificially induced thermal maturation at high temperatures. The correlation between gas adsorption and GRI results implies the multiscale pore network features of the samples, wherein a certain fraction of small pores could be partially or completely disconnected from the overall structure. Our work provides insights on useful information about the effects of fluids removal and thermal maturation for sample preparation procedures on laboratory measurements.

Jiang, L., George, S.C., 2019. Biomarker signatures of Upper Cretaceous Latrobe Group petroleum source rocks, Gippsland Basin, Australia: Distribution and geological significance of aromatic hydrocarbons. Organic Geochemistry 138, 103905.


Aromatic hydrocarbons extracted from Upper Cretaceous (Maastrichtian and Campanian) Latrobe Group coaly shales and shales from the Gippsland Basin were investigated by gas chromatography–mass spectrometry. A variety of 2-ring to 6-ring aromatic hydrocarbons were identified, including both higher-plant-derived and combustion-derived polycyclic aromatic hydrocarbons (PAHs). These aromatic compounds indicate that the Upper Cretaceous coaly shales and shales were deposited in a fluvial/deltaic environment with significant higher plant input and are at a relatively low thermal maturity stage. Higher plant parameters and angiosperm/gymnosperm indices based on aromatic components suggest that higher land plants, including both angiosperms and gymnosperms, were an important part of the palaeovegetation in the Upper Cretaceous. The aromatic angiosperm/gymnosperm index that includes chrysene- and picene-type PAHs is not as reliable for evaluation of relative angiosperm and gymnosperm contributions as the aliphatic indices due to input of combustion-derived PAHs and the complexity of burning conditions altering the relative contributions. However, combustion-derived PAHs and aromatic angiosperm/gymnosperm indices supplement the information from aliphatic hydrocarbons and provide further evidence to support the hypothesis that palaeoclimate cooled from the Campanian to the Maastrichtian.

Kaiser, K., Scriven, L.M., Schulz, F., Gawel, P., Gross, L., Anderson, H.L., 2019. An sp-hybridized molecular carbon allotrope, cyclo[18]carbon. Science 365, 1299-1301.

http://science.sciencemag.org/content/early/2019/08/14/science.aay1914.abstract

Carbon allotropes built from rings of two-coordinate atoms, known as cyclo[n]carbons, have fascinated chemists for many years, but until now they could not be isolated or structurally characterized, due to their high

reactivity. We generated cyclo[18]carbon (C18) using atom manipulation on bilayer NaCl on Cu(111) at 5 Kelvin by eliminating carbon monoxide from a cyclocarbon oxide molecule C24O6. Characterization of cyclo[18]carbon by high-resolution atomic force microscopy revealed a polyynic structure with defined positions of alternating triple and single bonds. The high reactivity of cyclocarbon and cyclocarbon oxides allows covalent coupling between molecules to be induced by atom manipulation, opening an avenue for the synthesis of other carbon allotropes and carbon-rich materials from the coalescence of cyclocarbon molecules.

Kantz, E.D., Tiwari, S., Watrous, J.D., Cheng, S., Jain, M., 2019. Deep neural networks for classification of LC-MS spectral peaks. Analytical Chemistry 91, 12407-12413.


Liquid chromatography–mass spectrometry (LC-MS)-based metabolomics has emerged as a valuable tool for biological discovery, capable of assaying thousands of diverse chemical entities in a single biospecimen. Processing of nontargeted LC-MS spectral data requires identification and isolation of true spectral features from the random, false noise peaks that comprise a significant portion of total signals, using inexact peak selection algorithms and time-consuming visual inspection of data. To increase the fidelity and speed of data processing, herein we establish, optimize, and evaluate a machine learning pipeline employing deep neural networks as well as a simpler multiple logistic regression model for classification of spectral features from nontargeted LC-MS metabolomics data. Machine learning-based approaches were found to remove up to 90% of false peaks from complex nontargeted LC-MS data sets without reducing true positive signals and exhibit excellent reproducibility across multiple data sets. Application of machine learning for nontargeted LC-MS-based peak selection provides for robust and scalable peak classification and data filtering, enabling handling and processing of large scale, complex metabolomics data sets.

Kato, S., Itoh, T., Yuki, M., Nagamori, M., Ohnishi, M., Uematsu, K., Suzuki, K., Takashina, T., Ohkuma, M., 2019. Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring. The ISME Journal 13, 2465-2474.

https://doi.org/10.1038/s41396-019-0447-3

A deep-branching clade of Thaumarchaeota, conventionally called Terrestrial hot spring creanarchaeotic group (THSCG), is a missing link between thaumarchaeotic ammonia oxidizers and the deeper-branching non-ammonia oxidizers, such as Crenarchaeota and Candidatus Korarchaeota. Here, we report isolation of the first cultivated representative from the THSCG, named as NAS-02. Physiological characterization demonstrated that the isolate was a thermoacidophilic, sulfur- and iron-reducing organoheterotroph, which was supported by gene contents encoded in its complete genome. There was no evidence for ammonia oxidation by the isolate. Members in THSCG are likely thermophiles, and may play roles in degrading cell debris as a scavenger and in biogeochemical cycling of sulfur and iron in the hot environments, as suggested by the physiological characteristics of the isolate and the geographical distribution of the 16S rRNA gene sequences of THSCG in terrestrial hot springs and marine hydrothermal fields. Phylogenetic analysis suggests that the THSCG lineage represented by NAS-02 has gained the ability of sulfur reduction via horizontal gene transfer. Based on the phylogeny and physiology, we propose the name Conexivisphaera calidus gen. nov., sp. nov. to accommodate the isolate.

Khalid, P., Qureshi, J., Din, Z.U., Ullah, S., Sami, J., 2019. Effect of kerogen and TOC on seismic characterization of Lower Cretaceous shale gas plays in Lower Indus Basin, Pakistan. Journal of the Geological Society of India 94, 319-327.

https://doi.org/10.1007/s12594-019-1312-8

Unconventional energy resources such as shale gas are becoming an increasingly important exploration and production targets. Organic-rich shales are widely distributed in the sedimentary basins of Pakistan. Among these shales, organic-rich Sembar shale of the lower Cretaceous age is a strong potential shale gas play in the

lower Indus basin of Pakistan. However, seismic and petrophysical characterization of this organic-rich shale is not well understood because of the complex dependency of the seismic and petrophysical properties of these rocks on mineralogical, heterogeneities, organic matter, clay content and thermal maturity. Therefore, to understand the seismic and elastic character of Sembar shales, rock physics modeling and seismic attribute analysis have been done. The results reveal that in-situ mineral composition, total organic content (TOC) and thermal maturity can influence significantly in inverse order to the seismic and elastic parameters of organic-rich shale. This work will facilitate the workers to interpret shale gas play and develop the exploration and production strategies for gas exploration and production.

Khatun, S., Iwata, T., Kojima, H., Fukui, M., Aoki, T., Mochizuki, S., Naito, A., Kobayashi, A., Uzawa, R., 2019. Aerobic methane production by planktonic microbes in lakes. Science of The Total Environment 696, 133916.


Methanogenesis in freshwater lakes has classically been considered to arise from anaerobic methanogens in oxygen-depleted sediments. However, the accumulation of supersaturated methane in fully oxygenated water columns is commonly observed in many lakes, and factors responsible for the formation of the subsurface methane maximum (SMM) remain largely unknown. The present study conducted in 14 Japanese freshwater lakes showed that the SMM formation during the summer stratification period is a common feature in large and deep oligotrophic lakes. The seasonal survey of a deep oligotrophic lake revealed that SMM formation may be uncoupled with the dissolution of atmospheric methane, as well as with the transport of methane from tributary rivers, littoral sediments, and hypolimnetic anoxic sources, suggesting the contribution of in situ methane production. In fact, batch-culture experiments confirmed that bacterioplankton present in lake subsurface waters produce methane aerobically through the decomposition of methylphosphonic acid. Moreover, the development of SMM was closely associated with the seasonal dynamics of planktonic cyanobacteria such as Synechococcus, which may carry the enzyme to catabolize organophosphonate compounds. Therefore, we suggest that the predominance of Synechococcus during the thermal stratification period plays a significant role in SMM formation, and likely the methane flux from lakes to the atmosphere.

Khoo, C.G., Dasan, Y.K., Lam, M.K., Lee, K.T., 2019. Algae biorefinery: Review on a broad spectrum of downstream processes and products. Bioresource Technology 292, 121964.


Algae biomass comprises variety of biochemicals components such as carbohydrates, lipids and protein, which make them a feasible feedstock for biofuel production. However, high production cost mainly due to algae cultivation remains the main challenge in commercializing algae biofuels. Hence, extraction of other high value-added bioproducts from algae biomass is necessary to enhance the economic feasibility of algae biofuel production. This paper is aims to deliberate the recent developments of conventional technologies for algae biofuels production, such as biochemical and chemical conversion pathways, and extraction of a variety of bioproducts from algae biomass for various potential applications. Besides, life cycle evaluation studies on microalgae biorefinery are presented, focusing on case studies for various cultivation techniques, culture medium, harvesting, and dewatering techniques along with biofuel and bioenergy production pathways. Overall, the algae biorefinery provides new opportunities for valorisation of algae biomass for multiple products synthesis.

Killops, S.D., Nytoft, H.P., di Primio, R., 2019. Biodegradative production and destruction of norhopanes – An example from residual oil in a Paleogene paleomigration conduit on the Utsira High, Norwegian North Sea. Organic Geochemistry 138, 103906.


Biodegradation of the more resistant hopanoids was examined using residual stains in a Paleogene paleomigration conduit on the Utsira High, Norwegian North Sea, together with related less degraded oils.

Under currently anoxic conditions, the most severely biodegraded samples contain 25-nor, 28-nor and 25,28-dinorhopanes, in addition to regular hopanes, neohopanes, diahopanes and didiahopanes [9,15-dimethyl-25,27-dinorhopanes]. The C27 member of the 25,28-dinorhopanes comprises closely eluting 17α,21β and 17β,21α isomers. A pair of C31 compounds eluting just after the 17α-homohopanes were tentatively identified as the 22S/R isomers of homo-18α-neohopane. The 28,30-dinorhopane peak seems to comprise 17α,21β and 17β,21α isomers, with relatively more of the less thermodynamically stable 17α,21β contributing under the most severe biodegradation.

The approximate order of increasing susceptibility to biodegradation was: gammacerane ≈ triaromatic 23,24-dimethylcholesteroids ≈ triaromatic dinosteroids < C21–C22 C-ring-monoaromatic steroids ≈ C21–C22 steranes < C21–C22 diasteranes < C31 methylhopanes < 22,29,30-trinorneohopane (27Ts) < C30 TPPs ≈ diahopane ≈ didiahopane ≈ 22,29,30-trinorhopane (27Tm) < 30-norneohopane (29Ts) ≈ C28+ 28-norhopanes/moretanes < C29+ hopanes ≈ C27+ diasteranes < C27+ steranes. This information can inform the selection of correlation parameters for heavily biodegraded oils, although the sequence should not be considered universally applicable. Regular hopanes declined steadily with increasing biodegradation. The 25-norhopane homologues may be initially produced, but are then also degraded, although the C26 component appears stable. There is a relative increase in 25,28-dinorhopane abundance with increasing biodegradation, which is likely to result from demethylation of 25- and 28-norhopanes; if so, there must also be some shortening of the E-ring side-chain. Concentration estimates suggest that there is an overall loss of the hopanoid skeleton with increasing severity of biodegradation.

Kingsley, I., Oliver, C., Slavich, E., 2019. Hidden in the figures: What students are telling us about the effectiveness of astrobiology outreach. Astrobiology 19, 1103-1116.

https://doi.org/10.1089/ast.2019.2048

Astrobiology is an ideal context to engage students with the processes of science. However, there is a problem in measuring the effectiveness of engaging students with astrobiology where the learning outcome is aimed at improving student views of science. Most studies suggest little to no change in students' views of science, especially in short experiences of hours or days. These studies mostly use quantitative methods, such as numerical scores derived from survey rating scales and responses. We propose that hidden in those figures, the words of students in written survey responses are telling us about the effectiveness of astrobiology outreach at improving understanding of science. We sampled 483 students from multiple high schools involved in an established astrobiology outreach program in Australia, using pre- and postintervention data collected from an open- and closed-form survey to identify the impacts of the program on students' views of science. We applied both conventional quantitative score analysis methods and computer-based qualitative analysis methods?NVivo and Linguistic Inquiry and Word Count (LIWC) programs. While there was little difference in postsurvey scores, there is evidence in the qualitative data that the astrobiology program creates cognitive conflict in students, a trigger to the learning process that can open students to the first steps in understanding the creative, subjective, and tentative nature of science.

Kirk, A.T., Bohnhorst, A., Raddatz, C.-R., Allers, M., Zimmermann, S., 2019. Ultra-high-resolution ion mobility spectrometry—current instrumentation, limitations, and future developments. Analytical and Bioanalytical Chemistry 411, 6229-6246.

https://doi.org/10.1007/s00216-019-01807-0

With recent advances in ionization sources and instrumentation, ion mobility spectrometers (IMS) have transformed from a detector for chemical warfare agents and explosives to a widely used tool in analytical and bioanalytical applications. This increasing measurement task complexity requires higher and higher analytical performance and especially ultra-high resolution. In this review, we will discuss the currently used ion mobility spectrometers able to reach such ultra-high resolution, defined here as a resolving power greater than 200. These instruments are drift tube IMS, traveling wave IMS, trapped IMS, and field asymmetric or differential IMS. The basic operating principles and the resulting effects of experimental parameters on resolving power are

explained and compared between the different instruments. This allows understanding the current limitations of resolving power and how ion mobility spectrometers may progress in the future.

Kjeldsen, K.U., Schreiber, L., Thorup, C.A., Boesen, T., Bjerg, J.T., Yang, T., Dueholm, M.S., Larsen, S., Risgaard-Petersen, N., Nierychlo, M., Schmid, M., Bøggild, A., van de Vossenberg, J., Geelhoed, J.S., Meysman, F.J.R., Wagner, M., Nielsen, P.H., Nielsen, L.P., Schramm, A., 2019. On the evolution and physiology of cable bacteria. Proceedings of the National Academy of Sciences 116, 19116-19125.


Significance: Cable bacteria are globally occurring multicellular filamentous bacteria that are electrically conductive: they transfer electrons from sulfide oxidation at one end over centimeter distances to oxygen reduction at the other end. Unlike any other organism known, cable bacteria thus split their central energy-conserving redox reaction into 2 half-reactions that occur in different cells as far as several centimeters apart. Before this study, the molecular foundation, evolutionary origin, and genomic basis of this unique metabolism were unknown. Here we reconstructed 5 genomes from single filaments and 1 from a cable bacterium enrichment culture to shed light on the evolution and physiology of cable bacteria; and, together with proteomic and experimental data, we propose a metabolic model of how cable bacteria work.

Abstract: Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood–Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.



Significance: Our findings highlight the ubiquitous occurrence of methane (CH4)-rich fluid inclusions in olivine-bearing rocks that, collectively, may constitute one of the largest reservoirs of abiotic CH4 on Earth. Because serpentinization in olivine-hosted fluid inclusions takes place in isolation from the surrounding rock, hydrogen (H2) and CH4 can form in any rock type containing olivine that hosts aqueous fluid inclusions, including those that do not undergo serpentinization on a macroscopic scale. Serpentinization and associated CH4 formation within olivine-hosted fluid inclusions has likely supplied microbial ecosystems with abiotic CH4 throughout most of Earth’s history and may be a source of H2 and CH4 on other planetary bodies in our solar system, even those where liquid water is no longer present.

Abstract: The conditions of methane (CH4) formation in olivine-hosted secondary fluid inclusions and their prevalence in peridotite and gabbroic rocks from a wide range of geological settings were assessed using confocal Raman spectroscopy, optical and scanning electron microscopy, electron microprobe analysis, and thermodynamic modeling. Detailed examination of 160 samples from ultraslow- to fast-spreading midocean

ridges, subduction zones, and ophiolites revealed that hydrogen (H2) and CH4 formation linked to serpentinization within olivine-hosted secondary fluid inclusions is a widespread process. Fluid inclusion contents are dominated by serpentine, brucite, and magnetite, as well as CH4(g) and H2(g) in varying proportions, consistent with serpentinization under strongly reducing, closed-system conditions. Thermodynamic constraints indicate that aqueous fluids entering the upper mantle or lower oceanic crust are trapped in olivine as secondary fluid inclusions at temperatures higher than ∼400 °C. When temperatures decrease below ∼340 °C, serpentinization of olivine lining the walls of the fluid inclusions leads to a near-quantitative consumption of trapped liquid H2O. The generation of molecular H2 through precipitation of Fe(III)-rich daughter minerals results in conditions that are conducive to the reduction of inorganic carbon and the formation of CH4. Once formed, CH4(g) and H2(g) can be stored over geological timescales until extracted by dissolution or fracturing of the olivine host. Fluid inclusions represent a widespread and significant source of abiotic CH4 and H2 in submarine and subaerial vent systems on Earth, and possibly elsewhere in the solar system.

Kleinen, T., Mikolajewicz, U., Brovkin, V., 2019. Terrestrial methane emissions from Last Glacial Maximum to preindustrial. Climate of the Past Discussions 2019, 1-32.


We investigate the changes in terrestrial natural methane emissions between the Last Glacial Maximum (LGM) and preindustrial (PI) by performing time-slice experiments with a methane-enabled version of MPI-ESM, the Max Planck Institute for Meteorology Earth System Model. We consider all natural sources of methane except for emissions from wild animals and geological sources, i.e. emissions from wetlands, fires, and termites. Changes are dominated by changes in tropical wetland emissions, with mid-to-high latitude wetlands playing a secondary role, and all other natural sources being of minor importance. The emissions are determined by the interplay of vegetation productivity, a function of CO2 and temperature, source area size, affected by sea level and ice sheet extent, and the state of the West African Monsoon, with increased emissions from north Africa during strong monsoon phases.

We show that it is possible to explain the difference in atmospheric methane between LGM and PI purely by changes in emissions. As emissions more than double between LGM and PI, changes in the atmospheric lifetime of CH4, as proposed in other studies, are not required.

Kobayashi, K., Makabe, A., Yano, M., Oshiki, M., Kindaichi, T., Casciotti, K.L., Okabe, S., 2019. Dual nitrogen and oxygen isotope fractionation during anaerobic ammonium oxidation by anammox bacteria. The ISME Journal 13, 2426-2436.

https://doi.org/10.1038/s41396-019-0440-x

Natural abundance of stable nitrogen (N) and oxygen (O) isotopes are invaluable biogeochemical tracers for assessing the N transformations in the environment. To fully exploit these tracers, the N and O isotope effects (15ε and 18ε) associated with the respective nitrogen transformation processes must be known. However, the N and O isotope effects of anaerobic ammonium oxidation (anammox), one of the major fixed N sinks and NO3

− producers, are not well known. Here, we report the dual N and O isotope effects associated with anammox by three different anammox bacteria including “Ca. Scalindua japonica”, a putative marine species, which were measured in continuous enrichment culture experiments. All three anammox species yielded similar N isotope effects of NH4

+ oxidation to N2 (15εNH4→N2) ranging from 30.9‰ to 32.7‰ and inverse kinetic isotope effects of NO2

− oxidation to NO3− (15εNO2→NO3 = −45.3‰ to −30.1‰). In contrast, 15εNO2→N2 (NO2

− reduction to N2) were significantly different among three species, which is probably because individual anammox bacteria species might possess different types of nitrite reductase. We also report the combined O isotope effects for NO2

− oxidation (18ENO2→NO3) by anammox bacteria. These obtained dual N and O isotopic effects could provide significant insights into the contribution of anammox bacteria to the fixed N loss and NO2

− reoxidation (N recycling) in various natural environments.

Kohl, L., Koskinen, M., Rissanen, K., Haikarainen, I., Polvinen, T., Hellén, H., Pihlatie, M., 2019. Technical note: Interferences of volatile organic compounds (VOCs) on methane concentration measurements. Biogeosciences 16, 3319-3332.


Studies that quantify plant methane (CH4) emission rely on the accurate measurement of small changes in the mixing ratio of CH4 that coincide with much larger changes in the mixing ratio of volatile organic compounds (VOCs). Here, we assessed whether 11 commonly occurring VOCs (e.g. methanol, α- and β-pinene, Δ3-carene) interfered with the quantitation of CH4 by five laser-absorption spectroscopy and Fourier-transformed infrared spectroscopy (FTIR) based CH4 analysers, and quantified the interference of seven compounds on three instruments. Our results showed minimal interference with laser-based analysers and underlined the importance of identifying and compensating for interferences with FTIR instruments. When VOCs were not included in the spectral library, they exerted a strong bias on FTIR-based instruments (64–1800 ppbv apparent CH4 ppmv−1 VOC). Minor (0.7–126 ppbv ppmv−1) interference with FTIR-based measurements were also detected when the spectrum of the interfering VOC was included in the library. In contrast, we detected only minor (<20 ppbv ppmv−1) and transient (< 1 min) VOC interferences on laser-absorption spectroscopy-based analysers. Overall, our results demonstrate that VOC interferences have only minor effects on CH4 flux measurements in soil chambers, but may severely impact stem and shoot flux measurements. Laser-absorption-based instruments are better suited for quantifying CH4 fluxes from plant leaves and stems than FTIR-based instruments; however, significant interferences in shoot chamber measurements could not be excluded for any of the tested instruments. Our results furthermore showed that FTIR can precisely quantify VOC mixing ratios and could therefore provide a method complementary to proton-transfer-reaction mass spectrometry (PTR-MS).

Koleini, M.M., Badizad, M.H., Kargozarfard, Z., Ayatollahi, S., 2019. Interactions between rock/brine and oil/brine interfaces within thin brine film wetting carbonates: A molecular dynamics simulation study. Energy & Fuels 33, 7983-7992.


The thin brine film that wets rock surfaces governs the wettability of underground reservoirs. The ionic composition and salinity of this nanosized brine film influence the wetting preference of the rock pore space occupied by hydrocarbons. Despite numerous investigations over the last decades, a unanimous fundamental understanding that concerns the contribution of ions in the original wetting state of the reservoir is lacking and hence the mechanisms responsible for the wettability reversal of the mineral are still unclear. This wettability reversal is the main consequence of ion-tuned waterflooding. Although the method is widely accepted in practice, there is no universal consensus on the underlying mechanisms involved. Molecular dynamics simulation is an excellent choice to remove such ambiguities. This method can capture an atomic-level picture of the phenomena that affect reservoir wettability upon injecting low-salinity water. For the purpose, we performed simulations of brine films confined between a calcite substrate and a layer of an oil model. The films were at two different salinities to represent the initial state of high-salinity connate water and low-salinity brine. We found the development of ionic aggregates, mainly comprising Na+ and Cl–, within the high-salinity thin brine film. These aggregates act as pinning entities to localize polar oil components within oil/brine interface and connect the hydrocarbon phase to the calcite surface. This results in the adhesion of oil components to the rock surface though a high-salinity thin brine film. Simulation results suggest that the aggregates do not form after the change of the brine content to low salinity. From these observations, we concluded that diluting the brine content of the reservoir leads to the disintegration of such ionic aggregates. As a consequence, electrical double layers (EDLs) form at both rock/brine and brine/oil interfaces, which is supposed to be reflected by additional oil recovery at the macroscopic scale. Furthermore, we pointed out that EDL at an oil interface is established by negatively charged oleic polar species and cations around those compounds. Likewise, the EDL in proximity to calcite is composed of a positive Stern layer of Na+ cations and a negative diffuse layer of Cl– anions beyond that.

Krencker, F.-N., Lindström, S., Bodin, S., 2019. A major sea-level drop briefly precedes the Toarcian oceanic anoxic event: implication for Early Jurassic climate and carbon cycle. Scientific Reports 9, 12518.

https://doi.org/10.1038/s41598-019-48956-x

Sea-level change is an important parameter controlling the expansion of oxygen-depleted conditions in neritic settings during oceanic anoxic events (OAEs). Despite this fundamental role, it remains on a short timescale (<1 Myr) one of the least constrained parameters for numerous OAEs. Here we present sedimentological and geochemical evidence from Morocco and East Greenland showing that a forced regression shortly precedes (ca.102 kyr) the major transgression associated with the Toarcian OAE. The forced regression can be correlated over distances greater than 3000 km in numerous Tethyan and Boreal basins, indicating that the relative sea-level change was driven by eustastic fluctuations. The major amplitude (>50 m) and short duration of the forced regression suggests that it was most likely related to the transient waxing and waning of polar ice sheet. We suggest that this short-lived glaciation might have a genetic link with the inception of the Toarcian OAE. Indeed, during the deglaciation and the accompanying sea-level rise, the thawing permafrost may have released important quantities of methane into the atmosphere that would have contributed to the Toarcian OAE rapid warming and its characteristic negative carbon isotope excursion. This study offers a hypothesis on how some hyperthermal events might be rooted in short-lived “cold-snap” episodes.

Kröger, B., Franeck, F., Rasmussen, C.M.Ø., 2019. The evolutionary dynamics of the early Palaeozoic marine biodiversity accumulation. Proceedings of the Royal Society B: Biological Sciences 286, 20191634.

https://doi.org/10.1098/rspb.2019.1634

The early Palaeozoic Era records the initial biodiversification of the Phanerozoic. The increase in biodiversity involved drastic changes in taxon longevity, and in rates of origination and extinction. Here, we calculate these variables in unprecedented temporal resolution. We find that highly volatile origination and extinction rates are associated with short genus longevities during the Cambrian Period. During the Ordovician and Silurian periods, evolutionary rates were less volatile and genera persisted for increasingly longer intervals. The 90%-genus life expectancy doubled from 5 Myr in the late Cambrian to more than 10 Myr in the Ordovician–Silurian periods. Intervals with widespread ecosystem disruption are associated with short genus longevities during the Cambrian and with exceptionally high longevities during the Ordovician and Silurian periods. The post-Cambrian increase in persistence of genera, therefore, indicates an elevated ability of the changing early Palaeozoic marine ecosystems to sustainably maintain existing genera. This is evidence of a new level of ecosystem resilience which evolved during the Ordovician Period.



In this paper, a molecular analytical approach for detecting hydrocarbonoclastic bacteria in water is suggested as a proxy measurement for tracking petroleum discharges in industrialized or pristine aquatic environments. This approach is tested for general application in cold marine regions (freezing to 5 °C). We used amplicon sequencing and qPCR to quantify 16S rRNA and GyrB genes from oleophilic bacteria in seawater samples from two different crude oil enrichments. The first experiment was conducted in a controlled environment using laboratory conditions and natural North Sea fjord seawater (NSC) at a constant temperature of 5 °C. The second was performed in the field with natural Arctic seawater (ARC) and outdoor temperature conditions from −7 °C to around 4 °C.

Although the experimental conditions for NSC and ARC differed, the temporal changes in bacterial communities were comparable and reflected oil biotransformation processes. The common bacterial OTUs for NSC and ARC had the highest identity to Colwellia rossensis and Oleispira antarctica rRNA sequences and were enriched within a few days in both conditions. Other typical oil degrading bacteria such as Alcanivorax (n-

alkane degrader) and Cycloclasticus (polycyclic aromatic hydrocarbons degrader) were rapidly enriched only in NSC conditions.

Both the strong correlation between Oleispira SSU gene copies and oil concentration, and the specificity of the Oleispira assay suggest that this organism is a robust bioindicator for seawater contaminated by petroleum in cold water environments. Further optimization for automation of the Oleispira assay for in situ analysis with a genosensing device is underway. The assay for Colwellia quantification requires more specificity to fewer Colwellia OTUs and a well-established dose-response relationship before those taxa are used for oil tracking purposes.

Kulyk, D.S., Swiner, D.J., Sahraeian, T., Badu-Tawiah, A.K., 2019. Direct mass spectrometry analysis of complex mixtures by nanoelectrospray with simultaneous atmospheric pressure chemical ionization and electrophoretic separation capabilities. Analytical Chemistry 91, 11562-11568.


Accurate and rapid analysis of complex microsamples are challenging tasks in translational research. Nanoelectrospray ionization (nESI) is the method of choice for analyzing small sample volumes by mass spectrometry (MS), but this technique works well only for polar analytes. Herein, we describe a versatile dual noncontact nESI/nAPCI (nanoatmospheric pressure chemical ionization) source that allows simultaneous detection of both polar and nonpolar analytes in microliter quantities of samples under ambient conditions and without pretreatment. The same device can be activated to enable electrophoretic separation. The noncontact nESI/nAPCI MS platform was applied to analyze different samples, including high sensitive direct analysis of biofluids and the efficient detection of proteins in buffers with high concentration of nonvolatile salts. Excellent linearity, accuracy and limits of detection were achieved for compounds with different chemical properties in different matrices. The high sensitivity, universality, simplicity, and ease of operation make this MS technique promising for use in clinical and forensic applications.

Kuo, T.-H., Chung, H.-H., Chang, H.-Y., Lin, C.-W., Wang, M.-Y., Shen, T.-L., Hsu, C.-C., 2019. Deep lipidomics and molecular imaging of unsaturated lipid isomers: A universal strategy initiated by mCPBA epoxidation. Analytical Chemistry 91, 11905-11915.


Cellular lipidome is highly regulated through lipogenesis, rendering diverse double-bond positional isomers (C═C isomer) of a given unsaturated lipid species. In recent years, there are increasing reports indicating the physiological roles of C═C isomer compositions associated with diseases, while the biochemistry has not been broadly investigated due to the challenge in characterizing lipid isomers inherent to conventional mass spectrometry-based lipidomics. To address this challenge, we reported a universal, user-friendly, derivatization-based strategy, MELDI (mCPBA Epoxidation for Lipid Double-bond Identification), which enables both large-scale identification and spatial mapping of biological C═C isomers using commercial mass spectrometers without any instrument modification. With the developed liquid-chromatography mass spectrometry (LC-MS) lipidomics workflow, we elucidated more than 100 isomers among monounsaturated and polyunsaturated fatty acids and glycerophospholipids in human serum, where uncommon isomers of low abundance were quantified for the first time. The capability of MELDI-LC-MS in lipidome analysis was further demonstrated using the differentiated 3T3-L1 adipocytes, providing an insight into the cellular lipid reprogramming upon stearoyl-coenzyme A desaturase 1 (SCD1) inhibition. Finally, we highlighted the versatility of MELDI coupled with ambient mass spectrometry imaging to spatially resolve cancer-associated alteration of lipid isomers in a metastatic mouse tissue section. Our results suggested that MELDI will contribute to current lipidomics pipelines with a deeper level of structural information, allowing us to investigate the underlying lipid biochemistry.

Küpper, H., Bokhari, S.N.H., Jaime-Pérez, N., Lyubenova, L., Ashraf, N., Andresen, E., 2019. Ultratrace metal speciation analysis by coupling of sector-field ICP-MS to high-resolution size exclusion and reversed-phase liquid chromatography. Analytical Chemistry 91, 10961-10969.


Techniques for metal speciation analysis with subnanomolar (ppt) detection limits in complex matrices, with simultaneous quantification of matrix elements, have become a necessity for investigating targets of trace metal binding to macromolecules and pigments at environmentally relevant concentrations. In this work we optimized the analysis of such metal binding in a custom-built HPLC-ICP-MS system. Key elements of the optimization were the choice of components for the metal-free HPLC-DAD system and sector-field ICP-MS detection (ICF-sfMS) with desolvating injection and optimization of sample handling. Protein analysis was done using ammonium bicarbonate buffer and size exclusion chromatography (SEC-ICP-sfMS), with possible addition of anion exchange chromatography. Detection of metal exchange in pigments (chlorophylls and bacteriochlorophylls) was based on reversed-phase chromatography with a methanol-acetone gradient and coupling to the ICP-sfMS via a dedicated organic matrix interface (RPC-ICP-sfMS). The resulting HPLC-DAD-ICP-sfMS system has detection limits in the picomolar range in protein buffer, limited by the maximal achievable purity of buffers/solvents and not by system sensitivity. Tests for method optimization showed that sonication, meant to increase protein solubilization, leads to artifacts of metal loss from metalloproteins. Examples for Cd binding to soybean proteins and chlorophyll, Cr binding to Arabidopsis thaliana proteins, La binding to Desmodesmus quadricauda proteins, and Cu binding to Rhodospirillum rubrum proteins and pigments are shown. These application examples demonstrate that the system is sensitive enough to detect binding of metals to proteins and pigments at background concentration levels of typical nutrient solutions made from analytical grade chemicals, equivalent to ultratrace metal concentrations in nonpolluted environments.

Kurison, C., Kuleli, H.S., Mubarak, A.H., 2019. Unlocking well productivity drivers in Eagle Ford and Utica unconventional resources through data analytics. Journal of Natural Gas Science and Engineering 71, 102976.


North America's unconventional resources are viewed as statistical plays because of the wide variability in the performance of hydraulically fractured wells. Attempts to unlock the primary drivers of productivity yield different interpretations because of the over-parameterized stimulation processes, diverse geoscience concepts and non-unique solutions of associated reservoir flow modeling. An opportunity to derive insights on the yet-to-be fully understood flow mechanisms lies in the interrogation of acquired stimulation and production data. In search of causation relationships, a data analytics approach was used to profile and associate well productivity with multiple hydraulic fracturing stimulation parameters for Eagle Ford and Utica horizontal wells in areas with similar geological settings. Data for the study was retrieved from public-accessible databases managed by the Rail Road Commission of Texas, Department of Natural Resources of Ohio and Chemical Disclosure Registry of FracFocus. Results from the approach show multiple apparent causal relationships between production and stimulation parameters with the latter evolving in tandem. As a result, a priori knowledge was incorporated in decoupling dependencies for sole contributions of parameters. Among the most critical trends, the amount of proppant and fracturing fluid volume correlated with productivity. The average proppant concentration, used to decouple this association, correlated poorly with cumulative hydrocarbon production. Better performing wells in which the amount of proppant was high coincidentally had been stimulated with large amounts of fracturing fluid; thus, motivating the latter to be interpreted as a primary driver for Eagle Ford and Utica production enhancement. It was speculated that the induced hydraulic fracture length is effective; thus, use of large amounts of high quality proppant to create conductive fractures might be yielding limited value. Additional results provided insights on interdependences between injected proppant, lateral length, fracturing stages, perforation clusters and fracturing fluid volume. The identification of stimulation parameters that correlated with well productivity provided ground for speculating that unconventional resources are not statistical as portrayed and repeatable well performance can be realized if stimulation operations are systematically constrained. Further reflection on the results backed postulations on attributes of reservoir flow physics such as matrix permeability, fracture conductivity and effective fracture length. In conclusion, data

analytics shed light on dominant productivity drivers in the subject unconventional resources and provided ground for hypotheses that will improve knowledge-driven simulation models.

Labbé, T., Pfister, C., Brönnimann, S., Rousseau, D., Franke, J., Bois, B., 2019. The longest homogeneous series of grape harvest dates, Beaune 1354–2018, and its significance for the understanding of past and present climate. Climate of the Past 15, 1485-1501.

https://www.clim-past.net/15/1485/2019/

Records of grape harvest dates (GHDs) are the oldest and the longest continuous phenological data in Europe. However, many available series, including the well-known (Dijon) Burgundy series, are error prone because scholars so far have uncritically drawn the data from 19th century publications instead of going back to the archives. The GHDs from the famous vine region of Beaune (Burgundy) were entirely drawn from the archives and critically cross-checked with narrative evidence. In order to reconstruct temperature, the series was calibrated against the long Paris temperature series comprising the 360 years from 1659 to 2018. The 664-year-long Beaune series from 1354 to 2018 is also significantly correlated with tree-ring and documentary proxy evidence as well as with the central European temperature series (from 1500). The series is clearly subdivided into two parts. From 1354 to 1987 grapes were on average picked from 28 September on, whereby during the last 31-year-long period of rapid warming from 1988 to 2018 harvests began 13 d earlier. Early harvest dates are shown to be accompanied by high pressure over western–central Europe and atmospheric blocking over Denmark. The 33 extremely early harvests comprising the fifth percentile bracket of GHDs are unevenly distributed over time; 21 of them occurred between 1393 and 1719, while this is the case for just 5 years between 1720 and 2002. Since the hot summer of 2003, 8 out of 16 spring–summer periods were outstanding according to the statistics of the last 664 years, no less than 5 among them within the last 8 years. In the Paris temperature measurements since 1659, April-to-July temperature reached the highest value ever in 2018. In sum, the 664-year-long Beaune GHD series demonstrates that outstanding hot and dry years in the past were outliers, while they have become the norm since the transition to rapid warming in 1988.

Łaciak, D., Borowski, M.P., Łydżba-Kopczyńska, B., Baron, J., Furmanek, M., 2019. Archaeometric characterisation and origin of black coatings on prehistoric pottery. Geochemistry 79, 453-466.


Black or dark grey vessel surfaces with characteristic metallic lustre are recognised from various archaeological contexts throughout Europe. This feature is commonly attributed to the application of graphite-bearing coatings onto ceramic vessels. However, recent experimental studies have shown that a very similar visual effect can alternatively be achieved by polishing and, subsequently, firing in a reducing atmosphere (so-called smudging). In this study, experimentally manufactured ceramics as well as samples of prehistoric ware (dated to the Neolithic Age, late Bronze Age and early Iron Age) have been analysed to find the distinguishing features between graphite-based and non-mineral black coatings. In the low-magnification BSE images the well-preserved graphite-coated surfaces are characterized by a distinctive spotty pattern with numerous dark grey angular fragments of monomineralic or nearly monomineralic metamorphic rocks scattered in the clay groundmass. Provided that polished thin sections are skilfully prepared, individual graphite plates can be easily recognized in the near-surface layer of the sherds using polarized reflected light microscopy. A relatively homogeneous appearance is typical of the low-magnification BSE images of surfaces coated by smudging. At higher magnifications, presence of blurred darkish stains (presumably organic-derived, as indicated by elevated levels of biogenic elements) is characteristic of this kind of non-mineral black coatings. SEM-EDS and optical microscopy have been supplemented by micro-Raman spectroscopy, which allows differentiation between various carbonaceous phases.



Dissolved organic matter (DOM) in river water dynamically changes with respect to its major sources during heavy rain events. However, there has been no established tool to estimate the relative contributions of different organic sources to river water DOM. In this study, the evolution in the contributions of ten different organic matter (OM) sources to storm water DOM was explored with a selected urban river, the Geumho River in South Korea, during storm events via an end-member mixing analysis (EMMA) based on fluorescence indices and Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The OM source materials included treated effluent, road runoff, groundwater, topsoil, deep soil, leaves, reeds, riparian plants, attached algae, and suspended algae. The EMMA results provided quantitative estimates of the variations in the dominant OM sources with the progress of storms. Treated effluent was the prevailing source at the beginning period of the storm, while topsoil, leaves, riparian plants, and groundwater predominated during and after the peak period. The fluorescence indices-based evaluation was consistent with the statistical comparison of the molecular formulas derived from FT-ICR-MS conducted on the ten potential OM sources and the storm samples. The observed variations in the OM sources agreed with the typical characteristics of urban rivers in connection with anthropogenic inputs and the impact of surrounding impervious surfaces. This study demonstrates the application of intuitive and facile tools in estimating the relative impacts of OM sources in urban watersheds.

Lee, M.R., Cohen, B.E., King, A.J., Greenwood, R.C., 2019. The diversity of CM carbonaceous chondrite parent bodies explored using Lewis Cliff 85311. Geochimica et Cosmochimica Acta 264, 224-244.


Lewis Cliff (LEW) 85311 is classified as a Mighei-like (CM) carbonaceous chondrite, yet it has some unusual properties that highlight an unrealised diversity within the CMs, and also questions how many parent bodies are sampled by the group. This meteorite is composed of rimmed chondrules, chondrule fragments and refractory inclusions that are set in a fine-grained phyllosilicate-rich matrix. The chondrules are of a similar size to those in the CMs, and have narrow fine-grained rims. LEW 85311 has been mildly aqueously altered, as evidenced by the preservation of melilite and kamacite, and X-ray diffraction results showing a low phyllosilicate fraction and a high ratio of cronstedtite to Fe, Mg serpentine. The chemical composition of LEW 85311 matrix, fine-grained rims, tochilinite and P-rich sulphides is similar to mildly aqueously altered CMs. LEW 85311 is enriched in refractory elements and REEs such that its CI-normalised profile falls between the CMs and CVs, and its oxygen isotopic composition plots in the CV-CK-CO field. Other distinctive properties of this meteorite include the presence of abundant refractory inclusions, and hundreds of micrometer size objects composed of needle-fibre calcite. LEW 85311 could come from part of a single CM parent body that was unusually rich in refractory inclusions, but more likely samples a different parent body to most other members of the group that accreted a subtly different mixture of materials. The mineralogical and geochemical evolution of LEW 85311 during subsequent aqueous alteration was similar to other CMs and was arrested at an early stage, corresponding to a petrologic subtype of CM2.7, probably due to an unusually low proportion of accreted ice. The CM carbonaceous chondrites sample multiple parent bodies whose similar size and inventory of accreted materials, including radiogenic isotopes, led to a comparable post-accretionary evolution.

Lei, Z.-y., Zhang, L., Su, M., Luo, S.-b., Qian, X., Zhang, B.-d., 2019. Types, characteristics and implication for hydrocarbon exploration of the Middle Miocene deep-water sediments in Beikang Basin, southern South China Sea. China Geology 2, 85-93.


ABSTRACT The internal seismic architectures of the Middle Miocene in Beikang Basin, southern South China Sea, were investigated and described using regional 2D seismic data from Guangzhou Marine Geology Survey. In particular, five typical seismic facies were identified based on an integrated analysis of the amplitude, continuity, contact relationship, and morphologies of seismic reflections. Bathyal-abyssal fine-grained sediments, deltaic front sandy bodies, turbidites, and small-scale turbidite channels were developed in the Middle Miocene according to the tectonic-sedimentary evolution of the sedimentary basins in the southern South China Sea. The findings of this study suggest that deltaic front sandy bodies and turbidites can be

considered as the two major types of deep-water clastic reservoirs for the depression stage of Beikang Basin. A well-developed source-reservoir-cap assemblage was composed by deep rift-stage source rocks, deep-water clastic reservoirs of the Middle Miocene, and bathyal-abyssal deep-water fine-grained sediments after the Middle Miocene, implying a good potential for hydrocarbon exploration. ©2019 China Geology Editorial Office.

Lejay, M., Alexis, M.A., Quénéa, K., Anquetil, C., Bon, F., 2019. The organic signature of an experimental meat-cooking fireplace: The identification of nitrogen compounds and their archaeological potential. Organic Geochemistry 138, 103923.


A better understanding of the operation and use of prehistoric fires is fundamental to interpreting the organization of living spaces. Following a previous study that focused on the organic signatures of fireplaces fueled with wood and/or bones, this study targeted the completion of an experimental reference database through the addition of a wood-fueled fireplace dedicated to the cooking of meat. Different sedimentary features of this experimental fireplace were visually identified (e.g. darkening, reddening), sampled, and subjected to geochemical analysis. Corg and N contents were quantified, samples were extracted with organic solvents and analyzed through GC–MS and bulk organic matter was characterized through py(TMAH)-GC–MS. Five different samples were studied and compared with a control sample, representative of the local background. A significant increase of Corg and N contents was measured for the three samples presenting darkened or charred caracteristics. The meat-cooking fireplace seems to be characterized by the strong contribution of nitrogen, which was visible in elementary analyses as well as in the molecular composition of solvent extracts, and bulk organic matter. More specifically, compounds containing nitrile functions, amides, N-heterocyclic and N-aromatic compounds could be detected in solvent extracts. Amines, amides, N-heterocyclic and N-aromatic compounds could be identified in py(TMAH)-GC–MS. Some of these compounds present a relative stability in soils and could therefore aid in our comprehension and functional interpretations of archaeological fireplaces, and may, more particularly, make it possible to highlight the use of fireplaces for the cooking of meat.

Levitan, O., Chen, M., Kuang, X., Cheong, K.Y., Jiang, J., Banal, M., Nambiar, N., Gorbunov, M.Y., Ludtke, S.J., Falkowski, P.G., Dai, W., 2019. Structural and functional analyses of photosystem II in the marine diatom Phaeodactylum tricornutum. Proceedings of the National Academy of Sciences 116, 17316-17322.


Significance: Despite distinctions in the architecture of thylakoid membranes, the fundamental machinery responsible for photosynthetic electron transfer is highly conserved in all oxygenic organisms. Using cryo-electron tomography in conjunction with proteomic and biophysical analyses, we show the distribution of photosystem II in thylakoid membranes of a diatom is heterogeneous. There are 2 subpopulations of the PSII supercomplexes; one contains antennae complexes, and the other does not. The former is functional, while the latter appears to be photochemically inactive. We suggest, based on tomography and biophysical analysis, that photochemically damaged reaction centers are physically isolated to repair stations where the inactive proteins can be removed and replaced.

Abstract: A descendant of the red algal lineage, diatoms are unicellular eukaryotic algae characterized by thylakoid membranes that lack the spatial differentiation of stroma and grana stacks found in green algae and higher plants. While the photophysiology of diatoms has been studied extensively, very little is known about the spatial organization of the multimeric photosynthetic protein complexes within their thylakoid membranes. Here, using cryo-electron tomography, proteomics, and biophysical analyses, we elucidate the macromolecular composition, architecture, and spatial distribution of photosystem II complexes in diatom thylakoid membranes. Structural analyses reveal 2 distinct photosystem II populations: loose clusters of complexes associated with antenna proteins and compact 2D crystalline arrays of dimeric cores. Biophysical measurements reveal only 1 photosystem II functional absorption cross section, suggesting that only the former population is photosynthetically active. The tomographic data indicate that the arrays of photosystem II cores are physically separated from those associated with antenna proteins. We hypothesize that the islands of photosystem cores are

repair stations, where photodamaged proteins can be replaced. Our results strongly imply convergent evolution between the red and the green photosynthetic lineages toward spatial segregation of dynamic, functional microdomains of photosystem II supercomplexes.

Li, C., Reimers, C.E., Alleau, Y., 2019. Inducing the attachment of cable bacteria on oxidizing electrodes. Biogeosciences Discussions 2019, 1-20.


The scope of the present study is to introduce electrochemical reactors as a tool for investigating the growth of novel filamentous cable bacteria and their unique extracellular electron transfer ability. New evidence that cable bacteria are widely distributed in sediments throughout an estuarine system connected to the NE Pacific Ocean is also presented. Cable bacteria found within Yaquina Bay, Oregon, USA, appear to cluster with the genus, Candidatus Electrothrix. Results of a 135-day bioelectrochemical reactor experiment confirm a previous observation that cable bacteria can grow on oxidatively poised electrodes suspended in anaerobic seawater above reducing sediments. However, several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the carbon fibers of the suspended electrodes including encrusted chains of cells. These observations provide new information to suggest what conditions will induce cable bacteria to perform electron donation to an electrode surface, further informing future experiments to culture cable bacteria apart from a sediment matrix.

Li, C., Zhu, H., Yang, F., Liu, H., Wang, F., Sun, G., Yao, B., 2019. Effect of asphaltene polarity on wax precipitation and deposition characteristics of waxy oils. Energy & Fuels 33, 7225-7233.


Asphaltenes are natural pour point depressants, and the effect of asphaltene polarity on the low-temperature rheology of waxy oils has been well studied. In this paper, the influence of asphaltene polarity on the wax precipitation and deposition characteristics of synthetic waxy oils was investigated through a differential scanning calorimeter (DSC), a rheometer, a polarizing microscope, and a Couette wax deposition experimental device. It was found that the asphaltenes with lower polarity have higher H/C ratio and can disperse into smaller associating particles in the synthetic waxy oils, which is beneficial for the cocrystallization interaction between asphaltenes and wax molecules, and also provide more nucleating sites for wax molecules. With the decrease of asphaltene polarity, the wax crystals of synthetic waxy oils are gradually changed from long needle-like to small needle-like or nearly spherical, which is not conducive to the overlap and insertion of wax crystals, thus greatly improving the rheological properties of synthetic waxy oils. The addition of asphaltenes with lower polarity can significantly reduce the wax deposition rate but increase the aging rate; that is, a thinner and harder wax deposit tends to form with the decrease of asphaltene polarity. Meanwhile, the formed wax deposits become heterogeneous along the radial direction after the asphaltenes addition; the wax contents of the wax deposits increase gradually from the bottom layer to the surface layer. On the one hand, with the decrease of asphaltene polarity, the low-temperature structural strength of synthetic waxy oils is continuously decreased. Therefore, the initial wax deposit layers require higher solid wax contents to resist shearing of pipe flow. On the other hand, the lower viscosity and smaller aspect ratio of wax crystals are also beneficial for the diffusion of wax molecules in the bulk oil and wax deposit, which increases the aging rate of wax deposits. Therefore, with the decrease of asphaltene polarity, the difference of wax content between the surface and bottom wax deposits in the formed heterogeneous wax deposit structure becomes larger and larger.

Li, D., Ren, S., Xu, Y., Rui, H., 2019. Experimental study on kinetic behaviors of natural gas hydrate production via continuous simulated seawater injection. Energy & Fuels 33, 8222-8230.


Natural gas hydrate (NGH) is a kind of potential energy with shallow buried depth, high energy density, huge reserves, and cleanliness. In this study, continuous seawater injection is adopted for NGH production

experiments with applying a self-designed reactor which can simulate an NGH-bearing reservoir with a mini well, given that the surface seawater stores tremendous heat. Continuous seawater injection for NGH production can keep the balance between productivity and sand production through controlling production pressure with its thermodynamic and technical feasibilities. Kinetic behaviors of NGH production by continuous seawater injection are investigated using the simulated NGH-bearing reservoir. Meanwhile, the dissociation of NGH and its influence factors are analyzed. The threshold value of temperature for NGH dissociation is also discussed. The experimental results show that the changes in temperature and pressure keep constant at the initial stage of the continuous seawater injection process. However, temperature and pressure show obvious variation with injecting more seawater, which increase first and decrease subsequently. Especially, the methane production rate shows a high level after the temperature exceeded the threshold value for NGH dissociation. But the methane production rate drops quickly after a short period of high level and keeps a low level until the end of the experiment. The maximum value of the methane production rate and cumulative methane production become higher with the presence of a larger overheat and NGH saturation. The existence of a threshold value of the temperature for NGH dissociation is demonstrated by experimental works. Minimum threshold values of the temperature for NGH dissociation vary with the presence of different corresponding reservoir pressures.



Zinc (Zn) and cadmium (Cd) are two important biological-sensitive elements, and their isotopes are strongly fractionated during biological processes. To develop the potential application of Zn and Cd isotopes for tracing the contribution of bacteria to metal mineralization, in this study we investigate for the first time the ranges and causes of isotope fractionation of Zn and Cd in a large hydrothermal system with bacteria from the world-class Jinding Zn-Pb deposit, southwest China. Extremely negative δ34SCDT values of sulfides (−48.6‰ to +7.7‰) obtained in this study and literature reveal the dominant biogenic sulfur associated with bacterial sulfate reduction. Both Zn and Cd isotope ratios are highly variable and significantly lighter compared with most of Zn-Pb ore deposits worldwide. The extremely negative δ66ZnJMC 3-0749L (down to −0.69‰) exceeds the range of Rayleigh fractionation during inorganic precipitation of ZnS. Zinc isotope ratios display a well-defined positive correlation with Zn/Cd ratios and the samples with lightest δ66Zn have lowest Zn/Cd ratios. This reflects that sphalerites formed in the early stages of mineralization already have extremely light Zn isotopic compositions. There is a negative relationship between δ34SCDT and δ66Zn, indicating that lighter Zn isotope ratios are related to stronger bacterial sulfate reduction, which results in heavier sulfur isotope ratios. Since organic compounds (e.g., Zn-carboxylate) in fluids are strongly enriched in heavy isotopes relative to free Zn2+ and Zn-sulfide, sulfides formed in the bacteria-rich hydrothermal systems would acquire light δ66Zn. Therefore, the extremely negative δ34SCDT and δ66Zn ratios demonstrate for the first time that bacterial metabolisms not only induced sulfate reduction, but also were directly involved in the formation of metals (e.g., Zn) in a large hydrothermal system. A similar process may have also partly contributed to the substantial fractionation of cadmium isotopes in the hydrothermal system. Overall, our studies show that zinc and cadmium isotopes may act as an effective tool in deciphering the specific role of organisms in formation of sulfides in hydrothermal systems and other settings.

Li, M., Wang, X.R., 2019. Peak alignment of gas chromatography–mass spectrometry data with deep learning. Journal of Chromatography A 1604, 460476.


We present ChromAlignNet, a deep learning model for alignment of peaks in Gas Chromatography-Mass Spectrometry (GC–MS) data. In GC–MS data, a compound’s retention time (RT) may not stay fixed across multiple chromatograms. To use GC–MS data for biomarker discovery requires alignment of identical analyte’s RT from different samples. Current methods of alignment are all based on a set of formal, mathematical rules. We present a solution to GC–MS alignment using deep learning neural networks, which are more adept at complex, fuzzy data sets. We tested our model on several GC–MS data sets of various complexities and

analysed the alignment results quantitatively. We show the model has very good performance (AUC ∼ 1 for simple data sets and AUC ∼ 0.85 for very complex data sets). Further, our model easily outperforms existing algorithms on complex data sets. Compared with existing methods, ChromAlignNet is very easy to use as it requires no user input of reference chromatograms and parameters. This method can easily be adapted to other similar data such as those from liquid chromatography. The source code is written in Python and available online.

Li, Q., Wu, S., Xia, D., You, X., Zhang, H., Lu, H., 2020. Major and trace element geochemistry of the lacustrine organic-rich shales from the Upper Triassic Chang 7 Member in the southwestern Ordos Basin, China: Implications for paleoenvironment and organic matter accumulation. Marine and Petroleum Geology 111, 852-867.


Lacustrine organic-rich shales are widespread in the Upper Triassic Yanchang Formation Chang 7 Member of the Ordos Basin. However, information on the short-term climate evolution within the Chang 7 Member is still lacking, and the mechanism of organic accumulation in the shales remains controversial. To address these issues, this study analyzes the palaeoenvironment and depositional setting of different intervals in the Chang 7 Member of the southwestern Ordos Basin and constrains the main control factors on accumulation and preservation of organic matter based on organic, major, and trace element data. The lower Chang 73 shale, which contains a high abundance of thermally mature Type I and II kerogen, has excellent original hydrocarbon generative potential. The lower Chang 73 interval has the most humid climatic condition, the strongest weathering condition, a euxinic bottom water condition, a high paleo-productivity, and a low terrigenous input. During the period of upper Chang 73 and Chang 72, the climate became somewhat drier and hotter, which was marked by relatively weak weathering conditions, suboxic to anoxic conditions, low paleoproductivity, and high terrigenous input. The Chang 71 was characterized by a moderately humid climate, moderate weathering conditions, paleoproductivity, and terrigenous input. The relationship among the primary productivity, redox conditions, clastic influx indicators and TOC content suggests that primary productivity was the most critical factor controlling the enrichment of organic matter. The high primary productivity during the early Chang 73 interval was probably driven by the deposition of volcanic ash and was influenced by marine incursion events. A warm and humid paleoclimate, combined with input of volcanic ash and seawater, resulted in eutrophic, nutrient-rich, and stratified surface water during the early Chang 73 period, which led to algal blooms with high primary productivity. A stratified water column with high primary productivity, together with oxygen-deficit bottom water conditions and low terrigenous input, resulted in the greatest enrichment of organic matter in the lower part of Chang 73 shale.

Li, S., Wang, X.-C., Li, C.-F., Wilde, S.A., Zhang, Y., Golding, S.D., Liu, K., Zhang, Y., 2019. Direct rubidium-strontium dating of hydrocarbon charge using small authigenic illitic clay aliquots from the Silurian bituminous sandstone in the Tarim Basin, NW China. Scientific Reports 9, 12565.

https://doi.org/10.1038/s41598-019-48988-3

Illitic clay is ubiquitous in clastic hydrocarbon reservoirs, and the host for several radiometric isotopes such as the potassium-argon (K-Ar) and rubidium-strontium (Rb-Sr) systems. This study applied the isotope-dilution thermal ionization mass spectrometry technique for small samples (3–4 mg) to conduct illite Rb-Sr isotope dating of five illitic clay samples from the Silurian bituminous sandstone (SBS) intersected by five drillholes in the Tarim Basin, NW China. The 87Rb/86Sr ratio of clays is fractionated mainly by the addition of Rb during the illitization of mixed-layer illite/smectite (I/S), which is the dominant clay species in the Tarim Basin samples. The subsample-scale Rb/Sr isotope values suggest that each subsample may contain I/S particles of slightly variable degrees of illitization. Three of the analyzed samples (H6, KQ1 and TZ67) generated Rb-Sr isochron ages of 141 ± 61 Ma, 332 ± 32 Ma and 235 ± 8 Ma (errors quoted at 2σ), respectively. These results are similar to the corresponding K-Ar ages (125 Ma, 389 Ma and 234 Ma). The isotopic ages are consistent with the timing of hydrocarbon charge which varies in different drillholes as constrained by basin modelling, indicating that a closed-system behavior is attained by the hydrocarbon charge that inhibits the illitization of I/S. The Rb-Sr

isotope analyses of the other two samples (YM35-1 and Q1) that did not yield isochron ages suggest the conditions for producing isochrons were not satisfied, which may be caused by disturbance of the isotope system by a post-charge hydrothermal event. The outcomes of this study show the robust potential of Rb-Sr clay subsample geochronology for cross-checking isotopic ages yielded by other systems (e.g. K-Ar system) and constraining the timing of hydrocarbon charge.

Li, T., Li, J., Zhang, H., Sun, K., Xiao, J., 2019. DFT study on the dibenzothiophene pyrolysis mechanism in petroleum. Energy & Fuels 33, 8876-8895.


Dibenzothiophene sulfur (DBTs), the most stable sulfur species, is present in remarkable concentration in petroleum. Removal of DBTs is with profound significance in environmental protection. In this work, a density functional theory method was adopted to investigate the pyrolysis mechanism of DBT. It was found that the pyrolysis of DBT is possibly started by H-migration or S–C bond rupture. Three main reaction pathways were found. Two dominating pyrolysis pathways are through thiol intermediate pyrolysis and another is through DBT carbene direct dissociation. The dominating products are sulfur-free atoms, 2-ethynyl-benzothiophene, 3-ethynyl-benzothiophene, ethyne, biphenylene, and 1,8-dihydrocyclopentaindene, with a certain amount of benzothiophene and SH radicals. For DBT, BT, and thiophene, the most difficult step is the initial step. The highest energy barrier of DBT is about 17 kcal/mol higher than BT and thiophene, indicating that pyrolysis of DBT needs more intense reaction conditions. Thiophenes can be stable in extreme conditions, which is possibly caused by the high energy barrier of the initial reaction step. After the initial reaction steps, BT and DBT can be desulfurized more easily through thiol intermediates. Searching the catalyst that could lower the energy barrier of the initial step and the reagent that could convert thiophenes directly into thiols may be a potential desulfurization approach for thiophenes.

Li, T., Song, F., Zhang, J., Liu, S., Xing, B., Bai, Y., 2020. Pyrolysis characteristics of soil humic substances using TG-FTIR-MS combined with kinetic models. Science of The Total Environment 698, 134237.


The incorporation and cycling of pyrogenic organic matter in soil is a potential carbon sink, while the pyrolysis behaviors of soil organic matter are still lacking. Pyrolysis characteristics of soil fulvic acid (FA) and humic acid (HA) were investigated using thermogravimetry combined with Fourier transform infrared spectrometer-mass spectrometer (TG-FTIR-MS) and kinetic models. Four reaction stages corresponding to four pseudo-components were distinguished for both FA and HA. FA exhibited greater transformation contributions of hemicellulose-like and cellulose-like pseudo-components, while HA exhibited greater transformation contributions of lignin-like pseudo-components. Compared to HA, higher levels of heat-resistant aromatic compounds, phenolic groups, and carboxylic groups were recognized in FA. Values of both activation energy (Ea, 246.13–661.40 kJ·mol−1) and pre-exponential factor (lnA, 53.49–107.16 min−1) of FA were greater than corresponding Ea (241.74–466.70 kJ·mol−1) and lnA (51.99–74.36 min−1) values of HA determined by Flynn-Wall-Ozawa method and Distributed Activation Energy Model. The main pyrolysis reaction mechanisms of both FA and HA closely matched with the order-based model corresponding to 2nd and 3rd order random nucleation on an individual particle. The evolved gas species of H2, CH4, H2O, and CO2 were dominant for FA and HA pyrolysis. Generally, the total H2/CO2 and CH4/H2O releases were relatively larger for FA and HA pyrolysis, respectively. TG-FTIR-MS is shown to be an effective method to provide valuable and qualitative analysis of the gaseous volatile species evolved during HS pyrolysis. Findings from this systematic study of soil organic matter responding to pyrolysis will be critical for predicting the changes of soil systems or carbon cycle affected by future climate and fire regimes.

Li, X., Jiang, Z., Jiang, S., Li, Z., Song, Y., Jiang, H., Qiu, H., Cao, X., Miao, Y., 2020. Various controlling factors of matrix-related pores from differing depositional shales of the Yangtze Block in south China: Insight from organic matter isolation and fractal analysis. Marine and Petroleum Geology 111, 720-734.


In this study, matrix-related pores from differing depositional shales were explored comparatively. Among of them, Lower Cambrian shale (3.83%Ro) and Lower Silurian shale (2.61%Ro) were marine sediments with abundant oil-prone kerogen and rich siliceous minerals, while Upper Permian shale (2.44%Ro) were transitional sediments with redundant gas-prone kerogen and rich clay. The morphology and geometry of pores were investigated via fractal analyses based on N2 adsorption and direct imaging. The effects of organic matter (OM) within different shales were also highlighted through N2 adsorption before and after OM isolation. Lower Cambrian shale possessed the lowest pore volumes (PV) (averaging 0.0109 ml/g) and the lowest pore surface areas (PSA) (averaging 9.09 m2/g) as well as the smallest average pore diameters (APD) (averaging 5.47 nm). Dissolved pore with dead-end openings was the main type. The PV and PSA of isolated OM were only approximately 1 and 2 times higher than that of corresponding samples, respectively. In contrast, Lower Silurian shale possessed the highest PV (averaging 0.0109 ml/g) and the highest PSA (averaging 9.09 m2/g) as well as relatively large APD (averaging 13.43 nm). Organic-hosted pores (OMP) with cellular structure is the main type. The PV and PSA of isolated OM were approximately 8.5 and 3 times higher than that of corresponding samples, respectively. Upper Permian shale with the largest averaging pore diameters (averaging 18.82 nm) presented high PV (averaging 0.0209 ml/g) similar to that of Lower Silurian shale, and a low PSA (averaging 10.85 m2/g) like that of Lower Cambrian shale. Pore associated with clay flakes was the main type. The PV and PSA of isolated OM were only approximately 0.6 times and 1 times higher than that of corresponding samples, respectively.

For marine shale, matrix-related pore features are synergy effects of the matrix basis where pre-existing space controls the occurrence of porous OM and functions as the shelter for OMP with an appropriate thermal maturity. However, extensive diagenesis can overprint the effects of matrixes on pore properties, because oil-prone kerogen is sensitive to thermal maturity. The specific material composition of transitional shale limit pore properties, because dominant structured OM is thermally stable with limited migration ability and pore contribution. Hence, diagenetic differences and material diversities may be attributed to the discrepancies of pore properties between marine shale and transitional shale.

Li, Y., Sun, L.-L., Sun, Y.-Y., Cha, Q.-Q., Li, C.-Y., Zhao, D.-L., Song, X.-Y., Wang, M., McMinn, A., Chen, X.-L., Zhang, Y.-Z., Qin, Q.-L., 2019. Extracellular enzyme activity and its implications for organic matter cycling in northern Chinese marginal seas. Frontiers in Microbiology 10, 2137. doi: 10.3389/fmicb.2019.02137.


Extracellular enzymes, initiating the degradation of organic macromolecules, are important functional components of marine ecosystems. Measuring in situ seawater extracellular enzyme activity (EEA) can provide fundamental information for understanding the biogeochemical cycling of organic matter in the ocean. Here we investigate the patterns of EEA and the major factors affecting the seawater EEA of Chinese marginal seas. The geographic distribution of EEA along a latitudinal transect was examined and found to be associated with dissolved organic carbon. Compared with offshore waters, inshore waters had higher enzyme activity. All the tested substrates were hydrolyzed at different rates and phosphatase, β-glucosidase and protease contributed greatly to summed hydrolysis rates. For any particular enzyme activity, the contribution of dissolved to total EEA was strongly heterogenous between stations. Comparisons of hydrolysis rates of the polymers and their corresponding oligomers suggest that molecule size does not necessarily limit the turnover of marine organic matter. In addition, several typical enzyme-producing clades, such as Bacteroidetes, Planctomycetes, Chloroflexi, Roseobacter, Alteromonas, and Pseudoalteromonas, were detected in the in situ environments. These enzyme-producing clades may be responsible for the production of different enzymes. Overall, each enzyme was found to flexibly respond to environmental conditions and were linked to microbial community composition. It is likely that this activity will profoundly affect organic matter cycling in the Chinese marginal seas.

Li, Y., Sun, P., Liu, Z., Wang, J., Li, Y., Zhang, M., 2019. Lake level controls on oil shale distribution in the Lucaogou Formation, Wujiawan area, Junggar Basin, northwest China. Energy & Fuels 33, 8383-8393.


In a thick section of the upper Permian, high-quality oil shale is present in the Lucaogou Formation on the northern flanks of Bogda Mountain, which is located in the southern Junggar Basin, northwest China. However, the distribution of these oil shales has yet to be studied. Based on 56 boreholes and associated oil yield analytical data in the area of Wujiawan in the south Junggar Basin, we investigated the distribution and formation of these oil shales. The oil shales in the Lucaogou Formation have an average oil yield of 6.09 wt %, and the maximum is 22.27 wt %. According to the borehole and oil yield data, the oil shale formed in a third-order sequence and was deposited mainly in the transgressive system (TST) and high stand tracts (HST). The oil shale has an average TOC content of 12.12 wt %, and the average petroleum potential is 66.54 mg/g. The TST oil shale mainly contains type II kerogen, which was derived from terrestrial sources and lake algae. The oil shale deposited during the early stages of the TST occurs locally distributed and occurs as lens-shaped bodies. As the lake level rose, the area over which the oil shale was deposited gradually increased, along with the thickness, extent, and oil yield. The oil shale layers increase in the average thickness from 6.69 to 11.36 m, from the base to top of the TST, and the average oil yield increases from 5.66 to 6.90 wt %. In the HST, the oil shale has an average TOC content of 20.56 wt %. Also, the average petroleum generation potential (S1 + S2) is up to 130.41 mg/g. Additionally, the organic matter type is largely type I kerogen and dominantly lake algae. The HST oil shale is thick (up to 130 m), layered, and continuously and widely distributed. Several parasequences can be identified in a single layer of oil shale, and the average thickness and oil yield of each parasequence are 10.13–12.47 m and 5.27–7.07 wt %, respectively. The curve change trends of V/(V + Ni), Ni/Co, and Cu/Zn are divided into three stages: phase I, rise (TST); phase II, high-Value zone (HST); and phase III, stable zone (HST). A similar trend of change was found in comparisons between the central and eastern regions, which showed that with the rise of a lake plane, the lake changes from an oxygen-poor to oxygen-deficient condition, which increases the space and is conducive to the formation of oil shale.

Li, Y., Yang, Z., Li, X., 2019. Molecular simulation study on the effect of coal rank and moisture on CO2/CH4 competitive adsorption. Energy & Fuels 33, 9087-9098.


The CO2-enhanced coalbed methane recovery (CO2-ECBM) technique is based on competitive adsorption. In this study, three models of different coal ranks were established using the molecular dynamics (MD) method. A combination of MD and grand canonical Monte Carlo (GCMC) simulations was used to investigate the competitive adsorption of CO2/CH4 on dry and moist coal. The effects of coal rank and moisture content on pore structure, chemical structure, mixed gas adsorption capacity, and adsorption selectivity are discussed in detail. Simulation results show that from low- to high-rank coals, the total pore volume, porosity, and proportion of effective pores increase, which leads to an increase in their adsorption capacity. In addition, the oxygen-containing functional groups on the pore surface of coal enhance the displacement effect of CO2 on CH4, and with an increase in coal rank the adsorption selectivity of CO2/CH4 decreases. Moreover, the adsorption capacity of CO2 and CH4 will decrease owing to moisture. Water molecules will preferentially occupy the high-energy adsorption sites on the pore surface of coal, and then hydrogen bonding and capillary condensation will form water clusters. Therefore, in the case of moist coal, the adsorption selectivity of CO2 to CH4 fluctuates and shows different patterns of variation according to the different effective pore volumes of different coal ranks. From the perspective of CO2-ECBM, achieving a certain moisture content can have a beneficial effect, and the optimal moisture content of medium- and high-rank coal should be higher than that of low-rank coal. Under low-pressure conditions, the adsorption selectivity of CO2/CH4 of dry and moist coal is larger than that of high-pressure conditions. In our work, we advance the understanding of the microscopic mechanism of competitive adsorption of CO2/CH4, which provides a theoretical basis for improving CO2-ECBM technology.

Li, Z., Kang, W., Bai, B., Wu, H., Gou, C., Yuan, Y., Xu, D., Lu, Y., Hou, J., 2019. Fabrication and mechanism study of the fast spontaneous emulsification of crude oil with anionic/cationic surfactants as an enhanced oil recovery (EOR) method for low-permeability reservoirs. Energy & Fuels 33, 8279-8288.


An emulsion that can be fast and spontaneously formed in reservoirs will be greatly beneficial to the oil recovery improvement in low-permeability reservoirs. Herein, an ultralow interfacial tension spontaneous emulsification (SE) system consisting of a novel anionic alkyl polyglucoside sodium hydroxypropyl sulfonate surfactant (APGSHS) surfactant and a cationic cetyltrimethylammonium bromide (CTAB) surfactant was proposed and studied for low-permeability reservoirs. The spontaneous emulsions were characterized in terms of morphology and size distribution of droplets. Multiple-light scattering method was applied to evaluate the stability and dynamic instability mechanism of O/W emulsions. In addition, the viscoelasticity and shear-recovery performance of emulsions were also investigated. The combined SE systems can form the spontaneous emulsions via once bottom-up cycle, and the average droplets size of optimum emulsion with 6:4 molar ratio is ∼0.2 μm, which is small enough to migrate in the porous media at low-permeability reservoirs. Besides, the coalescence and creaming of oil droplets, as well as clarification thickness, are well-deferred. The viscoelasticity and shear-recovery capacity can also be improved with the presence of combined SE systems. The efficient interfacial activity and emulsion performances can be attributed to the strong electrostatic attraction between anionic and cationic surfactants, which enables the formation of a tighter arrangement film on an oil/water interface. Ultimately, the core flooding experiments show that the optimum SE system can effectively enhance oil recovery by 14.14% of the initial oil in place and significantly decrease the injected pressure. Hence, the newly formulated spontaneous emulsification system with anionic/cationic surfactants exhibit remarkable performances and can be used as an ideal candidate for EOR in low-permeability reservoirs.

Liang, F., Zhang, Q., Cui, H., Meng, Q., Ma, C., Liang, P., Guo, W., 2019. Controlling factors of organic nanopore development: A case study on marine shale in the middle and upper Yangtze region, South China. Acta Geologica Sinica - English Edition 93, 1047-1059.

https://doi.org/10.1111/1755-6724.13800

The Upper Ordovician Wufeng-Lower Silurian Longmaxi and the Lower Cambrian Qiongzhusi shales are the major targets for shale gas exploration and development in China. Although the two organic-rich shales share similar distribution ranges and thicknesses, they exhibit substantially different exploration and development results. This work analyzed the nanopore structures of the shale reservoirs in this region. Pore development of 51 shale samples collected from various formations and locations was compared using the petromineralogical, geochemical, structural geological and reservoir geological methods. The results indicate that the reservoir space in these shales is dominated by organic pores and the total pore volume of micropores, mesopores, macropores in different tectonic areas and formations show different trends with the increase of TOC. It is suggested that organic pores of shale can be well preserved in areas with simple structure and suitable preservation conditions, and the shale with smaller maximum ancient burial depth and later hydrocarbon-generation-end-time is also more conducive to pore preservation. Organic pore evolution models are established, and they are as follows: ? Organic matter pore development stage, ? Early stage of organic matter pore destruction, and ? late stage of organic matter pore destruction. The areas conducive to pore development are favorable for shale gas development. Research results can effectively guide the optimization and evaluation of favorable areas of shale gas.

Liang, F., Zhang, Q., Xiong, X., Cui, H., Liang, P., Ma, C., 2019. Sedimentary evolution model of Upper Ordovician Wufeng-Lower Silurian Longmaxi organic-rich shale in the Sichuan Basin and its surrounding area. Acta Sedimentologica Sinica 37, 847-857.

http://www.cjxb.ac.cn/EN/abstract/abstract4027.shtml

The Upper Ordovician Wufeng-Lower Silurian Longmaxi organic-rich shale in the Sichuan Basin and its peripheral regions,whose thickness is 20-60 m,is the main focus for the exploration and development of shale gas in China. According to our research in recent years,the temporal and spatial distribution of the organic-rich shale varies greatly. Based on the observation of key sections,core drilling,lithosphere biostratigraphy,geochemistry and miner-al analysis,the spatial-temporal distribution characteristics of the organic-rich shale in the Sichuan Basin and its sur-rounding areas were clarified. Three types of organic-rich shale depositional evolutionary models were established, which are described as follows:(1) The "two sags

sandwiched between three uplifts" model in the Changning-Weiyu-an area:the organic-rich shale deposits at WF2-LM5 in Changning and at LM1-LM8 in Weiyuan. The thickness of the organic-rich shale in the uplift is much thinner than that in the sags. (2) The "stage-progressive distribution pat-tern" model in the Chongqing and Qianjiang area:The closer the area is to the interior of the basin,the later the sedi-mentation of the organic-rich shale tends to end. The Jiaoshiba area is the depositional center of the shale,while the thickness of other areas is relatively thin. (3) The "stable uplifting" model in northeastern Sichuan:The organic-rich shale in Well Wuxi 2 in the center of the basin has a large thickness and a long depositional duration (WF2-LM9). The thickness of the shale in the marginal area of the basin is significantly thinner,and the region presents an overall upward trend. With the passage of time,the organic shale depositional area becomes smaller and smaller. In general, the deposition of these shales is mainly influenced by the Guangxi movement. The organic-rich shale sedimentary cen-ters tend to move northward gradually,and the shale only deposits in the Weiyuan and Wuxi areas after the Aeronian stage in the Sichuan Basin. The research results have an important guiding significance for the micro-layer division and fine reservoirs contrast of the Wufeng-Longmaxi shale in this area.



1. Objective. Fluid inclusions are the only way to obtain the volatile components in the process of hydrocarbon accumulation. The Marine Paleozoic strata in the South Yellow Sea Basin are of great thickness and widely distributed. The Lower Paleozoic source rocks, reservoirs and caprocks are developed and have generally good hydrocarbon geological conditions. Fluid inclusion analysis of Silurian drilling core samples can restore the hydrocarbon accumulation process, so as to deepen the understanding of marine hydrocarbon accumulation and guide oil and gas exploration in this area.

2. Methods. Eight samples came from Silurian and were collected from the South Yellow Sea Basin, derived from the continental shelf scientific drilling program. About 100 g of the core sample was placed into the grinding tank each time and vacuumed it to below 10 Pa. Afterwards, the ball mill was started to pulverize the sample to 300–500 mesh to ensure the sample gas was completely released. The gas in the grinding tank was collected by the liquid discharging method and directly delivered to the instruments of gas chromatography (PE. Clarus600), chromatography mass spectrometry (Agilent 6890GC/5975iMS), isotope mass spectrometry (Trace GC ULTRA-MAT 253 IRMS), to study the composition of fluid inclusions, isotopic characteristics, and characteristics of saturated hydrocarbon biomarkers. The data for the eight samples studied are included in Table 1.

3. Results. 3.1. Fluid inclusion gas compositions: Gas chromatography analysis of eight Silurian sandstone samples, the gas composition of the inclusions is mainly CH4, followed by N2 and H2 with very low content (Table 1).

3.2. Isotopic geochemical characteristics of inclusion gas: Carbon isotope analysis of hydrocarbon inclusions show that the δ13C1 value ranges from −43.3‰ to −36.6‰ and the δ13Cco2 value is generally less than −10‰, from −14.2‰ to −11.6‰, reflecting the natural gas is of organic origin (Dai JX et al., 2014). The δ13C2 value varies from −34.3‰ to −30.3‰, and the δ13C3 value is between −33.8‰ and −28.4‰, which is characterized by oil-type gas (Dai JX et al., 2014). Ro is thus calculated to be in the range of 0.85% and 2.24% according to δ13C1-Ro relationship, indicating a stage of mature to high-mature.

3.3. Analysis of geochemical characteristics of hydrocarbon inclusions: Based on the biomarker analysis of saturated hydrocarbon in hydrocarbon inclusions, n-alkanes are mainly nC14–nC29, with the number of carbons in the main peak mostly nC16–nC18, presenting a bimodal state. Gammacerane is contained, belonging to the reducing environment (Ju YW et al., 2018). The relative contents of sterane in ααα20RC27, ααα20RC28, and ααα20RC29 show an asymmetric “V” distribution, indicating that the aquatic animals such as algae have a large contribution to source rocks. Ts<Tm suggests it is likely to be a late hydrocarbon generation stage (Maravelis AG et al., 2017). The “UCM” drum and 25-norhopane series coexist and the Pr/Ph value is 0.87–1.34, indicating the existence of second hydrocarbon emplacement stage in the Silurian reservoir (Fig. 1).

4. Conclusions

(i) The fluid inclusion analysis confirms that large-scale natural gas accumulation was developed in the Silurian strata in the South Yellow Sea Basin. The main component is proved to be methane, which is of organic origin, indicating a stage of mature to high-mature.

(ii) The type of natural gas of the Silurian reservoir is mature-high mature based on saturated hydrocarbon biomarkers analysis. The existence of a second hydrocarbon emplacement stage is found, and source rocks mainly are formed from the aquatic animals.

Liang, Y., Shan, X., Makeen, Y.M., Abdullah, W.H., Hao, G., Tong, L., Lawal, M., Zhao, R., Ayinla, H.A., 2019. Geochemical characteristics of oil from Oligocene Lower Ganchaigou Formation oil sand in northern Qaidam Basin, China. Natural Resources Research 28, 1521-1546.

https://doi.org/10.1007/s11053-019-09466-9

Oil from the Oligocene oil sands of the Lower Ganchaigou Formation in the Northern Qaidam Basin and the related asphaltenes was analyzed using bulk and organic geochemical methods to assess the organic matter source input, thermal maturity, paleo-environmental conditions, kerogen type, hydrocarbon quality, and the correlation between this oil and its potential source rock in the basin. The extracted oil samples are characterized by very high contents of saturated hydrocarbons (average 62.76%), low contents of aromatic hydrocarbons (average 16.11%), and moderate amounts of nitrogen–sulfur–oxygen or resin compounds (average 21.57%), suggesting that the fluid petroleum extracted from the Oligocene oil sands is of high quality. However, a variety of biomarker parameters obtained from the hydrocarbon fractions (saturated and aromatic) indicate that the extracted oil was generated from source rocks with a wide range of thermal maturity conditions, ranging from the early to peak oil window stages, which are generally consistent with the biomarker maturity parameters, vitrinite reflectance (approximately 0.6%), and Tmax values of the Middle Jurassic carbonaceous mudstones and organic-rich mudstone source rocks of the Dameigou Formation, as reported in the literature. These findings suggest that the studied oil is derived from Dameigou Formation source rocks. Furthermore, the source- and environment-related biomarker parameters of the studied oil are characterized by relatively high pristane/phytane ratios, the presence of tricyclic terpanes, low abundances of C27 regular steranes, low C27/C29 regular sterane ratios, and very low sterane/hopane ratios. These data suggest that the oil was generated from source rocks containing plankton/land plant matter that was mainly deposited in a lacustrine environment and preserved under sub-oxic to oxic conditions, and the data also indicate a potential relationship between the studied oil and the associated potential source rocks. The distribution of pristane, phytane, tricyclic terpanes, regular steranes and hopane shows an affinity with the studied Oligocene Lower Ganchaigou Formation oil to previously published Dameigou Formation source rocks. In support of this finding, the pyrolysis–gas chromatography results of the analyzed oil asphaltene indicate that the oil was primarily derived from type II organic matter, which is also consistent with the organic matter of the Middle Jurassic source rocks. Thus, the Middle Jurassic carbonaceous mudstones and organic rock mudstones of the Dameigou Formation could be significantly contributing source rocks to the Oligocene Lower Ganchaigou Formation oil sand and other oil reservoirs in the Northern Qaidam Basin.

Liduino, V.S., Payão Filho, J.C., Cravo-Laureau, C., Lutterbach, M.T., Camporese Sérvulo, E.F., 2019. Comparison of flow regimes on biocorrosion of steel pipe weldments: Fluid characterization and pitting analysis. International Biodeterioration & Biodegradation 144, 104750.


Pitting corrosion in microalloyed steel and its welded joints occur in fabricated structures, such as pipelines for oil and gas transport, which are exposed to corrosive environments. Although the formation of the pits consumes only a relatively small mass of material, the role of the pits as defect sites for crack initiation and continuing corrosion can be substantial. Furthermore, in natural and industrial environments where microorganisms are widely distributed, pitting corrosion is aggravated by the release of many reactive microbial metabolites. This is a report of a 28-day study aimed at the microbiologically influenced corrosion of joint

welds by gas tungsten arc welding (GTAW) and shielded metal arc welding (SMAW) exposed to laminar and turbulent flows. The characterization of the planktonic microbial community indicated that laminar flow created an anoxic environment promoting the dominance of anaerobic microorganisms, in particular sulfate reducing bacteria (SRB). Both types of welded joints showed similar pit densities in the base metal (BM), heat-affected zone (HAZ) and weld metal (WM), nevertheless the pit depth was higher in the HAZ than the BM and WM. On the other hand, turbulent flow retained dissolved oxygen content, ensuring the presence of aerobic microorganisms, but there was no inhibition of SRB growth. Although the pit depth was low in both types of welded joints, the pit density was exacerbated in only one HAZ of each welded joint due to WM reinforcement height, while the other HAZ showed low pit density. This study demonstrates that turbulent flow can reduce the biocorrosion of non-welded areas but can aggravate welded joints biocorrosion.

Lincy, J., Manohar, C., 2019. High-throughput screening of sediment bacterial communities from Oxygen Minimum Zones of the northern Indian Ocean. Biogeosciences Discussions 2019, 1-28.


The Northern Indian Ocean host two recognized Oxygen Minimum Zones (OMZ): one in the Arabian Sea and the other in the Bay of Bengal region. The next-generation sequencing technique was used to understand the total bacterial diversity from the surface sediment of off Goa within the OMZ of Arabian Sea, and from off Paradip within the OMZ of Bay of Bengal. The dominant phyla identified include Firmicutes (33.06 %) and Proteobacteria (32.44 %) from the Arabian Sea, and Proteobacteria (52.51 %) and Planctomycetes (8.63 %) from the Bay of Bengal. Statistical analysis indicates that bacterial diversity from sediments of the Bay of Bengal OMZ is ~ 48 % higher than the Arabian Sea OMZ. Diverse candidate bacterial clades were also detected, whose function is unknown, but many of these were reported from other OMZs as well, suggesting their putative role in sediment biogeochemistry. Bacterial diversity from the present study reveals that the off Paradip site of Bay of Bengal OMZ is highly diverse and unexplored in comparison to the off Goa site of the Arabian Sea OMZ. Functional diversity analysis indicates that the relative percentage distribution of genes involved in methane, nitrogen, sulfur and many unclassified energy metabolisms is almost the same in both sites, reflecting a similar ecological role, irrespective of the differences in phylotypic diversity.

Lindgren, J., Nilsson, D.-E., Sjövall, P., Jarenmark, M., Ito, S., Wakamatsu, K., Kear, B.P., Schultz, B.P., Sylvestersen, R.L., Madsen, H., LaFountain, J.R., Alwmark, C., Eriksson, M.E., Hall, S.A., Lindgren, P., Rodríguez-Meizoso, I., Ahlberg, P., 2019. Fossil insect eyes shed light on trilobite optics and the arthropod pigment screen. Nature 573, 122-125.

https://doi.org/10.1038/s41586-019-1473-z

Fossilized eyes permit inferences of the visual capacity of extinct arthropods1–3. However, structural and/or chemical modifications as a result of taphonomic and diagenetic processes can alter the original features, thereby necessitating comparisons with modern species. Here we report the detailed molecular composition and microanatomy of the eyes of 54-million-year-old crane-flies, which together provide a proxy for the interpretation of optical systems in some other ancient arthropods. These well-preserved visual organs comprise calcified corneal lenses that are separated by intervening spaces containing eumelanin pigment. We also show that eumelanin is present in the facet walls of living crane-flies, in which it forms the outermost ommatidial pigment shield in compound eyes incorporating a chitinous cornea. To our knowledge, this is the first record of melanic screening pigments in arthropods, and reveals a fossilization mode in insect eyes that involves a decay-resistant biochrome coupled with early diagenetic mineralization of the ommatidial lenses. The demonstrable secondary calcification of lens cuticle that was initially chitinous has implications for the proposed calcitic corneas of trilobites, which we posit are artefacts of preservation rather than a product of in vivo biomineralization4–7. Although trilobite eyes might have been partly mineralized for mechanical strength, a (more likely) organic composition would have enhanced function via gradient-index optics and increased control of lens shape.

Liu, H., Liu, Z., Zhao, C., Liu, W., 2019. n-Alkyl lipid concentrations and distributions in aquatic plants and their individual δD variations. Science China Earth Sciences 62, 1441-1452.

https://doi.org/10.1007/s11430-019-9370-8

Aquatic plants are major input sources of autochthonous organic matter in lake sediments, but investigations on fatty acid (FA) and n-alkane distributions in aquatic plants are currently limited, greatly hindering the applications of their isotope geochemistry in lacustrine environments. Here, the reported n-alkyl lipid distributions of aquatic plants in globally studied lakes, together with newly obtained aquatic plant n-alkyl lipid data in Chinese lakes (Yunnan and Inner Mongolia), are used to understand their distribution characteristics. The results show that aquatic plants have predominantly mid-chain lipids (C23–C25n-alkanes and C22–C24 FAs), differing from that of terrestrial plants (dominant by long-chain lipids), but the long-chain n-alkanes (e.g., C27 and C29) and long-chain FAs (e.g., C26 and C28) also show high abundances in most samples. Submerged plants have high concentrations of long-chain n-alkanes (avg. 47 µg g−1) and long-chain FAs (avg. 170 µg g−1), close to those in terrestrial plants, indicating that submerged plants may make large contributions of long-chain n-alkyl lipids to lake sediments, while the contributions of long-chain n-alkyl lipids derived from algae to lake sediments may be small because of their low concentrations (avg. 2 µg g−1 for n-alkanes and 9 µg g−1 for FAs). We find that lipid molecular proxies (including ACL14–32 and ATR14–18) can be reliably used to distinguish the FAs sourced from algae and other plants, and Paq’ values can be utilized to distinguish the n-alkane sources between submerged plants and terrestrial plants. Aquatic plants do not have significant δD differences among different chain-length n-alkanes and FAs for each sample, suggesting that the offset between δD values of different chain-length n-alkyl lipids in lake sediments can help determine sedimentary lipid input sources and infer paleohydrological changes.

Liu, H., Zartman, R.E., Ireland, T.R., Sun, W.-d., 2019. Global atmospheric oxygen variations recorded by Th/U systematics of igneous rocks. Proceedings of the National Academy of Sciences 116, 18854-18859.


Significance: Scientists have been working on the dating of atmospheric oxygenation in Earth’s history for decades. However, most previous studies relied on evidence from sedimentary rocks. Here, we show that igneous rocks can also be linked with surface oxidation by a key geological process: plate subduction. We here make an attempt to apply the Th/U of worldwide arc igneous rocks as an indicator for the timing of atmospheric oxygenation over the Earth’s history. The results are coincident with the previously defined Great Oxidation Event and Neoproterozoic Oxygenation Event.

Abstract: Atmospheric oxygen has evolved from negligible levels in the Archean to the current level of about 21% through 2 major step rises: The Great Oxidation Event (GOE) in the early Proterozoic and the Neoproterozoic Oxygenation Event (NOE) during the late Proterozoic. However, most previous methods for constraining the time of atmospheric oxygenation have relied on evidence from sedimentary rocks. Here, we investigate the temporal variations of the Th/U of arc igneous rocks since 3.0 billion y ago (Ga) and show that 2 major Th/U decreases are recorded at ca. 2.35 Ga and ca. 0.75 Ga, coincident with the beginning of the GOE and NOE. The decoupling of U from Th is predominantly caused by the significant rise of atmospheric oxygen. Under an increasingly oxidized atmosphere condition, more uranium in the surface environment became oxidized from the water-insoluble U4+ to the water-soluble U6+ valance and incorporated in the sea water and altered oceanic crust. Eventually, the subduction of this altered oceanic crust produced the low-Th/U signature of arc igneous rocks. Therefore, the sharp decrease of Th/U in global arc igneous rocks may provide strong evidence for the rise of atmospheric oxygen. We suggest that the secular Th/U evolution of arc igneous rocks could be an effective geochemical indicator recording the global-scale atmospheric oxygen variation.

Liu, J., An, Z., Wu, H., Yu, Y., 2019. Comparison of n-alkane concentrations and δD values between leaves and roots in modern plants on the Chinese Loess Plateau. Organic Geochemistry 138, 103913.


Sedimentary δDn-alkane values have been widely used as a valuable proxy for paleoenvironmental reconstruction. A number of studies have focused on δDn-alkane values that derived exclusively from leaves, while less attention has been paid to the root-derived n-alkanes and their impact on sedimentary δDn-alkane values. In this study, we sampled modern plant leaf and root materials from different growth contexts (slopes and seasons) on the Chinese Loess Plateau to compare leaf-derived n-alkanes with root-derived n-alkanes. Our results demonstrated that total n-alkane (C27–C33) concentrations varied substantially between leaf and root materials, with average values of 209  and 29.5 μg/g observed in leaves and roots respectively. The results suggest that ca. 12% of the n-alkane concentrations in sediments may be derived from plant roots. Furthermore, leaf-derived δDn-alkane values for Stipa bungeana (grass), Artemisisa vestita (shrub) and Bothriochloa ischaemum (grass) averaged −184‰, −152‰ and −198‰, compared with their root-derived δDn-alkane values of −199‰, −179‰ and −163‰, respectively. These statistically significant differences in concentrations and δD values between leaf-derived and root-derived n-alkanes suggest that the contribution of n-alkanes derived from plant roots is important for evaluating the resultant n-alkane compositions of sediments for paleoenvironmental reconstruction. Our findings indicates that the effects of root-derived n-alkanes on total sedimentary δDn-alkane values should be considered carefully in future paleoenvironmental reconstruction efforts.

Liu, K., Li, S., 2020. Biosynthesis of fatty acid-derived hydrocarbons: perspectives on enzymology and enzyme engineering. Current Opinion in Biotechnology 62, 7-14.


Enormous fuel consumption and growing environmental concerns have been spurring development of renewable biofuels. Among various biofuels, fatty acid-derived biohydrocarbons are ideal alternatives to non-renewable fossil fuels due to their closest properties to petroleum-based fuels. In the past decade, novel hydrocarbon-producing enzymes have continuously been discovered and engineered. Here, we review the recent advances in biosynthesis of fatty acid-derived hydrocarbons with emphasis on enzymology and enzyme engineering, based on which some outlooks are provided.

Liu, L.-h., Wang, C.-l., Zhao, X.-m., 2019. First report of TSR origin minerals filled in anhydrite dissolved pores in southeastern Ordos Basin. China Geology 2, 245-247.


1. Objective. Yican 1 well, drilled in Southeastern Ordos Basin by Oil & Gas Survey, China Geological Survey in 2014 produced 3.7×104 m3 natural gas daily, which is the most productive well in the area by far. However, the reservoir quality is poor compared with those of Jingbian gas field in the middle of the Basin, which is mainly caused by the pores filling in karst reservoir. The minerals filled in karst pores in southeastern Ordos Basin is mainly calcite, which filled more than 90% anhydrite dissolved pores and resulted in the loss of the porosity, whereas in Jingbian gas field, the pores are mainly filled by dolomite of less than 70% remaining much reservoir space. Therefore, the pores filling composition and filling degree control the spatial distribution of the reservoir. It’s favorable to find reservoir to study the characteristics and the formation mechanism of pores filling minerals.

2. Methods. More than 22 core samples were taken from Yican1 well in Southeast of Ordos Basin from a range of depths (600–3200 m) and were examined petrographically. Petrographic studies were performed with an optical microscope and thin section which were stained to discriminate between calcite and dolomite. The filled minerals in pores and matrix dolomite were separated by microdrill to compare the isotope composition. Carbon isotope analysis of the filled minerals was performed using a laser sampling device linked to a conventional mass spectrometer. The authors calculated the homogenization temperature and salinity of the fluid inclusion in quartz, calcite and dolomite for comparison.

3. Results. The anhydrite dissolved pores are mainly filled with quartz, calcite, dolomite and pyrite et al. (Fig. 1). Through homogenization temperature and salinity analysis of the fluid inclusion, the homogenization temperature of quartz, calcite and dolomite filled in anhydrite dissolved pores is 113‒154 °C, 140‒174 °C and 190‒196 °C, respectively. The temperature of dolomite precipitated is significantly higher than the maximum

temperature of the strata, which may be affected by hydrothermal fluid. The salinity calculated from the freezing temperature in three minerals is all between 15.47% and 23.18%, which indicates that the minerals filled in pores are formed in high temperature and high salinity diagenetic fluid in buried condition. The δ34S value varies from 10.50‰–24.00‰, average of 17.33‰, which shows the characteristics of TSR (Thermo-Chemical Sulfate Reduction) origin.

The carbon and oxygen isotope analysis result reveals that the average δ13C value is −4.66‰ and average δ18O value of filled minerals is −12.12 ‰ respectively; both values are significantly lower than those in corresponding dolomite, which is −1.84 ‰ and −8.47 ‰ respectively. The homogenization temperature and salinity result of the fluid inclusion suggest that the extreme low δ13 C value is caused by the organic carbon in deep buried strata, whereas the relative high δ18O value is caused by the high temperature of deep strata.

Previous studies considered that the anhydrite dissolved pores are filled in near surface environment as soon as the anhydrite is dissolved from meteoric water (Zhang JT et al., 2016). However, based on above analysis, the minerals filled in anhydrite dissolved pores in southeastern Ordos basin are mainly precipitated in buried condition. The basic principle is according to retrograde solubility model of carbonate, namely with the increasing of formation temperature, the carbonate mainly precipitates but not dissolves (Huang SJ et al., 2009). Since uplifted and erosion in Caledonian, the Ordovician stratum is buried continually until late Cretaceous (Fig. 2) (Ren ZL et al., 2017). The carbonate solubility decreases with the increasing of temperature in deep buried depth. The pore fluid becomes saturated with respect to minerals such as calcite and dolomite, which precipitate in the pores and cause the reservoir quality worse.

Besides, under the high temperature of deep buried condition, TSR occurred in the high salinity fluid, which caused the authigenic calcite precipitated with low δ13C value and pyrite precipitated with high δ34S value (Fig. 1c, d). H+ will be released when TSR occurred, which reduced the PH value of the strata fluid and facilitated the authigene quartz precipitated, which can interpret the closely connection of calcite and quartz in time and space.

4. Conclusion. Based on the above analysis, it can be concluded that the anhydrite dissolved pores are mainly filled in deep buried condition, where TSR provides CO2 for calcite precipitation and H2S for the formation of pyrite, which is different from the diagenisis in meteoric water.

Liu, P., Harman, C.E., Kasting, J.F., Hu, Y., Wang, J., 2019. Can organic haze and O2 plumes explain patterns of sulfur mass-independent fractionation during the Archean? Earth and Planetary Science Letters 526, 115767.


The existence of mass-independently fractionated sulfur in Archean rocks is almost universally accepted as evidence for low atmospheric O2 and O3 concentrations at that time. But the detailed patterns of the Δ33S values and of the ratios Δ33S/δ34S and Δ36S/Δ33S remain to be explained, and the mechanism for producing the mass-independent fractionation remains controversial. Here, we explore the hypothesis that the relatively low Δ33S values seen during the Mid-Archean, 2.7-3.5 Ga, were caused by the presence of organic haze produced from photolysis of methane. This haze helped shield SO2 from photolysis, while at the same time providing surfaces on which unfractionated short-chain sulfur species could condense. The evolution of oxygenic photosynthesis, and the concomitant disappearance of organic haze towards the end of the Archean allowed more negatively fractionated S4 and S8 to form, thereby generating large positive fractionations in other sulfur species, including sulfate and H2S. Reduction of this sulfate to H2S by bacteria, followed by incorporation of H2S into pyrite, produced the large positive Δ33S values observed in the Neoarchean rock record, 2.5-2.7 Ga.

Liu, S., Liu, H., Wang, Z., Cui, Y., Chen, R., Peng, Z., Yuan, S., Shi, L., 2019. Benzene promotes microbial Fe(III) reduction and flavins secretion. Geochimica et Cosmochimica Acta 264, 92-104.


The microbial reduction of Fe(III) (oxyhydr)oxide is widespread in subsurface and plays a critical role in both the biogeochemical cycle of iron and the fate of contaminants. Monocyclic aromatic compounds are ubiquitous

constituents of organic matter in many geologic environments and contaminated subsurface. Benzene is a typical monocyclic aromatic compound and frequently occurs in the subsurface environment. Due to its carcinogenicity and cytotoxicity, benzene may be toxic to the coexisted Fe(III)-reducing bacteria and thereby inhibit the microbial Fe(III) reduction. However, there is limited knowledge about the impact of the coexisting monocyclic aromatic compounds on the microbial Fe(III) reduction. In this study, the reduction of ferrihydrite by the dissimilatory iron-reducing bacterium Shewanella oneidensis MR-1 (MR-1) was investigated in the presence of benzene. Results showed that benzene had a negligible impact on the growth, cell morphology and integrity of MR-1, but it promoted the microbial Fe(III) reduction. The promotion of microbial Fe(III) reduction is maximum at benzene concentration of 3.8 μM. In the presence of 3.8 μM benzene, the produced Fe(II) from microbial Fe(III) reduction in 60 h doubled that in the absence of benzene, and the Fe(II)-O content of mineral surface after reduction experiment increased 4.73%. The promotion of microbial Fe(III) reduction was ascribed to the benzene induced increase of cell membrane permeability, which facilitated extracellular electron transfer and the secretion and release of flavin mononucleotide (FMN) as electron shuttle or cofactor. The impacts of benzene on the FMN secretion and microbial Fe(III) reduction have broad implications for both the cycling of iron and the biogeochemical transformation of redox-sensitive elements and contaminants in the benzene-containing subsurface environments.

Liu, X., Li, S., Zhang, J., Li, X., Zhao, S., Dai, L., Wang, G., 2019. Meso-Neoproterozoic strata and target source rocks in the North China Craton: A review. Precambrian Research 334, 105458.


Along with the breakup of the supercontinent Nuna and Rodinia during the Mesoproterozoic and Neoproterozoic, a series of sedimentary basins formed within or at the periphery of the ancient cratons. Under the regime of breakup of the supercontinent, these basins underwent different evolutionary history hence formed different geological elements constituting the petroleum systems. In this contribution, the distribution and the stratigraphic successions of the Meso-Neoproterozoic basins in the North China Craton (NCC) were examined, as well as the retrospective review for the mechanisms of the basin formation. The synthesized geological and geochronological data support a long-term extensional environment for the basins in the northern NCC. The Mesoproterozoic basins in the Yanshan, western Liaoning (Yan-Liao) and the Zhaertai areas formed at the intracratonic position later than that in the Bayan Obo, which possibly deposited in the continental margin. The further efforts still need to be devoted to decipher the huge controversial around the tectonic nature of the basins in the southern NCC, as well as their stratigraphic correlations with the basins in the north and central. The distribution and organic geochemical characteristics of the Mesoproterozoic source rock were also summarized. Three sets of source rock in the central NCC, namely the Chuanlinggou, Hongshuizhuang and Xiamaling Formations developed favorable geological and geochemical conditions for the generation of the hydrocarbon. While in the south, the Cuizhuang Formation was the only interval feasible for potential source rock. The progress in seismic geophysics and borehole drilling suggested the existence of the Mesoproterozoic beneath deep Ordos Basin. This open a new window for the reconstruction of the Mesoproterozoic paleogeography as well as the evaluation of the source potential of the Mesoproterozoic basins in the North China Craton.

Liu, Y., Hou, J., 2019. Investigation on the potential relationships between geophysical properties and CH4 adsorption in a typical shale gas reservoir. Energy & Fuels 33, 8354-8362.


The Longmaxi Formation is considered to be a potential shale gas reservoir in Sichuan Basin of China. In this work, 28 typical shale core samples are collected from the Longmaxi Formation and a comprehensive characterization of the geophysical and petrochemical properties of these core samples is obtained. Thermogravimetric method is applied to measure the excess CH4 adsorption on these shale samples; the adsorbed CH4 density is then calculated using the grand canonical Monte Carlo simulation method, which is consequently used to determine the absolute CH4 adsorption. Based on the converted absolute adsorption, the Langmuir adsorption model is employed to determine the maximum adsorption capacity of CH4 on these shale

samples. The inter-relationships between the adsorption capacity of CH4 and the geophysical properties of the 28 Longmaxi shale cores are analyzed. The geophysical and petrochemical characterization results show that the Longmaxi Formation generally possesses pores with diameter in the range of 1–10 000 nm, while mesopores (i.e., 2–50 nm) account for the most proportion. The Longmaxi shale has a complex mineral composition, wherein clay minerals constitute more than half of the total minerals. The maximum adsorption capacity of CH4 on these typical shale increases as the burial depth increases, indicating a higher potential for the commercial development of the Longmaxi shale with deep formations; in addition, the maximum adsorption capacity has a positive and linear relationship with the total organic carbon content. The CH4 adsorption presents linear and positive inter-relationships with clay minerals, i.e., illite and montmorillonite, other than kaolinite.

Liu, Y., Wu, B., Gong, Q., Cao, H., 2019. Geochemical characteristics of the lower Silurian Longmaxi Formation on the Yangtze Platform, South China: Implications for depositional environment and accumulation of organic matters. Journal of Asian Earth Sciences 184, 104003.


The organic-rich lower Silurian Longmaxi Formation is now regarded as the favorable target for shale gas exploration and production. However, the mechanism of organic matter accumulation in these deposits remains highly controversial. In this study, we investigate the total organic carbon (TOC) content and the major and trace element abundances of a newly recovered core from the Yangtze Platform to reconstruct the paleo-environment and to elucidate the factors that control organic matter accumulation. Our results suggest that the greenhouse conditions during the early Silurian were punctuated by several cooling events. Bottom water redox conditions improve gradually upsection with a transition from anoxic water conditions in the lower Longmaxi Formation to suboxic-oxic water conditions in the upper Longmaxi Formation. The primary productivity on the Yangtze Platform appears to have been high during deposition of the Longmaxi Formation, especially in its lower part, due to an enhanced phosphorus recycling. The strong correlations between TOC and copper and nickel imply that the productivity was especially critical to the organic matter accumulation in the lower Longmaxi Formation. Furthermore, the rapid consumption of dissolved oxygen in bottom water favored the establishment of anoxic water conditions, which facilitated organic matter preservation. The poor correlations between TOC and barium and phosphorus in the lower Longmaxi Formation likely reflect intense recycling of nutrients. The evolution of water redox conditions and accumulation of organic matters in the Longmaxi Formation can be related to global fluctuations in sea level and regional tectonic uplift of the Yangtze Platform.


http://advances.sciencemag.org/content/5/9/eaax3009.abstract

Multimodal microscopy that combines complementary nanoscale imaging techniques is critical for extracting comprehensive chemical, structural, and functional information, particularly for heterogeneous samples. X-ray microscopy can achieve high-resolution imaging of bulk materials with chemical, magnetic, electronic, and bond orientation contrast, while electron microscopy provides atomic-scale spatial resolution with quantitative elemental composition. Here, we combine x-ray ptychography and scanning transmission x-ray spectromicroscopy with three-dimensional energy-dispersive spectroscopy and electron tomography to perform structural and chemical mapping of an Allende meteorite particle with 15-nm spatial resolution. We use textural and quantitative elemental information to infer the mineral composition and discuss potential processes that occurred before or after accretion. We anticipate that correlative x-ray and electron microscopy overcome the limitations of individual imaging modalities and open up a route to future multiscale nondestructive microscopies of complex functional materials and biological systems.

Löhr, K., Borovinskaya, O., Tourniaire, G., Panne, U., Jakubowski, N., 2019. Arraying of single cells for quantitative high throughput laser ablation ICP-TOF-MS. Analytical Chemistry 91, 11520-11528.


Arraying of single cells for mass spectrometric analysis is a considerable bioanalytical challenge. In this study, we employ a novel single cell arraying technology for quantitative analysis and isotopic fingerprinting by laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS). The single cell arraying approach is based on a piezo-acoustic microarrayer with software for automated optical detection of cells within the piezo dispense capillary (PDC) prior to arraying. Using optimized parameters, single cell occupancy of >99%, high throughput (up to 550 cells per hour), and a high cell recovery of >66% is achieved. LA-ICP-TOF-MS is employed to detect naturally occurring isotopes in the whole mass range as fingerprints of individual cells. Moreover, precise quantitative determination of metal-containing cell dyes is possible down to contents of ∼100 ag using calibration standards which were produced using the same arrayer.


https://doi.org/10.1080/01490451.2019.1641770

Microbiological and geochemical data are presented to characterize the hydrogeochemistry and to investigate extant microbial life in fracture waters 2.4 km below surface, at the Kidd Creek Observatory in Canada. Previous studies identified the world’s oldest groundwaters with mean residence times on the order of millions to billions of years trapped in fractures in Precambrian host rock here. In this study, major ion chemistry, δ18O and δ2H isotopic signatures and dissolved gases in the fracture waters are shown to be distinct from potential contamination end-members, demonstrating the fracture waters are not impacted by waters used in mining operations. A previous work on sulfur isotope signatures suggested a longstanding indigenous population of sulfate-reducing bacteria in these highly reducing fluids and sufficient sulfate to support microbial activity. Here, we report the first evidence for extant visible and cultivable microbial life at this location. Anaerobic metabolisms were investigated using the Most Probable Number (MPN) method. The fracture fluids contained extant cells at low biomass density (∼103–104 cells/mL) and showed a strong response from autotrophic sulfate-reducers and alkane-oxidizing sulfate reducers. These lines of evidence provide the interpretational framework (chemical, hydrogeologic, and microbiologic) essential to the on-going genomic and metagenomic investigations at the Kidd Creek Observatory – the world’s most longstanding location for investigation of subsurface fluids and deep life at such profound depth.

Lopez, J.V., Peixoto, R.S., Rosado, A.S., 2019. Inevitable future: space colonization beyond Earth with microbes first. FEMS Microbiology Ecology 95, fiz127.

https://doi.org/10.1093/femsec/fiz127

Based on modern microbiology, we propose a major revision in current space exploration philosophy and planetary protection policy, especially regarding microorganisms in space. Mainly, microbial introduction should not be considered accidental but inevitable. We hypothesize the near impossibility of exploring new planets without carrying and/or delivering any microbial travelers. In addition, although we highlight the importance of controlling and tracking such contaminations—to explore the existence of extraterrestrial microorganisms—we also believe that we must discuss the role of microbes as primary colonists and assets, rather than serendipitous accidents, for future plans of extraterrestrial colonization. This paradigm shift stems partly from the overwhelming evidence of microorganisms’ diverse roles in sustaining life on Earth, such as symbioses and ecosystem services (decomposition, atmosphere effects, nitrogen fixation, etc.). Therefore, we propose a framework for new discussion based on the scientific implications of future colonization and terraforming: (i) focus on methods to track and avoid accidental delivery of Earth's harmful microorganisms and genes to extraterrestrial areas; (ii) begin a rigorous program to develop and explore ‘Proactive Inoculation Protocols’. We outline a rationale and solicit feedback to drive a public and private research agenda that optimizes diverse organisms for potential space colonization.

Loughery, J.R., Marentette, J.R., Frank, R.A., Hewitt, L.M., Parrott, J.L., Martyniuk, C.J., 2019. Transcriptome profiling in larval fathead minnow exposed to commercial naphthenic acids and extracts from fresh and aged oil sands process-affected water. Environmental Science & Technology 53, 10435-10444.

https://doi.org/10.1021/acs.est.9b01493

Surface mining and extraction of oil sands results in the generation of and need for storage of large volumes of oil sands process-affected water (OSPW). More structurally complex than classical naphthenic acids (NAs), naphthenic acid fraction components (NAFCs) are key toxic constituents of OSPW, and changes in the NAFC profile in OSPW over time have been linked to mitigation of OSPW toxicity. Molecular studies targeting individual genes have indicated that NAFC toxicity is likely mediated via oxidative stress, altered cell cycles, ontogenetic differentiation, endocrine disruption, and immunotoxicity. However, the individual-gene approach results in a limited picture of molecular responses. This study shows that NAFCs, from aged or fresh OSPW, have a unique effect on the larval fathead minnow transcriptome and provides initial data to construct adverse outcome pathways for skeletal deformities. All three types of processed NAs (fresh, aged, and commercial) affected the immunome of developing fish. These gene networks included immunity, inflammatory response, B-cell response, platelet adhesion, and T-helper lymphocyte activity. Larvae exposed to both NAFCs and commercial NA developed cardiovascular and bone deformities, and transcriptomic networks reflected these developmental abnormalities. Gene networks found only in NAFC-exposed fish suggest NAFCs may alter fish cardiovascular health through altered calcium ion regulation. This study improves understanding regarding the molecular perturbations underlying developmental deformities following exposure to NAFCs.

Lovley, D.R., Walker, D.J.F., 2019. Geobacter protein nanowires. Frontiers in Microbiology 10, 2078. doi: 10.3389/fmicb.2019.02078.


The study of electrically conductive protein nanowires in Geobacter sulfurreducens has led to new concepts for long-range extracellular electron transport, as well as for the development of sustainable conductive materials and electronic devices with novel functions. Until recently, electrically conductive pili (e-pili), assembled from the PilA pilin monomer, were the only known Geobacter protein nanowires. However, filaments comprised of the multi-heme c-type cytochrome, OmcS, are present in some preparations of G. sulfurreducens outer-surface proteins. The purpose of this review is to evaluate the available evidence on the in vivo expression of e-pili and OmcS filaments and their biological function. Abundant literature demonstrates that G. sulfurreducens expresses e-pili, which are required for long-range electron transport to Fe (III) oxides and through conductive biofilms. In contrast, there is no definitive evidence yet that wild-type G. sulfurreducens express long filaments of OmcS extending from the cells, and deleting the gene for OmcS actually increases biofilm conductivity. The literature does not support the concern that many previous studies on e-pili were mistakenly studying OmcS filaments. For example, heterologous expression of the aromatic-rich pilin monomer of Geobacter metallireducens in G. sulfurreducens increases the conductivity of individual nanowires more than 5,000-fold, whereas expression of an aromatic-poor pilin reduced conductivity more than 1,000-fold. This more than million-fold range in nanowire conductivity was achieved while maintaining the 3-nm diameter characteristic of e-pili. Purification methods that eliminate all traces of OmcS yield highly conductive e-pili, as does heterologous expression of the e-pilin monomer in microbes that do not produce OmcS or any other outer-surface cytochromes. Future studies of G. sulfurreducens expression of protein nanowires need to be cognizant of the importance of maintaining environmentally relevant growth conditions because artificial laboratory culture conditions can rapidly select against e-pili expression. Principles derived from the study of e-pili have enabled identification of non-cytochrome protein nanowires in diverse bacteria and archaea. A similar search for cytochrome appendages is warranted. Both e-pili and OmcS filaments offer design options for the synthesis of protein-based “green” electronics, which may be the primary driving force for the study of these structures in the near future.

Lu, G., Wei, C., Wang, J., Zhang, J., Quan, F., Tamehe, L.S., 2019. Variation of surface free energy in the process of methane adsorption in the nanopores of tectonically deformed coals: A case study of middle-rank tectonically deformed coals in the Huaibei coalfield. Energy & Fuels 33, 7155-7165.


Methane adsorption of coal is essentially a process of energy and material state transformation. It is a complex process especially for tectonically deformed coals (TDCs). In order to clarify this process, 12 middle-rank TDCs were screened for the experimental and theoretical study. On the basis of the liquid nitrogen adsorption experiment and methane isothermal adsorption experiment, the nanopore structure and the methane adsorption capacity of the TDC samples were analyzed. Using the theories of Polanyi adsorption potential and surface free energy reduction (SFER), the variation of energy in the process of methane adsorption in nanopores was explored. The following results were obtained. (1) The Langmuir volume has a stronger positive relationship with the specific surface area of the ultra-micropore, mild-micropore, and micropore than with those of the transitional pore. The adsorption potential decreases as the adsorption space grows; however, it rises as tectonic deformation enhances. The increase in the ratio of specific surface area for the mild-micropore and ultra-micropore indicates that the tectonic deformation can enhance both the available adsorption area and adsorption potential for methane in TDCs, eventually resulting in the increase of the Langmuir volume and the SFER. (2) The methane molecules preferentially occupy the sites with strong adsorption potential on the coal surface during the strong adsorption stage, resulting in the sharp increase of the methane adsorption volume and SFER. Then, the number of sites with strong adsorption potential decreases and the methane molecules have to settle at the energetically suboptimal sites during the weak adsorption stage, leading to the slight increase of methane adsorption volume and SFER. The above results may help to improve the accuracy of coalbed methane resource estimations and gas outburst prediction in the area where TDCs are developed.

Luan, G., Zhang, S., Lu, X., 2020. Engineering cyanobacteria chassis cells toward more efficient photosynthesis. Current Opinion in Biotechnology 62, 1-6.


Cyanobacteria photosynthetic biomanufacturing provides a promising technology route for green development, but an efficient photosynthesis system is required for economical competitive performance. Synthetic biology approaches have been adopted to improve photosynthesis productivity in cyanobacteria chassis cells and cell factories by remodeling cyanobacterial metabolism and physiology for more efficient absorption and utilization of solar energy and carbon dioxide. In addition, systematic assays of a newly identified cyanobacterium which performs efficient photosynthesis has provided extensive data elucidating new directions for tailoring cyanobacteria chassis cells with improved productivity. In this review, we summarize these two aspects of recent progress and suggest trends for future development.

Lukens, W.E., Eze, P., Schubert, B.A., 2019. The effect of diagenesis on carbon isotope values of fossil wood. Geology 47, 987-991.

https://doi.org/10.1130/G46412.1

The carbon isotope (δ13C) value of modern and fossil wood is widely used as a proxy for environmental and climatic change. Many researchers who study stable carbon isotopes in modern and recently deceased trees chemically extract cellulose (δ13Ccell) rather than analyzing whole wood (δ13Cwood) due to concerns that molecular variability across tree rings could influence δ13Cwood values, and that diagenesis may preferentially degrade cellulose over lignin. However, the majority of deep-time researchers analyze δ13Cwood without correcting for possible diagenetic effects due to cellulose loss. We measured δ13Ccell, δ13Cwood, and cellulose content of 38 wood fossils that span ∼50 m.y. in age from early Eocene to late Miocene, using variability across such a large range of geologic ages and settings as a natural laboratory in diagenesis. For comparison with our measurements, we produced a literature compilation of 1210 paired δ13Ccell and δ13Cwood values made on fossil and modern trees. We report that, on average, the apparent enrichment factor (ε) between δ13Ccell and δ13Cwood (ε = δ13Ccell – δ13Cwood) is 1.4‰ ± 0.4‰ larger in deep-time samples than Holocene wood, and this can be explained by loss of

cellulose during degradation, independent of atmospheric chemistry or climate conditions during growth. A strong linear correlation exists between δ13Cwood and δ13Ccell in both deep-time (r2 = 0.92) and Holocene (r2 = 0.87) samples, suggesting that either substrate can provide a reliable record of environmental conditions during growth. However, diagenetic effects must be corrected if δ13Cwood values are compared to extant trees or across long time scales, where cellulose content may vary.

Luo, S., Chen, X., Liu, A., Li, H., Sun, C., 2019. Characteristics and geological significance of canister desorption gas from the Lower Cambrian Shuijingtuo Formation shale in Yichang area, Middle Yangtze region. Acta Petrolei Sinica 40, 941-955.

http://www.syxb-cps.com.cn/EN/abstract/abstract5738.shtml

As displaying good gas reserves, the Lower Cambrian Shuijingtuo Formation shale in Yichang area, Middle Yangtze region is a new exploration area of shale gas in Sichuan Basin. Based on the onsite analysis of gas-bearing property for 64 pieces of Shuijingtuo Formation gas shale from two shale gas exploration wells, this paper determines the analytical gas content, gas composition, carbon and hydrogen stable isotopic composition of analytical gas, analyzes the changes in the analytical gas composition and the gaseous hydrocarbon and carbon dioxide isotope during analytical process, and explores the occurrence state of shale gas, inversion characteristics and geological significance of gas stable isotope. The results show that Shuijingtuo Formation shale contains the analytical gas of 0.32-5.48 m3/t, and the formation with continuous gas content greater than 2 m3/t is 44.05 m thick, demonstrating a strong positive correlation between gas content and TOC. The analytical gas contains methane and ethane of 81.90% -95.48% and 0.78% -3.95%, respectively and also a trace of propane, classified as a typical dry gas; the content of nitrogen is a bit high in non-hydrocarbon gases, with an average of about 6.7%, and the carbon dioxide content is less than 1%, free of H2S. The adsorption gas and free gas accounts for 50% -60% and 40% -50% respectively. In the early stage of adsorption, CH4 and N2, with weak adsorbability, are first desorbed, followed by C2H6 and CO2, with strong adsorbability; until the end of gas analysis, a considerable amount of C2H6 and CO2 still has not been desorbed. During the analytical process, the carbon and hydrogen isotopes have changed, the variation range of δ13CH4, δ13C2H6, δ13C3H8, δ13CO2, δDCH4 and δDC2H6 is -39.92 ‰--25.86 ‰, -41.57 ‰--39.34 ‰, -40.89 ‰--35.46 ‰, -23.42 ‰--19.23 ‰, -136.90 ‰--128.00 ‰ and -160.45 ‰--155.30 ‰, respectively. Due to the mass fractionation effect of isotope, the methane carbon isotope and methane hydrogen isotope remained in the analytical process is increased by 5.15 ‰ -13.33 ‰ and 1.64 ‰ -8.90 ‰ respectively; the ethane carbon, hydrogen isotope and carbon isotope of carbon dioxide is basically unchanged. The gaseous carbon isotope fractionation is also affected by the physical properties of shale, and the larger pore volume will lead to a more significant methane carbon isotope fractionation effect, as well as a difference in the volume content of ethane. The isotope value of the gas sample taken by desorbing the half volume represents the average value of all gases; the average value of δ13CH4, δ13C2H6 and δ13C3H8 is -33.19 ‰, -40.04 ‰ and -39.07 ‰, respectively; the shale gas shows the "reverse order" feature of isotope:δ13CH4 > δ13C2H6,δ13C2H6 < δ13C3H8, δDCH4 > δDC2H6. Similar to the Lower Cambrian Qizhusi Formation in Weiyuan, Shuijingtuo Formation shale gas in Yichang area is also in the early stage of reversal of gaseous hydrocarbon isotope, and has the characteristics of multi-source composite thermogenic gas.

Luong, J., Hua, Y., Gras, R., Shellie, R.A., 2019. Uniformity and sensitivity improvements in comprehensive two-dimensional gas chromatography using flame ionization detection with post-column reaction. Analytical Chemistry 91, 11223-11230.


A 3D-printed microreactor for post-column reactions was successfully integrated with comprehensive two -dimensional gas chromatography. A two-stage post-column reaction provided a carbon-independent response, enhanced the flame ionization detection uniformity, and improved the detector sensitivity. These enhancements are critical to overcome challenges in analyses using comprehensive two-dimensional gas chromatography and flame ionization detection, which aim to separate and quantify multiple components. Post-column reaction flame ionization detection eliminated the requirement of multilevel and multicompound calibration, it enabled the determination of target analytes with a single-carbon-containing calibration compound with an accuracy of

±10%, and it improved the sensitivity for compounds that were not efficiently ionized by flame ionization detection. Extra column band-broadening caused by the incorporation of the 3D-printed microreactor was minimized using optimized reactor operating parameters and intercolumn connectivity. Chromatographic fidelity was in the practical domain of comprehensive 2D gas chromatography. Typical peak widths at half-height using the described approach ranged from 165 to 235 ms for probe compounds with retention factors spanning 5 < k < 40.

Lv, D., Lu, C., Wen, Z., Song, H., Yin, S., 2019. Coal-bed methane geology of the No. 2 coal seam in Fengfeng Coalfield, North China. Arabian Journal of Geosciences 12, 529.

https://doi.org/10.1007/s12517-019-4703-7

The Fengfeng Coalfield is an important coal production base in the Hebei Province of North China. It has been reported that higher coal-bed methane (CBM) contents exist in this area showing good prospects for the exploration of CBM. However, there are few studies on CBM investigation in Fengfeng Coalfield. In order to better understand the geological controls on CBM in the Fengfeng Coalfield, geological surveys and laboratory experiments were conducted that included coal petrology analysis, proximate analysis, mercury intrusion, low-temperature liquid nitrogen adsorption, coal permeability analysis, and methane adsorption/desorption. The results show that the organic compositions are dominated by vitrinites, followed by inertinites, and minor liptinites. The CBM contents are range between 0.83 and 11.52 m3/t, with an average of 4.72 m3/t. The moisture contents are range from 0.76 to 2.54%, with an average of 1.21%, and the ash yields are range from 11.46 to 24.5%, with an average of 17.07%. Low-temperature nitrogen gas adsorption indicates the micropores provide most of the pore specific surface and the pore volume is mainly determined by small pores and mesopores. The geologic structures, coal-bearing strata, and the coal depositional environments were studied through field geological research and laboratory tests. The coals were deposited in a river-dominated shallow delta environment to form the mudstones or siltstones of the coal roof and floor that were used to seal the CBM. The CBM were mainly generated during stages of the Hercynian–Indosinian and the Early-Middle Yanshanian orogeny. Underground water flowed to the Dashucun Mine and its adjacent mines in the northeast of the Gushan Anticline to form a semi-closed hydrodynamic system that created the CBM emission and preservation. The coal rank increases from the southern to the northern areas. Then, it can be speculated that the CBM formation and preservation conditions in the north are better than in the south. The best prospective targets for CBM are in the northern areas. The results of this study may be useful for CBM exploration in North China.

Ma, J., Xu, X., Yu, C., Liu, H., Wang, G., Li, Z., Xu, B., Shi, R., 2020. Molecular biomarkers reveal co-metabolism effect of organic detritus in eutrophic lacustrine sediments. Science of The Total Environment 698, 134328.


In eutrophic lacustrine ecosystems, drifting algal blooms are easily trapped by emergent macrophytes in downwind littoral zones, potentially altering carbon cycling processes; yet, knowledge remains limited about the mechanisms driving these changes. In this study, Microcystis and Phragmites, two dominant photosynthetic organisms in a hypereutrophic (Lake Taihu, China), were collected to simulate their co-decomposition processes. We demonstrate how molecular-level biomarkers could be used to elucidate the degradation dynamics of these two distinct organic forms in mixtures. Microcystis-derived carbon accelerated the decomposition rate of mixed systems (positive co-metabolism effect), rather than retarding it. The decomposition rate of TOC (total organic carbon) directly measured in the mixed treatments was 14% higher than when the two substrates were incubated alone. The use of specific fatty acid biomarkers facilitated more accurate tracking, demonstrating 1.09 times higher decomposition rates for Phragmites detritus in mixed treatments than in single Phragmites treatments. Furthermore, Microcystis showed 0.98 times higher decomposition rates in mixed treatments than in single treatments. The addition of Microcystis detritus to Phragmites detritus might meet microbial stoichiometric requirements, increasing the abundance of decomposing bacteria in Phragmites detritus, and accelerating decomposition rates, resulting in the co-metabolism of Microcystis and Phragmites carbon. Given the increasing occurrence of algal blooms in

eutrophic lakes, the processes documented here might enhance greenhouse gas emissions from lakes with continued global climate warming.

Ma, W., Hou, L., Luo, X., Tao, S., Guan, P., Liu, J., Lin, S., 2020. Role of bitumen and NSOs during the decomposition process of a lacustrine Type-II kerogen in semi-open pyrolysis system. Fuel 259, 116211.


The purpose of this work is to investigate the generation characteristics of bitumen, NSO compounds, oil, and HC compounds during the artificial maturation of a lacustrine Type-II kerogen (which has not been given enough attention before) in order to determine its decomposition process. The analysis is based on the data itself, on the premise of jumping out of the generally accepted sequential reaction model. By taking the kerogen of the Chang 7 shale as an example, seven parallel experiments, in the temperature range from 300 °C to 420 °C were conducted on newly designed temperature-based semi-open pyrolysis system. The overall products are classified into oil and bitumen according to their phase, the C15+ fractions are classified into C15+sat, C15+aro and NSOs based on chemical compositions, and the NSOs are further classified into n-pentane NSOs and DCM NSOs according to Behar et al., (2008) and (2010). Results show that large proportion of oil is not merely a result of thermal cracking of bitumen, but also directly from the decomposition of kerogen itself. Both C15+sat and C15+aro are generated as soon as kerogen starts to decompose. It is not until the initial productivity of kerogen is basically exhausted that NSOs become the main precursor of hydrocarbons. The comparison with Behar et al. [2008, organic geochemistry 39, 1–22] further reveals that, for Chang 7 kerogen, initial decomposition of kerogen generates much more HCs than DCM NSOs. These results contradict the sequential reaction model described as: kerogen → bitumen → oil or kerogen → NSOs → hydrocarbons. Instead, they confirm the “alternate pathway” mechanism proposed by Burnham et al. [ACS symposium, 1989] in which hydrocarbons can be formed immediately from kerogen in parallel with NSOs and the formation of the two species are controlled by bond-breaking reactions that are independent of each other. This study adds geochemical insights into the decomposition mechanism of lacustrine Type-II kerogen.

Machale, J., Majumder, S.K., Ghosh, P., Sen, T.K., 2019. Development of a novel biosurfactant for enhanced oil recovery and its influence on the rheological properties of polymer. Fuel 257, 116067.


Surfactant plays a major role in enhanced oil recovery (EOR). However, most of the commonly-used surfactants are toxic, non-biodegradable, and can adsorb on the surface of the porous rocks. This work is focused on the development of an alternative sustainable biosurfactant derived from the weed Eichhornia crassipes and its utilization in EOR. The surfactant has been characterized by the FTIR, GC–MS, 1H NMR, FESEM, and FETEM analyses. The surface and interfacial tension have been measured. The influence of the synthesized surfactant on the rheological properties of xanthan gum has been studied and compared with that of a commercially used surfactant (i.e., sodium dodecyl sulfate). An effective improvement in the rheological properties and stability against heat and salinity suggest its potential application in EOR.

Macreadie, P.I., Anton, A., Raven, J.A., Beaumont, N., Connolly, R.M., Friess, D.A., Kelleway, J.J., Kennedy, H., Kuwae, T., Lavery, P.S., Lovelock, C.E., Smale, D.A., Apostolaki, E.T., Atwood, T.B., Baldock, J., Bianchi, T.S., Chmura, G.L., Eyre, B.D., Fourqurean, J.W., Hall-Spencer, J.M., Huxham, M., Hendriks, I.E., Krause-Jensen, D., Laffoley, D., Luisetti, T., Marbà, N., Masque, P., McGlathery, K.J., Megonigal, J.P., Murdiyarso, D., Russell, B.D., Santos, R., Serrano, O., Silliman, B.R., Watanabe, K., Duarte, C.M., 2019. The future of Blue Carbon science. Nature Communications 10, 3998.

https://doi.org/10.1038/s41467-019-11693-w

The term Blue Carbon (BC) was first coined a decade ago to describe the disproportionately large contribution of coastal vegetated ecosystems to global carbon sequestration. The role of BC in climate change mitigation and adaptation has now reached international prominence. To help prioritise future research, we assembled leading

experts in the field to agree upon the top-ten pending questions in BC science. Understanding how climate change affects carbon accumulation in mature BC ecosystems and during their restoration was a high priority. Controversial questions included the role of carbonate and macroalgae in BC cycling, and the degree to which greenhouse gases are released following disturbance of BC ecosystems. Scientists seek improved precision of the extent of BC ecosystems; techniques to determine BC provenance; understanding of the factors that influence sequestration in BC ecosystems, with the corresponding value of BC; and the management actions that are effective in enhancing this value. Overall this overview provides a comprehensive road map for the coming decades on future research in BC science.

Magalhães, N., Farquhar, J., Bybee, G., Penniston-Dorland, S., Rumble III, D., Kinnaird, J., McCreesh, M., 2019. Multiple sulfur isotopes reveal a possible non-crustal source of sulfur for the Bushveld Province, southern Africa. Geology 47, 982-986.

https://doi.org/10.1130/G46282.1

The source of sulfur for sulfide mineralization is a major question for the origin of platinum group element deposits such as the Rustenburg Layered Suite (RLS) of the Bushveld Complex and the nearby Waterberg Project (WP; a large palladium-dominant deposit) in southern Africa. Both deposits are mafic-ultramafic intrusions associated with the ca. 2.06 Ga Bushveld magmatism but are hosted in distinct country rocks. This contrast allows a critical assessment of the contribution upper crustal assimilation provides to sulfide mineralization, and refinement of our understanding of sources of mass-independent fractionated sulfur (MIF-S) to these intrusions. The WP has a signature of anomalous sulfur (average Δ33S = 0.113‰ ± 0.016‰, 1 s.d.), similar to the RLS (avgerage Δ33S = 0.137‰ ± 0.025‰, 1 s.d.). There is no evidence for influence of host rock as a source of anomalous sulfur. The lack of a significant variation of Δ33S values within the WP stratigraphy, and the distinct upper continental crust into which the WP magmas would have been emplaced, shows that addition of upper crustal sulfur is not necessary for PGE formation. This suggests that contamination of WP and RLS magmas with a surface-derived component of Archean age occurred at depth, prior to emplacement.

Maiorano, P., Marino, M., De Lange, G.J., 2019. Dynamic surface-water alterations during sapropel S1 preserved in high-resolution shallow-water sediments of Taranto Gulf, central Mediterranean. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109340.


The high sedimentation rate and shallow-water depositional depth of the sediments at site DP 30 in the Gulf of Taranto (central Mediterranean) provide unique biogenic signals that are usually not preserved in deeper records. This permits the reconstruction of long and short-term surface water modifications across the sapropel S1 period (10–6.5 ka), including calcareous nannofossil data at centennial-scale resolution.

The peculiar patterns of key taxa allowed the recognition of distinct long to short-term surface water changes that provide valuable evidence on climate conditions leading to sapropel deposition. As a long-term pattern, S1 is marked by a distinct increase of Helicosphaera carteri, thought to reflect increased detrital input/land-derived nutrients in the surface water, related to a higher influence of the Western Adriatic Current. A concomitant pattern of increased black organic particles in the sediments supports a connection between organic matter preservation at the seafloor and nutrient availability in the surface water. Decreased salinity in the surface water, testified by an increase of Braurudosphaera bigelowii, develops from 9.2 up to 6.5 ka.

At higher frequencies, additional changes occurred in surface-subsurface waters during the formation of S1 at shallow depths. Starting from 11 ka, the relative abundance pattern of Florisphaera profunda indicates a gradual nutrient enrichment in the subsurface waters and the development of a deep chlorophyll maximum (DCM), which becomes well established at the onset of sapropel S1, between 10 and 9 ka. A further change in the plankton ecosystem occurs between 9 and 8.2 ka, when reduced coccolithophore production is concomitant with diatom occurrence and enhanced Br/Ti level, implying a productivity increase. From 8 to 6.5 ka, coccolithophore productivity is re-established in relation to a reduction both in surface-water stratification and turbidity/nutrient availability, characterizing the final phase of sapropel formation. The turbidity in the surface

waters was briefly reduced at 8.2 and 7.3 ka, when also oxygen conditions at the seafloor improved. A centennial variability in turbidity/low light conditions in surface waters is evident across S1 and is illustrated by the abundance patterns of H. carteri and Gladiolithus flabellatus. The occurrence of ascidian spicules also represents a distinct biotic signal across the S1 layer, indicating an increase of shallow-water biogenic carbonate or an aragonitic near-coastal source. Surface-water modifications at longer and shorter time scales, accompanying the deposition of sapropel S1 in the Gulf of Taranto, occurred nearly simultaneously and with a magnitude that is comparable to changes observed in S1 deposits in the central and eastern Mediterranean basin and slope settings.

Makarov, A., 2019. Orbitrap journey: taming the ion rings. Nature Communications 10, 3743.

https://doi.org/10.1038/s41467-019-11748-y

The establishment of the Orbitrap analyzer as a major player in mass spectrometry based proteomics is traced back to the first public presentation of this technology 20 years ago; when a proof-of-principle application led the way to further advancements and biological applications.

Makled, W.A., El Ashwah, A.A.E., Lotfy, M.M., Hegazey, R.M., 2020. Anatomy of the organic carbon related to the Miocene syn-rift dysoxia of the Rudeis Formation based on foraminiferal indicators and palynofacies analysis in the Gulf of Suez, Egypt. Marine and Petroleum Geology 111, 695-719.


The syn-rift deposits from the Gulf of Suez witness different episodes of anoxia and dysoxia conditions. In many areas, the sediments of Rudeis Formation that represent the deposition in the time of maximum rift subsidence are considered as the principal organically rich and oil prone sources, while in other areas they are not. These differences are attributed to relative positions to the location of the syn-rift dysoxia and amounts of the carbon flux during active paleoproductivity time. In the present study, an extensive analysis of the syn-rift dysoxia and paleoproductivity during the Miocene is conducted in Burdigalian Rudeis Formation in Ramadan-1 well to determine their influence on the accumulation of organic carbon. The analysis depends on the statistical investigation of the benthic foraminiferal assemblages. The foraminiferal assemblages are discriminated into two biofacies in R-mode (suboxic and dysoxic) and three biotopes in Q-mode (suboxic (S), dysoxic DA and DB sample groups). The sediments are divided into three stratigraphic sequences. Five oxygen minimum zones are determined at the extreme oxygen depletion intervals and they are defined by suboxic (S) and dysoxic (DA) sample groups in descendent order of oxygen depletion intensity and mostly coincide with the high sea levels. The distribution of the organic matter showed large enrichment with partial fluorescence amorphous organic matter indicating kerogen type II in the three biotopes as clarified from palynofacies analysis. The organic carbon enrichment from the studied samples ranged from fair to very good (0.51 and 2.38 wt%) and the relatively larger enrichments are found to be correlated with dysoxic sample group (DA) of intermediate oxygen depletion. The pyrolysis gas chromatography (PGC) specifies the algal rich Type I kerogen that deposited in oxygen depleted marine environment. The mathematical calculation of the paleoproductivity (oligotrophic to eutrophic range 106–352 gCM−2yr−1), carbon flux (13.77 and 36.19 gCm−2yr−1) indicates that higher levels of organic productivity are correlated with dysoxic sample group (DA). The larger organic carbon values are found in the Rudeis Formation when the dysoxic conditions from the deeper topographic lows extend to the higher tectonic position of Ramadan-1 well during the sea level rise that furthermore enhances the paleoproductivity.

Mallah, K., Quanico, J., Raffo-Romero, A., Cardon, T., Aboulouard, S., Devos, D., Kobeissy, F., Zibara, K., Salzet, M., Fournier, I., 2019. Matrix-assisted laser desorption/ionization-mass spectrometry imaging of lipids in experimental model of traumatic brain injury detecting acylcarnitines as injury related markers. Analytical Chemistry 91, 11879-11887.


Identifying new lipid markers linked to traumatic brain injury (TBI) is of major importance in characterizing their central role in the regeneration process and inflammatory response in such an injury model. In the present study, an advanced lipidomics analysis using high spectral resolution matrix-assisted laser desorption/ionization-mass spectrometry imaging was performed on different brain regions in an experimental rat model of moderate controlled cortical impact (CCI) while considering different time points (1 day, 3 days, 7 days, and 10 days) assessing the acute and subacute phase after injury. Our results revealed a new family of lipids, the acylcarnitines, as TBI-lipid related markers, with maximum expression at 3 days after impact and main colocalization within resident microglia of the brain. Furthermore, our experiments highlighted the upregulation of these acylcarnitine lipids, secreted by microglia, in the ipsilateral substantia nigra, the main region in the brain affected in Parkinson’s disease (PD).

Mand, T.D., Metcalf, W.W., 2019. Energy conservation and hydrogenase function in methanogenic archaea, in particular the genus Methanosarcina. Microbiology and Molecular Biology Reviews 83, e00020-19.

http://mmbr.asm.org/content/83/4/e00020-19.abstract

The biological production of methane is vital to the global carbon cycle and accounts for ca. 74% of total methane emissions. The organisms that facilitate this process, methanogenic archaea, belong to a large and phylogenetically diverse group that thrives in a wide range of anaerobic environments. Two main subgroups exist within methanogenic archaea: those with and those without cytochromes. Although a variety of metabolisms exist within this group, the reduction of growth substrates to methane using electrons from molecular hydrogen is, in a phylogenetic sense, the most widespread methanogenic pathway. Methanogens without cytochromes typically generate methane by the reduction of CO2 with electrons derived from H2, formate, or secondary alcohols, generating a transmembrane ion gradient for ATP production via an Na+-translocating methyltransferase (Mtr). These organisms also conserve energy with a novel flavin-based electron bifurcation mechanism, wherein the endergonic reduction of ferredoxin is facilitated by the exergonic reduction of a disulfide terminal electron acceptor coupled to either H2 or formate oxidation. Methanogens that utilize cytochromes have a broader substrate range, and can convert acetate and methylated compounds to methane, in addition to the ability to reduce CO2. Cytochrome-containing methanogens are able to supplement the ion motive force generated by Mtr with an H+-translocating electron transport system. In both groups, enzymes known as hydrogenases, which reversibly interconvert protons and electrons to molecular hydrogen, play a central role in the methanogenic process. This review discusses recent insight into methanogen metabolism and energy conservation mechanisms with a particular focus on the genus Methanosarcina.

Mann, M., 2019. The ever expanding scope of electrospray mass spectrometry—a 30 year journey. Nature Communications 10, 3744.

https://doi.org/10.1038/s41467-019-11747-z

John Fenn’s electrospray mass spectrometry (ESMS) was awarded the chemistry Nobel Prize in 2002 and is now the basis of the entire field of MS-based proteomics. Technological progress continues unabated, enabling single cell sensitivity and clinical applications.

Manoharan, L., Kozlowski, J.A., Murdoch, R.W., Löffler, F.E., Sousa, F.L., Schleper, C., 2019. Metagenomes from coastal marine sediments give insights into the ecological role and cellular features of Loki- and Thorarchaeota. mBio 10, e02039-19.

http://mbio.asm.org/content/10/5/e02039-19.abstract

Abstract: The genomes of Asgard Archaea, a novel archaeal proposed superphylum, share an enriched repertoire of eukaryotic signature genes and thus promise to provide insights into early eukaryote evolution. However, the distribution, metabolisms, cellular structures, and ecology of the members within this superphylum are not well understood. Here we provide a meta-analysis of the environmental distribution of the Asgard archaea, based on available 16S rRNA gene sequences. Metagenome sequencing of samples from a salt-

crusted lagoon on the Baja California Peninsula of Mexico allowed the assembly of a new Thorarchaeota and three Lokiarchaeota genomes. Comparative analyses of all known Lokiarchaeota and Thorarchaeota genomes revealed overlapping genome content, including central carbon metabolism. Members of both groups contained putative reductive dehalogenase genes, suggesting that these organisms might be able to metabolize halogenated organic compounds. Unlike the first report on Lokiarchaeota, we identified genes encoding glycerol-1-phosphate dehydrogenase in all Loki- and Thorarchaeota genomes, suggesting that these organisms are able to synthesize bona fide archaeal lipids with their characteristic glycerol stereochemistry.

Importance: Microorganisms of the superphylum Asgard Archaea are considered to be the closest living prokaryotic relatives of eukaryotes (including plants and animals) and thus promise to give insights into the early evolution of more complex life forms. However, very little is known about their biology as none of the organisms has yet been cultivated in the laboratory. Here we report on the ecological distribution of Asgard Archaea and on four newly sequenced genomes of the Lokiarchaeota and Thorarchaeota lineages that give insight into possible metabolic features that might eventually help to identify these enigmatic groups of archaea in the environment and to culture them.

Martins, C., Rodrigo, A.P., Cabrita, L., Henriques, P., Parola, A.J., Costa, P.M., 2019. The complexity of porphyrin-like pigments in a marine annelid sheds new light on haem metabolism in aquatic invertebrates. Scientific Reports 9, 12930.

https://doi.org/10.1038/s41598-019-49433-1

True green pigments in the animal kingdom are scarce and are almost invariably porphyrinoids. Endogenous porphyrins resulting from the breakdown of haem are usually known as “bile pigments”. The pigmentation of intertidal Polychaeta has long gained attention due to its variety and vivid patterning that often seems incompatible with camouflage, as it occurs with Eulalia viridis, one of the few truly green Polychaeta. The present study combined UV and bright-field microscopy with HPLC to address the presence and distribution of pigments in several organs. The results showed two major types of porphyrin-like pigments, yellowish and greenish in colour, that are chiefly stored as intraplasmatic granules. Whereas the proboscis holds yellow pigments, the skin harbours both types in highly specialised cells. In their turn, oocytes and intestine have mostly green pigments. Despite some inter-individual variation, the pigments tend to be stable after prolonged storage at −20 °C, which has important implications for future studies. The results show that, in a foraging predator of the intertidal where melanins are circumscribed to lining the nervous system, porphyrinoid pigments have a key role in protection against UV light, in sensing and even as chemical defence against foulants and predators, which represents a remarkable adaptive feature.

Matys, E.D., Mackey, T., Grettenberger, C., Mueller, E., Jungblut, A., Sumner, D.Y., Hawes, I., Summons, R.E., 2019. Environmental controls on bacteriohopanepolyol profiles of benthic microbial mats from Lake Fryxell, Antarctica. Geobiology 17, 551-563.


Bacteriohopanepolyols (BHPs) are pentacyclic triterpenoid lipids that contribute to the structural integrity and physiology of some bacteria. Because some BHPs originate from specific classes of bacteria, BHPs have potential as taxonomically and environmentally diagnostic biomarkers. For example, a stereoisomer of bacteriohopanetetrol (informally BHT II) has been associated with anaerobic ammonium oxidation (anammox) bacteria and suboxic to anoxic marine environments where anammox is active. As a result, the detection of BHT II in the sedimentary record and fluctuations in the relative abundance of BHT II may inform reconstructions of nitrogen cycling and ocean redox changes through the geological record. However, there are uncertainties concerning the sources of BHT II and whether or not BHT II is produced in abundance in non-marine environments, both of which are pertinent to interpretations of BHT II signatures in sediments. To address these questions, we investigate the BHP composition of benthic microbial mats from Lake Fryxell, Antarctica. Lake Fryxell is a perennially ice-covered lake with a sharp oxycline in a density-stabilized water

column. We describe the diversity and abundance of BHPs in benthic microbial mats across a transect from oxic to anoxic conditions. Generally, BHP abundances and diversity vary with the morphologies of microbial mats, which were previously shown to reflect local environmental conditions, such as irradiance and oxygen and sulfide concentrations. BHT II was identified in mats that exist within oxic to anoxic portions of the lake. However, anammox bacteria have yet to be identified in Lake Fryxell. We examine our results in the context of BHPs as biomarkers in modern and ancient environments.

Maugeri, A., Medina-Inojosa, J.R., Kunzova, S., Barchitta, M., Agodi, A., Vinciguerra, M., Lopez-Jimenez, F., 2019. Dog ownership and cardiovascular health: Results from the Kardiovize 2030 Project. Mayo Clinic Proceedings: Innovations, Quality & Outcomes 3, 268-275.


Objective: To investigate the association of pet ownership, and specifically dog ownership, with cardiovascular diseases (CVD) risk factors and cardiovascular health (CVH) in the Kardiovize Brno 2030 study, a randomly selected prospective cohort in Central Europe.

Patients and Methods: We included 1769 subjects (aged from 25 to 64 years; 44.3% males) with no history of CVD who were recruited from January 1, 2013, to December 19, 2014. We compared sociodemographic characteristics, CVD risk factors, CVH metrics (ie, body mass index, healthy diet, physical activity level, smoking status, blood pressure, fasting glucose, and total cholesterol), and score between pet owners and non-pet owners or dog owners and several other subgroups.

Results: Approximately 42% of subjects owned any type of pet: 24.3% owned a dog and 17.9% owned another animal. Pet owners, and specifically dog owners, were more likely to report physical activity, diet, and blood glucose at ideal level, and smoking at poor level, which resulted in higher CVH score than non-pet owners (median, 10; interquartile range = 3 vs median, 9; interquartile range = 3; P=0.006). Compared with owners of other pets, dog owners were more likely to report physical activity and diet at ideal level. The comparison of dog owners with non-dog owners yielded similar results. After adjustment for covariates, dog owners exhibited higher CVH scores than non-pet owners (β=0.342; SE=0.122; P=0.005), other pet-owners (β=0.309; SE=0.151; P=0.041), and non-dog owners (β=0.341; SE=0.117; P=0.004).

Conclusion: Except for smoking, dog owners were more likely to achieve recommended level of behavioral CVH metrics (physical activity and diet) than non-dog owners, which translated into better CVH.

McGonigle, J.M., Bernau, J.A., Bowen, B.B., Brazelton, W.J., 2019. Robust archaeal and bacterial communities inhabit shallow subsurface sediments of the Bonneville Salt Flats. mSphere 4, e00378-19.

http://msphere.asm.org/content/4/4/e00378-19.abstract

Abstract: We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio. This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.

Importance: Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.

Meisner, J., Zhu, X., Martínez, T.J., 2019. Computational discovery of the origins of life. ACS Central Science 5, 1493-1495.


In silico reaction discovery using ab initio molecular dynamics shows that the chemistry of life could have originated from two simple inorganic molecules (HCN and water). Abiogenesis, the emergence of life, is an everlasting and intriguing question in biology and related fields. Compared to the long-time scale of evolution, it appears likely that life sprung up almost instantaneously when conditions permitted it. Indeed, a recent study(1) reported fossils with claimed biological origins dating back to the very oldest evidence of liquid water on Earth, not long after the planet formed 4.5 billion years ago. Despite the apparent effortlessness with which nature achieved abiogenesis, scientists did not know how any of the simple building blocks of life could have formed under early Earth conditions until Urey and Miller’s seminal experiments in 1952.(2) Urey and Miller applied heat and electric sparks to a mixture of simple molecules believed to be abundant on early Earth and obtained various different amino acids. This discovery kicked off the quest to find the chemical origins of life, and many plausible pathways for nonbiological synthesis of all basic building blocks of life have now been proposed, assuming different scenarios including UV radiation, lightning, or hydrothermal vents. Now, Das and co-workers(3) use novel computational methods to show that the chemistry of life could be generated with only two simple inorganic starting materials—water and HCN

Meister, P., Liu, B., Khalili, A., Böttcher, M.E., Jørgensen, B.B., 2019. Factors controlling the carbon isotope composition of dissolved inorganic carbon and methane in marine porewater: An evaluation by reaction-transport modelling. Journal of Marine Systems 200, 103227.


Carbon isotope compositions of dissolved inorganic carbon (DIC) and methane (CH4) in porewater of marine sediments at seafloor temperatures show very large variation covering a δ13C range from −100‰ to +35‰. These extreme values are the result of isotope fractionation during microbial carbon metabolism, but the combined effect of all factors controlling the isotope distributions is still not completely understood. We used a model approach to evaluate the effects of reaction and transport on carbon isotope distributions in modern sediment porewater under steady state. Simulated δ13CDIC profiles typically show negative values in the sulphate reduction zone and more positive values in the methanogenic zone. With increasing depth in the methanogenic zone, δ13C values approach a distribution where the offset of δ13CDIC from δ13C of total organic carbon (TOC) to more positive values is similar to the offset of δ13CCH4 to more negative values (δ13CDIC and δ13CCH4 approach a symmetric distribution relative to δ13CTOC). The model never exceeds this symmetry of the DIC-CH4 couple towards more positive values under steady-state conditions in a purely diffusive system.

Our model shows that to reach an offset in δ13C between DIC and CH4 in the order of 70‰, as frequently observed in methanogenic zones, a larger fractionation than reported from culture experiments with acetoclastic or autotrophic methanogens would be required. In fact, the observed isotope offset in natural systems would be consistent with the known inorganic equilibrium fractionation factor at in-situ temperature, which may suggest isotope exchange via a microbial pathway, during methanogenesis.

Furthermore, the model reproduces strongly negative δ13CCH4 values at the sulphate methane transition (SMT) as result of a reverse flux of carbon from DIC to CH4 during AOM. Such a reverse AOM has no influence on the

δ13CDIC at the SMT as methane is almost completely consumed. Only at high sedimentation rate combined with low porosity, δ13CDIC values significantly more negative than δ13CTOC occur at the SMT.

Methner, K., Lenz, O., Riegel, W., Wilde, V., Mulch, A., 2019. Paleoenvironmental response of midlatitudinal wetlands to Paleocene–early Eocene climate change (Schöningen lignite deposits, Germany). Climate of the Past 15, 1741-1755.

https://www.clim-past.net/15/1741/2019/

The early Paleogene is marked by multiple negative carbon isotope excursions (CIEs) that reflect massive short-term carbon cycle perturbations that coincide with significant warming during a high-pCO2 world, affecting both marine and terrestrial ecosystems. Records of such hyperthermals from the marine–terrestrial interface (e.g., estuarine swamps and mire deposits) are therefore of great interest as their present-day counterparts are highly vulnerable to future climate and sea level change. Here, we assess paleoenvironmental changes of midlatitudinal late Paleocene–early Eocene peat mire records along the paleo-North Sea coast. We provide carbon isotope data of bulk organic matter (δ13CTOC), organic carbon content (%TOC), and palynological data from an extensive peat mire deposited at a midlatitudinal (ca. 41∘ N) coastal site (Schöningen, Germany). The δ13CTOC data show a carbon isotope excursion of −1.3 ‰ (mean decrease in δ13CTOC; −1.7 ‰ at the onset of CIE) coeval with a conspicuous Apectodinium acme. Due to the exceptionally large stratigraphic thickness of the CIE at Schöningen (10 m of section) we established a detailed palynological record that indicates only minor changes in paleovegetation leading into and during this event. Instead, paleovegetation changes mostly follow natural successions in response to changes along the marine–terrestrial interface. The available age constraints for the Schöningen Formation hamper a solid assignment of the detected CIE to a particular hyperthermal such as the Paleocene–Eocene Thermal Maximum (PETM) or any succeeding hyperthermal event such as the Eocene Thermal Maximum 2 (ETM2).

Compared to other nearby peat mire records (Cobham, UK; Vasterival, F) it appears that wetland deposits around the Paleogene North Sea have a consistent CIE magnitude of ca. −1.3 ‰ in δ13CTOC. Moreover, the Schöningen record shares major characteristics with the Cobham Lignite PETM record, including evidence for increased fire activity prior to the CIE, minor plant species change during the hyperthermal, a reduced CIE in δ13CTOC, and drowning of the mire (marine ingressions) during much of the Schöningen CIE event. This suggests that either the Schöningen CIE reflects the PETM or that early Paleogene hyperthermals similarly affected paleoenvironmental conditions of a major segment of the paleo-North Sea coast.

Mettam, C., Zerkle, A.L., Claire, M.W., Prave, A.R., Poulton, S.W., Junium, C.K., 2019. Anaerobic nitrogen cycling on a Neoarchaean ocean margin. Earth and Planetary Science Letters 527, 115800.


A persistently aerobic marine nitrogen cycle featuring the biologically mediated oxidation of ammonium to nitrate has likely been in place since the Great Oxidation Event (GOE) some 2.3 billion years ago. Although nitrogen isotope data from some Neoarchaean sediments suggests transient nitrate availability prior to the GOE, these data are open to other interpretations. This is especially so as these data come from relatively deep-water environments that were spatially divorced from shallow-water settings that were the most likely sites for the accumulation of oxygen and the generation of nitrate. Here we present the first nitrogen isotope data from contemporaneous shallow-water sediments to constrain the nitrogen cycle in shallow Late Archaean settings. The BH-1 Sacha core through the Campbellrand-Malmani carbonate platform records a transition from a shallow siliciclastic/carbonate ramp to a rimmed carbonate shelf with the potential for reduced communication with the open ocean. In these settings nitrogen isotope (δ15N) data from sub- to peri-tidal and lagoonal settings are close to 0‰, indicating diazotrophy or the complete utilization of remineralised ammonium with an isotopic composition of near 0‰. Our dataset also includes negative δ15N values that suggest the presence of an ammonium pool of concentrations sufficient to have allowed for non-quantitative assimilation. We suggest that this condition may have been the result of upwelling of phosphorus-rich deep waters into the photic zone, stimulating primary productivity and creating an enhanced flux of organic matter that was subsequently

remineralised and persisted in the dominantly anoxic Neoarchaean marine environment. Notably, we find only limited evidence of coupled nitrification/denitrification, even in these shallow water environments, calling into question previous suggestions that the Late Archaean nitrogen cycle was characterized by widespread aerobic nitrogen cycling. Rather, aerobic nitrogen cycling was likely spatially heterogeneous and tied to loci of high oxygen production while zones of shallow water anoxia persisted.

Meyra, A.G., Ferrara, C.G., 2019. Study of nanoconfined mixtures of decane and water: Structure and dynamic. Fluid Phase Equilibria 502, 112279.


In the last years, the phase behaviour of multi-component hydrocarbon systems in shale reservoirs has received significant attention. The main complexities in modelling the phase behaviour is the confinement. It is presented in this work, the results obtained by molecular dynamics simulation in the NPT ensemble of n-decane/water liquid mixture confined in an amorphous hydrophobic nanometric tube. Nanotube walls are made up of a Lennard-Jones binary mixture similar to a Kob-Andersen system. As it happens in a macroscopic flow of biphasic fluid, a transition from drop to a thread is observed in this confined system when increasing water molar fraction. Different values of the water tetrahedral bond distribution, water density profiles, and the mean square-displacement of water were found for a drop to a thread transition. The calculated quantities, substantially differ from those corresponding to the bulk system.

Mihreteab, M., Stubblefield, B.A., Gilbert, E.S., 2019. Microbial bioconversion of thermally depolymerized polypropylene by Yarrowia lipolytica for fatty acid production. Applied Microbiology and Biotechnology 103, 7729-7740.

https://doi.org/10.1007/s00253-019-09999-2

Plastic production and waste generation will continue to rise as nations worldwide grow economically. In this work, we detail a pyrolysis-based bioconversion process for polypropylene (PP) to produce value-added fatty acids (FAs). PP pellets were depolymerized by pyrolysis, generating oil that consisted of mainly branched chain fatty alcohols and alkenes. The oil was mixed with biodegradable surfactants and trace nutrients and mechanically homogenized. The resulting medium, OP4, was used for fermentation by Yarrowia lipolytica strain 78-003. Y. lipolytica assimilated > 80% of the substrate over 312 h, including 86% of the fatty alcohols. Y. lipolytica produced up to 492 mg L−1 lipids, compared with 216 mg L−1 during growth in surfactant-based control medium. C18 compounds, including oleic acid, linoleic acid, and stearic acid, were the predominant products, followed by C16 compounds palmitic and palmitoleic acids. Two percent of the products was C 20 compounds. The majority of the products were unsaturated FAs. Growth on hydrophobic substrates (OP4 medium, hexadecane) was compared with growth on hydrophilic substrates (glucose, starch). The resulting FA profiles revealed an absence of short-chain fatty acids during growth on hydrophobic media, findings consistent with ex novo FA biosynthesis. Overall, FA profiles by Y. lipolytica during growth in OP4 medium were similar to FA profiles while growing on natural substrates. The process described here offers an alternative approach to managing postconsumer plastic waste.

Mitri, G., Lunine, J.I., Mastrogiuseppe, M., Poggiali, V., 2019. Possible explosion crater origin of small lake basins with raised rims on Titan. Nature Geoscience 12, 791-796.

https://doi.org/10.1038/s41561-019-0429-0

The Cassini mission discovered lakes and seas comprising mostly methane in the polar regions of Titan. Lakes of liquid nitrogen may have existed during the epochs of Titan’s past in which methane was photochemically depleted, leaving a nearly pure molecular nitrogen atmosphere and, thus, far colder temperatures. The modern-day small lake basins with sharp edges have been suggested to originate from dissolution processes, due to their morphological similarity to terrestrial karstic lakes. Here we analyse the morphology of the small lake basins that feature raised rims to elucidate their origin, using delay-Doppler processed altimetric and bathymetric data

acquired during the last close flyby of Titan by the Cassini spacecraft. We find that the morphology of the raised-rim basins is analogous to that of explosion craters from magma–water interaction on Earth and therefore propose that these basins are from near-surface vapour explosions, rather than karstic. We calculate that the phase transition of liquid nitrogen in the near subsurface during a warming event can generate explosions sufficient to form the basins. Hence, we suggest that raised-rim basins are evidence for one or more warming events terminating a nitrogen-dominated cold episode on Titan.

Mohammed, S., Opuwari, M., Titinchi, S., Bata, T., Abubakar, M.B., 2019. Evaluation of source rock potential and hydrocarbon composition of oil sand and associated clay deposits from the Eastern Dahomey Basin, Nigeria. Journal of African Earth Sciences 160, 103603.


Oil sands are classified as unconventional hydrocarbon plays and are being exploited to augment global energy needs. Nigeria has the largest conventional oil industry in Africa, but is also endowed with abundant oil sand deposits found within the Afowo Formation of the Eastern Dahomey Basin. In this study, outcrop samples of clay, oil sand, and bitumen seepage from a forestry reserve (J4) in Ogun State, South Western Nigeria were evaluated for organic matter maturity and hydrocarbon composition. Pyrolysis results for the clay indicate that the total organic carbon ranges from 5.95 to 18.46 wt % with a maturation temperature (Tmax) within the range of 417–426 °C. A complementary gas chromatography (GC) analysis of the free hydrocarbons in the clay reveals that both light and heavy hydrocarbon components are present. In contrast, oil sand and bitumen contain mostly heavy end hydrocarbon components with hydrocarbon chains C6–C12 missing, confirming oil biodegradation. This study demonstrates that these oil sands and clays represent viable exploration targets. With vast oil sand deposits in the Eastern Dahomey Basin, exploration and exploitation of this resource will open new frontiers to increase Nigeria's hydrocarbon production.

Mojarro, A., Hachey, J., Bailey, R., Brown, M., Doebler, R., Ruvkun, G., Zuber, M.T., Carr, C.E., 2019. Nucleic acid extraction and sequencing from low-biomass synthetic Mars analog soils for in situ life detection. Astrobiology 19, 1139-1152.

https://doi.org/10.1089/ast.2018.1929

Recent studies regarding the origins of life and Mars-Earth meteorite transfer simulations suggest that biological informational polymers, such as nucleic acids (DNA and RNA), have the potential to provide unambiguous evidence of life on Mars. To this end, we are developing a metagenomics-based life-detection instrument which integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG). Our goal is to isolate and sequence nucleic acids from extant or preserved life on Mars in order to determine if a particular genetic sequence (1) is distantly related to life on Earth, indicating a shared ancestry due to lithological exchange, or (2) is unrelated to life on Earth, suggesting convergent origins of life on Mars. In this study, we validate prior work on nucleic acid extraction from cells deposited in Mars analog soils down to microbial concentrations (i.e., 104 cells in 50 mg of soil) observed in the driest and coldest regions on Earth. In addition, we report low-input nanopore sequencing results from 2 pg of purified Bacillus subtilis spore DNA simulating ideal extraction yields equivalent to 1 ppb life-detection sensitivity. We achieve this by employing carrier sequencing, a method of sequencing sub-nanogram DNA in the background of a genomic carrier. After filtering of carrier, low-quality, and low-complexity reads we detected 5 B. subtilis reads, 18 contamination reads (including Homo sapiens), and 6 high-quality noise reads believed to be sequencing artifacts.

Montero, L., Herrero, M., 2019. Two-dimensional liquid chromatography approaches in Foodomics – A review. Analytica Chimica Acta 1083, 1-18.


Modern food analysis is directed to the characterization of as many components as possible in food and food-related materials. The use of –omics technologies within a Foodomics approach requires the use of high

throughput analytical techniques able to offer increased resolving power and capability to separate a high number of compounds. From this perspective, two-dimensional liquid chromatography has the potential to unravel very complex food matrices, providing with high resolving power and enhanced identification potential, particularly when coupled to mass spectrometry. This review presents an overview including the most notable two-dimensional liquid chromatography applications developed in the last ten years to study food safety, food quality and the relationship between health and food as well as for the characterization of particular groups of food components within a Foodomics perspective. Moreover, the latest developments and advances, limitations, future evolution and needs related to the use of this technique are critically discussed and commented.

Moosavi, S.R., Wood, D.A., Ahmadi, M.A., Choubineh, A., 2019. ANN-based prediction of laboratory-scale performance of CO2-foam flooding for improving oil recovery. Natural Resources Research 28, 1619-1637.

https://doi.org/10.1007/s11053-019-09459-8

Improving oil recovery by CO2 injection continues to gain momentum in mature oil fields due to its favorable industrial and environmental benefits. One remediation for the poor sweep efficiency of CO2 is co-injection of surfactants to generate CO2-foams in reservoirs. However, it is essential to minimize the expensive and time-consuming experiments required during the laboratory screening of this EOR process for a given reservoir. In this regard, methods to predict RF and Q from reservoir characteristics based on existing laboratory test data are worthwhile. In this paper, we develop the RF and Q prediction models involving optimized multi-layer perceptron (MLP) and radial basis function (RBF) neural networks. These models are applied to a compiled dataset of 214 data records of published CO2-foam injection tests into oil-reservoir cores. The RF and Q prediction derived applying these two models to the compiled dataset are compared. Statistical accuracy measures of the predictions achieved for an independent testing subset (20% of the data records) indicate for RF (MLP: RMSE = 0.0236, R2 = 0.9988; for RBF: RMSE = 0.0197, R2 = 0.9991) and for Q (MLP: RMSE = 0.0283, R2 = 0.9971; for RBF: RMSE = 0.0092, R2 = 0.9991) the excellent prediction performance of the developed networks.

Morgunova, I.P., Petrova, V.I., Litvinenko, I.V., Kursheva, A.V., Batova, G.I., Renaud, P.E., Granovitch, A.I., 2019. Hydrocarbon molecular markers in the Holocene bottom sediments of the Barents Sea as indicators of natural and anthropogenic impacts. Marine Pollution Bulletin 149, 110587.


The recent intensification of energy resource exploration and human activities in the Barents Sea (BS) requires a more thorough assessment of the natural and anthropogenic impact of hydrocarbons on the environment. We analyzed a wide set of sensitive indicators, including hydrocarbon molecular markers and organic matter (OM) maturity parameters in the Holocene sediments from three regions of the BS: the Kola-Kanin Monocline (KKM), the Svalbard shelf, and the Shtokman gas-condensate field (GCF). An increase in pyrogenic polycyclic aromatic hydrocarbons toward the core surface traces the intensification of anthropogenic contamination in the KKM region during last century. An input of highly mature OM from the eroded coal rocks of Barentsburg were confirmed by comparison of biomarker distribution in sediments and coals. An increase in biogenic hopanes and hopenes content down-core, and a crude-oil stage of OM maturity in surface sediments of the Shtokman GCF attests to hydrocarbons migration from subsurface strata.

Morley, M.W., Goldberg, P., Uliyanov, V.A., Kozlikin, M.B., Shunkov, M.V., Derevianko, A.P., Jacobs, Z., Roberts, R.G., 2019. Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia). Scientific Reports 9, 13785.

https://doi.org/10.1038/s41598-019-49930-3

Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few

fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal–Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.

Morozov, E.V., Yushmanov, P.V., Martyanov, O.N., 2019. Temperature-triggered rearrangement of asphaltene aggregates as revealed by pulsed-field gradient NMR. Energy & Fuels 33, 6934-6945.


The tendency of asphaltenes for aggregation followed by precipitation and deposition plays a crucial role in the petroleum industry since these processes present severe problems during the production, recovery, and processing of crude oils and fossil hydrocarbon feedstocks. The dynamics of oil asphaltene aggregates dissolved in chloroform at different concentrations varied in a wide range that was investigated at temperatures from 0 to 55 °C using the Pulsed-Field Gradient NMR technique. The components attributed to nanoaggregates and macroaggregates were successfully resolved, which allowed us to measure their diffusion coefficients. The diffusion coefficients for all types of aggregates grow as the asphaltene concentration decreases, whereas the partial weight of the aggregates increases with the increase of asphaltene concentration. The difference in diffusion behavior of the aggregates of different types was registered when passing the critical concentration range 10–20 g/L. The nano- and macroaggregates behave independently when the asphaltene concentration is higher than 20 g/L (concentrated regime), while below 20 g/L (semidiluted regime) the components related to the different types of aggregates cannot be properly resolved. It was found that regardless of the asphaltene concentration, the diffusion coefficients for nano- and macroaggregates demonstrate similar temperature behavior giving the straight lines in the Arrhenius coordinates which change their slopes when passing the temperature range 20–30 °C. The phenomenon evidences the thermally induced cleavage of noncovalent bonds with subsequent rearrangement of asphaltene aggregates that is observed for all concentration regimes covering the existence of asphaltene aggregates of all types. The data obtained are well consistent with the modern concept of asphaltene aggregate structure and fairly agree with the data obtained earlier. We believe these results will contribute essentially to a better understanding of the fundamental behavior of asphaltenes and their aggregates, providing a deep insight into aggregate transformation triggered by the temperature.

Morse, A.D., Chan, Q.H.S., 2019. Observations of cometary organics: A post Rosetta review. ACS Earth and Space Chemistry 3, 1773-1791.


Comets are relics from the formation of the solar system. During their formation, the comets captured organics in their vicinity that may have originated in interstellar space and survived the collapse of the solar system’s parent molecular cloud. The variety of organic compounds depends on the initial ingredients and formation conditions, subsequently modified through chemical processes in the solar nebula and on the comet. As a result, organic compounds record the history of their journey from interstellar space, through comets and perhaps onward to Earth. However, because of the fragile nature of comets, the pristine organics stored on the nucleus of a comet is difficult to detect directly. The composition of cometary organics has been gleaned from a variety of sources, remote sensing detection of volatiles in the coma of many comets, in situ spacecraft missions of a few targeted comets, and terrestrial analysis of refractory organics in potential cometary dust arriving on Earth. The spacecraft missions provide the link between the remote sensing and terrestrial analysis. We review these

observations in light of the recent completion of the Rosetta mission, with its lander Philae and long-term monitoring of 67P/Churyumov-Gerasimenko, which has greatly expanded our knowledge of cometary organics.

Mounier, A., Mirazón Lahr, M., 2019. Deciphering African late middle Pleistocene hominin diversity and the origin of our species. Nature Communications 10, 3406.

https://doi.org/10.1038/s41467-019-11213-w

The origin of Homo sapiens remains a matter of debate. The extent and geographic patterning of morphological diversity among Late Middle Pleistocene (LMP) African hominins is largely unknown, thus precluding the definition of boundaries of variability in early H. sapiens and the interpretation of individual fossils. Here we use a phylogenetic modelling method to predict possible morphologies of a last common ancestor of all modern humans, which we compare to LMP African fossils (KNM-ES 11693, Florisbad, Irhoud 1, Omo II, and LH18). Our results support a complex process for the evolution of H. sapiens, with the recognition of different, geographically localised, populations and lineages in Africa – not all of which contributed to our species’ origin. Based on the available fossils, H. sapiens appears to have originated from the coalescence of South and, possibly, East-African source populations, while North-African fossils may represent a population which introgressed into Neandertals during the LMP.

Mozhdehei, A., Hosseinpour, N., Bahramian, A., 2019. Dimethylcyclohexylamine switchable solvent interactions with asphaltenes toward viscosity reduction and in situ upgrading of heavy oils. Energy & Fuels 33, 8403-8412.


Because of the ever-increasing depletion rate of conventional oil resources, it is essential to design processes for heavy oil recovery from petroleum reservoirs. Heavy oils contain high quantities of large molecules, such as asphaltenes, giving rise to high viscosities during production. Solvent extraction processes are capable candidates for heavy oil recovery; however, the separation of conventional solvents is energy-intensive. Therefore, a solvent with not only a high capacity for heavy oil dissolution but also an easy and environmentally friendly separation is in demand. In this work, the N,N-dimethylcyclohexylamine switchable hydrophilicity solvent (SHS) was employed for viscosity reduction and upgrading of heavy oils. Optimum weight ratios of the SHS were added to three different dead heavy oil samples with 11.33 to 17.54 °API and a corresponding room-temperature viscosity of more than 4287.0 to 3365.4 cp. To shed light on the interactions of the SHS with asphaltenes, the solvent was also added to heavy oil model solutions of asphaltenes in toluene. The solutions containing the solvent and the recovered oil were exposed to pressurized CO2 in the presence of deionized water to switch the hydrophilicity of the solvent to water-miscible and separate the recovered oil. The thus-obtained aqueous solution was then warmed up to 65 °C in the presence of N2 gas bubbling through the liquid to switch the solvent hydrophilicity to water-immiscible form and recover the SHS. Results indicate that more than 52 wt % of the oils are recovered at the optimum solvent-to-oil ratio (SOR). The heavier the oil, the higher the optimum SOR is, resulting in the viscosity reductions of more than 70%. Dynamic light scattering shows that the size of asphaltene aggregates becomes smaller and considerably uniform by the SHS, indicating weakening of the asphaltene self-association interactions. Dynamic interfacial tension measurements calibrate the amount of impurity in the recovered SHS.

Musadji, N.Y., Lemée, L., Caner, L., Porel, G., Poinot, P., Geffroy-Rodier, C., 2020. Spectral characteristics of soil dissolved organic matter: Long-term effects of exogenous organic matter on soil organic matter and spatial-temporal changes. Chemosphere 240, 124808.


The aim of this study was to evaluate the long-term effect of urban and green waste compost exogenous organic matter (EOM) on soil dissolved organic matter (DOM). A luvic cambisol was amended 7 years before the study. DOM was investigated along a soil profile down to 1 m depth regarding seasonal variations (autumn and spring). DOM sampled by suction cups was characterized using dissolved organic carbon (DOC) content and

excitation emission matrix (EEM) fluorescence. The variability of DOM concentrations was pronounced but no major change in composition was determined. The results obtained, reinforced by statistical analysis, showed that the DOM quality was mainly influenced by soil management (organic matter amendment) whereas the quantity mainly depended on the season (heavy precipitation event). DOM humic characteristics were strongly dependent on amendment and changed with depth but was not affected by the season. Long term effect of compost organic matter was highlighted after a 7-years amendment.

Nagai, Y., Sato, F., Okamoto, S., Kamiya, Y., Honda, T., 2019. Pyrolysis behavior of Asian lacquer film in the presence of carbon nanotubes with potential application as a new sampling method. Journal of Analytical and Applied Pyrolysis 142, 104637.


This study aims to report the possibility of applying a sampling method using a carbon nanotube–based sampling tool for pyrolysis–gas chromatography/mass spectrometry (Py–GC/MS) to qualitative analysis of Asian lacquer. This sampling tool comprises multiwalled carbon nanotubes (MWCNTs) and emulates the adhesive mechanism of geckos. To apply this sampling method to lacquer-containing archaeological samples, the films of Toxicodendron vernicifluum, T. succedaneum and Gluta usitata, which are East Asian lacquers, were subjected to Py–GC/MS analysis. Similar to the conventional Py–GC/MS, the pyrolysis product characteristics of the three lacquer films were detected. However, compared with conventional Py–GC/MS, a difference was observed in the peak intensities of several pyrolyzates; this difference revealed the compositional change of pyrolyzates. To investigate the compositional change of pyrolyzates in detail, the T. vernicifluum film was analyzed by Py–GC/MS in the presence of MWCNTs, and the pyrolysis mechanism of T. vernicifluum film was discussed. The results suggest that MWCNTs promote side-chain cleavage and hydroxyl-group removal and alkylcatechols decompose into alkylbenzenes via alkylphenols.

Narasimhan, V.M., Patterson, N., Moorjani, P., Rohland, N., Bernardos, R., Mallick, S., Lazaridis, I., Nakatsuka, N., Olalde, I., Lipson, M., Kim, A.M., Olivieri, L.M., Coppa, A., Vidale, M., Mallory, J., Moiseyev, V., Kitov, E., Monge, J., Adamski, N., Alex, N., Broomandkhoshbacht, N., Candilio, F., Callan, K., Cheronet, O., Culleton, B.J., Ferry, M., Fernandes, D., Freilich, S., Gamarra, B., Gaudio, D., Hajdinjak, M., Harney, É., Harper, T.K., Keating, D., Lawson, A.M., Mah, M., Mandl, K., Michel, M., Novak, M., Oppenheimer, J., Rai, N., Sirak, K., Slon, V., Stewardson, K., Zalzala, F., Zhang, Z., Akhatov, G., Bagashev, A.N., Bagnera, A., Baitanayev, B., Bendezu-Sarmiento, J., Bissembaev, A.A., Bonora, G.L., Chargynov, T.T., Chikisheva, T., Dashkovskiy, P.K., Derevianko, A., Dobeš, M., Douka, K., Dubova, N., Duisengali, M.N., Enshin, D., Epimakhov, A., Fribus, A.V., Fuller, D., Goryachev, A., Gromov, A., Grushin, S.P., Hanks, B., Judd, M., Kazizov, E., Khokhlov, A., Krygin, A.P., Kupriyanova, E., Kuznetsov, P., Luiselli, D., Maksudov, F., Mamedov, A.M., Mamirov, T.B., Meiklejohn, C., Merrett, D.C., Micheli, R., Mochalov, O., Mustafokulov, S., Nayak, A., Pettener, D., Potts, R., Razhev, D., Rykun, M., Sarno, S., Savenkova, T.M., Sikhymbaeva, K., Slepchenko, S.M., Soltobaev, O.A., Stepanova, N., Svyatko, S., Tabaldiev, K., Teschler-Nicola, M., Tishkin, A.A., Tkachev, V.V., Vasilyev, S., Velemínský, P., Voyakin, D., Yermolayeva, A., Zahir, M., Zubkov, V.S., Zubova, A., Shinde, V.S., Lalueza-Fox, C., Meyer, M., Anthony, D., Boivin, N., Thangaraj, K., Kennett, D.J., Frachetti, M., Pinhasi, R., Reich, D., 2019. The formation of human populations in South and Central Asia. Science 365, eaat7487.

http://science.sciencemag.org/content/365/6457/eaat7487.abstract

Abstract: By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.

Editor's summary: Ancient human movements through Asia. Ancient DNA has allowed us to begin tracing the history of human movements across the globe. Narasimhan et al. identify a complex pattern of human migrations and admixture events in South and Central Asia by performing genetic analysis of more than 500 people who lived over the past 8000 years (see the Perspective by Schaefer and Shapiro). They establish key phases in the population prehistory of Eurasia, including the spread of farming peoples from the Near East, with movements both westward and eastward. The people known as the Yamnaya in the Bronze Age also moved both westward and eastward from a focal area located north of the Black Sea. The overall patterns of genetic clines reflect similar and parallel patterns in South Asia and Europe.

Structured Abstract

Rationale: To elucidate the extent to which the major cultural transformations of farming, pastoralism, and shifts in the distribution of languages in Eurasia were accompanied by movement of people, we report genome-wide ancient DNA data from 523 individuals spanning the last 8000 years, mostly from Central Asia and northernmost South Asia.

Results: The movement of people following the advent of farming resulted in genetic gradients across Eurasia that can be modeled as mixtures of seven deeply divergent populations. A key gradient formed in southwestern Asia beginning in the Neolithic and continuing into the Bronze Age, with more Anatolian farmer–related ancestry in the west and more Iranian farmer–related ancestry in the east. This cline extended to the desert oases of Central Asia and was the primary source of ancestry in peoples of the Bronze Age Bactria Margiana Archaeological Complex (BMAC). This supports the idea that the archaeologically documented dispersal of domesticates was accompanied by the spread of people from multiple centers of domestication.

The main population of the BMAC carried no ancestry from Steppe pastoralists and did not contribute substantially to later South Asians. However, Steppe pastoralist ancestry appeared in outlier individuals at BMAC sites by the turn of the second millennium BCE around the same time as it appeared on the southern Steppe. Using data from ancient individuals from the Swat Valley of northernmost South Asia, we show that Steppe ancestry then integrated further south in the first half of the second millennium BCE, contributing up to 30% of the ancestry of modern groups in South Asia. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the unique features shared between Indo-Iranian and Balto-Slavic languages.

The primary ancestral population of modern South Asians is a mixture of people related to early Holocene populations of Iran and South Asia that we detect in outlier individuals from two sites in cultural contact with the Indus Valley Civilization (IVC), making it plausible that it was characteristic of the IVC. After the IVC’s decline, this population mixed with northwestern groups with Steppe ancestry to form the “Ancestral North Indians” (ANI) and also mixed with southeastern groups to form the “Ancestral South Indians” (ASI), whose direct descendants today live in tribal groups in southern India. Mixtures of these two post-IVC groups—the ANI and ASI—drive the main gradient of genetic variation in South Asia today.

Conclusion: Earlier work recorded massive population movement from the Eurasian Steppe into Europe early in the third millennium BCE, likely spreading Indo-European languages. We reveal a parallel series of events leading to the spread of Steppe ancestry to South Asia, thereby documenting movements of people that were likely conduits for the spread of Indo-European languages.

Nelson, L.L., Smith, E.F., 2019. Tubey or not tubey: Death beds of Ediacaran macrofossils or microbially induced sedimentary structures? Geology 47, 909-913.

https://doi.org/10.1130/G46473.1

Within the upper Ediacaran Esmeralda Member of the Deep Spring Formation in southeastern California, USA, an ∼3 m stratigraphic interval contains multiple clastic bedding surfaces with enigmatic, three-dimensionally preserved corrugated tubes (<60 cm in length and 6 cm in width). When viewed as fragments and in situ on bedding planes, these resemble larger versions of annulated, tubular soft-bodied macrofossils that are common in late Ediacaran biotic assemblages regionally and globally. Despite superficial similarities to casts and molds

of body fossils preserved in correlative strata, we suggest these tubes are instead previously undescribed organosedimentary structures that developed through differential compaction of rippled heterolithic interbeds bound by pyritized microbial mat layers. These distinctive structures formed within peritidal settings in the latest Ediacaran Period as the result of specific ecological and environmental conditions marked by flourishing microbial mat communities and dysoxic sediments. This interpretation may inform the biogenicity of other structures previously reported as macroscopic body or trace fossils.

Nema, P., Paul, D., Karmalkar, N.R., Shouche, Y.S., 2019. Bacterial diversity in the metal-rich terrestrial deep subsurface sediments of Krishna Godavari Basin, India. Geomicrobiology Journal 36, 917-932.

https://doi.org/10.1080/01490451.2019.1654041

Krishna Godavari (KG) basin, located in the eastern continental margin of India, is a geological region well known for the abundance of economically important minerals. However, less is known about the microbial ecology of its subsurface sediments. The present study is the first report on the comprehensive culture-independent census of bacterial communities of deep subsurface of KG basin and their relationship with the geochemical environment. Elemental and mineralogical characterization of the sediments highlighted the presence of carbon and nitrogen deprived conditions along with the abundance of metalliferous minerals, especially rich in valuable elements like zirconium, vanadium, cesium, and rare earth elements. Diversity analysis based on Illumina MiSeq high-throughput sequencing platform revealed the predominance of Firmicutes (44.24%), Proteobacteria (34.17%), Bacteroidetes (15.18%), and Actinobacteria (3.81%) in the deep subsurface of this basin. ?Abundant? and ?rare? sub-communities analysis indicated that a large number of phyla like Acidobacteria, Armatimonadetes, Chloroflexi, and Deinococcus-Thermus were exclusively present as a rare community. Statistical analyses demonstrated that geochemical parameters, especially depth, pH, and metal content, showed significant influence on the microbial community structure. The present study should help future investigations for microbial mediated sustainable utilization of mineral-rich sediments of the region.

Nguyen, S.N., Kyle, J.E., Dautel, S.E., Sontag, R., Luders, T., Corley, R., Ansong, C., Carson, J., Laskin, J., 2019. Lipid coverage in nanospray desorption electrospray ionization mass spectrometry imaging of mouse lung tissues. Analytical Chemistry 91, 11629-11635.


Lipids are a naturally occurring group of molecules that not only contribute to the structural integrity of the lung preventing alveolar collapse but also play important roles in the anti-inflammatory responses and antiviral protection. Alteration in the type and spatial localization of lipids in the lung plays a crucial role in various diseases, such as respiratory distress syndrome (RDS) in preterm infants and oxidative stress-influenced diseases, such as pneumonia, emphysema, and lung cancer following exposure to environmental stressors. The ability to accurately measure spatial distributions of lipids and metabolites in lung tissues provides important molecular insights related to lung function, development, and disease states. Nanospray desorption electrospray ionization (nano-DESI) and other ambient ionization mass spectrometry techniques enable label-free imaging of complex samples in their native state with minimal to absolutely no sample preparation. However, lipid coverage obtained in nano-DESI mass spectrometry imaging (MSI) experiments has not been previously characterized. In this work, the depth of lipid coverage in nano-DESI MSI of mouse lung tissues was compared to liquid chromatography tandem mass spectrometry (LC-MS/MS) lipidomics analysis of tissue extracts prepared using two different procedures: standard Folch extraction method of the whole lung samples and extraction into a 90% methanol/10% water mixture used in nano-DESI MSI experiments. A combination of positive and negative ionization mode nano-DESI MSI identified 265 unique lipids across 20 lipids subclasses and 19 metabolites (284 in total) in mouse lung tissues. Except for triacylglycerols (TG) species, nano-DESI MSI provided comparable coverage to LC-MS/MS experiments performed using methanol/water tissue extracts and up to 50% coverage in comparison with the Folch extraction-based whole lung lipidomics analysis. These results demonstrate the utility of nano-DESI MSI for comprehensive spatially resolved analysis of lipids in tissue sections. A combination of nano-DESI MSI and LC-MS/MS lipidomics is particularly useful for

exploring changes in lipid distributions during lung development, as well as resulting from disease or exposure to environmental toxicants.

Nie, H., Jin, Z., Sun, C., He, Z., Liu, G., Liu, Q., 2019. Organic matter types of the Wufeng and Longmaxi formations in the Sichuan Basin, South China: Implications for the formation of organic matter pores. Energy & Fuels 33, 8076-8100.


Organic matter (OM) pores are crucial to porosity in many shale gas reservoirs, but the origin and types of OM pores remain controversial. In this paper, the OM types are systematically identified and analyzed in the Wufeng–Longmaxi Formations from wells JY 1 and JY 2 in the Jiaoshiba gas field, Sichuan Basin. The results indicate that the OM comprises several hydrocarbon-generating organisms, such as various algae (multi- and unicellular algae, colonial algae, acritarch, etc.), graptolite, sponge spicule, and other fossil fragments, as well as several amorphous OM types, such as solid bitumen and strongly compacted algae. The OM pores have inherited the morphology and structure of multicellular algae and are commonly hundreds of nanometers, some of which even reach micrometer size, exhibiting irregular, bubble-like, spherical, and/or elliptical shapes. In the unicellular algae, only a small amount of OM pores are observed, which are isolated and distributed randomly. The OM pores, either irregular or oval, are tens to more than 100 nm, which are developed by the arrangement gap between the unicellular algae, and some are generated inside the unicellular algae by hydrocarbon generation and expulsion. Two types of OM pores developed in solid bitumen, including bitumen–spherulite pores and vesicular pores. The bitumen–spherulite pores are formed by the arrangement of nanoscale bitumen–spherulite with a pore diameter of nanometer scale. The vesicular pores are formed by gas generation and expulsion after oil cracking, and the shape is mostly sporadic, isolated with various sizes ranging from 500 nm to 3 μm. The OM pores in graptolite, sponge spicule, radiolarian, and other fossil fragments are much fewer in quantity and smaller in size. The OM pores may have only developed on the surface of graptolite. The pores are commonly developed in the walls of the fossil fragments and in the solid bitumen by filling in the biological cavity of the sponge spicule. Therefore, it is concluded that the OM types are the pivotal causes of different OM pore types and properties. Multicellular algae are most beneficial to OM pore development, serving as the major producer of OM pores. In the profile of the Wufeng–Longmaxi shales, the vertical variation of OM types and OM pores are diverse in different graptolitic zones. The dominant hydrocarbon-generating organisms in the WF2–LM4 graptolitic zone are multicellular algae and graptolite, followed by a small number of unicellular algae, sponge spicule, radiolarian, and other fossil fragments. The OM pores are mainly developed in multicellular algae and graptolite, with only a few developed in solid bitumen and unicellular algae. In the LM5–LM8 graptolitic zone, however, the hydrocarbon-generating organisms are primarily unicellular algae, with little multicellular algae, graptolite, sponge spicule, and other fossil fragments. The OM pores are mainly developed in unicellular algae and solid bitumen. The new findings provide evidence to support the proposal that multicellular algae are the main hydrocarbon-generating organisms controlling the OM pore development. Moreover, the WF2–LM4 graptolitic zone is the target interval for shale gas exploration and development in the Upper Ordovician and Lower Silurian Formations in the Sichuan Basin and its surrounding areas.

Novoa, E.M., Jungreis, I., Jaillon, O., Kellis, M., 2019. Elucidation of codon usage signatures across the domains of life. Molecular Biology and Evolution 36, 2328-2339.

https://doi.org/10.1093/molbev/msz124

Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being “synonymous,” these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutational drift, is the major determinant of variation across species. Here, we find that in addition to GC content, interspecies codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding and show that domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain of life with high accuracy. We then wondered whether the inclusion of codon usage

codon autocorrelation patterns, which reflects the nonrandom distribution of codon occurrences throughout a transcript, might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to previous reports. Instead, our results suggest that codon autocorrelation patterns are a by-product of codon optimality throughout a sequence, where highly expressed genes display autocorrelated “optimal” codons, whereas lowly expressed genes display autocorrelated “nonoptimal” codons.

O'Keefe, J.H., O'Keefe, E.L., Lavie, C.J., 2019. The human-canine bond: A heart's best friend. Mayo Clinic Proceedings: Innovations, Quality & Outcomes 3, 249-250.


Humans have coevolved with dogs, beginning with the domestication of the wolf about 40,000 years ago.1 Since then, this symbiotic relationship between a human and a dog has favorably affected development bilaterally and intertwined the 2 species. In this issue of Mayo Clinic Proceedings, a study by Maugeri et al2 further strengthens the growing body of evidence indicating dogs' beneficial effect on cardiovascular health (CVH) and overall well-being. The investigators examined 1769 patients from the Kardiovize Brno 2030 study and used a novel metric for CVH based on 7 key health factors emphasized by the American Heart Association. Pet owners reported higher levels of physical activity (PA), better adherence to a heart-healthy diet, higher levels of high-density lipoprotein cholesterol, and lower levels of blood glucose and diabetes. Moreover, PA and diet were even more favorable in dog owners than in owners of other animals. Dog ownership also correlated with a significantly higher overall CVH score compared with either ownership of a noncanine pet or no pet at all.

Experts on the topic have long recommended canine companionship as protection against cardiovascular disease (CVD) because of a dog's tendency to boost its owner's PA and mental health. Research indicates that bringing a dog into the home can improve adherence to an exercise regime, enhance fitness, and reduce visceral adiposity of its human coinhabitants.3 With CVD being the predominant cause of death worldwide and physical inactivity and overweight/obesity being major risk factors for CVD and premature death and disability, a commitment to regular PA, exercise, and fitness has the potential to substantially improve outcomes.4 In fact, PA has ameliorating effects on 5 of the 6 leading modifiable risk factors for myocardial infarction, including lipid profiles, stress, diabetes, hypertension, and abdominal obesity, as well as psychological risk factors and psychosocial stress (PSS).5 Dogs compel their owners to specifically do more outdoor exercise, which may even bolster health benefits further. Recently, a large cross-sectional study found that >120 min/wk spent in a natural outdoor environment was associated with higher reported levels of health and well-being.6

Higher levels of PA, exercise, and fitness not only improves CVD outcomes but also curb anxiety, hostility, depression, and emotional distress.7, 8, 9 In addition to increasing their owners' dose of outdoor exercise, dogs reduce PSS levels, aid in the treatment of depression, and act effectively as an anxiolytic intervention.10, 11 There exists a dangerous reciprocal relationship between CVD and mental health whereby PSS is associated with elevated rates of CVD, but CVD also stands as a major risk factor for developing or worsening mental health conditions.7 The strong emotional bond that typically develops between a human and a dog can bestow powerful therapeutic effects on both mental health and heart health.

A landmark study from Sweden analyzed the effects of dog ownership on CVD death and all-cause mortality in a prospective register-based nationwide cohort of 3,432,153 individuals, with 12 years of follow-up.12 In single-person households, dog ownership was associated with significantly lower risks of both all-cause mortality and CVD mortality (33% and 36% reductions, respectively). People living in multiple-person households also benefited from dog ownership with significantly lower risks of all-cause mortality and CVD mortality (11% and 15% reductions, respectively), though the benefits were less impressive than for those living alone.12

More evidence of the halo effect of canine companionship on heart health comes from the Cardiac Arrhythmia Suppression Trial,13 which concluded that high social support and dog ownership were 2 independent predictors of survival 1 year after myocardial infarction. Dog ownership, much like interactive physical play,14 improves risk factors for both CVD and mental illness in unique multidimensional ways. The human bond with dogs goes beyond emotion and sheds light on the shared evolutionary journey of these 2 species. More so than

chimpanzees, our closest genetic relative, and more so than wolves raised in human environments, dogs are uniquely sensitive to human forms of communication and have been proven to understand human intention far better than any other animal.15, 16 The observation suggests that this may be genetically inherent as these abilities are seen in untrained dogs as young as 6 weeks old.15 Hunting dogs were found to best understand human hand gestures.16 Similarly, in the Swedish nationwide cohort study, among all the various breeds, hunting dogs (such as retrievers, pointers, and setters) were associated with the lowest risks of CVD death.12

Over the past 40,000 years, Homo sapiens and Canis familiaris have become evolutionarily adapted to fill a niche in each other's environments and that relationship has translated into contemporary health benefits. Currently, the presence of a dog in the home portends a lifestyle shift for the better and is linked to a reduction in PSS levels; improvement in PA, exercise, and fitness levels; and decreased overall CVD burden, producing a true “Dog's Day Heaven.”

Ok, S., Mahmoodinia, M., Rajasekaran, N., Sabti, M.A., Lervik, A., van Erp, T.S., Cabriolu, R., 2019. Molecular structure and solubility determination of asphaltenes. Energy & Fuels 33, 8259-8270.


Due to their complex chemical structure, identification and characterization of asphaltenes remain a big challenge for researchers in the oil industry. In the current contribution, solution-state two-dimensional (2D) nuclear magnetic resonance (NMR) spectra of the asphaltenes, obtained from either heavy or light crude oil samples, provide information on the chemical structures of asphaltenes at the molecular level. Two-dimensional 1H–13C heteronuclear NMR measurements are particularly useful for differentiating among several structural environments whose signals overlap in the one-dimensional 13C spectra. Both, 2D 1H–13C heteronuclear and 1H–1H homonuclear NMR spectra indicate short- and long-range interactions between different functional groups of the asphaltene samples, revealing even “bay”- and “fjord”-type structures. Based on the NMR correlations between different protons and carbons with different chemical environments, we propose various chemical structures (polyaromatic cores with aliphatic chains, porphyrin derivatives, organic salts). Furthermore, through molecular dynamics simulations, we have obtained Hildebrand solubility parameters of different asphaltene solvents and of two experimental recovered asphaltene structures. Our calculated solubilities are consistent with previous experimental and simulation works.

Onojake, M.C., Abrakasa, S., 2019. Distribution of methylhopanes in some Niger Delta oils. Arabian Journal of Geosciences 12, 584.

https://doi.org/10.1007/s12517-019-4728-y

A suite of oil samples from Niger Delta oil fields were examined for compositional distribution of methylhopane. The samples were obtained from wellhead of oil wells and stored in sample bottles. The oil samples were fractionated and the saturate fraction was subjected to gas chromatography/mass spectrometry (GC–MS) analysis. The methylhopanes in the oils were identified, their abundance delineated, and are of potential use for oil characterization. The mass chromatograms of m/z 205 were extracted and the peaks identified using GC–MS library, literature, and mass spectra form the library. 2α–Methylhopanes and 3β–methylhopanes were identified in Nigerian Niger Delta oils. North Sea and Venezuelan Boscan oil were also examined. Generally, the Nigerian oils showed higher abundance of 2α–methylhopanes and lower abundance 3β–methylhopanes compared to the Boscan and North Sea oils. The plot of C30 hopane/C30 2α–methylhopane and C30 hopane/C30 3β–methylhopane for all the oils showed the discrimination of the oils into Niger Delta, North Sea, and Venezuelan Boscan oil. The ratio of C30 hopanes/methylhopanes can be applied as a correlation tool.

Ortega, A., Geraldi, N.R., Alam, I., Kamau, A.A., Acinas, S.G., Logares, R., Gasol, J.M., Massana, R., Krause-Jensen, D., Duarte, C.M., 2019. Important contribution of macroalgae to oceanic carbon sequestration. Nature Geoscience 12, 748-754.

https://doi.org/10.1038/s41561-019-0421-8

The role of macroalgae in Blue Carbon assessments has been controversial, partially due to uncertainties about the fate of exported macroalgae. Available evidence suggests that macroalgae are exported to reach the open ocean and the deep sea. Nevertheless, this evidence lacks systematic assessment. Here, we provide robust evidence of macroalgal export beyond coastal habitats. We used metagenomes and metabarcodes from the global expeditions Tara Oceans and Malaspina 2010 Circumnavigation. We discovered macroalgae worldwide at up to 5,000 km from coastal areas. We found 24 orders, most of which belong to the phylum Rhodophyta. The diversity of macroalgae was similar across oceanic regions, although the assemblage composition differed. The South Atlantic Ocean presented the highest macroalgal diversity, whereas the Red Sea was the least diverse region. The abundance of macroalgae sequences attenuated exponentially with depth at a rate of 37.3% km−1, and only 24% of macroalgae available at the surface were expected to reach the seafloor at a depth of 4,000 m. Our findings indicate that macroalgae are exported across the open and the deep ocean, suggesting that macroalgae may be an important source of allochthonous carbon, and their contribution should be considered in Blue Carbon assessments.

Pacheco, D.M., Bergerson, J.A., Alvarez-Majmutov, A., Chen, J., MacLean, H.L., 2019. Characterizing variability in oil sands upgrading greenhouse gas emissions intensity. Energy & Fuels 33, 8907-8919.


A better understanding of the greenhouse gas (GHG) emissions intensity of upgrading oil sands bitumen is needed to inform industry and government decisions related to climate change mitigation. We develop an enhanced version of the Oil Sands Technologies for Upgrading Model (OSTUM 2.0), a life cycle-based model that estimates energy use and GHG intensities of upgrading technologies at the process unit level. We apply OSTUM 2.0 to commercial upgrading technologies operating in Alberta, Canada, and propose baseline estimates and ranges of direct and indirect GHG intensities for delayed coking based- (DC), hydroconversion based- (HC), and combined hydroconversion and fluid coking based upgrading (HC/FC). We identify potential drivers of variability in upgrading GHG intensity. These include the application of different upgrading technologies (up to 36% variation in baseline GHG intensities), variation in the properties of upgrading products (up to 91% variation in baseline GHG intensities, a factor not previously modeled in the literature), and changes in the energy efficiency of operations and use of byproducts as fuels (up to 45% variation in baseline GHG intensities). OSTUM 2.0 improves upon life cycle-based literature by facilitating more detailed modeling, assessment, and comparison of the GHG intensity of commercial upgrading schemes, using consistent boundaries, assumptions, public data sources, and calculation methods. The systems-level modeling approach allows comprehensive characterization of upgrading GHG emissions and drivers of variability. Our findings suggest that modeling different technology configurations, product properties, and fuel mixes can increase the representativeness of upgrading GHG intensity estimates.



The Moon-forming giant impact extensively melts and partially vaporizes the silicate Earth and delivers a substantial mass of metal to Earth's core. The subsequent evolution of the magma ocean and overlying atmosphere has been described by theoretical models but observable constraints on this epoch have proved elusive. Here, we report thermodynamic and climate calculations of the primordial atmosphere during the magma ocean and water ocean epochs respectively and forge new links with observations to gain insight into the behavior of volatiles on the Hadean Earth. As accretion wanes, Earth's magma ocean crystallizes, outgassing the bulk of its volatiles into the primordial atmosphere. The redox state of the magma ocean controls both the chemical composition of the outgassed volatiles and the hydrogen isotopic composition of water oceans that remain after hydrogen escape from the primordial atmosphere. The climate modeling indicates that multi-bar H2-rich atmospheres generate sufficient greenhouse warming and rapid kinetics resulting in ocean-atmosphere H2O-H2 isotopic equilibration. Whereas water condenses and is mostly retained, molecular hydrogen does not

condense and can escape, allowing large quantities (∼102 bars) of hydrogen – if present – to be lost from the Earth in this epoch. Because the escaping inventory of H can be comparable to the hydrogen inventory in primordial water oceans, equilibrium deuterium enrichment can be large with a magnitude that depends on the initial atmospheric H2 inventory. With rapid kinetics, the water molecule concentrates deuterium and, to the extent that hydrogen in other forms (e.g., H2) are significant species in the outgassed atmosphere, pronounced D/H enrichments (∼1.5-2x) in the oceans are expected from equilibrium partitioning in this epoch. By contrast, the common view that terrestrial water has a carbonaceous chondritic source requires the oceans to preserve the isotopic composition of that source, undergoing minimal D-enrichment via equilibration with H2 followed by hydrodynamic escape. Such minimal enrichment places upper limits on the amount of primordial atmospheric H2 in contact with Hadean water oceans and implies oxidizing conditions (logfO2>IW+1, H2/H2O < 0.3) for outgassing from the magma ocean. Preservation of an approximate carbonaceous chondrite D/H signature in the oceans thus provides evidence that the observed oxidation of silicate Earth occurred before crystallization of the final magma ocean, yielding a new constraint on the timing of this critical event in Earth history. The seawater-carbonaceous chondrite “match” in D/H (to ∼10-20%) further constrains the prior existence of an atmospheric H2 inventory – of any origin – on post-giant-impact Earth to <20 bars, and suggests that the terrestrial mantle supplied the oxidant for the chemical resorption of metals during terrestrial late accretion.

Paradise, A., Menou, K., Valencia, D., Lee, C., 2019. Habitable snowballs: Temperate land conditions, liquid water, and implications for CO2 weathering. Journal of Geophysical Research: Planets 124, 2087-2100.

https://doi.org/10.1029/2019JE005917

Abstract: Habitable planets are commonly imagined to be temperate planets like Earth, with areas of open ocean and warm land. In contrast, planets in snowball states, where oceans are entirely ice covered, are believed to be inhospitable. However, we show using a general circulation model that terrestrial planets in the inner habitable zone are able to support large unfrozen areas of land while in a snowball state. Due to their lower albedo, these unfrozen regions reach summer temperatures in excess of 10 °C. Such conditions permit CO2 weathering, suggesting that continental weathering can provide a mechanism for trapping planets in stable snowball states. The presence of land areas with warm temperatures and liquid surface water motivates a more‐nuanced understanding of habitability during these snowball events.

Plain Language Summary: Studies examining the ability of Earth‐like planets to host life have often used conditions leading to “snowball” events, where sea ice extends all the way to the equator, as a limit to the range of habitable climates. This has been based on the assumption that snowball planets are always below freezing everywhere on their surfaces. As the chemical process by which CO2 is removed from the atmosphere and bound in surface rocks relies on warm temperatures and liquid water and therefore would not happen in globally cold conditions, this has also led to the conclusion that snowball events should be temporary, coming to an end when volcanoes release enough accumulated CO2 to warm the planet enough to melt the ice. We ran several thousand three‐dimensional computer simulations of Earth‐like climates and found that if there are inland areas of dark, bare ground under enough sunlight, those regions can be warm enough for liquid water and life without causing the sea ice to retreat. This suggests that snowball planets should not be excluded as inhospitable to life and that on some planets the burial of CO2 in surface rocks in these areas could balance volcanic emissions, resulting in permanent snowball conditions.

Pastor, A., Freixa, A., Skovsholt, L.J., Wu, N., Romaní, A.M., Riis, T., 2019. Microbial organic matter utilization in high-Arctic streams: Key enzymatic controls. Microbial Ecology 78, 539-554.

https://doi.org/10.1007/s00248-019-01330-w

In the Arctic, climate changes contribute to enhanced mobilization of organic matter in streams. Microbial extracellular enzymes are important mediators of stream organic matter processing, but limited information is available on enzyme processes in this remote area. Here, we studied the variability of microbial extracellular enzyme activity in high-Arctic fluvial biofilms. We evaluated 12 stream reaches in Northeast Greenland draining areas exhibiting different geomorphological features with contrasting contents of soil organic matter to

cover a wide range of environmental conditions. We determined stream nitrogen, phosphorus, and dissolved organic carbon concentrations, quantified algal biomass and bacterial density, and characterized the extracellular enzyme activities involved in catalyzing the cleavage of a range of organic matter compounds (e.g., β-glucosidase, phosphatase, β-xylosidase, cellobiohydrolase, and phenol oxidase). We found significant differences in microbial organic matter utilization among the study streams draining contrasting geomorphological features, indicating a strong coupling between terrestrial and stream ecosystems. Phosphatase and phenol oxidase activities were higher in solifluction areas than in alluvial areas. Besides dissolved organic carbon, nitrogen availability was the main driver controlling enzyme activities in the high-Arctic, which suggests enhanced organic matter mineralization at increased nutrient availability. Overall, our study provides novel information on the controls of organic matter usage by high-Arctic stream biofilms, which is of high relevance due to the predicted increase of nutrient availability in high-Arctic streams in global climate change scenarios.

Pattan, J.N., Parthiban, G., Amonkar, A., 2019. Productivity controls on the redox variation in the southeastern Arabian Sea sediments during the past 18 kyr. Quaternary International 523, 1-9.


Redox-sensitive elements (uranium, molybdenum and cadmium) and productivity proxies (total organic carbon, calcium carbonate and phosphorous) were analysed to assess the importance of productivity on redox variation for the last ∼18 kyr in a sediment core off Cochin at a water depth of 280 m in the southeastern Arabian Sea. These proxies document a combination of higher productivity and intense suboxic conditions during the last deglaciation (∼18–13 kyr) and late Holocene (5.5 kyr to Present) versus lower productivity and less suboxic conditions between these intervals (∼13–5.5 kyr). The productivity and redox proxies behave similar to one another suggesting that the variations in productivity controlled the redox conditions. This relationship is supported by patterns during the last deglaciation, when a decrease in productivity at ∼16 kyr preceded improved deep water oxygenation by ∼14 kyr. Therefore, productivity changes were responsible for the development of reducing conditions in shallow waters in the southeastern Arabian Sea.

Pederson, C.L., Klaus, J.S., Swart, P.K., McNeill, D.F., 2019. Deposition and early diagenesis of microbial mud in the Florida Everglades. Sedimentology 66, 1989-2010.


Abstract Microbial carbonate mud in the modern (<4 kyr) palustrine environment of the Florida Everglades is surprisingly susceptible to early diagenetic alteration. The low-Mg calcite crystals show an open, trellis-like crystal structure that yields a high surface area to volume ratio. This textural complexity, likely to be a result of organic influence, leads to abundant reaction sites vulnerable to both dissolution and subsequent precipitation. Rapid degradation of organics is attributed to both aerobic and anaerobic metabolisms. Geochemical signatures suggest increased denitrification within the freshwater environment and increased sulphate reduction at the (slightly) brackish mangrove transition zone. A transition from a freshwater to brackish depositional environment is likely to follow the Holocene sea-level transgression. The textural complexity in these microbial carbonates causes an unexpectedly low preservation potential of original textural and geochemical signatures, even in low-Mg calcite. Given the potential for early diagenesis of palustrine and perhaps other microbial carbonates, they should be used cautiously as archives for palaeoenvironmental proxies.



The bioremediation of petroleum spills in marine environments is still a challenge nowadays, and the technology available towards this goal must be improved. The search for efficient and applicable systems requires the prospection, isolation and characterization of autochthonous microorganisms with potential for bioremediation. Here, microorganisms were isolated from “Lagoa do Peixe” National Park, a site with a history of frequent petroleum spills in Brazil. The isolation methodology was based on the enrichment of microorganisms able to biodegrade petroleum hydrocarbons. After preliminary tests of 2,3,5-triphenyl tetrazolium chloride (TTC) redox indicator, two bacteria were able to produce biosurfactants and metabolize complex carbon sources in a solid medium: Bacillus methylotrophicus SSNPLPB5 and Pseudomonas sihuiensis SNPLPB7. Biodegradation assays using aliphatic and polycyclic aromatic hydrocarbons (PAHs) sources showed that both bacteria are able to biodegrade: (i) up to 92.1% and 42.4% of the medium (C8 to C19) and long (C20 to C33) chain aliphatic contaminant fraction, respectively; (ii) 31.1% of isoprenoid (pristane) and (iii) 46% of anthracene, 33.9% of phenanthrene and 35.3% of pyrene, after 46 days of incubation in seawater. The isolates were shown to produce biosurfactants such as surfactins, iturins, mono- and di-rhamnolipids, which reduced the surface tension, pH and showed emulsifying activity of the cell-free supernatant at the end of the incubation time, with potential application in petroleum spills bioremediation.

Pereira, O., Hochart, C., Auguet, J.C., Debroas, D., Galand, P.E., 2019. Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. MicrobiologyOpen 8, e00852.

https://doi.org/10.1002/mbo3.852

Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re‐analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co‐occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more specifically of MGII subgroups, and reveal their association to a number of gene‐coding sequences. In particular, we show that MGII proteorhodopsins were detected in both the surface and the deep chlorophyll maximum layer and that different clusters of these light harvesting proteins were present. Our approach helped describing the set of genes found together with specific MGII subgroups. We could thus define genomic environments that could theoretically describe ecologically meaningful units and the ecological niche that they occupy.

Perez Claro, Y.A., Schoeggl, F.F., Taylor, S.D., Yarranton, H.W., 2019. Phase behavior of mixtures of bitumen and n-butane. Energy & Fuels 33, 8530-8543.


The phase behavior of bitumen and n-butane mixtures was investigated at temperatures from 20 to 230 °C and pressures from 2 to 10 MPa. The measurements included saturation pressures, compositions at the onset of the second liquid phase, and the compositions and masses of the light n-butane-rich and heavy “pitch” phases in the liquid–liquid region. The phase compositions were measured in terms of the n-butane, maltenes, and C5-asphaltenes (pentane insolubles) contents. The bitumen component yields were reported as the mass of the component in the pitch phase divided by the mass of bitumen in the feed. The onsets, yields, and phase compositions were insensitive to temperature and pressure except possibly at 2 MPa and 20 °C. The phase boundary data were used to construct pressure–composition diagrams. The phase compositions were used to construct a ternary diagram from which equilibrium constants were determined. The equilibrium constants were correlated to the feed n-butane content and used in a flash calculation to confirm the consistency of the phase composition and yield data in the liquid–liquid region. The phase behavior data for mixtures of n-butane and bitumen were consistent with the trends observed with other n-alkane diluted bitumens.

Petersen, H.I., Hillock, P., Milner, S., Pendlebury, M., Scarlett, D., 2019. Monitoring gas distribution and origin in the Culzean Field, UK Central North Sea, using data from a continuous isotope logging tool and isotube and test samples. Journal of Petroleum Geology 42, 435-449.

https://doi.org/10.1111/jpg.12745

The high pressure – high temperature Culzean field, UK Central North Sea, contains lean gas condensate in the Triassic Joanne sandstones and the Middle Jurassic Pentland sandstones. A comprehensive gas analysis programme was installed as an integrated part of field development in order to monitor gas composition, distribution and origin in the reservoirs and overburden pre‐ production start‐up. Isotube OUT and isotube IN gas samples were collected. The isotube IN data show that some gas is recycled, including alkenes representing contamination from the degradation of mud additives; but concentrations are minor, and do not seem to affect the isotope values derived from the C2 and C3 isotube OUT gases significantly. 13C‐enriched methane derived from drill‐bit metamorphism is recorded in the isotube IN gas, but likewise in low concentrations. Gas data were also acquired from a Continuous Isotope Logging Tool (CILT) which measures real‐time gas concentrations and isotope values of C1–C3 each foot through the entire drilled section. The CILT thus provides a continuous trend of methane isotope values versus depth, and this trend is useful in identifying changes in gas composition. However, concerns related to CILT include: (i) C1–C3 stable carbon isotope detection limits for isotube OUT gas analyses are considerable lower than for CILT; due to the lower isotube gas concentrations required for measurement of C3 isotopes, isotubes are able to map a shallower vertical thermogenic gas migration front in the overburden. (ii) Discrepancies between isotube OUT and CILT isotope values may be significant and cannot be assigned to analytical uncertainty; by contrast, test gas and isotube OUT isotope values are comparable. Hence, CILT isotope values from specific depths cannot stand in isolation but must be complemented by isotube OUT isotope measurements.

Gas in the Pentland reservoir is the most coaly in composition due to self‐sourcing from the Pentland coals. The coals are the primary source rock for the gas encountered in the entire reservoir interval at Culzean, but the underlying Joanne sandstones contain contributions from highly mature marine shales in the Kimmeridge Clay Formation and/or Heather Formation. The Lower Cretaceous seal on top of the Pentland reservoir is relatively tight but some minor migration/leakage of thermogenic gas into the overburden is recorded by the detection of C3 isotopes. Thermogenic gas also occurs in high porosity intervals in the Upper Cretaceous succession but this gas is interpreted to have migrated laterally in porous carrier beds and did not enter these intervals at the well locations.

Pitarello, M.Z., Santos, T.J.S.d., Ancelmi, M.F., 2019. Syn-to post-depositional processes related to high grade metamorphic BIFs: Geochemical and geochronological evidences from a Paleo to Neoarchean (3.5–2.6 Ga) terrane in NE Brazil. Journal of South American Earth Sciences 96, 102312.


In the Borborema Province, iron formations occur in Archean-Paleoproterozoic nuclei including the highly metamorphosed and deformed Granjeiro Complex. In this work, we analyze the BIFs of the Granjeiro Complex from the petrographic, geochemical, and isotopic viewpoints and discuss their depositional conditions. Also, we evaluate the post-depositional processes that may have suppressed their original geochemistry. Petrographic and major element analysis divides the BIFs into grunerite magnetite meta-BIF (“Grunerite BIF”), magnetite/hematite meta-BIF (“Magnetite BIF”), and garnet magnetite meta-BIF (“Garnet BIF”). REY and Nd isotope analysis exhibit a distinct pattern and display two groups, according to ΣREY. Group I (low ΣREY) shows REY ratios consistent with sediments precipitated from seawater, such positive anomalies of LaSN, LREE-MREE depletion, and superchondritic Y/Ho wt.-ratios. In contrast, Group II has parameters that are different from seawater, including negative or absent LaSN anomalies, LREE-MREE enrichment, and subchondritic Y/Ho, that suggest the influence of other REY sources and post-depositional processes. Both groups present negative Ce anomalies, with higher values on Group II. Considering the results of the Nd isotopes, the Group I presents negative εNd and higher TDM ages, while Group II has positive εNd and lower TDM ages. An isochron could be defined, but the age obtained (635 ± 49 Ma) is probably metamorphic. Besides, five representative samples of the terrane where the BIFs are enclosed were dated using the LA-ICP-

MS U-Pb zircon method. The resulting ages range 3535 ± 14 Ma to 2384 ± 35 Ma, with the amphibolite of the metavolcano-sedimentary sequence dating back to 2654 ± 26 Ma. According to the results, it is possible to infer that the Granjeiro BIFs deposited in an environment with little contribution of terrigenous sediments attested by the low concentration of immobile elements. The depositional environment was probably distant from the continent, under the influence of high-temperature hydrothermal fluids. In contrast, the Garnet BIFs may represent sporadic terrigenous events or more proximity to the shore. Inconsistent Nd isotopes and REY data from the Group II rocks suggest the influence of processes after deposition. Our data show that, although REY and Nd isotopes are considered to be relatively immobile, metamorphism and hydrothermal alteration in areas of intense deformation can lead to remobilization. These should be analyzed before the interpretation of the depositional environment of the BIFs.



Hydrocarbon-degrading bacteria were isolated from 2% hydrocarbon enriched sample collected from vehicular repairing stations, garages and petrol bunk. Incubation of the isolated non-virulent strains in Bushnell-Haas (BH) medium supplemented with hydrocarbon, showed their ability to survive on hydrocarbon thereby reducing the total organic carbon content. Based on the degradation potential, different bacterial consortia were prepared and consortium CHM1 was found to grow best with maximum degradation. 16S rRNA gene sequencing of the strains revealed their identity with Klebsiella spp., Enterobacter sp. and Pantoea sp. high to moderate affinity towards hydrocarbon of the selected strains were indicated by Bacterial Adhesion To Hydrocarbon (BATH) test and Contact Angle. Gas Chromatography-Mass Spectrometric (GC-MS) analysis of the mixed hydrocarbon containing broth revealed the presence of benzene derivatives, aliphatic acids, naphthalene, aliphatic alkanes, cyclic aliphatics as major compounds. The efficiency of the selected bacterial consortium showed an overall 16.20% degradation of the mixed hydrocarbon after 4 days, where, aliphatic cyclic compound (1-(1,5-Dimethylhexyl)-4-(4-Methylpentyl)-Cyclohexane) were completely degraded, naphthalene derivatives were reduced to 36.72%, aliphatic acids were degraded to 78.13% and benzene derivatives to 24.16%. Degradation of the long-chain aliphatic alkanes was further observed through Fourier Transform Infrared spectrometric (FTIR) analysis.

Portnov, A., Cook, A.E., Sawyer, D.E., Yang, C., Hillman, J.I.T., Waite, W.F., 2019. Clustered BSRs: Evidence for gas hydrate-bearing turbidite complexes in folded regions, example from the Perdido Fold Belt, northern Gulf of Mexico. Earth and Planetary Science Letters 528, 115843.


We describe previously undocumented but extensive gas hydrate accumulations in the mouth of Perdido Canyon in the northern Gulf of Mexico. The accumulations are located within central parts of structural domes (four-way closures) and are characterized by stacked, high-amplitude bottom simulating reflections (BSRs) that we call clustered BSRs. Seismic data from Perdido Canyon show two clustered BSRs associated with turbidite sequences within two dome folds formed from tectonic folding and salt diapir rise. The northwestern (NW) and southeastern (SE) clustered BSRs have aerial extents of ∼25 km2 and 50 km2, respectively. Well log data confirm gas hydrate occurs above the NW clustered BSR, within a 225 m-thick consistently high-resistivity interval that we interpret as gas hydrate in near-vertical fractures and turbidite sands. The SE dome is only drilled at the edge of the BSR; nevertheless, the well log data indicate that a 30 m-thick gas hydrate accumulation is present. Gas chromatographic logs in both domes suggest a gradual transition from predominantly microbial gas below the BSR (500–1000 m below seafloor (mbsf)) to thermogenic gas at 1000–2000 mbsf. Based on the well log data and seismic stratigraphic analysis, we find gas hydrate is concentrated in fractures in marine mud, as well as in the pores of submarine fan turbidities, where saturations reach as high as 75%. An estimate of the total gas hydrate-bound gas volume at standard temperature and pressure is between 0.04 and 0.17 trillion cubic meters (TCM) assuming average hydrate saturation of 5-20% in a ∼45 m thick turbidite sand unit above the Perdido Canyon BSR area. Measured BSR extent and gas volume estimates

indicate that the NW and SE reservoirs are among the largest gas hydrate occurrences known in the Gulf of Mexico.

Portnov, A., Santra, M., Cook, A.E., Sawyer, D.E., 2020. The Jackalope gas hydrate system in the northeastern Gulf of Mexico. Marine and Petroleum Geology 111, 261-278.


We present a new gas hydrate system, Jackalope, in the US Gulf of Mexico ~110 km from the Louisiana coast primarily in Mississippi Canyon (MC) Blocks 127 and 128. Jackalope is a relatively shallow prospect (~1650 m water depth) and is associated with a submarine channel-levee depositional system. Several kilometers below the seafloor, an extended sub-circular salt ridge rooted into the allochthonous salt canopy creates a system of faulted anticlinal folds. Accordingly, the distribution of bottom simulating reflections mapped at ~250–300 m below seafloor (mbsf) is structurally controlled, indicating that gas tends to accumulate above the hinge of the salt ridge in sand-dominated turbidites. The Jackalope system is not a single accumulation; it comprises two primary prospects (Saint Petersburg and Columbus) and several secondary prospects. The primary prospects are defined based on seismic data by peak-leading reflections and phase reversals at the base of the gas hydrate stability zone: a strong peak-leading amplitude above it changes to trough-leading amplitude below. We interpret strong peak-leading amplitudes as gas hydrate in sand-rich intervals, which is confirmed by resistivity and gamma ray logs at the margin of the Saint Petersburg prospect. Continuous gas-water contacts below the primary prospects characterize them as permeable three-component reservoirs comprising gas hydrate above gas, and gas above water. Both prospects are located at ~230–300 mbsf occupying a total area of ~5.9 km2. Low and high estimates of in place gas at standard pressure and temperature conditions in the primary prospects range between 1.5 and 10.6 BCM. These characteristics define Jackalope as a promising, cost- and time-efficient gas hydrate system for further drilling exploration. Moreover, Jackalope demonstrates there is potential for new discoveries in the US Gulf of Mexico in particular due to expanding public 3D seismic and well log datasets.

Pourkarimi, S., Hallajisani, A., Alizadehdakhel, A., Nouralishahi, A., 2019. Biofuel production through micro- and macroalgae pyrolysis – A review of pyrolysis methods and process parameters. Journal of Analytical and Applied Pyrolysis 142, 104599.


Bio-fuels derived from biomass with zero net CO2 emission seem to be a promising alternative for fossil fuels. Algal biomasses are promising sources of lipids, proteins and carbohydrates which can convert them into energy in the different forms of fuel depend on the type of conversion process. Transesterification, anaerobic digestion, fermentation, thermochemical conversion, and biophotolysis can convert algal biomass into biodiesel, bio-methane, bioethanol, bio-oil and hydrogen biofuels respectively. Among developed pathways for producing biofuel from algal biomass, thermochemical conversion especially pyrolysis is one of the most studied and discussed techniques in recent years. The yield and quality of pyrolysis products strongly depend on the process parameters such as temperature, heating rate, catalyst, etc. The aim of this article is to present a review of bio-fuel production from algal biomasses (micro- and macroalgae) through pyrolysis processes. After an overview of the algae characteristics and their potential as a source of biofuel production, we focus on the pyrolysis process for algal biomass conversion to biofuel in terms of various types of pyrolysis, affecting parameters on algae pyrolysis products, and the economical challenges and opportunities for commercial algal biofuel production through pyrolysis. It was found that pyrolysis processes are potential routes to convert algal biomass to solid, liquid and gaseous biofuels and they can be a good substitute of the unsustainable fossil fuels to meet the growing global energy demand. Additionally, despite the extensive research on pyrolysis of algal biomass which can provide promising information for use in commercial applications, the producing algal biofuel from pyrolysis is not commercially feasible yet and needs to more in-depth studies.

Praetzel, L.S.E., Plenter, N., Schilling, S., Schmiedeskamp, M., Broll, G., Knorr, K.-H., 2019. Organic matter and sediment properties determine in-lake variability of sediment CO2 and CH4 production and emissions of a small and shallow lake. Biogeosciences Discussions 2019, 1-39.


Inland waters are significant sources of CO2 and CH4 to the atmosphere, following recent studies this is particularly the case for small and shallow lakes. The spatial in-lake heterogeneity of CO2 and CH4 production processes and their drivers in the sediment yet remain poorly studied. We thus measured potential CO2 and CH4 production in sediment incubations from 12 sites within the small and shallow crater lake Windsborn in Germany as well as fluxes at the water-atmosphere interface at four sites. Production rates were highly variable and ranged from 7.2 and 38.5 µmol CO2 g C−1 d−1 and from 5.4 to 33.5 µmol CH4 g C−1 d−1. Fluxes lay between 4.5 and 26.9 mmol CO2 m−2 d−1 and between 0 and 9.8 mmol CH4 m−2 d−1. Both CO2 and CH4 production rates and CH4 fluxes were significantly negative (p < 0.05, rho < − 0.6) correlated with the prevalence of recalcitrant organic matter compounds in the sediment as identified by FTIR spectroscopy. The C / N ratio was significantly (p < 0.01, rho = − 0.88) correlated with CH4 fluxes, but neither with production rates nor CO2 fluxes. Inorganic (nitrate, sulfate, ferric iron) and organic (humic acids) electron acceptors together could explain differences in CH4 production rates (R2 = 0.22) whereas we did not find clear relationships between organic matter quality, methanogenic pathways (acetoclastic vs. hydrogenotrophic) and electron accepting capacity of the organic matter. Grain size distribution could sufficiently (p < 0.05, rho = ± 0.65) explain differences in CH4 fluxes. Surprisingly, sediment gas storage, potential production rates and water–atmosphere fluxes were decoupled from each other and did not show any correlations. Our results show that there exists a significant spatial variability of sediment gas production even within small lakes which can be explained by the origin and pre-processing, and therefore the degradability of the organic matter. We highlight that measuring production rates is not a suitable way to replace in-situ flux measurements as it neglects physical sediment properties and production and oxidation processes in the water column.

Price, M., 2019. Stunning skull shakes human family tree. Science 365, 850.


For months, herder Ali Bereino had been trying to get a job working for a team of fossil hunters in northeastern Ethiopia. The Afar man hung around, watching and learning. One day in February 2016, Bereino dug a burrow to keep his baby goats safe from hyenas. He noticed teeth protruding from the hard-packed sand and pulled out a jawbone, which he brought to the team's leader, Ethiopian paleoanthropologist Yohannes Haile-Selassie of the Cleveland Museum of Natural History in Ohio. Shoveling aside nearly half a meter of old goat droppings and sieving through sediment, the team unearthed the nearly complete skull of an enigmatic human ancestor, the oldest member of the genus that eventually led to our own.

After 3 years of analysis, researchers have dated the fossil to 3.8 million years old and identified it as Australopithecus anamensis, a hominin long thought to be the direct predecessor of the famed “Lucy” species, A. afarensis. The new fossil could reshuffle that ancient relationship, the authors argue this week in two papers in Nature.

Researchers hail the skull as one of the most significant hominin discoveries in decades. “It's a spectacular find,” says Carol Ward, an evolutionary anatomist at the University of Missouri School of Medicine in Columbia. “A number of teams—mine included—have been looking for an australopith skull like this. … This is the specimen we've been waiting for.”

Still, not everyone is convinced it clarifies the relations of the australopithecines, a genus of upright apes that lived between 4.2 million and 2 million years ago throughout eastern and southern Africa.

A. anamensis was first identified in 1995, mostly on the basis of 4-million-year-old teeth and jaws from Kenya. Given the dates, plus several telltale anatomical similarities, most researchers concluded that A. anamensis gradually transitioned into and was replaced by A. afarensis, which lived from about 3.7 million to 3 million years ago.

The new Ethiopian specimen, named MRD after Miro Dora, the site where it was found, was probably a male with a brain size of about 370 cubic centimeters, about that of a chimpanzee. He had jutting cheekbones, elongated canine teeth and oval-shaped earholes—all features that strongly suggest membership in A. anamensis rather than the bigger-brained, flatter-faced A. afarensis, Haile-Selassie says. The team dated the skull using the radioactive decay of isotopes of argon in the surrounding sediments.

Fred Spoor, a paleoanthropologist at the Natural History Museum in London, says features such as MRD's projecting cheekbones and primitive earholes resemble those of later hominins, including South Africa's A. africanus and Kenya's Kenyanthropus platyops. The similarities, he says, may make some researchers wonder whether A. anamensis—and not A. afarensis, as thought—was the ancestor of those later hominins.

MRD's anatomy also helps pin down the identity of a puzzling 3.9-million-year-old forehead bone found in Ethiopia in 1981; Haile-Selassie says the comparison suggests the skull fragment belonged to A. afarensis. If he's correct, Lucy's species would predate the new anamensis skull. Haile-Selassie concludes that the two species overlapped for about 100,000 years. The team still thinks A. afarensis descends from A. anamensis, but suggests Lucy's species branched off anamensis, rather than simply replacing it.

Ward and William Kimbel, a paleoanthropologist at Arizona State University in Tempe, agree that the new skull belongs to A. anamensis, but both say it will take more fossils to convince them that two distinct species of australopithecines roamed the Afar region at the same time. “That issue rests on the comparison of the new specimen with the single frontal” bone, which is the only A. afarensis specimen suspected of such antiquity, Kimbel says. “It's difficult to make a strong argument because we have only the two specimens.”

In a statement, Tim White, a paleoanthropologist at the University of California, Berkeley, who served as Haile-Selassie's doctoral adviser years ago, praised the discovery but says the studies' evolutionary implications are “a bridge too far.” He thinks individual variation alone can account for the differences between the two specimens, and that the idea that afarensis replaced anamensis still makes sense.

Regardless of how things shake out for hominin taxonomy, the finding proved a boon for Bereino. “Obviously, it guaranteed him a hire,” Haile-Selassie says.



Combining a Gas-Injection System (GIS) with the Focused Ion Beam (FIB) has a broad scope of applications in sample preparation such as protective layer deposition, increasing material sputtering rates, and reducing FIB-related artifacts. On the other hand, injecting certain specific gases during a Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) analysis can significantly increase element ionization probability and, therefore, improve the quality of 3D representation of a sample elemental structure. In this work, for the first time, the potential of GIS for enhancing secondary ion signals acquired using a TOF detector incorporated into a commercial Ga+ FIB-SEM (Focused Ion Beam combined with Scanning Electron Microscope) instrument is presented. The depth profiles of pure metals (thin films of Cu, Zr, Ag, and W with the thickness in the order of 100 nm) were acquired under ambient vacuum conditions as well as under an exposure to water and fluorine gases. The influence of supplementary gases on the ion yields and sputtering rates was studied. Simulations were performed to assess the local gas pressure at the location of FIB-TOF-SIMS analysis. The highest enhancement of ionization probability was achieved in the case of the Cu thin film (10 times during water vapor coinjection and 510 times when using a fluorine gas). Regarding the sputtering rates, the response of Zr to the effect of the gases was the strongest. Compared to standard background pressure measurements, this thin film was milled around 6 times faster under exposure to water vapor and over 2 times faster when fluorine gas was supplied.

Pugh, T.A.M., Arneth, A., Kautz, M., Poulter, B., Smith, B., 2019. Important role of forest disturbances in the global biomass turnover and carbon sinks. Nature Geoscience 12, 730-735.

https://doi.org/10.1038/s41561-019-0427-2

Forest disturbances that lead to the replacement of whole tree stands are a cornerstone of forest dynamics, with drivers that include fire, windthrow, biotic outbreaks and harvest. The frequency of disturbances may change over the next century with impacts on the age, composition and biomass of forests. However, the disturbance return time, that is, the mean interval between disturbance events, remains poorly characterized across the world’s forested biomes, which hinders the quantification of the role of disturbances in the global carbon cycle. Here we present the global distribution of stand-replacing disturbance return times inferred from satellite-based observations of forest loss. Prescribing this distribution within a vegetation model with a detailed representation of stand structure, we quantify the importance of stand-replacing disturbances for biomass carbon turnover globally over 2001–2014. The return time varied from less than 50 years in heavily managed temperate ecosystems to over 1,000 years in tropical evergreen forests. Stand-replacing disturbances accounted for 12.3% (95% confidence interval, 11.4–13.7%) of the annual biomass carbon turnover due to tree mortality globally, and in 44% of the forested area, biomass stocks are strongly sensitive to changes in the disturbance return time. Relatively small shifts in disturbance regimes in these areas would substantially influence the forest carbon sink that currently limits climate change by offsetting emissions.

Qi, Y., Volmer, D.A., 2019. Chemical diversity of lignin degradation products revealed by matrix-optimized MALDI mass spectrometry. Analytical and Bioanalytical Chemistry 411, 6031-6037.

https://doi.org/10.1007/s00216-019-01984-y

Lignin is the most abundant natural resource of aromatic moieties and the second most abundant natural biopolymer. Analytical techniques that obtain as much information as possible on the exact structural content of lignin species are essential for developing efficient processes that transform highly complex lignin wastes into value chemicals and biofuels. For mass spectrometric analysis of lignin samples, usually electrospray ionization, atmospheric pressure chemical ionization, or atmospheric pressure photoionization are used as ionization techniques. Matrix-assisted laser desorption/ionization (MALDI) is less frequently applied but offers a much more rapid screening option for lignin mixtures. In this study, we compared several common MALDI matrices for analysis of alkali lignin and discovered that different chemical matrices exhibited very different ionization efficiencies and selectivity with respect to the structures of the lignin-related compounds as well as the presence of heteroatoms. Importantly, the results highlight that the choice of matrix strongly determines the analytical coverage of molecular species in the complex lignin degradation mixtures.


https://doi.org/10.1007/s12517-019-4708-2

This study first employed micro-computed tomography technique for scanning the gas-fat coal sample; then, using Avizo software, coal’s micro-pore structure model was established; finally, seepage behaviors of gas and water in the coal under a pressure of 3 MPa were simulated. Through comparison, it can be concluded that both gas pressure and water pressure decreased gradually along the seepage direction; at a same seepage length, water’s maximum seepage pressure significantly exceeded that of gas; gas’s velocity flow lines were overall fuller than water’s flow lines; using a same pore model, gas’s migration velocity far exceeded that of water; In terms of mass flow rate, water exceeded gas. The effluent mass flow rate at the outlet was smaller than the influent mass flow rate at the inlet. Overall, with the increase in the seepage length, gas and water’s mean seepage pressures and mass flow rates all decreased gradually, while their mean seepage velocities fluctuated greatly. Since the pores at the different coal cross-sections were developed to different degrees, the heterogeneity of the coal structure meant that the cross-sectional area of the pore channel varied irregularly along the seepage direction. The fitting curve can be reduced to three classes: logistic linear regression curve, Boltzmann function curve, Exp Dec curve, or poly curve.



The crustal subseafloor is the least explored and largest biome on Earth. Interrogating crustal life is difficult due to habitat inaccessibility, low-biomass and contamination challenges. Subseafloor observatories have facilitated the study of planktonic life in crustal aquifers, however, studies of life in crust-attached biofilms are rare. Here, we investigate biofilms grown on various minerals at different temperatures over 1-6 years at subseafloor observatories in the Eastern Pacific. To mitigate potential sequence contamination, we developed a new bioinformatics tool –TaxonSluice. We explore ecological factors driving community structure and potential function of biofilms by comparing our sequence data to previous amplicon and metagenomic surveys of this habitat. We reveal that biofilm community structure is driven by temperature rather than minerology, and that rare planktonic lineages colonize the crustal biofilms. Based on 16S rRNA gene overlap, we partition metagenome assembled genomes into planktonic and biofilm fractions and suggest that there are functional differences between these community types, emphasizing the need to separately examine each to accurately describe subseafloor microbe-rock-fluid processes. Lastly, we report that some rare lineages present in our warm and anoxic study site are also found in cold and oxic crustal fluids in the Mid-Atlantic Ridge, suggesting global crustal biogeography patterns.

Rasmussen, B., Muhling, J.R., 2019. Evidence for widespread oil migration in the 1.88 Ga Gunflint Formation, Ontario, Canada. Geology 47, 899-903.

https://doi.org/10.1130/G46469.1

The abundance of Precambrian organic-rich shales, heated beyond the oil and gas window, requires that enormous volumes of hydrocarbons were generated and transported through the ancient crust. However, the former passage of fluid hydrocarbons rarely leaves a trace, so evidence for this process in the early Precambrian rock record is sparse. Here, we report the widespread presence of solidified oil (pyrobitumen) in the iron formation of the 1.88 Ga Gunflint Formation, Ontario, Canada. Petrographic textures indicate at least two phases of oil migration, an early phase marked by pyrobitumen in granules and intergranular pores, synchronous with synsedimentary silica cementation, and a later phase restricted to crosscutting fractures. The paragenetic relationships between the pyrobitumen and iron oxides indicate that oil migration commenced before hematite and some magnetite growth. Our evidence for early oil migration can be explained by petroleum generation during the 1.86–1.80 Ga Penokean orogeny, expelling hydrocarbons generated in the core of the fold-and-thrust belt outwards and updip through the sediments of the Gunflint Formation.

Rauball, J.F., Sachsenhofer, R.F., Bechtel, A., Coric, S., Gratzer, R., 2019. The Oligocene–Miocene Menilite Formation in the Ukrainian Carpathians: A world-class source rock. Journal of Petroleum Geology 42, 393-415.


This study investigates the hydrocarbon potential of Oligocene–Miocene shales in the Menilite Formation, the main source rock in the Ukrainian Carpathians. The study is based on the analysis of 233 samples collected from outcrops along the Chechva River in western Ukraine in order to analyse bulk parameters (TOC, Rock‐Eval), biomarkers and maceral composition.

In Ukraine, the Menilite Formation is conventionally divided into Lower (Lower Oligocene), Middle (Upper Oligocene) and Upper (Lower Miocene) Members. The Early Oligocene and Early Miocene ages of the lower and upper members are confirmed by new nannoplankton data. The Lower Menilite Member is approximately 330 m thick in the study area and contains numerous chert beds and turbidite sandstones in its lower part together with organic‐rich black shales. The shales have a high content of silica which was probably derived from siliceous micro‐organisms. The TOC content of the shales frequently exceeds 20 wt.% and averages 9.76

wt.%. HI values range between 600 and 300 mgHC/gTOC (max. 800 mgHC/gTOC). The Middle Member contains thin black shale intervals but was not studied in detail. The Upper Member is about 1300 m thick in the study area and is composed mainly of organic‐rich shales. Chert layers are present near the base of the Member, and a prominent tuff horizon in the upper part represents a volcanic phase during shale deposition. The member grades into overlying molasse sediments. The average TOC content of the Upper Menilite succession is 5.17 wt.% but exceeds 20 wt.% near its base.

Low Tmax and vitrinite reflectance measurements for the Lower (419°C and 0.24–0.34 %Rr, respectively) and Upper (425°C and 0.26–0.32 %Rr, respectively) Menilite Member successions indicate thermal immaturity. Biomarker and maceral data suggest a dominantly marine (Type II) organic matter input mixed with varying amounts of land‐plant derived material, and indicate varying redox and salinity conditions during deposition.

Determination of the Source Potential Index (SPI) shows that the Menilite Formation in the study area has the potential to generate up to 74.5 tons of hydrocarbons per m2. The Chechva River outcrops therefore appear to have a significantly higher generation potential than other source rocks in the Paratethys realm. These very high SPI values for the Menilite Formation may explain why a relatively small area in Ukraine hosts about 70% of the known hydrocarbon reserves in the northern and eastern Carpathian fold‐thrust belt.

Remusat, L., Bonnet, J.-Y., Bernard, S., Buch, A., Quirico, E., 2019. Molecular and isotopic behavior of insoluble organic matter of the Orgueil meteorite upon heating. Geochimica et Cosmochimica Acta 263, 235-247.


Organic matter contained in carbonaceous chondrites may have evolved due to aqueous and/or thermal evolution on the parent body. The thermal behavior of the insoluble organic matter (IOM) of the Orgueil meteorite was investigated. The evolutions of structural and molecular properties were assessed by Raman, infrared and XANES spectroscopies, the H- and N-isotopic compositions by NanoSIMS. The starting IOM is a disordered organic macromolecule presenting a high degree of cross-linking. Hydrogen and Nitrogen isotope distributions are heterogeneous with the occurrence of numerous micron-sized hot spots enriched in heavy isotopes of H or N. After 1 h at 300 °C, there is subtle modification of the structural ordering and the isotopic compositions. After 1 h at 500 °C, the structure evolves toward condensation. Indeed, FTIR and XANES data are consistent with a continuous evolution of the molecular structure toward an increase of aromatization, starting at 300 °C and becoming more intense at 500 °C. The bulk D-enrichment is significantly reduced and D-rich hot spots are lost at 500 °C. The experimental evolution of the δD is consistent with observations of IOM isolated from lightly altered carbonaceous chondrites. In contrast, the 15N-rich hot spots seem insensitive to high temperature up to 500 °C and bulk δ15N remains constant. The thermal evolution of H- and N-isotopes is decoupled, indicating that the D-rich and 15N-rich moieties exhibit different thermal recalcitrance.



Molecular compositions and stable carbon isotope ratios (δ13C) of n-alkanes and fatty acids (FA) were investigated in urban aerosols from Beijing, China. Seasonal trends for n-alkanes showed a higher carbon preference index (CPI) and Cmax at C29 in spring indicating the enhanced emission of higher plant waxes. Lower CPIs and Cmax at C23 were found in winter that should be associated with fossil fuel combustion. 13C-depletion in C29n-alkane was observed during an extreme rainfall event, during which the inflow of air masses were originated from lower latitude regions. Higher concentrations of 13C-enriched C23n-alkane in winter together with the air mass trajectories suggested that the Beijing aerosols were affected by the air masses transported from the southern regions. Fatty acids were abundant in fall and showed a bimodal pattern with Cmax at C16:0 and C18:0. Higher C24:0/FA ratios with 13C-enrichment occurred as influenced by southerly air masses, and lower C24:0/FA ratios with 13C-depletion was observed with northerly air masses in fall and winter. These results suggested that C24:0 fatty acid was more abundantly transported from the southwestern air masses and may be a

powerful tool to distinguish polluted aerosol source regions. Moreover, the δ13C values of C24:0 fatty acid showed a positive correlation with levoglucosan, implying that the biomass-burning process may contribute 13C-enriched C24:0 fatty acid.



Peatlands are a large source of methane (CH4) to the atmosphere, yet the uncertainty around the estimates of CH4 flux from peatlands is large. To better understand the spatial heterogeneity in temperate peatland CH4 emissions and their response to physical and biological drivers, we studied CH4 dynamics throughout the growing seasons of 2017 and 2018 in Flatiron Lake Bog, a kettle-hole peat bog in Ohio. The site is composed of six different hydro-biological zones: an open water zone, four concentric vegetation zones surrounding the open water, and a restored zone connected to the main bog by a narrow channel. At each of these locations, we monitored water level (WL), CH4 pore-water concentration at different peat depths, CH4 fluxes from the ground and from representative plant species using chambers, and microbial community composition with a focus here on known methanogens and methanotrophs. Integrated CH4 emissions for the growing season were estimated as 315.4±166 mgCH 4 m −2 d −1 in 2017 and 362.3±687 mgCH 4 m −2 d −1 in 2018. Median CH4 emission was highest in the open water, then it decreased and became more variable through the concentric vegetation zones as the WL dropped, with extreme emission hotspots observed in the tamarack mixed woodlands (Tamarack) and low emissions in the restored zone (18.8–30.3 mgCH 4 m −2 d −1 ). Generally, CH4 flux from above-ground vegetation was negligible compared to ground flux (<0.4 %), although blueberry plants were a small CH4 sink. Pore-water CH4 concentrations varied significantly among zones, with the highest values in the Tamarack zone, close to saturation, and the lowest values in the restored zone. While the CH4 fluxes and pore-water concentrations were not correlated with methanogen relative abundance, the ratio of methanogens to methanotrophs in the upper portion of the peat was significantly correlated to CH4 transfer velocity (the CH4 flux divided by the difference in CH4 pore-water concentration between the top of the peat profile and the concentration in equilibrium with the atmosphere). Since ebullition and plant-mediated transport were not important sources of CH4 and the peat structure and porosity were similar across the different zones in the bog, we conclude that the differences in CH4 transfer velocities, and thus the flux, are driven by the ratio of methanogen to methanotroph relative abundance close to the surface. This study illustrates the importance of the interactions between water-level and microbial composition to better understand CH4 fluxes from bogs and wetlands in general.

Rizzi, M., Fyhn, M.B.W., Schovsbo, N.H., Korte, C., Hovikoski, J., Olivarius, M., Thomsen, T.B., Keulen, N., Thuy, N.T.T., Hoang, B.H., Dung, B.V., Toan, D.M., Abatzis, I., Nielsen, L.H., 2020. Hinterland setting and composition of an Oligocene deep rift-lake sequence, Gulf of Tonkin, Vietnam: Implications for petroleum source rock deposition. Marine and Petroleum Geology 111, 496-509.


Most SE Asian oil accumulations are sourced from Paleogene lacustrine mudstones. Even so, the mechanisms controlling formation of these source rocks are not fully understood. Bach Long Vi Island, located in the northwestern South China Sea, offers a unique opportunity to study these mechanisms. A continuous, 800 m thick, organic rich and highly oil-prone, lacustrine section was investigated in outcrop and in a continuously cored section. The Oligocene deep-lake succession formed in the Bach Long Vi Graben that connects the Beibuwan Basin with the Yinggehai-Song Hong Basin. Petrography, detrital zircon U-Th-Pb geochronology and heavy mineral assemblages of sandstone intervals document a locally derived sediment source isolated from the Red River. Orientations of ripple cross lamination in gravity flow sands indicate axial sediment transport along the graben. Combined with the local structural configuration, this suggests that sediments were derived from the Qixi High through a relay ramp located about 10 km south of the island. Rare earth and major elements, detrital zircon ages, sandstone petrography and garnet composition, suggest a dominantly Ordovician

– Silurian aged felsic and metasedimentary hinterland. The limited sediment supply from the small hinterland allowed tectonic subsidence to keep pace with graben infill. This promoted the establishment of a long-lived, deep lake favorable for source rock generation. In addition, heavy mineral and geochemical data document an unusually high content of detrital phosphate minerals in the investigated section indicative of a phosphate-rich hinterland. Tropical leaching resulted in an extraordinary high phosphorus input into the lake that catalyzed a high organic productivity and promoted the generation of highly prolific, oil-prone source rocks. The study documents that hinterland size and composition play a primary role in lacustrine source rock deposition. Comparable petroleum source rocks are likely to exist in other ancient rift basins surrounded by small, phosphate-rich hinterlands sheltered from significant sediment input.

Rodrigues, B., Silva, R.L., Reolid, M., Mendonça Filho, J.G., Duarte, L.V., 2019. Sedimentary organic matter and δ13CKerogen variation on the southern Iberian palaeomargin (Betic Cordillera, SE Spain) during the latest Pliensbachian–Early Toarcian. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109342.


The Early Toarcian Oceanic Anoxic Event (T-OAE) is characterised by major palaeoenvironmental and palaeoceanographical changes (ocean anoxia, global warming, ocean acidification, among other), and a severe perturbation of the global carbon cycle. Although widespread oceanic anoxia was a significant control on the occurrence of organic-rich facies during the T-OAE in several locations of the northern Tethyan margin, the effects of anoxia, oceanic productivity, and dilution are poorly understood in other worldwide locations, such as the southern Tethyan and Iberian margins.

In this study, we report new geochemical [total organic carbon (TOC), total sulphur (TS), total carbonate content (CaCO3), δ13C from kerogen isolates (δ13CKerogen)], palynofacies and thermal maturation data from the Upper Pliensbachian–Lower Toarcian successions in La Cerradura and Fuente Vidriera, External Subbetic domain, Betic Cordillera (SE Spain). The obtained results indicate that these successions have low TOC contents (~ 0.3 wt.%), with TOC reaching up to 0.46 wt.% around the Polymorphum–Serpentinum ammonite zone boundary in La Cerradura. δ13CKerogen negative carbon isotope excursions (CIE) are observed at the base of the Polymorphum Zone, the Pliensbachian–Toarcian Event (Pl-Toa), and base of the Serpentinum Zone (T-OAE). Overall, the low maturity kerogen assemblages are dominated by terrestrial OM and with a minor marine component. Small increments in terrestrial OM, non-opaque phytoclasts, and palynomorphs are observed just before and during the T-OAE in the studied area.

During the Early Toarcian, in the External Subbetic domain, accumulation and preservation of OM was low and with a significant terrestrial contribution, similarly to other locations around the southern margins of Iberia and Tethys. The dominance of the opaque phytoclast subgroup, the occurrence of Classopollis, and the relatively more positive δ13C of terrestrial kerogen suggest that OM was mostly sourced from an area characterised by a semi-arid climate (i.e. with pronounced arid periods) during most of the Polymorphum Zone. The T-OAE negative CIE is accompanied by an increase in terrestrial OM, with a slight increase in the non-opaque phytoclast subgroup and terrestrial palynomorph subgroup. The increase of non-opaque phytoclast and terrestrial palynomorphs are in line with the posited enhancements of the hydrological cycle and export of terrestrial OM into marine environments during the T-OAE. This study suggests a link between 13C fractionation during photosynthesis in C3 plants and climate during the Early Toarcian. This link suggests coupling of the water and terrestrial carbon cycles before and during the T-OAE.

Ropartz, D., Fanuel, M., Ujma, J., Palmer, M., Giles, K., Rogniaux, H., 2019. Structure determination of large isomeric oligosaccharides of natural origin through multipass and multistage cyclic traveling-wave ion mobility mass spectrometry. Analytical Chemistry 91, 12030-12037.


Carbohydrate isomers with identical atomic composition cannot be distinguished by mass spectrometry. By separating the ions according to their conformation in the gas phase, ion mobility (IM) coupled to mass spectrometry is an attractive approach to overcome this issue and extend the limits of mass spectrometry in

structural glycosciences. Recent technological developments have significantly increased the resolving power of ion mobility separators. One such instrument features a cyclic traveling-wave IM separator integrated in a quadrupole/time-of-flight mass spectrometer. This system allows for multipass ion separations and for pre-, intra-, and post-IM fragmentation. In the present study, we utilize this system to explore a complex mixture of oligoporphyrans derived from the enzymatic digestion of the cell wall of the red alga P. umbilicalis. We are able to deduce their complete structure using IM arrival times and the m/z of specific fragments. This approach was successfully applied for sequencing of oligoporphyrans of up to 1500 Da and included the positioning of the methyl ether and sulfate groups. The structures defined in this study by IM-MS/MS agree with those found in the past but use much more time-consuming analytical approaches. This study also revealed some so far undescribed structures, present at very low abundance. In addition, the results made it possible to compare the abundance of the different isomers released by the enzyme and to draw further conclusions on the specificity of β-porphyranase and more particularly on its accommodation tolerance of anhydro-bridges in subsites. Finally, a separation of two isomers with very similar mobility was obtained after 58 passes around the cIM, with an estimated resolving power of 920 for these triply charged species, confirming the structures attributed to these two isomers.

Rose, C.V., Webb, S.M., Newville, M., Lanzirotti, A., Richardson, J.A., Tosca, N.J., Catalano, J.G., Bradley, A.S., Fike, D.A., 2019. Insights into past ocean proxies from micron-scale mapping of sulfur species in carbonates. Geology 47, 833-837.

https://doi.org/10.1130/G46228.1

Geological reconstructions of global ocean chemistry and atmospheric oxygen concentrations over Earth history commonly rely on the abundance and stable isotopic composition (δ34S) of sulfur-bearing compounds. Carbonate-associated sulfate (CAS), sulfate bound within a calcium carbonate mineral matrix, is among the most commonly interrogated sulfur mineral phases. However, recent work has revealed variability in δ34SCAS values that cannot be explained by evolution of the marine sulfate reservoir, challenging the common interpretation that CAS is inherently a high-fidelity record of seawater sulfate. To investigate the source of this inconsistency, we used X-ray spectromicroscopy to map the micron-scale distribution of S-bearing sedimentary phases in Ordovician-aged (ca. 444 Ma) shallow marine carbonates from Anticosti Island, Québec, Canada. Clear differences in the abundance of CAS are observed between cements and fossils, suggesting that variance in bulk-rock data could be a consequence of component mixing and that coupled synchrotron-petrographic screening can identify the carbonate components that are most likely to retain primary CAS. Furthermore, we observe multiple, distinct forms of sulfate (both inorganic and organic). Differences in these forms among fossil clades could provide new insights into biomineralization mechanisms in extinct organisms.



This paper presents a method for upscaling permeability of fractured coal using the cubic law to quantify permeability of the fracture system. The version of the cubic law that incorporates the length/tortuosity effect available in the literature was modified by including a connectivity parameter. All parameters of the modified cubic law (fracture aperture, porosity, length, and connectivity) were estimated for a set of coal samples using quantitative methods available in the literature. The geometry of the fracture system within the coal samples was determined from micro computed tomography scans. Parameters of the modified cubic law estimated from the scans were validated by comparison of the resulting permeability to the numerical simulation of single-phase fluid flow in fractures, which was developed at the previous stage of this study. The modified cubic law was then used for upscaling of permeability from the millimeter scale to the centimeter scale. It produced the results that match the literature data for the coal from the same region as well as the experimental data for the studied area.

Roth, V.-N., Lange, M., Simon, C., Hertkorn, N., Bucher, S., Goodall, T., Griffiths, R.I., Mellado-Vázquez, P.G., Mommer, L., Oram, N.J., Weigelt, A., Dittmar, T., Gleixner, G., 2019. Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nature Geoscience 12, 755-761.

https://doi.org/10.1038/s41561-019-0417-4

Dissolved organic matter affects fundamental biogeochemical processes in the soil such as nutrient cycling and organic matter storage. The current paradigm is that processing of dissolved organic matter converges to recalcitrant molecules (those that resist degradation) of low molecular mass and high molecular diversity through biotic and abiotic processes. Here we demonstrate that the molecular composition and properties of dissolved organic matter continuously change during soil passage and propose that this reflects a continual shifting of its sources. Using ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, we studied the molecular changes of dissolved organic matter from the soil surface to 60 cm depth in 20 temperate grassland communities in soil type Eutric Fluvisol. Applying a semi-quantitative approach, we observed that plant-derived molecules were first broken down into molecules containing a large proportion of low-molecular-mass compounds. These low-molecular-mass compounds became less abundant during soil passage, whereas larger molecules, depleted in plant-related ligno-cellulosic structures, became more abundant. These findings indicate that the small plant-derived molecules were preferentially consumed by microorganisms and transformed into larger microbial-derived molecules. This suggests that dissolved organic matter is not intrinsically recalcitrant but instead persists in soil as a result of simultaneous consumption, transformation and formation.

Royle, S.H., Watson, J.S., Zhang, Y., Chatzitheoklitos, G., Sephton, M.A., 2019. Solid phase micro extraction: Potential for organic contamination control for planetary protection of life-detection missions to the icy moons of the outer solar system. Astrobiology 19, 1153-1166.

https://doi.org/10.1089/ast.2018.1968

Conclusively detecting, or ruling out the possibility of, life on the icy moons of the outer Solar System will require spacecraft missions to undergo rigorous planetary protection and contamination control procedures to achieve extremely low levels of organic terrestrial contamination. Contamination control is necessary to avoid forward contamination of the body of interest and to avoid the detection of false-positive signals, which could either mask indigenous organic chemistry of interest or cause an astrobiological false alarm. Here we test a new method for rapidly and inexpensively assessing the organic cleanliness of spaceflight hardware surfaces using solid phase micro extraction (SPME) fibers to directly swab surfaces. The results suggest that the method is both time and cost efficient. The SPME–gas chromatography–mass spectrometry (SPME-GC-MS) method is sensitive to common midweight, nonpolar contaminant compounds, for example, aliphatic and aromatic hydrocarbons, which are common contaminants in laboratory settings. While we demonstrate the potential of SPME for surface sampling, the GC-MS instrumentation restricts the SPME-GC-MS technique's sensitivity to larger polar and nonvolatile compounds. Although not used in this study, to increase the potential range of detectable compounds, SPME can also be used in conjunction with high-performance liquid chromatography/liquid chromatography–mass spectrometry systems suitable for polar analytes (Kataoka et al.,2000). Thus, our SPME method presents an opportunity to monitor organic contamination in a relatively rapid and routine way that produces information-rich data sets.

Rubin, M., Bekaert, D.V., Broadley, M.W., Drozdovskaya, M.N., Wampfler, S.F., 2019. Volatile species in comet 67P/Churyumov-Gerasimenko: Investigating the link from the ISM to the terrestrial planets. ACS Earth and Space Chemistry 3, 1792-1811.


Comets contain abundant amounts of organic and inorganic species. Many of the volatile molecules in comets have also been observed in the interstellar medium and some of them even with similar relative abundances, indicating formation under similar conditions or even sharing a common chemical pathway. There is a growing amount of evidence that suggests comets inherit and preserve substantial fractions of materials inherited from

previous evolutionary phases, potentially indicating that commonplace processes occurred throughout comet-forming regions. Through impacts, part of this material has also been transported to the inner planetary system, including the terrestrial planets. While comets have been ruled out as a major contributor to terrestrial ocean water, substantial delivery of volatile species to the Earth’s atmosphere, and as a consequence also organic molecules to its biomass, appears more likely. Comets contain many species of prebiotic relevance and molecules that are related to biological processes on Earth, and have hence been proposed as potential indicators for the presence of biological processes in the search of extraterrestrial life. Although the delivery of cometary material to Earth may have played a crucial role in the emergence of life, the presence of such alleged biosignature molecules in the abiotical environment of comets complicates the detection of life elsewhere in the universe.

Ruiz-Morales, Y., Miranda-Olvera, A.D., Portales-Martínez, B.n., Domínguez, J.M., 2019. Determination of 13C NMR chemical shift structural ranges for polycyclic aromatic hydrocarbons (PAHs) and PAHs in asphaltenes: An experimental and theoretical density functional theory study. Energy & Fuels 33, 7950-7970.


Nowadays, 13C nuclear magnetic resonance (NMR) is used in the structural study of asphaltenes. However, the different carbon types in the polycyclic aromatic hydrocarbon (PAH) core of asphaltenes, to be able to establish their main backbone, have been reported to have different 13C NMR chemical shift ranges by different authors in the literature. Therefore, in the present study, the 13C NMR chemical shift ranges for the structural carbon types—(a) Y-carbons (CY) or internal triple bridgehead aromatic carbons; (b) external peripheral aromatic carbon atoms at the junction of two fused rings, or external double bridgehead aromatic carbons (CAP3); (c) aromatic carbon atoms bonded to hydrogen atoms (CAH); and (d) carbon atoms bonded to heteroatoms (CAX) and carbon atoms bonded to hydrogen in the β position to a heteroatom (CAHβX)—have been determined by combining calculated 13C NMR chemical shifts, at the gauge-independent atomic orbital-density functional theory level (GIAO-DFT), with measured experimental 13C NMR chemical shifts for PAHs that have been identified as being asphaltene-PAH cores and for PAHs that are not examples of asphaltene-PAH cores. The determined 13C NMR chemical shift ranges are reported.

Rule, R.G., Pratt, B.R., 2019. The pseudofossil Horodyskia: Flocs and flakes on microbial mats in a shallow Mesoproterozoic sea (Appekunny Formation, Belt Supergroup, western North America). Precambrian Research 333, 105439.


Horodyskia moniliformis Yochelson and Fedonkin (2000) is found abundantly in its type area, the lower Appekunny Formation (Belt Supergroup; ca. 1.45 Ga) of northwestern Montana and adjacent southwestern Alberta. It has a distinct curving to meandering string-of-beads appearance on bedding planes of thin-bedded, laminated argillaceous siltstone, and has been regarded by some as one of the oldest eukaryotic organisms in the fossil record. The beads are disc-shaped to lenticular, ~1–5 mm in diameter, circular to elliptical to polygonal in outline, and composed of variably silty clay. They are interpreted as mud flocs and small intraclasts. The beads in individual specimens are fairly uniform in size and spacing, but string length varies from about one to 15 cm depending in part on bead size. The radius of curvature varies from tight to open, but strings never form loops. Isolated beads are also present and smaller ones become indistinguishable from pustules which, along with mud-cored wrinkles and blisters, are associated on many bedding surfaces. These are regarded as evidence for a benthic microbial mat with variable topography ranging from crudely linear or stellate ridges to small domes and pinnacles. Rather than representing a semi-infaunal colonial eukaryote, fungal bladders or macroalgae, Horodyskia is here interpreted to be large mud particles that were trapped on small protrusions of the microbial mat probably consisting of filament tufts. Commonly, the tufts were oriented in rows of similar-sized and generally evenly spaced elevations and these bound suspended flocs and flakes of a more or less uniform size, resulting in the features that appear organized as strings-of-beads. Horodyskia is therefore considered to be a microbially-induced sedimentary structure specific to a muddy, relatively low-energy, subtidal marine setting with just the right combination of sediment type and depositional factors.



Polyaromatic compounds (PACs) are by-products of combustion and are the major pollutants from the oil and gas industry. However, the mechanism of PACs induced toxicity still remains elusive. The aim of this study was to elucidate the effects of a typical mixture of PACs found in oil sand extract (OSE) on the respiratory, hepatic and nervous systems in humans using in vitro cell culture models followed by non-targeted metabolomics analysis. OSE collected from Alberta, Canada was fractionated into PAC and alkane fractions, and their effects after 24 h exposure on the cell viability measured by MTT assay in three human cell lines (A549, HepG2, and SK-N-SH) were studied. The PAC fractions showed significant dose-dependent cytotoxicity. A549 cells showed the highest sensitivity to OSE extracts, followed by SK-N-SH and HepG2. In contrast, the alkane fractions showed no effects on cell viability. The three human cell lines were further exposed with the PACs at 10% and 20% lethal concentration for 24 h. Metabolomics analysis of the cell extracts indicated that PACs treatments showed different disruptions on possible metabolic pathways on the three cell lines. PACs altered the sex steroid hormone metabolism and regulated the levels of leukotrienes metabolites in all three cell types. The amino acids L-cysteine, L-glutamine, L-tyrosine that are known to cause respiratory effects were significantly up-regulated in A549 cells. The PACs treated HepG2 cells showed down-regulation in metabolites responsible for the inflammatory mediation. Treatment of the differentiated SK-N-SH cells showed up-regulated metabolites involved with butanoate, fatty acid, and pyrimidine metabolism. Leukotriene metabolites were found to be significantly increased in all PACs treated cells. In conclusion, our results showed that PACs in OSE can alter the metabolism of the human lung, liver and neuronal cells and may induce toxicity in multiple target organs.

Saylor, B.Z., Gibert, L., Deino, A., Alene, M., Levin, N.E., Melillo, S.M., Peaple, M.D., Feakins, S.J., Bourel, B., Barboni, D., Novello, A., Sylvestre, F., Mertzman, S.A., Haile-Selassie, Y., 2019. Age and context of mid-Pliocene hominin cranium from Woranso-Mille, Ethiopia. Nature 573, 220-224.

https://doi.org/10.1038/s41586-019-1514-7

A fossil hominin cranium was discovered in mid-Pliocene deltaic strata in the Godaya Valley of the northwestern Woranso-Mille study area in Ethiopia. Here we show that analyses of chemically correlated volcanic layers and the palaeomagnetic stratigraphy, combined with Bayesian modelling of dated tuffs, yield an age range of 3.804 ± 0.013 to 3.777 ± 0.014 million years old (mean ± 1σ) for the deltaic strata and the fossils that they contain. We also document deposits of a perennial lake beneath the deltaic sequence. Mammalian fossils associated with the cranium represent taxa that were widespread at the time and data from botanical remains indicate that the vegetation in the lake and delta catchment was predominantly dry shrubland with varying proportions of grassland, wetland and riparian forest. In addition, we report high rates of sediment accumulation and depositional features that are typical of a steep topographic relief and differ from younger Woranso-Mille fossil localities, reflecting the influence of active rift processes on the palaeolandscape.

Sazykin, I., Makarenko, M., Khmelevtsova, L., Seliverstova, E., Rakin, A., Sazykina, M., 2019. Cyclohexane, naphthalene, and diesel fuel increase oxidative stress, CYP153, sodA, and recA gene expression in Rhodococcus erythropolis. MicrobiologyOpen 8, e00855.


In this study, we compared the expression of CYP153, sodA, sodC, and recA genes and ROS generation in hydrocarbon‐degrading Rhodococcus erythropolis in the presence of cyclohexane, naphthalene, and diesel fuel. The expression of cytochrome P450, sodA (encoding Fe/Mn superoxide dismutase), recA, and superoxide anion radical generation rate increased after the addition of all studied hydrocarbons. The peak of CYP153, sodA, and

recA gene expression was registered in the presence of naphthalene. The same substrate upregulated the Cu/Zn superoxide dismutase gene, sodC. Cyclohexane generated the highest level of superoxide anion radical production. Hydrogen peroxide accumulated in the medium enriched with diesel fuel. Taken together, hydrocarbon biotransformation leads to oxidative stress and upregulation of antioxidant enzymes and CYP153 genes, and increases DNA reparation levels in R. erythropolis cells.

Sazykin, I.S., Minkina, T.M., Grigoryeva, T.V., Khmelevtsova, L.E., Sushkova, S.N., Laikov, A.V., Antonenko, E.M., Ismagilova, R.K., Seliverstova, E.Y., Mandzhieva, S.S., Sazykina, M.A., 2019. PAHs distribution and cultivable PAHs degraders’ biodiversity in soils and surface sediments of the impact zone of the Novocherkassk thermal electric power plant (Russia). Environmental Earth Sciences 78, 581.

https://doi.org/10.1007/s12665-019-8584-6

The qualitative and quantitative composition of polycyclic aromatic hydrocarbons (PAHs) pollutants at 13 points of the impact zone of the Novocherkassk thermal electric power plant (NchPP) has been determined. This territory has been polluted with emissions from brown coal combustion for several decades. A total of 200 isolates from PAH-degrading bacteria were selected from the soils and surface sediments, heavily contaminated with PAHs. Taxonomic identification of isolates was carried out by sequencing of the 16S rRNA genes and by MALDI-TOF analysis of protein spectra. Soil cultivable PAH-degrading microorganisms were represented by six species of four genera of actinobacteria (Arthrobacter, Rhodococcus, Oerskovia and Isoptericola). Surface sediments cultivable PAH degraders were represented by six species of the genus Pseudomonas. R. erythropolis was the most numerous of soil isolated strains. The studied soils heavily contaminated with PAHs display low biodiversity of cultivable PAH-degrading bacteria and do not have a connection between the quantity of PAHs in the soil samples and taxonomic variety of PAH degraders. Cultivable PAH degraders were represented in the soils exclusively by Gram-positive bacteria, and in the surface sediments only by Gram-negative bacteria.

Schaefer, N.K., Shapiro, B., 2019. New middle chapter in the story of human evolution. Science 365, 981-982.


By comparing genetic information from extant humans worldwide, researchers have painted a broadstrokes picture of human prehistory. However, these data reveal only the oldest and most recent chapters of the story of human evolution. On page 999 of this issue, Narasimhan et al. (1) capitalize on recent advances in high-throughput genome sequencing techniques and access to well-preserved ancient human remains to write a key middle chapter of this story.

Over the past 100,000 years or so, humans dispersed across Africa and then throughout the rest of the world, consequently adapting to a wide variety of lands, climates, and ecosystems (2). This basic narrative illuminates questions—about local adaptation, ecosystem disruption, linguistic evolution, and human prehistory—that genomic data from extant humans fails to answer. To address this deficiency, Narasimhan et al. built on previous large-scale studies of human migration history conducted with ancient DNA obtained from human remains across Eurasia (3–6) (see the figure). The authors sequenced more than 500 genomes of humans belonging to ancient cultures from archaeological sites across a large part of Asia. They then used an array of allele frequency–based statistics and algorithms to model human populations across time as mixtures of other, earlier populations and investigated outstanding questions about human dispersals in South and Central Asia. Although this effort does not rewrite the history of humans in South Asia, it does fill in several missing pieces.

Despite the archaeological and historical importance of the Copper Age Indus Valley Civilization in the northwest regions of South Asia, the genetic origins of the people of this culture remain uncharacterized. Narasimhan et al. identified 11 individuals who lived in regions adjacent to, but outside of, South Asia between 3300 and 2000 BCE and whose genetic signatures indicate that they were migrants from the south. Each of these migrant genomes was a mixture of one population comprising mostly early Iranian farmers and another resembling hunter-gatherers from the Andaman Islands south of India. These two groups mixed between 5400 and 3700 BCE, forming a genetic signature detectable in South Asian genomes today. Because these South Asian migrants were contemporaneous with the Indus Valley Civilization, Narasimhan et al. inferred that the

migrants' genetic profile was probably typical of members of the Indus Valley Civilization. Thus, their study provides evidence of the genomic origins of the Indus Valley Civilization despite not including any ancient genomes from the Indus Valley Civilization itself.

These new data also suggest that, after the fall of the Indus Valley Civilization, several migrations into South Asia led to the formation of two distinct populations therein, one more ancestral to modern North Indians and the other more ancestral to modern South Indians. The ancestry of most present-day Indians is probably composed of these two populations along with a handful of others (6–8). The ancestral South Indian population formed as individuals typical of the Indus Valley Civilization continued to mix with a population related to today's Andaman Islanders; this genomic mixing likely persisted until as late as 1700 to 400 BCE.

The ancestral North Indian population, by contrast, contains ancestry from migrants thought to have moved south from the Eurasian steppe—a flat, unforested grassland—but the source of this ancestry is controversial (6, 8). During the Bronze Age, a culture of steppe pastoralists called the Yamnaya spread ancestry and probably technology and Indo-European languages as far west as Spain and as far east as the Altai Mountains in Siberia (4, 5). Whereas some have suggested that the Yamnaya arrived in North India around 3000 to 2500 BCE (8), others argue that steppe ancestry in North India also contains a European Neolithic component, which implies that it came from a later eastward expansion around 2300 to 1200 BCE (6). Narasimhan et al. date the arrival of steppe ancestry to 1900 to 1500 BCE, which supports the latter hypothesis. Thus, steppe ancestry and the associated Indo-European languages arrived later in India than in Europe and likely arrived by way of Europe.

The amount of genome-wide data available from ancient humans has exploded in recent years, and the study by Narasimhan et al. is the largest contribution to date, with more than 500 ancient human genomes sequenced (see the figure). This scale of genomic data enabled the authors to compare genomes across a large number of locations and time points and to home in on increasingly specific questions that would have been unanswerable even a few years ago.

These new data also suggest that, after the fall of the Indus Valley Civilization, several migrations into South Asia led to the formation of two distinct populations therein, one more ancestral to modern North Indians and the other more ancestral to modern South Indians. The ancestry of most present-day Indians is probably composed of these two populations along with a handful of others (6–8). The ancestral South Indian population formed as individuals typical of the Indus Valley Civilization continued to mix with a population related to today's Andaman Islanders; this genomic mixing likely persisted until as late as 1700 to 400 BCE.

The ancestral North Indian population, by contrast, contains ancestry from migrants thought to have moved south from the Eurasian steppe—a flat, unforested grassland—but the source of this ancestry is controversial (6, 8). During the Bronze Age, a culture of steppe pastoralists called the Yamnaya spread ancestry and probably technology and Indo-European languages as far west as Spain and as far east as the Altai Mountains in Siberia (4, 5). Whereas some have suggested that the Yamnaya arrived in North India around 3000 to 2500 BCE (8), others argue that steppe ancestry in North India also contains a European Neolithic component, which implies that it came from a later eastward expansion around 2300 to 1200 BCE (6). Narasimhan et al. date the arrival of steppe ancestry to 1900 to 1500 BCE, which supports the latter hypothesis. Thus, steppe ancestry and the associated Indo-European languages arrived later in India than in Europe and likely arrived by way of Europe.

The amount of genome-wide data available from ancient humans has exploded in recent years, and the study by Narasimhan et al. is the largest contribution to date, with more than 500 ancient human genomes sequenced (see the figure). This scale of genomic data enabled the authors to compare genomes across a large number of locations and time points and to home in on increasingly specific questions that would have been unanswerable even a few years ago.

The human story revealed by Narasimhan et al. in South Asia is similar to those from elsewhere in Eurasia: Successive waves of migration altered the genetic makeup of, but did not completely replace, preexisting groups (4–6). Modern South Asians appear to be a mixture of Iranian-like hunter-gatherers, a population ancestral to the Andaman Islands, and Eurasian steppe herders who first settled in Europe. Some South Asian populations later received immigrants from other outside groups. As more genomes become available from previously unexamined historical cultures around the world, stories like this one will fill other middle chapters in the book of human history.

References and Notes1. V. M. Narasimhan et al., Science 365, eaat7487 (2019).2. M. Slatkin, F. Racimo, Proc. Natl. Acad. Sci. U.S.A. 113, 6380 (2016).3. I. Lazaridis et al., Nature 513, 409 (2014).4. W. Haak et al., Nature 522, 207 (2015).5. M. E. Allentoft et al., Nature 522, 167 (2015).6. P. de Barros Damgaard et al., Science 360, eaar7711 (2018).7. D. Reich et al., Nature 461, 489 (2009).8. A. Basu et al., Proc. Natl. Acad. Sci. U.S.A. 113, 1594 (2016).9. M. Raghavan et al., Science 345, 1255832 (2014).10. I. Lazaridis et al., Nature 536, 419 (2016).11. M. Lipson et al., Nature 551, 368 (2017).12. I. Olalde et al., Nature 555, 190 (2018)

Scheingross, J.S., Hovius, N., Dellinger, M., Hilton, R.G., Repasch, M., Sachse, D., Gröcke, D.R., Vieth-Hillebrand, A., Turowski, J.M., 2019. Preservation of organic carbon during active fluvial transport and particle abrasion. Geology 47, 958-962.

https://doi.org/10.1130/G46442.1

Oxidation of particulate organic carbon (POC) during fluvial transit releases CO2 to the atmosphere and can influence global climate. Field data show large POC oxidation fluxes in lowland rivers; however, it is unclear if POC losses occur predominantly during in-river transport, where POC is in continual motion within an aerated environment, or during transient storage in floodplains, which may be anoxic. Determination of the locus of POC oxidation in lowland rivers is needed to develop process-based models to predict POC losses, constrain carbon budgets, and unravel links between climate and erosion. However, sediment exchange between rivers and floodplains makes differentiating POC oxidation during in-river transport from oxidation during floodplain storage difficult. Here, we isolated in-river POC oxidation using flume experiments transporting petrogenic and biospheric POC without floodplain storage. Our experiments showed solid phase POC losses of 0%–10% over ∼103 km of fluvial transport, compared to ∼7% to >50% losses observed in rivers over similar distances. The production of dissolved organic carbon (DOC) and dissolved rhenium (a proxy for petrogenic POC oxidation) was consistent with small POC losses, and replicate experiments in static water tanks gave similar results. Our results show that fluvial sediment transport, particle abrasion, and turbulent mixing have a minimal role on POC oxidation, and they suggest that POC losses may accrue primarily in floodplain storage.

Schmidt, F., Swiderek, P., Bredehöft, J.H., 2019. Formation of formic acid, formaldehyde, and carbon dioxide by electron-induced chemistry in ices of water and carbon monoxide. ACS Earth and Space Chemistry 3, 1974-1986.


The processing of cryogenic ices consisting of water and carbon monoxide by different types of radiation is known to lead to the formation of carbon dioxide, formic acid, formaldehyde, and also methanol. In this study, we have investigated these reactions upon electron irradiation with energies between 2 and 20 eV, an energy range typically found in secondary electrons. This is the first time that the reactions have been monitored with a sufficiently fine step width in energy to resolve and identify the primary electron–molecule interactions leading to the specific products. This enables us to elucidate reaction mechanisms by linking these primary electron–molecule interactions to final products. In these reactions, HCO• and HOCO• radicals are key intermediates. Our results show that the HCO• intermediate predominantly leads to formaldehyde, while HOCO• is intermediate to the formation of formic acid. Noticeably, the formation of both formaldehyde and formic acid is enhanced within characteristic energy ranges by resonant electron attachment processes. In contrast, the reactions leading to carbon dioxide show no resonant energy dependence but can be traced back to nonresonant neutral dissociation processes. This reveals that carbon dioxide is linked to neither of these two intermediates. This is in contrast to prior experimental studies, which have proposed that carbon dioxide is formed by loss of a H• radical

from HOCO•. However, our results confirm theoretical studies that have predicted that carbon dioxide formation from HOCO• is not very efficient, because HOCO• presents an energetic well and quickly loses any excess energy it might have in an ice matrix. Instead, we provide evidence that the primary electron–molecule interaction leading to the formation of carbon dioxide in cryogenic ices of water and carbon monoxide is the neutral dissociation of water into O atoms and H2. The so-formed O atoms then react directly with carbon monoxide to yield carbon dioxide.

Schmidt, P., Blessing, M., Rageot, M., Iovita, R., Pfleging, J., Nickel, K.G., Righetti, L., Tennie, C., 2019. Birch tar production does not prove Neanderthal behavioral complexity. Proceedings of the National Academy of Sciences 116, 17707-17711.


Significance: We found a previously unknown way to produce birch tar. Instead of creating cognitively demanding structures (underground or in containers), this method consists of simply burning bark close to cobbles in a hearth. The tar is deposited on the stones and can be scraped off for use. This approach to interpreting early tar resolves the mystery of the associated and still not understood early technical complexity and provides a “discoverable” pathway to one of the earliest pyrotechnologies. These results have implications for our interpretation of birch tar in the archaeological record: Birch tar from early archaeological contexts alone can no longer indicate the presence of modern cognition and/or cultural behaviors in Neanderthals.

Abstract: Birch tar production by Neanderthals—used for hafting tools—has been interpreted as one of the earliest manifestations of modern cultural behavior. This is because birch tar production per se was assumed to require a cognitively demanding setup, in which birch bark is heated in anaerobic conditions, a setup whose inherent complexity was thought to require modern levels of cognition and cultural transmission. Here we demonstrate that recognizable amounts of birch tar were likely a relatively frequent byproduct of burning birch bark (a natural tinder) under common, i.e., aerobic, conditions. We show that when birch bark burns close to a vertical to subvertical hard surface, such as an adjacent stone, birch tar is naturally deposited and can be easily scraped off the surface. The burning of birch bark near suitable surfaces provides useable quantities of birch tar in a single work session (3 h; including birch bark procurement). Chemical analysis of the resulting tar showed typical markers present in archaeological tar. Mechanical tests verify the tar’s suitability for hafting and for hafted tools use. Given that similarly sized stones as in our experiment are frequently found in archaeological contexts associated with Neanderthals, the cognitively undemanding connection between burning birch bark and the production of birch tar would have been readily discoverable multiple times. Thus, the presence of birch tar alone cannot indicate the presence of modern cognition and/or cultural behaviors in Neanderthals.

Schmitz, B., Farley, K.A., Goderis, S., Heck, P.R., Bergström, S.M., Boschi, S., Claeys, P., Debaille, V., Dronov, A., van Ginneken, M., Harper, D.A.T., Iqbal, F., Friberg, J., Liao, S., Martin, E., Meier, M.M.M., Peucker-Ehrenbrink, B., Soens, B., Wieler, R., Terfelt, F., 2019. An extraterrestrial trigger for the mid-Ordovician ice age: Dust from the breakup of the L-chondrite parent body. Science Advances 5, eaax4184.


The breakup of the L-chondrite parent body in the asteroid belt 466 million years (Ma) ago still delivers almost a third of all meteorites falling on Earth. Our new extraterrestrial chromite and 3He data for Ordovician sediments show that the breakup took place just at the onset of a major, eustatic sea level fall previously attributed to an Ordovician ice age. Shortly after the breakup, the flux to Earth of the most fine-grained, extraterrestrial material increased by three to four orders of magnitude. In the present stratosphere, extraterrestrial dust represents 1% of all the dust and has no climatic significance. Extraordinary amounts of dust in the entire inner solar system during >2 Ma following the L-chondrite breakup cooled Earth and triggered Ordovician icehouse conditions, sea level fall, and major faunal turnovers related to the Great Ordovician Biodiversification Event.

Schuetz, R., Maragh, J.M., Weaver, J.C., Rabin, I., Masic, A., 2019. The Temple Scroll: Reconstructing an ancient manufacturing practice. Science Advances 5, eaaw7494.

http://advances.sciencemag.org/content/5/9/eaaw7494.abstract

The miraculously preserved 2000-year-old Dead Sea Scrolls, ancient texts of invaluable historical significance, were discovered in the mid-20th century in the caves of the Judean desert. The texts were mainly written on parchment and exhibit vast diversity in their states of preservation. One particular scroll, the 8-m-long Temple Scroll is especially notable because of its exceptional thinness and bright ivory color. The parchment has a layered structure, consisting of a collagenous base material and an atypical inorganic overlayer. We analyzed the chemistry of the inorganic layer using x-ray and Raman spectroscopies and discovered a variety of evaporitic sulfate salts. This points toward a unique ancient production technology in which the parchment was modified through the addition of the inorganic layer as a writing surface. Furthermore, understanding the properties of these minerals is particularly critical for the development of suitable conservation methods for the preservation of these invaluable historical documents.

Schuhmann, M., Altwegg, K., Balsiger, H., Berthelier, J.-J., De Keyser, J., Fuselier, S.A., Gasc, S., Gombosi, T.I., Hänni, N., Rubin, M., Sémon, T., Tzou, C.-Y., Wampfler, S.F., 2019. CHO-bearing molecules in comet 67P/Churyumov-Gerasimenko. ACS Earth and Space Chemistry 3, 1854-1861.


In 2004, the Rosetta spacecraft was sent to comet 67P/Churyumov-Gerasimenko for the first ever long-term investigation of a comet. After its arrival in 2014, the spacecraft spent more than 2 years in immediate proximity to the comet. During these 2 years, the ROSINA Double Focusing Mass Spectrometer (DFMS) onboard Rosetta discovered a coma with an unexpectedly complex chemical composition that included many oxygenated molecules. Determining the exact cometary composition is an essential first step to understanding of the organic rich chemistry in star forming regions and protoplanetary disks that are ultimately conserved in cometary ices. In this study, a joint approach of laboratory calibration and space data analysis was used to perform a detailed identification and quantification of CHO compounds in the coma of 67P/Churyumov-Gerasimenko. The goal was to derive the CHO compound abundances relative to water for masses up to 100 u. For this study, the May 2015 postequinox period represents the best bulk abundances of comet 67P/Churyumov-Gerasimenko. A wide variety of CHO compounds were discovered, and their bulk abundances were derived. Finally, these results are compared to abundances of CHO-bearing molecules in other comets, obtained mostly from ground-based observations and modeling.

Seidl, C., Bell, D.S., Stoll, D.R., 2019. A study of the re-equilibration of hydrophilic interaction columns with a focus on viability for use in two-dimensional liquid chromatography. Journal of Chromatography A 1604, 460484.


In recent years there has been increasing interest in the use of HILIC separations in two-dimensional liquid chromatography (2D-LC), mainly because the selectivity of HILIC separations complement that of reversed-phase separations for a variety of molecules. Historically, the re-equilibration of HILIC phases following gradient elution has been perceived as too slow to be useful in the second dimension of 2D-LC separations in particular. Recent studies of re-equilibration of HILIC phases by McCalley and coworkers using a limited set of conditions showed that highly repeatable gradient separations could be obtained with re-equilibration times as short as 4.3 min [1], [2]. In this study we aimed to study re-equilibration of HILIC phases under a broader set of conditions, and at much shorter re-equilibration times, in the interest of determining whether or not HILIC separations can be generally considered as a viable option for use in the second dimension of 2D-LC separations. To this end we studied the effects of mobile phase pH, buffer concentration, and preparation method, flow rate, analyte and stationary phase chemistry, column length, and re-equilibration time on retention of a variety of small molecule probe solutes following gradient elution. In general, we have found that excellent separation repeatability can be obtained with quite short (≪10 min) re-equilibration times, even when progress

toward full equilibration of the column is quite slow (≫10 min). In other words, even if the stationary phase is not fully equilibrated, as long as it is partially equilibrated in a highly precise manner, highly repeatable retention times can be obtained. Higher flow rate has a positive effect on both the rate of progress toward full equilibration and the repeatability of separation. No significant, consistent effects of eluent pH or buffer concentration on repeatability of gradient separation were observed for the stationary phases studied. Excellent gradient separation repeatability was obtained with shorter columns (30 mm length) with re-equilibration times as short as 3 s. A proof-of-concept 2D-LC separation of several small molecule probes using HILIC separations in both dimensions was performed to illustrate that re-equilibration of these columns can be fast enough for HILIC columns to be considered as a viable option for the second dimension of comprehensive 2D-LC separations.

Serovaiskii, A.Y., Kolesnikov, A.Y., Kutcherov, V.G., 2019. Formation of iron hydride and iron carbide from hydrocarbon systems at ultra-high thermobaric conditions. Geochemistry International 57, 1008-1014.

https://doi.org/10.1134/S001670291909009X

The chemical interaction of hydrocarbon systems and iron-bearing minerals was investigated under extreme upper mantle pT conditions. As a result, the formation of iron carbide and iron hydride was detected. The experiments were carried out in diamond anvil cells with laser heating. Natural crude oil from the Korchaginskoe deposit and a synthetic mixture of paraffin hydrocarbons were used as hydrocarbon systems and pyroxene-like glass and ferropericlase (57Fe enriched) were used as iron-bearing minerals. The experiments were carried out in the pressure range of 26–95 kbar and the temperature range of 1000–1500°C (± 100°C). The formation of iron hydride was detected at pressure of 26–69 kbar (corresponds to a depth of 100–200 km), and a mixture of iron carbide and iron hydride is formed at pressure of 75–95 kbar (corresponds to a depth of 210–290 km). The formation of iron hydrides and carbides through the interaction of hydrocarbon systems with iron-bearing minerals may indicate the possible existence of these compounds in the upper mantle.

Servais, T., Cascales-Miñana, B., Cleal, C.J., Gerrienne, P., Harper, D.A.T., Neumann, M., 2019. Revisiting the Great Ordovician Diversification of land plants: Recent data and perspectives. Palaeogeography, Palaeoclimatology, Palaeoecology 534, 109280.


Recent molecular clock data suggest with high probability a Cambrian origin of Embryophyta (also called land plants), indicating that their terrestrialization most probably started about 500 Ma. The fossil record of the ‘Cambrian Explosion’ was limited to marine organisms and not visible in the plant fossil record. The most significant changes in early land plant evolution occurred during the Ordovician. For instance, the earliest bryophyte-like cryptospores and the oldest fragments of the earliest land plants are from the Middle and Late Ordovician, respectively. Organic geochemistry studies on biomarker compositions hint at a transition from green algae to land plants during the ‘Great Ordovician Biodiversification Event’ (GOBE). The colonization of the terrestrial realms by land plants clearly had an impact on marine ecosystems. Interactions between the terrestrial and marine biospheres have been proposed and the radiation of land plants potentially impacted on CO2 and O2 concentrations and on global climate. In addition, the shift of strontium isotopes during the Ordovician is probably linked to changing terrestrial landscapes, affected by the first massive land invasion of eukaryotic terrestrial life. The land plants seem unaffected by the first global mass extinction at the end of the Ordovician that eliminated many marine invertebrate taxa.

Severino, R., Froufe, H.J.C., Barroso, C., Albuquerque, L., Lobo-da-Cunha, A., da Costa, M.S., Egas, C., 2019. High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria. MicrobiologyOpen 8, e00840.


Gaiella occulta strain F2‐233T (=CECT 7815 = LMG 26412), isolated from a 150 meter deep mineral water aquifer, was deemed a candidate for high‐quality draft genome sequencing because of the rare environment from which it was isolated. The draft genome sequence (QQZY00000000) of strain F2‐233T is composed of approximately 3 Mb, predicted 3,119 protein‐coding genes of which 2,545 were assigned putative functions. Genome analysis was done by comparison with the other deep‐branching Actinobacteria neighbors Rubrobacter radiotolerans, Solirubrobacter soli and Thermoleophilum album. The genes for the tricarboxylic acid cycle, gluconeogenesis and pentose phosphate pathway, were identified in G. occulta, R. radiotolerans, S. soli and T. album genomes. Genes of the Embden–Meyerhof–Parnas pathway and nitrate reduction were identified in G. occulta, R. radiotolerans and S. soli, but not in the T. album genome. Alkane degradation is precluded by genome analysis in G. occulta. Genes involved in myo‐inositol metabolism were found in both S. soli and G. occulta genomes. A Calvin–Benson–Bassham (CBB) cycle with a type I RuBisCO was identified in G. occulta genome, as well. However, experimental growth under several conditions was negative and CO2 fixation could not be proven in G. occulta.



Improving the crude oil properties can solve serious operational problems in oil production and reduce the production costs. In this study, the possibility of improving the quality of an Iranian heavy crude oil sample using two asphaltene-degrading bacterial consortia was investigated. So, two bacterial consortia were isolated from oil-contaminated soil and reservoir water samples and their impact on the composition, pour point, °API (The American Petroleum Institute gravity), and viscosity of crude oil at 30 and 60 °C after 14 days of incubation was assessed. The results showed that the pour point, °API, and viscosity of the samples decreased significantly. The maximum reduction in the viscosity of the crude oil at room temperature, 25 °C, was 95.73%, which is caused by isolated bacterial consortium from oil-contaminated soil and incubation sample at 60 °C. The results of gas chromatography–mass spectrometry analysis indicated that the amount of nC14 and nC18 in the Soil-60 and RW-60 samples and that of nC15 and nC16 in the Soil-60 and RW-60 samples increased. In addition, some complex polycyclic aromatic hydrocarbons spilled up simpler components, and the content of the simple aromatic hydrocarbon components increased significantly. Although the main criterion of the bacteria isolation was the ability to consume asphaltene, in the presence of lighter hydrocarbons, particularly saturated compounds, strains prefer to use them as carbon and energy sources and cause a decrease in the °API and viscosity of the crude oil. Consequently, the effect of these bacterial consortia on viscosity reduction of crude oil can improve the transportability of the crude oil in the well column and surface pipelines.

Shang, M., Tang, D., Shi, X., Zhou, L., Zhou, X., Song, H., Jiang, G., 2019. A pulse of oxygen increase in the early Mesoproterozoic ocean at ca. 1.57–1.56 Ga. Earth and Planetary Science Letters 527, 115797.


The relationship between oxygen and evolution of early eukaryotes including algae and primitive animals in geological history has been debated, partly due to the varying estimates of oxygen levels in the mid-Proterozoic (ca. 1.8–0.8 Ga) ocean and atmosphere. The upper part of the Gaoyuzhuang Formation (ca. 1.60–1.54 Ga) in North China hosts decimeter-scale multicellular eukaryotic fossils and is documented with a decrease in cerium anomaly indicative of ocean oxygenation. However, the atmospheric oxygen level across this interval and its subsequent oxidation state require further investigation using additional redox proxies. Here we report I/(Ca+Mg) ratios, carbonate/organic carbon isotopes (δ13Ccarb and δ13Corg), and phosphorous (P) contents across the ca. 1.57–1.56 Ga fossil-bearing interval in the North China Platform. High I/(Ca+Mg) ratios (≥2.6 μmol/mol; up to 3.8 μmol/mol) from shallow-water carbonates of the Gaoyuzhuang Formation suggest an episode of significant oxygen increase up to ≥4% PAL (present atmospheric level). The I/(Ca+Mg) ratios return back to ≤0.5 μmol/mol shortly after the peak values without evidence for increasing water depth or diagenetic alteration, implying a short-lived oxidation event. The increase of I/(Ca+Mg) ratios is associated with a −3.5‰ negative δ13Ccarb and δ13Corg anomaly and an increase in P/Al ratios that are best explained by oxidation of

dissolved organic carbon (DOC) in the ocean. Oxygen consumption through oxidation of DOC may have quickly lowered marine and atmospheric O2 levels to the early mid-Proterozoic (1.8–1.4 Ga) background oxygen concentration of ≤0.1–1% PAL. Short-lived oxidation events in an overall anoxic mid-Proterozoic ocean and atmosphere best explain the existing geochemical data and evolutionary stasis of eukaryotes during the “Boring Billion”.

Shields, G.A., Mills, B.J.W., Zhu, M., Raub, T.D., Daines, S.J., Lenton, T.M., 2019. Unique Neoproterozoic carbon isotope excursions sustained by coupled evaporite dissolution and pyrite burial. Nature Geoscience 12, 823-827.

https://doi.org/10.1038/s41561-019-0434-3

The Neoproterozoic era witnessed a succession of biological innovations that culminated in diverse animal body plans and behaviours during the Ediacaran–Cambrian radiations. Intriguingly, this interval is also marked by perturbations to the global carbon cycle, as evidenced by extreme fluctuations in climate and carbon isotopes. The Neoproterozoic isotope record has defied parsimonious explanation because sustained 12C-enrichment (low δ13C) in seawater seems to imply that substantially more oxygen was consumed by organic carbon oxidation than could possibly have been available. We propose a solution to this problem, in which carbon and oxygen cycles can maintain dynamic equilibrium during negative δ13C excursions when surplus oxidant is generated through bacterial reduction of sulfate that originates from evaporite weathering. Coupling of evaporite dissolution with pyrite burial drives a positive feedback loop whereby net oxidation of marine organic carbon can sustain greenhouse forcing of chemical weathering, nutrient input and ocean margin euxinia. Our proposed framework is particularly applicable to the late Ediacaran ‘Shuram’ isotope excursion that directly preceded the emergence of energetic metazoan metabolisms during the Ediacaran–Cambrian transition. Here we show that non-steady-state sulfate dynamics contributed to climate change, episodic ocean oxygenation and opportunistic radiations of aerobic life during the Neoproterozoic era.

Shikhov, I., Thomas, D.S., Arns, C.H., 2019. On the optimum aging time: Magnetic resonance study of asphaltene adsorption dynamics in sandstone rock. Energy & Fuels 33, 8184-8201.


Wettability is a key factor defining ultimate hydrocarbon recovery. Extensive experimentation is required to replicate the wetting state of reservoir rocks. This involves a rock sample wettability restoration procedure, including an aging step and a concept of an optimum aging time, in which asphaltene chemistry plays a major role. There are numerous reports on significance of various crude oil components and elements of asphaltene structure to their tendency to interact with the solid phase, though subject evidence is contradictory. We investigate a possible relationship between the composition of oil, kinetics of an aging process, and a change of sandstone rock wettability. Wettability state of the cores was monitored using low-field NMR relaxometry. The composition and key components of accumulated deposits were established by matching 1H solution-state NMR and X-band EPR spectra of deposits to the spectra of SARA (saturates-aromatics-resins-asphaltenes) fractions of aging fluids. We determined adsorption rate as a function of aging fluid type, monitored free radical and vanadyl content of deposits, and wettability state (through surface relaxivity) over extended aging time interval. EPR data suggest no correlation between the concentration of free radicals in deposits and wettability of the cores. We observe two distinctive periods in the aging process: (i) early-time adsorption best described by a pseudo-second-order kinetic model similar for all aging fluids used in this study, suggesting a common reaction-limited process; (ii) a late-time adsorption process of a faster rate proportional to a bulk diffusion coefficient of aging fluids approximated by an intraparticle diffusion kinetic model. The transition time interval between the two can be used as a definition of an “optimum aging time” in special core analysis. Results provide a link between oil chemistry and wettability phenomena in rocks and may contribute to the development of a model predicting wettability reversal and more accurate reservoir modeling.

Shiraishi, K., Yamada, Y., Nibe, T., 2019. Thermogenic petroleum potential of the Nankai Subduction Zone, offshore SW Japan. Journal of Petroleum Geology 42, 417-434.


In the Kumano forearc basin, offshore SW Japan, the potential occurrence of hydrocarbons has been inferred from both geophysical surveys which point to the presence of natural gas hydrates, and geochemical analyses of gas samples recovered from boreholes and submarine mud volcanoes. The forearc basin is located in the inner part of the Nankai Trough where the Philippine Sea plate is subducting northwards beneath SW Japan. The basin succession unconformably overlies a deformed accretionary prism complex. Hydrocarbons with both microbial and thermogenic origins have been recorded in the Kumano Basin, but the thermogenic petroleum potential is poorly constrained because the regional‐scale geological architecture of the Nankai subduction zone is not well understood.

In this paper, the regional‐scale petroleum potential of the Nankai Trough is investigated based on the geological interpretation of new seismic reflection images. The images were derived from legacy seismic survey data using advanced processing techniques such as reverse time migration, which make use of both primary and multiple reflections in wide‐angle seismic data collected with ocean‐bottom seismographs. In the study area, a seaward‐dipping reflector was identified which terminates at the plate boundary décollement and which is interpreted as part of the boundary between previously‐identified older (>14 Ma) and younger (<6 Ma) accretionary prisms. A triangle body at the base of the younger accretionary prism is interpreted to consist of underthrusted sediments including thick hemipelagic mudstones with source rock potential which were scraped off the down‐going oceanic plate. These tentatively identified, deeply‐buried mudstones may have the potential to generate thermogenic hydrocarbons which may then migrate upwards along dipping carrier beds or faults and fractures to the unconformity at the base of the Kumano forearc basin succession. The presence of hydrocarbons in the accretionary prism may be inferred from positive amplitude anomalies which have been identified in the reprocessed multi‐channel seismic data.

The new reflection interpretations therefore allow the potential for thermogenic petroleum to be proposed in the study area. The hydrocarbon potential at this subduction margin may therefore rely not only on shallow microbial methane, but may also involve deeper, thermogenic petroleum generated within the underlying accretionary prism.

Shurigin, V., Hakobyan, A., Panosyan, H., Egamberdieva, D., Davranov, K., Birkeland, N.-K., 2019. A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups. MicrobiologyOpen 8, e00850.


During the last five decades, the Aral Sea has gradually changed from a saline water body to a hypersaline lake. Microbial community inhabiting the Aral Sea has been through a succession and continuous adaptation during the last 50 years of increasing salinization, but so far, the microbial diversity has not been explored. Prokaryotic diversity of the Large Aral Sea using cultivation‐independent methods based on determination of environmental 16S rRNA gene sequences revealed a microbial community related to typical marine or (hyper) saline‐adapted Bacteria and Archaea. The archaeal sequences were phylogenetically affiliated with the order Halobacteriales, with a large number of operational taxonomic units constituting a novel cluster in the Haloferacaceae family. Bacterial community analysis indicated a higher diversity with representatives belonging to Proteobacteria, Actinobacteria and Bacteroidetes. Many members of Alphaproteobacteria and Gammaproteobacteria were affiliated with genera like Roseovarius, Idiomarina and Spiribacter which have previously been found in marine or hypersaline waters. The majority of the phylotypes was most closely related to uncultivated organisms and shared less than 97% identity with their closest match in GenBank, indicating a unique community structure in the Large Aral Sea with mostly novel species or genera.

Si, W., Liu, Y., Xiao, Y., Guo, Z., Jin, G., Yan, J., Shen, A., Zhou, H., Yang, F., Liang, X., 2020. An offline two-dimensional supercritical fluid chromatography × reversed phase liquid chromatography tandem quadrupole time-of-flight mass spectrometry system for comprehensive gangliosides profiling in swine brain extract. Talanta 208, 120366.


Gangliosides, widely distributed in tissues and body fluid, have been connected to the therapy of cancer and brain related diseases. The complexity of the gangliosides structures with different polar moieties coexisting, a carbohydrate moiety and a ceramide chain, make it a great challenge in separation and analysis science. This study aimed to develop a strategy on the basis of high-accuracy data collected by an offline two-dimensional (2D) supercritical fluid chromatography (SFC) × reversed phase liquid chromatography (RPLC)/quadrupole time-of-flight (Q-ToF) system, and to integrate an in-house library with self-developed software for fast screening and identification of gangliosides from a complex sample (swine brain extract). Subsequent positive-mode MS/MS was used to validate the identified gangliosides. Finally, 153 gangliosides were separated and 79 of them were identified by the in-house library and self-developed software, 4-fold more than those by manual identification (18 gangliosides). Among the identified ones, 20 were detected in swine brain for the first time. This study established an offline 2D SFC × RPLC system and provided a new method for fast screening and automatic identification of gangliosides in complex mixtures. It will be conducive to further study of biological functions of gangliosides.

Sim, M.S., 2019. Effect of sulfate limitation on sulfur isotope fractionation in batch cultures of sulfate reducing bacteria. Geosciences Journal 23, 687-694.

https://doi.org/10.1007/s12303-019-0015-x

Dissimilatory reduction of sulfate to sulfide produces a wide range of sulfur isotope effects, enriching heavy isotopes of sulfur in the remaining sulfate. This isotope fractionation is known to decrease at low sulfate concentrations, which has been used to assess marine sulfate levels throughout the geologic record. So far, the relationships of fractionations to the sulfate concentrations have been examined exclusively in continuous cultures or cell suspensions with continuous removal of the metabolic product sulfide, although sulfate respiration often results in the accumulation of high levels of sulfide in nature. High sulfide levels, as opposed to the effect of sulfate depletion, can increase the magnitude of sulfur isotope fractionation. Thus, I investigate the sulfur isotope fractionation by sulfate reducing bacteria, Desulfovibrio alaskensis and Desulfovibrio sp. DMSS1, in pyruvate batch cultures, where low sulfate but high sulfide concentrations can be achieved. The improved sensitivity of the new analytical method using multicollector ICP-MS makes it easier to measure the sulfur isotope composition of residual sulfate. Both species of Desulfovibrio fractionate sulfur isotopes by 11 to 12‰ with sulfate in excess, but as sulfate is used up in the culture medium, sulfur isotope fractionations decrease down to 0‰ and 3‰ for D. alaskensis and DMSS1, respectively. The results here suggest that elevated sulfide levels are likely secondary to the sulfate availability in determining the magnitude of isotope fractionation. However, the threshold sulfate concentrations at which isotope effect diminishes are apparently different between the two species studied.

Sindhuja, C.S., Khelen, A.C., Manikyamba, C., 2019. Geochemistry of Archean–Proterozoic shales, Dharwar Craton, India: Implications on depositional environment. Geological Journal 54, 2759-2778.

https://doi.org/10.1002/gj.3467

Shales are significant sedimentary units in the Archean greenstone belts and Proterozoic Cuddapah sequence of Dharwar Craton. We present the geochemical studies of the Archean shales from the Chitradurga greenstone belt and the Proterozoic Vempalle Formation of the Cuddapah Basin to evaluate their chemical composition, weathering, provenance, and depositional conditions. The Archean shales are depleted in transition metals (Ni and Co) but enriched in V, Cr, and Sc relative to upper continental crust, while the Proterozoic shales are depleted in Cr, Co, Ni, Sc, and V compared with Post-Archean Australian shale reflecting on negligible mafic source during their deposition. The REE patterns of these shales are uniform with moderately flat LREE and negative to positive Ce anomalies reflecting on marine conditions of their deposition. The presence of both positive and negative Ce anomalies indicate fluctuating oxic and anoxic conditions. The Archean and Proterozoic shales show negative and positive Eu anomalies, respectively, along with slightly enriched HREE. Compositional variation is observed in the Archean shales, whereas the Proterozoic counterparts were affected by sediment recycling as displayed by the Th/Sc and Zr/Sc relationship. Th/U and Th along with (Gd/Yb)n

ratios display significant heavy mineral enrichment in these shales. The chemical index of alteration (CIA) and chemical index of weathering (CIW) of these shales suggest moderate to intense chemical weathering during the Archean and low to moderate weathering during Proterozoic times. The overall geochemical signatures collectively indicate granitic and tonalitic provenance for the Archean and Proterozoic shales, which were deposited in an active and passive continental margins.

Smrzka, D., Zwicker, J., Misch, D., Walkner, C., Gier, S., Monien, P., Bohrmann, G., Peckmann, J., 2019. Oil seepage and carbonate formation: A case study from the southern Gulf of Mexico. Sedimentology 66, 2318-2353.


Oil seeps from the southern Gulf of Mexico can be regarded as natural laboratories where the effect of crude oil seepage on chemosynthesis‐based communities and carbonate precipitation can be studied. During R/V Meteor cruise 114 the seep sites UNAM (Universidad Nacional Autónoma de México) Ridge, Mictlan Knoll and Tsanyao Yang Knoll (Bay of Campeche, southern Gulf of Mexico) were investigated and sampled for authigenic carbonate deposits containing large amounts of liquid oil and solid asphalt. The δ13C values of individual carbonate phases including: (i) microcrystalline matrix aragonite and calcite; (ii) grey, cryptocrystalline to microcrystalline aragonite; and (iii) clear, fibrous aragonite cement, are between −30‰ and −20‰, agreeing with oil as the primary carbon source. Raman spectra reveal that residual heavy oils from all sites are immature and most likely originate from the same reservoir. Geochemical batch modelling using the software code PHREEQC demonstrates how sulphate‐driven oxidation of oil‐derived low‐molecular to high‐molecular weight hydrocarbons affects carbonate saturation state, and shows that the oxidation state of carbon in hydrocarbon compounds and oxidation rates of hydrocarbons control carbonate saturation and precipitation at oil seeps. Phase‐specific trace and rare earth element contents of microcrystalline aragonite and calcite, grey cryptocrystalline aragonite and clear aragonite were determined, revealing enrichment in light rare earth elements for grey aragonite. By comparing trace element patterns of carbonates with those of associated oils, it becomes apparent that liquid hydrocarbons constitute an additional source of trace metals to sedimentary pore waters. This work not only demonstrates that the microbial degradation of oil at seeps may result in the precipitation of carbonate minerals, it also elucidates that trace metal inventories of seep carbonates archive diagnostic elemental patterns, which can be assigned to the presence of heavy hydrocarbons in interstitial pore waters.

Soderlund, K.M., 2019. Ocean dynamics of outer solar system satellites. Geophysical Research Letters 46, 8700-8710.

https://doi.org/10.1029/2018GL081880

Abstract: Ocean worlds are prevalent in the solar system. Focusing on Enceladus, Titan, Europa, and Ganymede, I use rotating convection theory and numerical simulations to predict ocean currents and the potential for ice‐ocean coupling. When the influence of rotation is relatively strong, the oceans have multiple zonal jets, axial convective motions, and most efficient heat transfer at high latitudes. This regime is most relevant to Enceladus and possibly to Titan and may help explain their long‐wavelength topography. For a more moderate rotational influence, fewer zonal jets form, Hadley‐like circulation cells develop, and heat flux peaks near the equator. This regime is predicted for Europa, where it may help drive geologic activity via thermocompositional diapirism in the ice shell, and is possible for Titan. Weak rotational influence allows concentric zonal flows and overturning cells with no preferred orientation. Predictions for Ganymede's ocean span multiple regimes.

Plain Language Summary: The outer solar system is host to a large number of diverse satellites, many of which likely have global oceans beneath their outer icy shells. I use theoretical arguments and numerical models to make predictions about ocean currents and heat transfer across such oceans. Our results suggest that strong ocean currents exist in Enceladus, Titan, Europa, and Ganymede and cause the transfer of heat to vary with latitude that may modify the overlying ice shell.



The location of double bond in unsaturated fatty acids (FAs) plays a critical role in their physiological properties. However, structural identification and quantification of unsaturated FAs by mass spectrometry are still challenging. In this work, we reported the coupling of epoxidation reaction of the C=C in unsaturated FAs and liquid chromatography-mass spectrometry (LC-MS) with multiple reaction monitoring (MRM) mode for accurate identification and quantification of C=C isomers of FAs. Epoxidation of the C=C in unsaturated FAs was induced by a dioxide of ketone, tetrahydrothiopyran-4-one 1,1-dioxide, as a catalyst and Oxone as an oxidant in less than 5 min with nearly 100% yield. All the C=C bonds were epoxidized to obtain a single product, simplifying the chromatographic separation of epoxidation products to enable more accurate quantification analysis. The epoxidation products were stable at room temperature and can produce highly abundant diagnostic ions indicative of C=C locations by tandem mass spectrometry using collision-induced association (CID). The application of this approach for the analysis of FAs isomers in human plasma demonstrated the potential of our method for the qualitative and quantitative analysis of unsaturated FAs in complex biological samples, which is valuable in biological and medical analysis.



Gas transport in shale nanopores is controlled by the complex transport mechanisms and pore structure characteristics. So far much work has been done on the single pore and regular structure based pore network but little is known on real gas transport behavior on a realistic shale pore structure model. In this work, a dynamic pore network model is proposed to describe single component methane transport in nano-scale porous media. Gas transport behavior takes transport mechanisms of slip flow, transition flow, surface diffusion and ad/desorption into account. Real gas effect under high pressure and temperature is considered when calculating gas properties. A three dimensional pore network model is built from a three dimensional image that is reconstructed using multi-point statistics from a small organic-rich area on a two dimensional shale SEM image. This pore network model is used to analyze dynamic gas transport and pressure drop transmission process. Our simulated results reveal that there exists a time period that gas permeability on the pore network is influenced by the pressure drop transmission process and pore structure that flows on. When pressure drop reaches outlet, gas transport turns steady state. At steady state period gas permeability becomes constant and is influenced by the effective stress, pressure, temperature and shale rock property.

Sorokin, D.Y., Yakimov, M., Messina, E., Merkel, A.Y., Bale, N.J., Sinninghe Damsté, J.S., 2019. Natronolimnobius sulfurireducens sp. nov. and Halalkaliarchaeum desulfuricum gen. nov., sp. nov., the first sulfur-respiring alkaliphilic haloarchaea from hypersaline alkaline lakes. International Journal of Systematic and Evolutionary Microbiology 69, 2662-2673.

https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003506

Eight pure cultures of alkaliphilic haloaloarchaea capable of growth by dissimilatory sulfur reduction (previously only shown for neutrophilic haloarchaea) were isolated from hypersaline alkaline lakes in different geographic locations. These anaerobic enrichments, inoculated with sediments and brines, used formate, butyrate and peptone as electron donors and elemental sulfur as an electron acceptor 4 M total Na+ and at pH 9–10. According to 16S rRNA gene sequencing, the isolates fell into two distinct groups. A major group, comprising seven obligate alkaliphilic isolates from highly alkaline soda lakes, represents a new species-level branch within the genus Natronolimnobius (order Natrialbales ), while a single moderately alkaliphilic isolate from the less alkaline Searles Lake forms a novel genus-level lineage within the order Haloferacales . The cells of the isolates are either flat rods or coccoid. They are facultative anaerobes using formate or H2 (in the

presence of acetate or yeast extract as carbon source), C4–C9 fatty acids or peptone (the major group) as electron donors and either sulfur or DMSO (the major group) as electron acceptors. Aerobic growth is only possible with organic acids and peptone–yeast extract. All isolates are extreme halophiles, growing optimally at 4 M total Na+. On the basis of their unique physiological properties and distinct phylogeny, we propose that the seven isolates from the soda lakes are placed into a novel species, Natronolimnobius sulfurireducens sp. nov. (type strain AArc1T=JCM 30663T=UNIQEM U932T), and the Searles Lake isolate, AArc-SlT, into a new genus and species Halalkaliarchaeum desulfuricum (=JCM 30664T=UNIQEM U999T).

Souza-Corrêa, J.A., da Costa, C.A.P., da Silveira, E.F., 2019. Compaction and destruction cross-sections for α-glycine from radiolysis process via 1.0 keV electron beam as a function of temperature. Astrobiology 19, 1123-1138.

https://doi.org/10.1089/ast.2018.1986

Glycine is an amino acid that has already been detected in space. It is relevant to estimate its resistance under cosmic radiation. In this way, a sublimate of glycine in α-form on KBr substrate was exposed in the laboratory to a 1.0 keV electron beam. The radiolysis study was performed at 40 K, 80 K, and 300 K sample temperatures. These temperatures were chosen to cover characteristics of the outer space environment. The evolution of glycine compaction and degradation was monitored in real time by infrared spectroscopy (Fourier-transform infrared) by investigation in the spectral ranges of 3500–2100, 1650–1200, and 950–750 cm−1. The compaction cross-section increases as the glycine temperature decreases. The glycine film thickness layer of ∼160 nm was depleted completely after ∼15 min at 300 K under irradiation with ∼1.4 μA beam current on the target, whereas the glycine depletion at 40 K and 80 K occurred after about 4 h under similar conditions. The destruction cross-section at room temperature is found to be (13.8 ± 0.2) × 10−17 cm2, that is, about 20 times higher than the values for glycine depletion at lower temperatures (<80 K). Emerging and vanishing peak absorbance related to OCN− and CO bands was observed in 2230–2100 cm−1 during the radiolysis at 40 K and 80 K. The same new IR bands appear in the range of 1600–1500, 1480–1370, and 1350–1200 cm−1 after total glycine depletion for all temperature configurations. A strong N-H deformation band growing at 1510 cm−1 was observed only at 300 K. Finally, the destruction cross-section associated to tholin decay at room temperature is estimated to be (1.30 ± 0.05) × 10−17 cm2. In addition, a correlation between the formation cross-sections for daughter and granddaughter molecules at 300 K is also obtained from the experimental data.

Spacapan, J.B., D'Odorico, A., Palma, O., Galland, O., Rojas Vera, E., Ruiz, R., Leanza, H.A., Medialdea, A., Manceda, R., 2020. Igneous petroleum systems in the Malargüe fold and thrust belt, Río Grande Valley area, Neuquén Basin, Argentina. Marine and Petroleum Geology 111, 309-331.


The Río Grande Valley (Neuquén Basin, Argentina) is a large oil field where voluminous igneous sill complexes are emplaced in different levels of the sedimentary sequence in a fold and thrust belt setting. These sills are predominantly emplaced in organic-rich units such as Vaca Muerta and Agrio Formations and are critical elements of the defined petroleum system, as they affect the thermal maturity of the surrounding source rocks, and also act as naturally fractured reservoirs. In this contribution, we integrated structural sections, borehole data, core descriptions, petrophysical laboratory tests and organic geochemistry measurements to characterize the impact of the magmatism in the petroleum system of the Río Grande Valley oil field. Especially, we focused in evaluating the impact of the sill-complexes in hydrocarbon generation, migration and accumulation. Our data shows that: (1) intrusions are preferably emplaced in organic rich units; (2) a large number of intrusions is observed in areas intensely deformed by imbricated thrusts; (3) an increase in the number of intrusions drives stronger and more extensive maturation processes in the Vaca Muerta formation, enhancing notably the cracking of kerogen to hydrocarbon within this unit; (4) where the number of intrusions increases, the concentration of total gas and methane also increases, given that all sills are suitable reservoirs; (5) igneous rocks provide a low resistance path for fluids flow and act as the main reservoirs in the study area; (6) the reservoir quality of igneous intrusions is dominated by the combination of matrix and fracture framework properties; (7) zeolites are the most common type of cement in these reservoirs; (8) deep sills

located in the Vaca Muerta formation produce larger volumes of hydrocarbons relative to shallower intrusive reservoirs. The Río Grande Valley oil field offers a world-class example of the implications of igneous complexes in hydrocarbon generation, migration and accumulation in a compressive tectonic setting of fold and thrust belt.

Šponer, J.E., Šponer, J., Di Mauro, E., 2019. Structural and energetic compatibility: The driving principles of molecular evolution. Astrobiology 19, 1117-1122.

https://doi.org/10.1089/ast.2018.1978

In this work, we provide an answer to the question formulated by Albert Eschenmoser: ?How would you envisage the bridge between potentially primordial geochemistry that had been disordered and one that gradually became self-organizing?? Analysis of the free-energy profiles of some of the key reactions leading to formation of nucleotides and their oligomers shows that, whereas the first part of the pathway, up to nucleotides, is energy-driven, in the second low-energy part entropic control in the form of structural compatibility becomes more important. We suggest that the birth of modern metabolism requires structural compatibility, which is enabled by the commensurability of the thermodynamics of the synthetic steps with the stabilizing effect of those intermolecular interactions that play a key role in dictating entropic control of these reactions.

Sponheimer, M., Ryder, C.M., Fewlass, H., Smith, E.K., Pestle, W.J., Talamo, S., 2019. Saving old bones: a non-destructive method for bone collagen prescreening. Scientific Reports 9, 13928.

https://doi.org/10.1038/s41598-019-50443-2

Bone collagen is an important material for radiocarbon, paleodietary, and paleoproteomic analyses, but it degrades over time, making such analyses more difficult with older material. Collagen preservation between and within archaeological sites is also variable, so that much time, effort, and money can go into the preparation and initial analysis of samples that will not yield meaningful results. To avoid this, various methods are employed to prescreen bone for collagen preservation (e.g., %N, microporosity, and FTIR spectroscopic analyses), but these are often destructive and/or require exportation for analysis. Here, we explore near-infrared spectroscopy as a tool for gauging the collagen content of ground and whole bone from about 500 to 45,000 years ago. We show that a portable spectrometer’s ability to quantify collagen content and classify specimens by preservation status is comparable to that of other popular prescreening methods. Moreover, near-infrared spectroscopy is non-destructive and spectra can be acquired in a few seconds.

Spoor, F., 2019. Elusive cranium of early hominin found. Nature 573, 200-202.

https://www.nature.com/articles/d41586-019-02520-9

A 3.8-million-year-old hominin fossil reveals what the cranium of the oldest known Australopithecus species looked like, casting doubt on assumptions about how these ancient relatives of humans evolved.

Human evolution often captures the imagination, not least because some of our extinct hominin relatives are personified by well-preserved fossils with catchy nicknames. For example, a partial skeleton of Australopithecus afarensis is named Lucy, and an Australopithecus africanus cranium (the skull without its lower jaw) is called Mrs Ples. However, the oldest known species that is unambiguously part of the human evolutionary tree1, Australopithecus anamensis, has mainly languished away from the limelight because of its small and not particularly glamorous fossil record. Until now, A. anamensis was known only from partial upper and lower jaw bones, isolated teeth, a small part of the braincase and a few limb bones. These specimens were found in Kenya and Ethiopia and are between 4.2 million and 3.9 million years old2.

Writing in Nature, Haile-Selassie et al. 3 and Saylor et al .4 report the discovery of a mostly complete 3.8-million-year-old cranium found in the Woranso-Mille area of Ethiopia. The fossil is of an adult, probably male, and was

identified as A. anamensis mainly on the basis of the characteristics of its jaw and canine teeth. This cranium looks set to become another celebrated icon of human evolution.

A complete skull is not essential for a good understanding of the morphology of an extinct species. For example, A. afarensis had already been well documented from a large collection of fragmentary remains when the first skull from an adult of this species was found5. However, the newly discovered cranium of A. anamensis, casually named MRD after its collection number, MRD-VP-1/1, provides a wealth of information about A. anamensis by revealing for the first time what its full face and braincase looked like (Fig. 1).

MRD offers insight into the shape of hominin skulls at an early stage of the better understood part of human evolution, from about 4.2 million years ago to the present. The new information will help scientists to determine which skull features are primitive (ancestral) and which are derived (evolved — that is, different from the corresponding feature in an ancestor); this, in turn, will affect inferences about the evolutionary relationships between species. The discovery will also trigger a re-evaluation of the sparse hominin fossil record from before 4.2 million years ago. Whether previously discovered fossils assigned to species of Ardipithecus, Orrorin and Sahelanthropus are all indeed part of the human evolutionary tree or are extinct apes is controversial1,6. MRD provides information that will advance this debate.

By comparing A. anamensis with other species, and including their new evidence, the authors generated evolutionary family trees in which A. anamensis was consistently placed as the most ancestral of all Australopithecus species and later hominins. This result confirms previous findings6, and reflects the fact that the cranium shows predominantly primitive features — including some in parts never documented before in A. anamensis fossils. MRD has a distinctly protruding face (Fig. 1) and a notably long and narrow braincase. The latter feature is remarkably similar in this respect to that of the 7-million-year-old cranium of Sahelanthropus7, and these two species both had a small brain. The new fossil has several features that are assumed by the authors to be derived rather than primitive. Most striking is the forward projection of the cheek bones, which creates a facial appearance reminiscent of much younger Paranthropus hominin species, particularly the 2.5-million-year-old Paranthropus aethiopicus8. The authors conclude that this facial characteristic evolved independently in A. anamensis and later species, but the resemblance might inspire alternative interpretations.

On the basis of previous comparisons in which only information about jaws and teeth was available for A. anamensis, it has been widely accepted that A. anamensis and A. afarensis were successively part of a single evolving lineage through time, and were represented in the fossil record, respectively, from 4.2 million to 3.9 million years ago, and from 3.8 million to 3.0 million years ago2,9. Thus, it has been argued that A. anamensis and A. afarensis should be considered a single evolutionary species9.

The MRD cranium now increases the number of A. anamensis features that can be compared with those of the other species to explore this issue further, and the authors present evidence that is not consistent with the two species being part of a single evolving lineage. First, they identify a number of features that are derived in A. anamensis but are primitive in A. afarensis. Second, with the shape of MRD as a basis, the authors conclude that a 3.9-million-year-old frontal bone (part of the forehead) from Ethiopia represents A. afarensis rather than A. anamensis. This attribution, along with the discovery of the 3.8-million-year-old MRD cranium of A. anamensis (dating evidence reported by Saylor et al.), provides a revised timeframe indicating that A. anamensis existed from at least 4.2 million to 3.8 million years ago, and A. afarensis from at least 3.9 million to 3.0 million years ago — so the temporal overlap between the two species was at least 100,000 years.

The model of a single, evolving lineage is certainly challenged by this new evidence, but more aspects will need to be considered. The isolated frontal bone attributed to A. afarensis might instead belong to Kenyanthropus platyops or Australopithecus deyiremeda, other broadly contemporary hominin species from eastern Africa10. Moreover, little is known about the face of early A. afarensis2,9, and in particular, whether it showed more similarities to the face of the MRD cranium than does the face of later A. afarensis.

One way in which Haile-Selassie and colleagues’ analysis of the fossil specimen stands out is in their use of wide-ranging digital reconstruction that corrects distortions of the fossil’s shape, and estimates missing parts. These digital methods are readily available and offer unique opportunities for research. However, many more shapes can be morphed and matched this way than would be possible with conventional methods, and care is

needed to generate only the most realistic options. It is therefore essential that any digital reconstruction is carried out with detailed, first-hand knowledge of the original fossil, including how it is preserved and distorted.

This point is particularly relevant with respect to the forward-projecting cheekbones of the newly discovered fossil. After reconstruction, this area looks smoothed, with hardly any sign of the original bone surface. One prominent aspect of MRD where the reconstruction could be improved is the front of the upper jaw. Here, digital processing resulted in a less accurate idea of what the characteristic, strongly projecting subnasal area would have looked like before the fossil was broken.

MRD is a great addition to the fossil record of human evolution. Its discovery will substantially affect our thinking on the origin of the genus Australopithecus specifically, and on the evolutionary family tree of early hominins more broadly. This work demonstrates the importance that a single fossil can have in palaeontology, something we should remember when we get puzzled looks and sighs from our colleagues in the experimental biosciences regarding excitement about a sample size of n = 1.

References1. Wood, B. & Harrison, T. Nature 470, 347–352 (2011).2. Kimbel, W. H. in Handbook of Paleoanthropology: Vol III: Phylogeny of Hominids (eds Henke, W. &

Tattersall, I.) 2071–2105 (Springer, 2015).3. Haile-Selassie, Y., Melillo, S. M., Vazzana, A., Benazzi, S. & Ryan T. M. Nature 573, 214–219 (2019).4. Saylor, B. Z. et al. Nature 573, 220–224 (2019).5. Kimbel, W. H., Johanson, D. C. & Rak, Y. Nature 368, 449–451 (1994).6. Mongle, C. S., Strait, D. S. & Grine, F. E. J. Hum. Evol. 131, 28–39 (2019).7. Zollikofer, C. P. et al. Nature 434, 755–759 (2005).8. Walker, A., Leakey, R. E., Harris, J. M. & Brown, F. H. Nature 322, 517–522 (1986).9. Kimbel, W. H. et al. J. Hum. Evol. 51, 134–152 (2006).10. Spoor, F. Nature 521, 432–433 (2015).

St. Pierre, K.A., St. Louis, V.L., Schiff, S.L., Lehnherr, I., Dainard, P.G., Gardner, A.S., Aukes, P.J.K., Sharp, M.J., 2019. Proglacial freshwaters are significant and previously unrecognized sinks of atmospheric CO2. Proceedings of the National Academy of Sciences 116, 17690-17695.


Significance: Glacier melt is one of the most dramatic consequences of climate change in high-latitude and high-altitude environments. As meltwaters move across poorly consolidated landscapes, they transport vast quantities of highly reactive comminuted sediments prone to chemical weathering reactions that may consume atmospheric CO2. Using a whole watershed approach in the Canadian High Arctic, combined with additional dissolved CO2 measurements in glacial rivers in Greenland and the Canadian Rockies, we show that certain glacier-fed freshwater ecosystems are significant and previously unrecognized annual CO2 sinks due to chemical weathering. As many of the world’s rivers originate from glacial headwaters, we highlight the potential importance of this process for contemporary regional carbon budgets in rapidly changing high-latitude and high-altitude watersheds.

Abstract: Carbon dioxide (CO2) emissions from freshwater ecosystems are almost universally predicted to increase with climate warming. Glacier-fed rivers and lakes, however, differ critically from those in nonglacierized catchments in that they receive little terrestrial input of organic matter for decomposition and CO2 production, and transport large quantities of easily mobilized comminuted sediments available for carbonate and silicate weathering reactions that can consume atmospheric CO2. We used a whole-watershed approach, integrating concepts from glaciology and limnology, to conclusively show that certain glacier-fed freshwater ecosystems are important and previously overlooked annual CO2 sinks due to the overwhelming influence of these weathering reactions. Using the glacierized Lake Hazen watershed (Nunavut, Canada, 82°N) as a model system, we found that weathering reactions in the glacial rivers actively consumed CO2 up to 42 km downstream of glaciers, and cumulatively transformed the High Arctic’s most voluminous lake into an important CO2 sink. In conjunction with data collected at other proglacial freshwater sites in Greenland and the Canadian Rockies, we suggest that CO2 consumption in proglacial freshwaters due to glacial melt-enhanced

weathering is likely a globally relevant phenomenon, with potentially important implications for regional annual carbon budgets in glacierized watersheds.

Steinthorsdottir, M., Vajda, V., Pole, M., Holdgate, G., 2019. Moderate levels of Eocene pCO2 indicated by Southern Hemisphere fossil plant stomata. Geology 47, 914-918.

https://doi.org/10.1130/G46274.1

Reducing the uncertainty in predictions of future climate change is one of today’s greatest scientific challenges, with many significant problems unsolved, including the relationship between pCO2 and global temperature. To better constrain these forecasts, it is meaningful to study past time intervals of global warmth, such as the Eocene (56.0–33.9 Ma), serving as climatic analogues for the future. Here we reconstructed pCO2 using the stomatal densities of a large fossil Lauraceae (laurel) leaf database from ten sites across the Eocene of Australia and New Zealand. We show that mostly moderate pCO2 levels of ∼450–600 ppm prevailed throughout the Eocene, levels that are considerably lower than the pCO2 forcing currently needed to recreate Eocene temperatures in climate models. Our data record significantly lower pCO2 than inferred from marine isotopes, but concur with previously published Northern Hemisphere Eocene stomatal proxy pCO2. We argue that the now globally consistent stomatal proxy pCO2 record for the Eocene is robust and that climate sensitivity was elevated and/or that additional climate forcings operated more powerfully than previously assumed.

Stephens, L., Fuller, D., Boivin, N., Rick, T., Gauthier, N., Kay, A., Marwick, B., Geralda, C., Armstrong, D., Barton, C.M., Denham, T., Douglass, K., Driver, J., Janz, L., Roberts, P., Rogers, J.D., Thakar, H., Altaweel, M., Johnson, A.L., Sampietro Vattuone, M.M., Aldenderfer, M., Archila, S., Artioli, G., Bale, M.T., Beach, T., Borrell, F., Braje, T., Buckland, P.I., Jiménez Cano, N.G., Capriles, J.M., Diez Castillo, A., Çilingiroğlu, Ç., Negus Cleary, M., Conolly, J., Coutros, P.R., Covey, R.A., Cremaschi, M., Crowther, A., Der, L., di Lernia, S., Doershuk, J.F., Doolittle, W.E., Edwards, K.J., Erlandson, J.M., Evans, D., Fairbairn, A., Faulkner, P., Feinman, G., Fernandes, R., Fitzpatrick, S.M., Fyfe, R., Garcea, E., Goldstein, S., Goodman, R.C., Dalpoim Guedes, J., Herrmann, J., Hiscock, P., Hommel, P., Horsburgh, K.A., Hritz, C., Ives, J.W., Junno, A., Kahn, J.G., Kaufman, B., Kearns, C., Kidder, T.R., Lanoë, F., Lawrence, D., Lee, G.-A., Levin, M.J., Lindskoug, H.B., López-Sáez, J.A., Macrae, S., Marchant, R., Marston, J.M., McClure, S., McCoy, M.D., Miller, A.V., Morrison, M., Motuzaite Matuzeviciute, G., Müller, J., Nayak, A., Noerwidi, S., Peres, T.M., Peterson, C.E., Proctor, L., Randall, A.R., Renette, S., Robbins Schug, G., Ryzewski, K., Saini, R., Scheinsohn, V., Schmidt, P., Sebillaud, P., Seitsonen, O., Simpson, I.A., Sołtysiak, A., Speakman, R.J., Spengler, R.N., Steffen, M.L., Storozum, M.J., Strickland, K.M., Thompson, J., Thurston, T.L., Ulm, S., Ustunkaya, M.C., Welker, M.H., West, C., Williams, P.R., Wright, D.K., Wright, N., Zahir, M., Zerboni, A., Beaudoin, E., Munevar Garcia, S., Powell, J., Thornton, A., Kaplan, J.O., Gaillard, M.-J., Klein Goldewijk, K., Ellis, E., 2019. Archaeological assessment reveals Earth’s early transformation through land use. Science 365, 897-902.


Abstract: Environmentally transformative human use of land accelerated with the emergence of agriculture, but the extent, trajectory, and implications of these early changes are not well understood. An empirical global assessment of land use from 10,000 years before the present (yr B.P.) to 1850 CE reveals a planet largely transformed by hunter-gatherers, farmers, and pastoralists by 3000 years ago, considerably earlier than the dates in the land-use reconstructions commonly used by Earth scientists. Synthesis of knowledge contributed by more than 250 archaeologists highlighted gaps in archaeological expertise and data quality, which peaked for 2000 yr B.P. and in traditionally studied and wealthier regions. Archaeological reconstruction of global land-use history illuminates the deep roots of Earth’s transformation and challenges the emerging Anthropocene paradigm that large-scale anthropogenic global environmental change is mostly a recent phenomenon.

Editor's Summary: A synthetic history of human land use. Humans began to leave lasting impacts on Earth's surface starting 10,000 to 8000 years ago. Through a synthetic collaboration with archaeologists around the globe, Stephens et al. compiled a comprehensive picture of the trajectory of human land use worldwide during the Holocene (see the Perspective by Roberts). Hunter-gatherers, farmers, and pastoralists transformed the face

of Earth earlier and to a greater extent than has been widely appreciated, a transformation that was essentially global by 3000 years before the present.

Stevenson, K.A.J.M., Blumberg, L.M., Harynuk, J.J., 2019. Thermodynamics-based retention maps to guide column choices for comprehensive multi-dimensional gas chromatography. Analytica Chimica Acta 1086, 133-141.


Comprehensive two-dimensional gas chromatography (GC × GC) provides enhanced separation power over its one-dimensional counterpart – gas chromatography (GC). This enhancement is achieved by the inclusion of a secondary column, the choice of which is a major determinant on the quality of the ultimate separation. When developing and optimizing a new GC × GC method, the choices of stationary phase chemistries, geometries and configurations (which phase serves in which dimension) are of fundamental importance, and must often be addressed even before the manipulation of instrumental conditions. These choices are often made using educated guesses, literature searches, or trial and error. Thermodynamic models of GC separations; however, provide a fast and easy means of acquiring information for guiding these choices. By using characteristic thermodynamic parameters (characteristic temperatures, Tchar, and characteristic thermal constants, θchar), we demonstrate the generation of maps that can inform the choices of column chemistries, phase ratios and configurations for GC × GC separations.

Sun, W., Zhang, E., Chang, J., Shulmeister, J., Bird, M.I., Zhao, C., Jiang, Q., Shen, J., 2019. Microbial membrane tetraether lipid-inferred paleohydrology and paleotemperature of Lake Chenghai during the Pleistocene-Holocene transition. Climate of the Past Discussions 2019, 1-29.


Over the past few decades, paleoenvironmental studies in the Indian Summer Monsoon (ISM) region have mainly focused on precipitation change, with few published terrestrial temperature records from the region. We analyzed the distribution of isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs) in the sediments of Lake Chenghai in southwest China across the Pleistocene–Holocene transition, to extract both regional hydrological and temperature signals for this important transition period. Lake-level was reconstructed from the relative abundance of crenarchaeol in isoGDGTs (%cren) and the crenarchaeol'/crenarchaeol ratio. The %cren-inferred lake-level identified a single lowstand (15.4–14.4 cal ka BP), while the crenarchaeol'/crenarchaeol ratio suggests relatively lower lake-level between 15.4–14.4 cal ka BP and 12.5–11.7 cal ka BP, corresponding to periods of weakened ISM during the Heinrich 1 (H1) and Younger Dryas (YD) cold event. A filtered TetraEther indeX consisting of 86 carbon atoms (TEX86 index) revealed that lake surface temperature reached present-day values during the YD cold event, and suggests a substantial warming of ~ 4 °C from the early Holocene to the mid-Holocene. Our paleotemperature record is generally consistent with other records in southwest China, suggesting that the distribution of isoGDGTs in Lake Chenghai sediments has potential for quantitative paleotemperature reconstruction.

Sun, W., Zhang, E., Chen, R., Shen, J., 2019. Lacustrine carbon cycling since the last interglaciation in northeast China: Evidence from n-alkanes in the sediments of Lake Xingkai. Quaternary International 523, 101-108.


Organic carbon mineralization and storage in the inland water bodies is an important component of global carbon cycling. However, the mechanisms influencing carbon cycling in the inland water bodies remain uncertain. In this study, n-alkane data from a sediment core spanning the last glacial-interglacial cycle from Lake Xingkai in northeast China, were analyzed to determine response of regional carbon cycling to climate change. Prior to MIS 1 the sedimentary n-alkanes were mainly derived from terrigenous higher plants and helophytes in the wetland. By contrast, non-photosynthetic bacteria are probable major alternating source of sedimentary n-alkanes during MIS 1. The n-alkanes in the sediments are mainly influenced by the variations of lake level and deposition of mineral dust. The total organic carbon content (TOC) and TOC-normalized middle-

and long-chain n-alkane concentrations increased during glacial times and decreased during interglacial periods, reflecting higher rates of organic matter decomposition under warmer climatic conditions. The temperature dependence of lacustrine organic matter mineralization suggests that the carbon burial potential of lakes in northeast China will decrease in the future as global warming intensifies.

Sun, X., Kop, L.F.M., Lau, M.C.Y., Frank, J., Jayakumar, A., Lücker, S., Ward, B.B., 2019. Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones. The ISME Journal 13, 2391-2402.

https://doi.org/10.1038/s41396-019-0443-7

Oxygen minimum zones (OMZs) are marine regions where O2 is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes. We used metagenomic binning to construct metagenome-assembled genomes (MAGs) of nitrite oxidizers from OMZs. These MAGs represent two novel Nitrospina-like species, both of which differed from all known Nitrospina species, including cultured species and published MAGs. Relative abundances of different Nitrospina genotypes in OMZ and non-OMZ seawaters were estimated by mapping metagenomic reads to newly constructed MAGs and published high-quality genomes of members from the Nitrospinae phylum. The two novel species were present in all major OMZs and were more abundant inside ODZs, which is consistent with the detection of higher nitrite oxidation rates in ODZs than in oxic seawaters and suggests novel adaptations to anoxic environments. The detection of a large number of unclassified nitrite oxidoreductase genes in the dataset implies that the phylogenetic diversity of nitrite oxidizers is greater than previously thought.

Takagi, H., Kimoto, K., Fujiki, T., Saito, H., Schmidt, C., Kucera, M., Moriya, K., 2019. Characterizing photosymbiosis in modern planktonic foraminifera. Biogeosciences 16, 3377-3396.


Photosymbiosis has played a key role in the diversification of foraminifera and their carbonate production throughout geologic history. However, identification of photosymbiosis in extinct taxa remains challenging, and even among the extant species the occurrence and functional relevance of photosymbiosis remain poorly constrained. Here, we investigate photosymbiosis in living planktonic foraminifera by measuring active chlorophyll fluorescence with fast repetition rate fluorometry. This method provides unequivocal evidence for the presence of photosynthetic capacity in individual foraminifera, and it allows us to characterize multiple features of symbiont photosynthesis including chlorophyll a (Chl a) content, potential photosynthetic activity (Fv∕Fm), and light-absorption efficiency (σPSII). To obtain robust evidence for the occurrence and importance of photosymbiosis in modern planktonic foraminifera, we conducted measurements on 1266 individuals from 30 species of the families Globigerinidae, Hastigerinidae, Globorotaliidae, and Candeinidae. Among the studied species, 19 were recognized as symbiotic and 11 as non-symbiotic. Of these, six species were newly confirmed as symbiotic and five as non-symbiotic. Photosymbiotic species have been identified in all families except the Hastigerinidae. A significant positive correlation between test size and Chl a content, found in 16 species, is interpreted as symbiont abundance scaled to the growth of the host and is consistent with persistent possession of symbionts through the lifetime of the foraminifera. The remaining three symbiont-bearing species did not show such a relationship, and their Fv∕Fm values were comparatively low, indicating that their symbionts do not grow once acquired from the environment. The objectively quantified photosymbiotic characteristics have been used to design a metric of photosymbiosis, which allows the studied species to be classified along a gradient of photosynthetic activity, providing a framework for future ecological and physiological investigations of planktonic foraminifera.



The improvement of microbial induced calcium carbonate precipitate (MICP) using additives has attracted much attention due to its great influence on the quality of precipitate. In this paper, graphene oxide (GO) was used as an additive to induce CaCO3 precipitate. Using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS), the effects of GO on immobilization of bacteria, CaCO3 crystals and the consolidation of sand was studied. The addition of GO caused the rapid growth and the larger size of the CaCO3

crystals. Additionally, the morphology of the rhombohedral crystals was unchanged. The precipitation capability of CaCO3 during the MICP process was improved significantly. X-ray diffraction (XRD) noted that stable calcite was formed during the CaCO3 precipitate process with GO, compared to calcite and vaterite formed. More importantly, the unconfined compressive strength of the consolidated sand was significantly enhanced. These results show that GO has outstanding properties.

Tang, S., Zhou, Y., Yao, X., Feng, X., Li, Z., Wu, G., Zhu, G., 2019. The mercury isotope signatures of coalbed gas and oil-type gas: Implications for the origins of the gases. Applied Geochemistry 109, 104415.


The concentration of mercury vapor (elemental mercury, Hg0) in natural gases has been used to differentiate between coalbed gas and oil-type gas. However, the concentrations of Hg0 in coalbed gas and oil-type gas are highly variable, and its use as a genetic indicator is problematic. Here, for the first time, we report significant differences in the mass-dependent fractionation (MDF, measured with δ202Hg) and the mass-independent fractionation (MIF, measured with Δ199Hg, Δ200Hg and Δ201Hg) of Hg0 isotopes between coalbed gas and oil-type gas. Coalbed gas has an extremely negative δ202Hg (−5.8‰ to −3.08‰) and negative Δ199Hg (−0.19‰ to −0.01‰) relative to the assumed source, which is Permian coal from the Henan Province, China. Oil-type gas is characterized by less negative δ202Hg (−3.08‰ to −0.77‰) and positive Δ199Hg (0.06‰–0.30‰) relative to its E2-3s source rocks in the Liaohe oilfield (dark mudstones: δ202Hg = −1.96‰ to −2.48‰, Δ199Hg = 0.09‰–0.17‰). This significant difference in the MIF can be used to distinguish between coalbed gas and oil-type gas. Notably, the Δ200Hg values of our samples are as high as 0.15‰. We suggest that significant Hg0 MDF might occur during the formation of coalbed gas, but not during the formation of oil-type gas. This study highlights the potential of Hg0 isotopes as proxies for the source of natural gases.

Thakur, M.P., van der Putten, W.H., Cobben, M.M.P., van Kleunen, M., Geisen, S., 2019. Microbial invasions in terrestrial ecosystems. Nature Reviews Microbiology 17, 621-631.

https://doi.org/10.1038/s41579-019-0236-z

Human travel and global trade have tremendously increased the spread of invasive microorganisms in new regions. Experimental and observational studies in terrestrial ecosystems are beginning to shed light on processes of microbial invasions, their ecological impacts and implications for ecosystem functioning. We provide examples of terrestrial invasive microorganisms, including bacteria, fungi, oomycetes and other protists, and viruses, and discuss the impacts of pathogenic and non-pathogenic invasive microorganisms at levels ranging from host species to ecosystems. This Review highlights that despite the recent progress in microbial invasion research, we are only beginning to understand how alien microorganisms interact with native microorganisms, and the implications of those interactions. Finally, we propose three research themes — microbial interactions, impacts and climate change — to make microbial invasion research a truly integrative discipline.

Thibon, F., Blichert-Toft, J., Albarede, F., Foden, J., Tsikos, H., 2019. A critical evaluation of copper isotopes in Precambrian Iron Formations as a paleoceanographic proxy. Geochimica et Cosmochimica Acta 264, 130-140.


Trace metals in Iron Formations (IF) have been widely used as proxies for oceanic redox processes and oxygen evolution leading to the Great Oxidation Event (GOE). Copper has hitherto received comparatively little attention, with a single study reporting variation in δ65Cu between pre- and post-GOE black shales. This is attributed to postulated isotope fractionation effects in the pre-GOE ocean during widespread iron oxide deposition in IF. Here we focus on the application of Cu isotopes in two classic IF-containing sequences of the Neoarchean-Paleoproterozoic, namely the Hamersley (Australia) and Transvaal (South Africa) Supergroups. We specifically targeted the oxide-rich Joffre and Kuruman IF, the carbonate-rich Griquatown IF, and the Mn-rich Hotazel IF, which collectively record over 100 Ma of sustained IF deposition in the pre-GOE ocean. The aim was to assess the utility of Cu isotopes in IF as a paleoceanographic proxy in view of existing oxygen evolution models. Iron formation Cu concentrations are low compared to average crust and modern oceanic Fe-Mn oxide deposits, with average values between 1 and 5 ppm for all four IF data sets. Copper concentrations show no systematic variability with mineralogy, no statistical correlation with bulk Fe and Mn contents, good correlations with Ti (rCu-Ti = 0.73) for the Joffre data set and with Cr, Ni, and V for the South African data sets, and shale-like Cu/Ti ratios. Isotopic results show statistically invariant average δ65Cu values very close to 0‰ for all but the Joffre IF which has a marginally negative average δ65Cu value (−0.24 ± 0.22‰). Combined with other trace transition metal systematics, the Cu isotope data point to a Cu source that was controlled largely by inputs of fine volcanic-derived particles (ash), thus placing limitations on its utility as a paleoceanographic redox proxy during IF genesis.

Thiemens, M.M., Sprung, P., Fonseca, R.O.C., Leitzke, F.P., Münker, C., 2019. Early Moon formation inferred from hafnium–tungsten systematics. Nature Geoscience 12, 696-700.

https://doi.org/10.1038/s41561-019-0398-3

The date of the Moon-forming impact places an important constraint on Earth’s origin. Lunar age estimates range from about 30 Myr to 200 Myr after Solar System formation. Central to this age debate is the greater abundance of 182W inferred for the silicate Moon than for the bulk silicate Earth. This compositional difference has been explained as a vestige of less late accretion to the Moon than to the Earth after core formation. Here we present high-precision trace element composition data from inductively coupled plasma mass spectrometry for a wide range of lunar samples. Our measurements show that the Hf/W ratio of the silicate Moon is higher than that of the bulk silicate Earth. By combining these data with experimentally derived partition coefficients, we found that the 182W excess in lunar samples can be explained by the decay of the now extinct 182Hf to 182W. 182Hf was only extant for the first 60 Myr after the Solar System formation. We conclude that the Moon formed early, approximately 50 Myr after the Solar System, and that the excess 182W of the silicate Moon is unrelated to late accretion.

Thorell, K., Meier-Kolthoff, J.P., Sjöling, Å., Martín-Rodríguez, A.J., 2019. Whole-genome sequencing redefines Shewanella taxonomy. Frontiers in Microbiology 10, 1861. doi: 10.3389/fmicb.2019.01861.


The genus Shewanella encompasses a diverse group of Gram negative, primarily aquatic bacteria with a remarkable ecological relevance, an outstanding set of metabolic features and an emergent clinical importance. The rapid expansion of the genus over the 2000 s has prompted questions on the real taxonomic position of some isolates and species. Recent work by us and others identified inconsistencies in the existing species classification. In this study we aimed to clarify such issues across the entire genus, making use of the genomic information publicly available worldwide. Phylogenomic analyses, including comparisons based on genome-wide identity indexes (digital DNA-DNA hybridization and Average Nucleotide Identity) combined with core and accessory genome content evaluation suggested that the taxonomic position of 64 of the 131 analyzed strains should be revisited. Based on the genomic information currently available, emended descriptions for some Shewanella species are proposed. Our study establishes for the first time a whole-genome based phylogeny for Shewanella spp. including a classification at the subspecific level.

Thyng, K.M., 2019. Deepwater Horizon oil could have naturally reached Texas beaches. Marine Pollution Bulletin 149, 110527.


Following the Deepwater Horizon (DWH) spill, oil residues were found in all five Gulf states of the United States (Texas, Louisiana, Mississippi, Alabama and Florida). However, only a small amount was found in Texas, leading to speculation that it may have arrived there via ship through bilge water instead of naturally via currents. We report on a numerical modeling effort to simulate surface drifters during and after the DWH spill to demonstrate that surface water parcels – and therefore oil carried by those parcels – could reasonably have reached Texas waters at the appropriate time and location from known oiled locations without human interference. We additionally give context for the conditions in 2010 through a study of summer connectivity with the Galveston Bay coastline, which shows that in some years oil from the DWH pipe likely would not have reached Texas.

Tóth, A.B., Lyons, S.K., Barr, W.A., Behrensmeyer, A.K., Blois, J.L., Bobe, R., Davis, M., Du, A., Eronen, J.T., Faith, J.T., Fraser, D., Gotelli, N.J., Graves, G.R., Jukar, A.M., Miller, J.H., Pineda-Munoz, S., Soul, L.C., Villaseñor, A., Alroy, J., 2019. Reorganization of surviving mammal communities after the end-Pleistocene megafaunal extinction. Science 365, 1305-1308.


Abstract: Large mammals are at high risk of extinction globally. To understand the consequences of their demise for community assembly, we tracked community structure through the end-Pleistocene megafaunal extinction in North America. We decomposed the effects of biotic and abiotic factors by analyzing co-occurrence within the mutual ranges of species pairs. Although shifting climate drove an increase in niche overlap, co-occurrence decreased, signaling shifts in biotic interactions. Furthermore, the effect of abiotic factors on co-occurrence remained constant over time while the effect of biotic factors decreased. Biotic factors apparently played a key role in continental-scale community assembly before the extinctions. Specifically, large mammals likely promoted co-occurrence in the Pleistocene, and their loss contributed to the modern assembly pattern in which co-occurrence frequently falls below random expectations.

Editor's summary: Extinction leads to restructuring. By most accounts, human activities are resulting in Earth's sixth major extinction event, and large-bodied mammals are among those at greatest risk. Loss of such vital ecosystem components can have substantial impacts on the structure and function of ecological systems, yet fully understanding these effects is challenging. Tóth et al. looked at the loss of large-bodied mammals in the Pleistocene epoch to identify potential community assembly effects. They found that the demise of large mammals led to a restructuring and a shift from biotic to abiotic drivers of community structure. Understanding past changes may help predict the community-level effects of the extinctions we are currently driving.

Tuerena, R.E., Ganeshram, R.S., Humphreys, M.P., Browning, T.J., Bouman, H., Piotrowski, A.P., 2019. Isotopic fractionation of carbon during uptake by phytoplankton across the South Atlantic subtropical convergence. Biogeosciences 16, 3621-3635.


The stable isotopic composition of particulate organic carbon (δ13CPOC) in the surface waters of the global ocean can vary with the aqueous CO2 concentration ([CO2(aq)]) and affects the trophic transfer of carbon isotopes in the marine food web. Other factors such as cell size, growth rate and carbon concentrating mechanisms decouple this observed correlation. Here, the variability in δ13CPOC is investigated in surface waters across the south subtropical convergence (SSTC) in the Atlantic Ocean, to determine carbon isotope fractionation (εp) by phytoplankton and the contrasting mechanisms of carbon uptake in the subantarctic and subtropical water masses. Our results indicate that cell size is the primary determinant of δ13CPOC across the Atlantic SSTC in summer. Combining cell size estimates with CO2 concentrations, we can accurately estimate εp within the varying surface water masses in this region. We further utilize these results to investigate future changes in εp

with increased anthropogenic carbon availability. Our results suggest that smaller cells, which are prevalent in the subtropical ocean, will respond less to increased [CO2(aq)] than the larger cells found south of the SSTC and in the wider Southern Ocean. In the subantarctic water masses, isotopic fractionation during carbon uptake will likely increase, both with increasing CO2 availability to the cell, but also if increased stratification leads to decreases in average community cell size. Coupled with decreasing δ13C of [CO2(aq)] due to anthropogenic CO2 emissions, this change in isotopic fractionation and lowering of δ13CPOC may propagate through the marine food web, with implications for the use of δ13CPOC as a tracer of dietary sources in the marine environment.

Valyaeva, O.V., Ryabinkina, N.N., Bushnev, D.A., 2019. Composition of the thermolysis products of asphaltenes from natural bitumen of the Voya deposit in the Timan–Pechora Province. Petroleum Chemistry 59, 956-960.

https://doi.org/10.1134/S0965544119090159

The products of thermolysis of asphaltenes of Lower Visean natural bitumens mined from different parts of the Voya field in the Timan–Pechora province have been studied. It has been found that the thermolysis of asphaltenes results in generation of alkanes, isoprenanes, alkenes, steranes, and hopanes. Genetic indices determined from the composition of biomarkers identified in the thermolysis products of asphaltenes do not contradict the possible genetic relations of the bitumens under study and Domanik crude oils of the Timan–Pechora province.

van der Voort, T.S., Mannu, U., Hagedorn, F., McIntyre, C., Walthert, L., Schleppi, P., Haghipour, N., Eglinton, T.I., 2019. Dynamics of deep soil carbon – insights from 14C time series across a climatic gradient. Biogeosciences 16, 3233-3246.


Quantitative constraints on soil organic matter (SOM) dynamics are essential for comprehensive understanding of the terrestrial carbon cycle. Deep soil carbon is of particular interest as it represents large stocks and its turnover times remain highly uncertain. In this study, SOM dynamics in both the top and deep soil across a climatic (average temperature ∼ 1–9 ∘C) gradient are determined using time-series (∼20 years) 14C data from bulk soil and water-extractable organic carbon (WEOC). Analytical measurements reveal enrichment of bomb-derived radiocarbon in the deep soil layers on the bulk level during the last 2 decades. The WEOC pool is strongly enriched in bomb-derived carbon, indicating that it is a dynamic pool. Turnover time estimates of both the bulk and WEOC pool show that the latter cycles up to a magnitude faster than the former. The presence of bomb-derived carbon in the deep soil, as well as the rapidly turning WEOC pool across the climatic gradient, implies that there likely is a dynamic component of carbon in the deep soil. Precipitation and bedrock type appear to exert a stronger influence on soil C turnover time and stocks as compared to temperature.

van Elden, S., Meeuwig, J.J., Hobbs, R.J., Hemmi, J.M., 2019. Offshore oil and gas platforms as novel ecosystems: A global perspective. Frontiers in Marine Science 6, 548. doi: 10.3389/fmars.2019.00548.

https://www.frontiersin.org/article/10.3389/fmars.2019.00548

Offshore oil and gas platforms are found on continental shelves throughout the world’s oceans. Over the course of their decades-long life-spans, these platforms become ecologically important artificial reefs, supporting a variety of marine life. When offshore platforms are no longer active they are decommissioned, which usually requires the removal of the entire platform from the marine environment, destroying the artificial reef that has been created and potentially resulting in the loss of important ecosystem services. While some countries allow for these platforms to be converted into artificial reefs under Rigs-to-Reefs programs, they face significant resistance from various stakeholders. The presence of offshore platforms and the associated marine life alters the ecosystem from that which existed prior to the installation of the platform, and there may be factors which make restoration of the ecosystem unfeasible or even detrimental to the environment. In these cases, a novel ecosystem has emerged with potentially significant ecological value. In restoration ecology, ecosystems altered in this way can be classified and managed using the novel ecosystems concept, which recognizes the value of

the new ecosystem functions and services and allows for the ecosystem to be managed in its novel state, instead of being restored. Offshore platforms can be assessed under the novel ecosystems concept using existing decommissioning decision analysis models as a base. With thousands of platforms to be decommissioned around the world in coming decades, the novel ecosystems concept provides a mechanism for recognizing the ecological role played by offshore platforms.

Vanani, M.B., Daneshfar, R., Khodapanah, E., 2019. A novel MLP approach for estimating asphaltene content of crude oil. Petroleum Science and Technology 37, 2238-2245.

https://doi.org/10.1080/10916466.2018.1474223

Asphaltene is considering to be the most problematic part of oil that causes pipe plugging, permeability reduction, and ultimately loss of production through its separation process from oil body as result of any thermodynamic change. Its weight fraction is one of key inputs to any asphaltene related modeling, which requires an expensive and time consuming experimental procedure. In this research, for the first time a novel MLP-ANN structure is proposed to predict this critical parameter at wide range of operational conditions, with satisfactory precision. A dataset of over 300 experimental data was gathered from open literature and used to train and test the proposed construct. The results show network great performance and therefore, can be used as a universal tool to provide input for any asphaltene-related modeling, with assurance.

Wade, L., 2019. Ancient site in Idaho implies first Americans came by sea. Science 365, 848-49.


About 16,000 years ago, on the banks of a river in western Idaho, people kindled fires, shaped stone blades and spearpoints, and butchered large mammals. All were routine activities in prehistory, but their legacy today is anything but. The charcoal and bone left at that ancient site, now called Cooper's Ferry, are some 16,000 years old—the oldest radiocarbon-dated record of human presence in North America, according to work reported on p. 891.

The findings do more than add a few centuries to the timeline of people in the Americas. They also shore up a new picture of how humans first arrived, by showing that people lived at Cooper's Ferry more than 1 millennium before melting glaciers opened an ice-free corridor through Canada about 14,800 years ago. That implies the first people in the Americas must have come by sea, moving rapidly down the Pacific coast and up rivers. The dates from Cooper's Ferry “fit really nicely with the [coastal] model that we're increasingly getting a consensus on from genetics and archaeology,” says Jennifer Raff, a geneticist at the University of Kansas in Lawrence who studies the peopling of the Americas.

The Clovis people, big game hunters who made characteristic stone tools dated to about 13,000 years ago, were once thought to have been the first to reach the Americas, presumably through the ice-free corridor. But a handful of earlier sites have persuaded many researchers that the coastal route is more likely. Archaeologists have questioned the signs of occupation at some putative pre-Clovis sites, but the stone tools and dating at Cooper's Ferry pass the test with flying colors, says David Meltzer, an archaeologist at Southern Methodist University in Dallas, Texas. “It's pre-Clovis. I'm convinced.”

Over 10 years of excavations, the Cooper's Ferry team uncovered dozens of stone spear points, blades, and multipurpose tools called bifaces, as well as hundreds of pieces of debris from their manufacture. Although the site is near the Salmon River, most of the ancient bones belonged to mammals, including extinct horses. The team also found a hearth and pits dug by the site's ancient residents, containing stone artifacts and animal bones.

Radiocarbon dates on the charcoal and bone are as old as 15,500 years. In North America, few tree ring records can precisely calibrate such early radiocarbon dates, but a state-of-the-art probabilistic model placed the start of the occupation at between 16,560 and 15,280 years. “I may not think it goes back to 16,000 years ago, but I surely can believe it goes back 15,000 years,” says Michael Waters, an archaeologist at Texas A&M University in College Station.

The only rival to Cooper's Ferry as the oldest site in North America is the Gault site in Texas. Researchers dated that site to about 16,000 years ago by optical luminescence, a method with larger error bars than radiocarbon dating.

It's easy to see how seafaring people might have reached Cooper's Ferry, says Loren Davis, an archaeologist at Oregon State University in Corvallis who led the excavations. Although the site is more than 500 kilometers from the coast, the Salmon, Snake, and Columbia rivers link it to the sea. “As people come down the coast, the first left-hand turn to get south of the ice comes up the Columbia River Basin,” Davis says. “It's the first off-ramp.”

The area is now federal land but was long occupied by the Nez Perce Tribe, or the Niimíipuu. They know Cooper's Ferry as Nipéhe, an ancient village founded by a young couple after a flood destroyed their previous home, says Nakia Williamson, the tribe's director of cultural resources. “Our stories already tell us how long we've been here. … This [study] only reaffirms that,” Williamson says. He hopes the excavations—in which Nez Perce archaeologists and interns participated—will help others recognize the deep ties the Nez Perce have to their ancestral lands. “This is not just something that happened 16,000 years ago. It's something that is still important to us today,” he says.

Cooper's Ferry may also offer a glimpse of the tools carried by the first arrivals to the Americas. Many of the spearpoints found there belong to the western stemmed point tradition, smaller—about the size of a pinkie—and lighter than the hefty Clovis points. Such tools have been found at early sites from British Columbia to Peru, and as far inland as Texas. Similar points are known from Japan from about 16,000 to 13,000 years ago, Davis says. He and others argue that western stemmed points are emerging as the best markers of the first people to arrive in the Americas, and that they carried the tradition with them from Asia.

But Meltzer isn't convinced the western stemmed tradition conclusively predates Clovis or represents a coastal connection around the Pacific Rim. There are plenty of sites in Siberia in Russia without the technology, he says, and the complete points at Cooper's Ferry are almost the same age as Clovis. (The site's oldest tools are blades, bifaces, and fragments of points, fashioned with the same methods used to make western stemmed points.) Just as archaeology puts one debate about stone tools in the Americas to rest, it could be gearing up for the next one.

Wang, G., Li, S., Li, X., Zhao, W., Zhao, S., Suo, Y., Liu, X., Somerville, I., Liu, Y., Zhou, J., Wang, Z., 2019. Destruction effect on Meso-Neoproterozoic oil-gas traps derived from Meso-Cenozoic deformation in the North China Craton. Precambrian Research 333, 105427.


As the first extensively developed sedimentary cover in the North China Craton (NCC), the thick Meso- to Neoproterozoic strata have great exploration potential for hydrocarbons. However, the Meso-Cenozoic Indosinian, Yanshanian and Himalayan movements caused the Meso-Neoproterozoic strata in the NCC to experience various deformations and even destroyed Meso-Neoproterozoic primary oil-gas reservoirs, especially their trap conditions. Until now, how each Meso-Cenozoic tectonic movement influenced the development and evolution of Meso-Neoproterozoic oil-gas traps in different parts of the NCC has remained unclear. The Indosinian Movement caused Meso-Neoproterozoic rocks to undergo gentle folding, as well as limited thrusting, and mainly brought about the creation of contractional anticlinal traps in the NCC. In contrast, the early Yanshanian Movement mainly triggered their vertical movement and may have introduced some stratigraphic and faulted-related traps. The middle Yanshanian Movement led to the Meso-Neoproterozoic strata being involved in more intense differential folding, thrusting and strike-slip faulting in the western, central, and eastern NCC, at the cost of destroying the earlier-formed structures, especially those in the central-eastern NCC. Thus, the mid Yanshanian Movement showed both constructive and destructive effects on the formation and evolution of the Meso-Neoproterozoic oil-gas traps and made them develop incoherently in different parts of the NCC. The late Yanshanian and Himalayan movements did not affect the Meso-Neoproterozoic strata in the western NCC, but caused those in the middle NCC to be uplifted and eroded further, whilst strata in the eastern NCC became inverted, subsided and buried. As a consequence, it led to the continuous destruction of the Meso-Neoproterozoic structural-related traps for Meso-Neoproterozoic primary

hydrocarbons in the central-eastern NCC, and the formation of the Meso-Neoproterozoic buried-hill traps for Cenozoic hydrocarbons in the eastern NCC. Based on our structural analysis, it is suggested that the Meso-Neoproterozoic primary hydrocarbons could have accumulated in various Meso-Neoproterozoic structural-related traps with the overlying well-preserved Paleo-Mesozoic strata, especially, those in the southwest Ordos Basin. The promising Meso-Neoproterozoic buried-hill traps for Cenozoic hydrocarbons are mainly located in the western Bohai Bay Basin and the south part of the southern North China Basin.

Wang, K.J., O'Donnell, J.A., Longo, W.M., Amaral-Zettler, L., Li, G., Yao, Y., Huang, Y., 2019. Group I alkenones and Isochrysidales in the world’s largest maar lakes and their potential paleoclimate applications. Organic Geochemistry 138, 103924.


The Espenberg maar lakes on the Seward Peninsula, Alaska, are the largest volcanic crater lakes in the world and contain the longest known lacustrine sedimentary archives in Alaska. The lack of glacial-aged marine sedimentary archives around the Bering Land Bridge due to exposure of the shelf during sea level low-stands makes these lakes highly valuable for understanding the region’s past climate and environmental changes. Located en route to humanity’s last colonized American continents, the Seward Peninsula’s climate and environments during the last glacial period bear major anthropological significance. However, a lack of quantitative proxies has so far hampered exploration of these lakes for paleoclimate reconstructions. Here we report, for the first time, the discovery of abundant Group I alkenones and Isochrysidales in surface sediments from three maar lakes: White Fish, North Killeak and Devil Mountain, using a combination of lipid biomarker and 18S rRNA gene sequencing analyses. Our discovery adds to the expanding list of oligotrophic freshwater lakes where Group I alkenones are found, and water chemistry data contribute to the understanding of the environmental controls on Group I Isochrysidales. Our results further confirm the use of the U37K index of Group I alkenones as a proxy for the mean temperature of the spring isotherm (MTSI) and RIK37 as a quantitative measurement for Isochrysidales group mixing. We also demonstrate the analytical challenges for analyzing alkenones in freshwater lakes and the effectiveness of eliminating coelution using silver thiolate chromatographic material (AgTCM).

Wang, M.-j., Xiao, G.-l., Yang, C.-q., Yang, Y.-q., Chen, X., Huang, L., 2019. Characteristics and evaluation of Mesozoic source rocks in the southeastern East China Sea continental shelf. China Geology 2, 133-141.


Source rocks are the material basis of oil and gas generation and determine the potential resources of exploration blocks and have important research value. This paper studies the lithology, thickness, and geochemistry of Mesozoic source rocks in the southeastern East China Sea continental shelf. The results show that the Mesozoic source rocks are mainly dark mudstone and coal-bearing strata. The total thickness of Lower–Middle Jurassic source rocks ranges from 100 m to 700 m, and that of Lower Cretaceous source rocks ranges from 50 m to 350 m. The overall thickness of Mesozoic source rocks is distributed in the NE direction and their thickness center is located in the Jilong Depression. The Lower–Middle Jurassic source rocks are mainly developed shallow marine dark mudstone and transitional coal measure strata. Those of the Lower Cretaceous are mainly mudstone of a fan delta front. Lower–Middle Jurassic and Lower Cretaceous hydrocarbon source rocks are dominated by type III kerogen, with Lower–Middle Jurassic hydrocarbon source rocks having high organic matter abundance and being medium–good hydrocarbon source rocks, while Lower Cretaceous hydrocarbon source rocks have relatively poor quality. From northwest to southeast, the vitrinite reflectance Ro of Mesozoic source rocks increases gradually. Source rocks in the study area are divided into three types. The first hydrocarbon-generating area is mainly located in the southeastern region of the study area, and the Jilong Depression is the hydrocarbon-generating center. The results of this study can provide a basis for exploration of Mesozoic oil and gas resources in the southeastern East China Sea continental shelf. © 2019 China Geology Editorial Office.

Wang, Q., Huang, H., Li, Z., Li, Z., 2019. Novel thermal maturity parameters derived from alkylbiphenyls and alkyldiphenylmethanes. Energy & Fuels 33, 8491-8502.


A total of 13 Paleogene lacustrine source rocks from well LY1 in the Bohai Bay basin, East China, and 6 Carboniferous marine–continental transitional source rocks from well ZK5-1 in the Qaidam basin, Northwest China, have been analyzed by gas chromatography–mass spectrometry (GC–MS) to investigate the application of alkylbiphenyls and alkyldiphenylmethanes for maturity assessment. The Bohai Bay samples are marginally mature with vitrinite reflectance (Ro) values of below 0.8%, while the Qaidam samples are highly matured with Ro values of above 0.8%. In addition to validate some previous reported maturity parameters based on isomer distributions of methylbiphenyls and dimethylbiphenyls, several novel parameters based on isomer distributions, degree of alkylation, and compound types in alkylbiphenyls and alkyldiphenylmethanes have been provisionally proposed. These new parameters in the studied source rocks show good correlation with known maturity levels. Most maturity parameters are formed on the basis of relative stability of isomer substituent positions. Both meta and para substituents are confirmed to be more stable than ortho substituent counterparts, and various previously recognized maturity parameters, such as 3-/2-methylbiphenyl (MBP), 3,5-/2,5-dimethylbiphenyl (DMBP), and 3,4′-/(2,4- + 2,4′)-DMBP show linear correlation with measured Ro values. Noticeably, our limited data suggest that compounds with para substituents are even more stable than those with meta substituents, as evidenced by increasing ratios of 4-/3-MBP, 4-/3-EBP, 4,4′-/3,3′-DMBP, and 3,4′-/3,3′-DMBP with maturity levels. Ethylbiphenyl (EBP) seems less stable than the methylated isomer, and ratios of 4-MBP/4-EBP and 3-MBP/3-EBP can be used as potential maturity parameters. These two parameters are likely valid only at a high maturity range when the dealkylation process has been initiated. Diphenylmethane (DPM) and its alkylated homologues show overall lower thermal stability than alkylbiphenyls, and ratios of 4-MBP/4-MDPM and 3-MBP/3-MDPM increase with increasing maturity levels as well. The risk for this type of parameter is component concentration because concentrations of alkyldiphenylmethanes are usually below the minimal requirement for reliable parameter calculation. Nevertheless, a continuous increase of these novel parameters in data from the Bohai Bay and Qaidam basins may provide a powerful tool for maturity assessment of different maturated source rocks and oils in petroliferous basins, even though depositional facies may exert some impacts on the thermal evolution behavior of alkylbiphenyls and alkyldiphenylmethanes.

Wang, W., Liu, C., Zhang, D., Liu, W., Chen, L., Liu, W., 2019. Radioactive genesis of hydrogen gas under geological conditions: An experimental study. Acta Geologica Sinica - English Edition 93, 1125-1134.

https://doi.org/10.1111/1755-6724.14298

The coexistence of hydrogen‐containing materials and radioactive substances in source rocks is universal. Few documents have researched whether the latter can radiate the former to generate hydrogen gas (H2) as well as the factors controlling this process. This work conducted a series of radiation experiments to address this issue. Samples were placed in sealed Pyrex glass containers and subject to cobalt (60Co) γ irradiation and components and contents of resultant gases were analyzed using gas‐chromatography. The results show that all the samples released variable amounts of H2 after irradiation and that the yield (H2) of decane is lower than that of 3‐tetradecylthiophene but higher than that of distilled water, which implies that a weaker H‐X bond energy (X indicates O, C or other element) in homogeneous materials corresponds with increased yield (H2). The yields (H2) of samples decreased with the decreasing solutions concentrations in sequence from mixed salts solution, KCl solution, Yellow Sea water, oil field water, gypsum solution to distilled water. The experimental results also show that the yield (H2) of distilled water with montmorillonite is higher than that of distilled water with kaolinite, because due to the larger specific surface area, ion exchange capacity and more effective energy transfer effect of montmorillonite. Meanwhile, the irradiation of oxygen‐ and carbon‐containing materials also releases O2 and CH4. The production of H2 via the irradiation of hydrogen‐containing materials makes the involvement of exogenous H2 into hydrocarbon generation possible, which can enhance the hydrocarbon volume and optimize crude oil.

Wang, X., Bayon, G., Kim, J.-H., Lee, D.-H., Kim, D., Guéguen, B., Rouget, M.-L., Barrat, J.-A., Toffin, L., Feng, D., 2019. Trace element systematics in cold seep carbonates and associated lipid compounds. Chemical Geology 528, 119277.


Seeping of methane-rich fluids at submarine cold seeps drives intense microbial activity and precipitation of authigenic carbonates. Some trace elements play an important role in the biogeochemical processes operating at cold seeps, especially as specific enzymatic co-factors related to methanogenesis and the anaerobic oxidation of methane (AOM). However, it is unclear whether microbial trace metal utilization can be traced by the geochemical composition of seep carbonates. In this study, we analyzed a series of authigenic carbonate samples recovered from various seep settings worldwide and report for the first time trace element concentrations for total lipid fractions, combined with biomarker analyses and determination of elemental abundances in associated inorganic mineral phases (carbonate phases, sulfides, organic compounds and detrital fractions). Our results indicate marked enrichments of Co, Ni, Cu, Mo and W in the archaeal and bacterial lipids associated with authigenic carbonates, which can all be ascribed to previously identified enzymatic pathways. In addition to the microbial communities involved in AOM, which most likely control specific lipid-bound enrichments of Co, Ni, Mo and W in seep carbonates, Cu was found to display higher concentrations in the lipid fractions extracted from a few authigenic carbonate samples formed closer to the sediment-water interface, hence possibly related to the presence of aerobic methane-oxidizing bacterial assemblages in the near seafloor environment. While the above mentioned trace metals are relatively enriched in all studied inorganic and organic fractions, the very low W concentrations measured in carbonate phases, combined with their pronounced enrichment in associated lipid fractions and inferred microbial requirement, suggest that tungsten depletion in pore waters could possibly act as a limiting factor on AOM at cold seeps. Finally, two other trace elements (Li and Ti) also displayed particular enrichments in studied lipid fractions, which, despite no reported evidence, could possibly indicate that they are also involved as metalloenzymes in microbial methane oxidation processes at cold seeps.


https://doi.org/10.1111/1755-6724.13870

Kerogen plays an important role in shale gas adsorption, desorption and diffusion. Therefore, it is necessary to characterize the molecular structure of kerogen. In this study, four kerogen samples were isolated from the organic‐rich shale of the Longmaxi Formation. Raman spectroscopy was used to determine the maturity of these kerogen samples. High‐resolution transmission electron microscopy (HRTEM), 13C nuclear magnetic resonance (13C NMR), X‐ray diffraction (XRD) and Fourier transform infrared (FT‐IR) spectroscopy were conducted to characterize the molecular structure of the shale samples. The results demonstrate that VReqv of these kerogen samples vary from 2.3% to 2.8%, suggesting that all the kerogen samples are in the dry gas window. The macromolecular carbon skeleton of the Longmaxi Formation kerogen is mainly aromatic (fa'=0.56). In addition, the aromatic structural units are mainly composed of naphthalene (23%), anthracene (23%) and phenanthrene (29%). However, the aliphatic structure of the kerogen macromolecules is relatively low (fal

*+falH=0.08), which

is presumed to be distributed in the form of methyl and short aliphatic chains at the edge of the aromatic units. The oxygen‐containing functional groups in the macromolecules are mainly present in the form of carbonyl groups (fa

c=0.23) and hydroxyl groups or ether groups (falO=0.13). The crystallite structural parameters of

kerogen, including the stacking height (Lc=22.84 Å), average lateral size (La=29.29 Å) and interlayer spacing (d002=3.43 Å), are close to the aromatic structural parameters of anthracite or overmature kerogen. High‐resolution transmission electron microscopy reveals that the aromatic structure is well oriented, and more than 65% of the diffractive aromatic layers are concentrated in the main direction. Due to the continuous deep burial, the longer aliphatic chains and oxygen‐containing functional groups in the kerogen are substantially depleted. However, the ductility and stacking degree of the aromatic structure increases during thermal evolution. This study provides quantitative information on the molecular structure of kerogen samples based on multiple research methods, which may contribute to an improved understanding of the organic pores in black shale.

Wang, Y., Cao, J., Li, X., Zhang, J., Wang, Y., 2019. Cretaceous and Paleogene saline lacustrine source rocks discovered in the southern Junggar Basin, NW China. Journal of Asian Earth Sciences 185, 104019.


Saline lacustrine source rocks in China provide the resource basis for many giant oil fields. Here, we report the first discovery of such source rocks in the piedmont area of the northern Tianshan Mountains in the southern Junggar Basin of NW China. These source rocks are Cretaceous and Paleogene in age. Organic geochemistry and trace-element data suggest that these mudstones were formed in a brackish–saline lacustrine environment, characterized by deep-water and reducing conditions, and in a warm and dry paleoclimate. Evidence for this environment includes mudstone Pr/Ph values of <1.0, high gammacerane index ratios of >0.4, and negative Ce and Eu anomalies. The total organic carbon (TOC) contents of these Cretaceous and Paleogene mudstones are typically >0.5%, with maximum values of 1.45% and 2.22%, respectively, signifying moderate to high organic matter abundance. Rock-Eval and kerogen analyses suggest that the organic matter was dominated by type II kerogen. The mudstones are generally thermally mature, suggesting favorable conditions for hydrocarbon (particularly oil) generation. Oil–source correlation confirms the oil generation of these two sets of source rocks, whose development are controlled mainly by reducing environments. These Cretaceous and Paleogene mudstones should therefore be a target for regional exploration in the southern Junggar Basin in addition to the known gas-producing Jurassic rocks. This oil-bearing potential is unique amongst the Early Cretaceous and Eocene–Oligocene central Asian petroliferous basins, as the eastern portion of this realm is considered to host predominantly Jurassic coal-based source rocks, giving rise to numerous large gas fields rather than oil resources.

Wang, Y., Chen, J., Pang, X., Zhang, K., Shen, W., Chen, Z., Zhang, G., Luo, G., 2019. Analysis of Ordovician hydrocarbon migration in the Halahatang area, Tarim Basin, NW China. Carbonates and Evaporites 34, 1055-1075.

https://doi.org/10.1007/s13146-018-0465-7

Hydrocarbon migration mechanism in deep Ordovician reservoir of the Halahatang area, Tarim Basin, is investigated based on the analysis of the geological setting and geochemical parameters. The parameters successfully analyzed include oil–gas properties, crude oil maturity [Ts/(Ts + Tm) ratio], gas carbon isotopic ratios, and trace elements (B, V, Ni, and Cu) in crude oil. The results show that hydrocarbons migrate into the Ordovician of the Halahatang area from the Manjiaer Depression and the Halahatang area itself through unconformities and faults. The overall hydrocarbon migration orientation in the area is generally from south to north. The oil and gas migration process determine parameters vary regularly from south to north as follows: oil density, V/Ni ratio, Ni/Cu ratio, and concentrations of V, Ni and (Ni + B) in crude oil regularly increase, whereas Ts/(Ts + Tm), gas/oil ratio, and dryness coefficient gradually decrease, and methane show a trend toward depletion of heavy carbon isotopes. Additionally, there exist obvious anomalies of geochemical parameter values in the Repu3 well block, which indicates that a local fault intersection could provide a favorable hydrocarbon filling point. Based on these findings, further exploration activities in the deep Ordovician reservoir of the Halahatang area should be conducted in the southern part of the Halahatang area along the oil charging pathways, and fault intersection zones should be emphasized.

Weggler, B.A., Gruber, B., Dorman, F.L., 2019. Rapid screening of complex matrices: Utilizing Kendrick mass defect to enhance knowledge-based group type evaluation of multidimensional gas chromatography–high-resolution time-of-flight mass spectrometry data. Analytical Chemistry 91, 10949-10954.


Organic compound characterization of highly complex matrices involves scientific challenges, such as the diversity of “true” unknowns, the concentration ranges of various compound classes, and limited available amounts of sample. Therefore, discovery-based multidimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry (GC×GC-HRToFMS) is increasingly applied. Nevertheless, most studies focus on target analysis and tend to disregard important details of the sample composition. The

increased peak or separation capacity of GC×GC-ToFMS allows for in-depth chemical analysis of the molecular composition. However, high amounts of data, containing several thousands of compounds per experiment, are generally acquired during such analyses. Coupling GC×GC to high-resolution mass spectrometry further increases the amount of data and therefore requires advanced data reduction and mining techniques. Commonly, the main approach for the evaluation of GC×GC-HRToFMS data sets either focuses on the chromatographic separation (e.g., group type analysis), or utilizes exact mass data applying Kendrick mass defect analysis or van Krevelen plots. The presented approach integrates the accurate mass data and the chromatographic information by combining Kendrick mass defect information and knowledge-based rules. This combination allows for fast, visual data screening as well as quantitative estimation of the sample’s composition. Moreover, the resulting sample classification significantly reduces the number of variables, allowing distinct chemometric analysis in nontargeted studies, such as detailed hydrocarbon analyses and environmental and forensic investigations.

Wei, B., Jia, G., Hefter, J., Kang, M., Park, E., Mollenhauer, G., 2019. Comparison of the U37K', LDI, TEX86

H and RI-OH temperature proxies in the northern shelf of the South China Sea. Biogeosciences Discussions 2019, 1-26.


The temperature proxies U37K′, LDI, TEX86

H and RI-OH are derived from lipid biomarkers, namely long-chain alkenones from coccolithophorids, archaeal glycerol dialkyl glycerol tetraethers (GDGTs), long-chain diols ascribed tentatively to eustigmatophytes, and archaeal OH-GDGTs, respectively. The applicability of these proxies has been examined in the South China Sea (SCS), but most of these studies were focused on a single proxy and hence did not allow for a direct comparison between them. In this study, we investigated the above 4 proxies in the same set of surface sediment samples in the northern SCS shelf and related them to local sea surface temperature (SST), which allowed us to assess whether they represent certain seasons or are impaired by terrestrial influences, as well as to infer the preferred habitats of their source organisms. Terrestrial organic inputs appeared to have an impact on LDI, TEX86

H and RI-OH proxies near the coast and lead to colder LDI and TEX86

H derived temperatures, but a warmer RI-OH estimate in this region. After excluding samples influenced by terrestrial organic input, we found that LDI-derived temperature agreed well with annual SSTs, while U37

K′ reflected mainly spring SST and both TEX86

H and RI-OH indices were correlated with winter SST. The differential seasonal biases of these biomarker-derived temperatures observed here suggest that each biomarker’s source organism responds differently to regional marine environmental changes in an annual cycle. Specifically, marine eustigmatophytes are likely insensitive to nutrient variations and hence show the lowest seasonal variations, while coccolithophorids could have bloomed in late spring, when nutrient inputs by freshwater are usually highest. GDGT- and OH-GDGT-producing planktonic archaea likely thrive in winter, when conditions, such as relatively high nutrients levels, low light, and high concentrations of SPM in the upper water due to the enhancement of vertical mixing driven by a combination of surface cooling and strong winter monsoon winds, are favorable, although not clearly known.

Wei, Z., Wang, Y., Wang, G., Ma, X., He, W., Zhang, T., Yu, X., Zou, Y.-R., 2019. Isotopic composition of abiogenic gas produced in closed-system Fischer-Tropsch synthesis: Implications for the origins of the deep Songliao Basin gases in China. Geofluids 2019, 2823803.

https://doi.org/10.1155/2019/2823803

In this study, closed-system Fischer-Tropsch synthesis was conducted at 380°C and 30 MPa for 72 h with magnetite as a catalyst. The isotopic composition of the closed-system Fischer-Tropsch synthesis gas and the composition of known abiogenic gas were systematically studied, and the deep Songliao Basin gas was also investigated. The results show that closed-system Fischer-Tropsch synthesis of gaseous hydrocarbon isotopes exhibits a partial reverse order, which includes the reverse order of methane and ethane such as δ13C-C1>δ13C-C2<δ13C-C3 and δ2H-C1>δ2H-C2<δ2H-C3. Furthermore, experimental data on the control of NaBH4 content indicates that the carbon isotopes demonstrate a reverse order on condition that the H2/CO2 (mole ratio) is equal to or greater than 4.0; meanwhile, the hydrogen isotopes show a normal order. The deep Songliao Basin hydrocarbon gas component is similar to thermogenic gas and has a trend of a transition to oceanic

hydrothermal system abiogenic gas. In addition, the deep Songliao Basin gas isotopic pattern is different from both Lost City and Kidd Creek where the deep Basin gas carbon isotopic pattern has a reverse order, and the hydrogen isotopic pattern has a normal order. Therefore, the deep Basin gas might be a mixture of the oil-type gas and the coal-formed gas, which could be the cause of the isotopic reverse.

West, C., 2019. Recent trends in chiral supercritical fluid chromatography. TrAC Trends in Analytical Chemistry 120, 115648.


This paper presents a review of the recent literature covering separations of enantiomers achieved with supercritical fluid chromatography (SFC) or subcritical fluid chromatography. First of all, the recent progress in SFC technology are explained in relation to chiral separations. Mobile phases and operating conditions mostly encountered in current practise, instruments and stationary phases are discussed. Some elements related to fundamental studies are also given. While the pharmaceutical industry was long the principal user of chiral SFC for preparative purposes, it is now more and more in use for analytical purposes and especially pharmacokinetics. Other application fields are now emerging like the determination of different degradation rates in chiral agrochemicals, forensics, natural products and cosmetics. This review does not aim at being comprehensive but rather provides a global view of current practise of chiral resolution with SFC.

Wilkes, E.B., Pearson, A., 2019. A general model for carbon isotopes in red-lineage phytoplankton: Interplay between unidirectional processes and fractionation by RubisCO. Geochimica et Cosmochimica Acta 265, 163-181.


The carbon isotopic composition of organic matter preserved in marine sediments provides a window into the global carbon cycle through geologic time, including variations in atmospheric CO2 levels. Traditional models for interpreting isotope records of marine phytoplankton assume that these archives primarily reflect kinetic isotope discrimination by the carbon-fixing enzyme RubisCO. However, some in vivo and in vitro measurements appear to contradict this assumption, indicating that significant questions remain about the mechanistic underpinning of algal isotopic signatures, including the role of carbon concentrating mechanisms (CCMs). Here, we present a general model to explain photosynthetic carbon isotope fractionation (εP) in marine red-lineage phytoplankton groups; the model reproduces existing chemostat and batch culture datasets with a normalized root mean squared error (nRMSE) of 6.8%. Our framework proposes that a nutrient- and light-dependent step upstream of RubisCO is a kinetic barrier to carbon acquisition and therefore represents a significant source of isotopic fractionation. We suggest this step represents a carbon concentrating strategy that becomes favorable to cells under conditions of excess photon flux. The primary implications are that RubisCO is predicted to exert minimal isotopic control in photon-rich, nutrient-limited regimes but becomes influential as growth becomes light-limited. This framework enables both environment-specific and taxon-specific isotopic predictions. By refining the mechanistic understanding of marine photosynthetic carbon isotope fractionation, we may begin to reconcile existing datasets and reexamine Phanerozoic isotope records—including the resulting CO2 reconstructions—by emphasizing the influence of different types of resource limitation on photosynthetic carbon acquisition.

Wilson, S.T., Hawco, N.J., Armbrust, E.V., Barone, B., Björkman, K.M., Boysen, A.K., Burgos, M., Burrell, T.J., Casey, J.R., DeLong, E.F., Dugenne, M., Dutkiewicz, S., Dyhrman, S.T., Ferrón, S., Follows, M.J., Foreman, R.K., Funkey, C.P., Harke, M.J., Henke, B.A., Hill, C.N., Hynes, A.M., Ingalls, A.E., Jahn, O., Kelly, R.L., Knapp, A.N., Letelier, R.M., Ribalet, F., Shimabukuro, E.M., Tabata, R.K.S., Turk-Kubo, K.A., White, A.E., Zehr, J.P., John, S., Karl, D.M., 2019. Kīlauea lava fuels phytoplankton bloom in the North Pacific Ocean. Science 365, 1040-1044.


Abstract: From June to August 2018, the eruption of Kīlauea volcano on the island of Hawai‘i injected millions of cubic meters of molten lava into the nutrient-poor waters of the North Pacific Subtropical Gyre. The lava-impacted seawater was characterized by high concentrations of metals and nutrients that stimulated phytoplankton growth, resulting in an extensive plume of chlorophyll a that was detectable by satellite. Chemical and molecular evidence revealed that this biological response hinged on unexpectedly high concentrations of nitrate, despite the negligible quantities of nitrogen in basaltic lava. We hypothesize that the high nitrate was caused by buoyant plumes of nutrient-rich deep waters created by the substantial input of lava into the ocean. This large-scale ocean fertilization was therefore a unique perturbation event that revealed how marine ecosystems respond to exogenous inputs of nutrients.

Editor's Summary. Ocean greening off Hawai'i: From June to August 2018, the eruption of Kīlauea volcano triggered a diatom-dominated phytoplankton bloom. Wilson et al. set sail to sample the plume, deploying subsea gliders and using satellite monitoring to measure the dynamics of this rare event in the nutrient-poor Pacific (see the Perspective by Ducklow and Plank). They found subsurface chlorophyll maxima not visible by remote sensing, performed transcriptome and N isotope marker analysis, and measured nutrients, partitioning of biomass into different organisms, and primary production. Much of the data are corroborated by physical modeling of the ocean dynamics. The authors conclude that the plume was fed by the lava heating subsurface water and triggering upwelling of deepwater nutrients to the surface rather than by direct injection of micronutrients from lava.

Wu, D.-t., Ramaniraka, J.I., Xu, F.-m., Shao, J.-b., Zhou, Y.-h., Zhao, Y.-d., Ralison, B., 2019. Characteristics and potential analysis of Madagascar hydrocarbon-bearing basins. China Geology 2, 56-66.


ABSTRACT Madagascar becomes a large isolated island after its dislocation from East Africa at its western part during the opening of the Mozambique Channel and its separation from India at its eastern part during the opening of the basin of the Mascarene. From a stratigraphic point of view, Karroo of Madagascar shares substantial similarities with the stratigraphic strata of East Africa. While oil companies have taken a liking to the basins of East Africa, they also turn to the basins in the western part of Madagascar especially after the discovery of large oil fields at Tsimiroro and Bemolanga. According to the study of their geological history, the basins of Madagascar contain huge hydrocarbon potential. The western basins, which is more developed than the east coast of the island, have been the subject of many in-depth studies by numerous researchers. The cross-referencing of bibliographic data with geological studies, and knowledge of hydrocarbon formation and maturation stages, carried out in this study served to determine the nature of source rocks, reservoir rocks, bedrock and eventual trapping system of hydrocarbons in Madagascar. This study identified the properties of Madagascar source rocks, reservoir rocks, bedrock and the final oil and gas trap system by cross-referencing the literature and geological research, oil and gas formation and maturity stages, and shows that Madagascar has considerable hydrocarbon potential. ©2019 China Geology Editorial Office.


https://doi.org/10.1111/1755-6724.13860

A key target of shale gas exploration and production in China is the organic-rich black shale of the Wufeng Formation-Longmaxi Formation in the Sichuan Basin and its periphery. The set of black shale contains abundant graptolites, which are mainly preserved as flattened rhabdosomes with carbonized periderms, is an important organic component of the shale. However, few previous studies had focused on the organic matter (OM) which is derived from graptolite and its pore structure. In particular, the contributions of graptolites to gas generation, storage, and flow have not yet been examined. In this study, focused ion beam-scanning electron microscope (FIB-SEM) was used to investigate the characteristics of the graptolite-derived OM and the micro-nanopores of graptolite periderms. The results suggested that the proportion of OM in the graptolite was between 19.7% and 30.2%, and between 8.9% and 14.4% in the surrounding rock. The total organic carbon

(TOC) content of the graptolite was found to be higher than that of the surrounding rock, which indicated that the graptolite played a significant role in the dispersed organic matter. Four types of pores were developed in the graptolite periderm, including organic gas pores, pyrite moulage pores, authigenic quartz moldic pores, and microfractures. These well-developed micro-nano pores and fractures had formed an interconnected system within the graptolites which provided storage spaces for shale gas. The stacked layers and large accumulation of graptolites resulted in lamellation fractures openning easily, and provided effective pathways for the gas flow. A few nanoscale gas pores were observed in the graptolite-derived OM, with surface porosity lie in 1.5%?2.4%, and pore diameters of 5?20 nm. The sapropel detritus was determined to be rich in nanometer-sized pores with surface porosity of 3.1%?6.2%, and pore diameters of 20?80 nm. Due to the small amount of hydrocarbon generation of the graptolite, supporting the overlying pressure was difficult, which caused the pores to become compacted or collapsed.

Wu, Q., Xu, Y., Ji, H., Wang, Y., Zhang, Z., Lu, H., 2019. Enhancing coverage in LC–MS-based untargeted metabolomics by a new sample preparation procedure using mixed-mode solid-phase extraction and two derivatizations. Analytical and Bioanalytical Chemistry 411, 6189-6202.

https://doi.org/10.1007/s00216-019-02010-x

It is a challenge to expand the metabolome coverage of liquid chromatography (LC)–electrospray ionization (ESI) mass spectrometry (MS) based untargeted metabolomics analysis. The limited coverage is attributed to the weak signal of hydroxyl and carboxyl groups in ESI-MS and the limited capacity of LC separation for metabolites with a wide range of polarities. Here a new sample preparation procedure is proposed to solve these problems. Mixed-mode (reversed-phase and anion-exchange) solid-phase extraction sorbents were used to separate metabolites into hydrophilic amine, hydrophobic amine/alcohol, and organic acid groups. Then, alcohols and carboxylic acids in separated groups were tagged with pyridine with use of two derivatization systems for signal enhancement. Finally, hydrophilic amines were analyzed by LC–MS with a hydrophilic interaction LC column, and the two hydrophobic compound groups were analyzed by LC–MS with a C18 column. From the results for standard samples, the detection limits of the new method are lower than those of the classic solvent extraction–protein precipitation method by 3.3–70 times for five amino acids and by 65–1141 times for five fatty acids. Moreover, the detection limit of this new method is 125 ng mL-1 for cholesterol, which has no signal with the classic method even at 10 μg mL-1. In seminal plasma samples, 110 more metabolites were identified by this new method than by the traditional solvent extraction–protein precipitation method in positive-mode ESI (new method vs traditional method, 65 vs 22 identified by comparing MS/MS spectra with those of standards, 203 vs 136 identified by searching MS spectra in a published database). Among them, 53 carboxylic acids and 21 alcohols were identified only by the new method, and more hydrophilic amine metabolites, such as amino acids and nucleosides, were identified by the new method than by the classic method. Finally, in application to the study of male infertility, more potential biomarkers of oligoasthenoteratospermic infertility were found with the new method (46 potential biomarkers) than with the classic method (19 potential biomarkers) and previously reported methods (10–30 potential biomarkers). Thus, it is demonstrated that this new sample preparation method expands the detection coverage of LC–MS-based untargeted metabolomics methods and has application potential in biological research.



To investigate the adsorption characteristics and mechanisms of coal–microorganisms in the process of biogenic methane production from coal, simulation experiments of biogas production were conducted under suitable environmental conditions (initial pH = 7 and constant temperature at 35 °C) using highly volatile bituminous coal from China’s Yima coalfield. The microbial adsorption characteristics, organic liquid products, coal wettability, and adsorption heat were measured using scanning election microscopy, gas chromatography–mass spectrometry, contact angle measurement, and micro-calorimetry, respectively, to reveal the adsorption

characteristics of the coal and its interaction mechanisms with microorganisms. The results show the following: (1) The microbial adsorption capacity changed as fermentation time varied and the maximum values of optical density (at 600 nm) and RNA were 0.122 and 1772.73 μg, respectively, and occurred at 9 d. (2) The contact angle of the coal surface was <90° during the experiments, and the coal wettability reached its maximum on day 9 of heat production. (3) There was correspondence between the exothermic process and production of intermediate liquid products, and the content of small organic molecules was more and the heat output was higher. (4) The generation of gas products differed remarkably as adsorption capacity and adsorption heat during the reactions varied. The maximum methane production and adsorption heat values were, respectively, 1.849 mL/g (at 19 d) and 306.031 J/g (at 9 d). The adsorption heat showed a variable trend (first decreasing, then increasing, decreasing again, and finally increasing), but all phases resulted from an exothermic reaction. This research provides a reference for understanding the biogas production pathway, the degradation mechanism, and the improvement of biogas-producing efficiency as microorganisms degrade coal, and enhances knowledge about the potential concentrations of target products. The study further enriches the theory of biogenic gas production from coal.

Xia, F., Feng, R., Xu, F.-G., Su, H., He, C., Hu, Y.-J., Wan, J.-B., 2019. Quantification of phospholipid fatty acids by chemical isotope labeling coupled with atmospheric pressure gas chromatography quadrupole- time-of-flight mass spectrometry (APGC/Q-TOF MS). Analytica Chimica Acta 1082, 86-97.


Phospholipid fatty acids play the crucial role in biophysical properties and the function of cellular membranes. In the present study, an accurate and sensitive method was developed to quantify phospholipid fatty acids in biological samples by using chemical isotope labeling coupled with atmospheric pressure gas chromatography quadrupole-time-of-flight mass spectrometry (APGC/Q-TOF MS). APGC, a soft ionization source, was operated under proton-transfer condition by introducing methanol into the ionization source as a modifier, which provided high quantifiable molecular ion peaks to substantially enhance the sensitivity. Fatty acid standards were methylated with methanol-d4 to yield FAMEs-d3 that were used as one-to-one internal standards to ensure accurate quantification. Thirty fatty acids in phospholipids were accurately quantified in wide linear range with limit of quantification ranging from 84.6 to 113.2 pg/mL. The newly developed method was successfully applied to quantify phospholipid fatty acids in brain and liver tissues from both fat-1 and WT mice. This method might be expanded to quantify free fatty acids or other conjugated fatty acids in biological samples or other matrices.

Xie, T., Zhang, Q., Hu, S., Zhou, C., Huang, J., Wen, W., 2019. The Mesozoic maximum of 87Sr/86Sr ratio: a critical turning point after the end-Permian mass extinction. Carbonates and Evaporites 34, 1021-1029.

https://doi.org/10.1007/s13146-018-0475-5

The secular change in 87Sr/86Sr ratio of the Mesozoic recorded the highest value above 0.7083 in Early–Middle Triassic boundary, i.e., the Triassic maximum, suggesting that a major reform in oceanography occurred after the end-Permian mass extinction. We have detected correlative highest 87Sr/86Sr value from the Triassic carbonate, including our data. The stratigraphic horizon of the maximum was constrained to the Olenekian–Anisian boundary (OAB) (247.2 Ma), by conodont. As the oceanic data represent the global average, the present study confirmed the chemostratigraphical utility of the “Triassic maximum” of 87Sr/86Sr ratio in global correlation. After the sharp rise throughout Early Triassic since the end-Permian mass extinction, a remarkable turnover of seawater-87Sr/86Sr values appeared in the OAB. A major global change likely appeared in the OAB to change the Sr-isotope balance in seawater from a continental flux-dominated to a mantle flux-dominated regime. The sharp turning point in 87Sr/86Sr values likely has recorded the timing of the biological influence on the environment.

Xin, C., Chen, L., Guo, X., Wang, C., 2019. Geochemical characteristics of shale gas in the Silurian Longmaxi Formation, Jiaoshiba area, southeast Sichuan Basin, China. Energy & Fuels 33, 8045-8054.


On the basis of geochemistry tests, in combination with comparative studies of the Weiyuan-Changning shale gas field in the south Sichuan Basin and typical shale gas fields in North America (such as Barnett and Fayetteville), the geochemical characteristics of the Lower Silurian shale gas in the Jiaoshiba area were studied. The results show that (1) the average RO value of Longmaxi shale in Jiaoshiba area is about 2.65%, which is at the dry gas stage. The content of CH4ranges from 94.02% to 98.95%, and the contents of ethane and propane are lower. The weight anomaly average values of δ(13C1) and δ(13C2) are −30.18‰ and −35.45‰, respectively. (2) Non-hydrocarbon gases are dominated by CO2 and N2. The CO2 in the Longmaxi shale gas in the Jiaoshiba has three origins: the thermogenic CO2, the abiogenic CO2, and the biogenic CO2. The N2 in the Longmaxi shale gas comes from the released N2 during the thermal evolution process of sedimentary organic matter under the control of maturity and kerogen type. (3) The natural gas genetic type discriminating signs and plates indicate that the shale gas in the Jiaoshiba area belongs to an organic pyrolysis oil type gas at high temperature. (4) With an increasing degree of thermal evolution, the wetness of the shale gas decreases gradually, the carbon isotopic composition of methane becomes heavier, and the carbon isotopic composition of ethane and propane will reverse. In the Jiaoshiba, a complete reversal phenomenon of carbon isotopes (δ(13C1) > δ(13C2) > δ(13C3)) is caused by the reaction among water, ferrous metals, and hydrocarbon gas which was mainly generated from the mixed gas caused during the secondary cracking, wet gas cracking, and Rayleigh fractionation at the high formation temperature.

Xiong, P., Lu, H., Xie, X., Zhang, G., Fu, S., Jiang, L., Zhang, P., 2020. Geochemical responses and implications for gas hydrate accumulation: Case study from site SHC in Shenhu Area within northern South China Sea. Marine and Petroleum Geology 111, 650-661.


A knowledge of gas hydrates is critical for understanding complex geological, geophysical, and biogeochemical processes and for explaining the proposed link between gas hydrate destabilization and global sea level changes. With the aim of discussing the geochemical characteristics and implications for gas hydrate accumulation, this study assesses the changes in a series of organic and inorganic geochemical gas hydrate-bearing sediments within a core section obtained at site SHC in the Shenhu Area of the northern South China Sea that range from the Late Miocene to the present. High S/C ratios (0.53–5.6) and low TOC contents (<0.5%) suggest that strong ancient anaerobic oxidation of methane (AOM) occurred in sediments between 96 mbsf and 182 mbsf at site SHC. Therefore, the high total inorganic carbon (TIC) content (with a peak value of 47%) in sediments close to the gas hydrates-bearing sediment zone (GHBSZ) can be partially attributed to the AOM, and this also provides a reasonable explanation for the high concentrations of captured acid-extraction CH4 (58.38–576.1 μl/g) in the samples. The relatively lower 13C values (−4.10‰ to −1.69‰) in the carbonate indicate that the contribution of dissolve inorganic carbon is partially from methanogenesis gas within the GHBSZ. However, the relatively higher values of δ 18O, as well as the inverse correlation between values of the δ 18O and the δ 13C observed in the GHBSZ, likely suggest a dissociation event of gas hydrates. These features are effective for indicating the presence of AOM in ancient times and implicate the formation of authigenic carbonates in sediments. The high value of authigenic carbonates by the AOM overly the GHBSZ in sediments, which implies the authigenic carbonate may have played an important role in the accumulation and sealing of gas hydrates at the SHC site. The relatively high contents of branched glycerol dialkyl glycerol tetraethers (B-GDGTs) and the relatively high values of the BIT index in the GHBSZ at SHC site are consistent with an increase in terrestrial source inputs which are marked by fine sands and silty deposits. These features also coincide with the change trend in the TOC/TN ratio and δ 13C org value, which imply an increase in terrestrial organic mass. Such significant paleoenvironment change is consistent with the results of previous studies based on sediment cores and seismic reflection data. It is thus suggested that those proxies are related to a relative sea level fall caused by the global “Messina carbon shift” in the South China Sea. Such geochemical imprints not only reveal that the ancient AOM played an important role in the formation of the reservoir-cap assemblage, but also suggest that reservoir generation at SHC site is related to a relative sea level change. We propose that the formation of authigenic carbonates and their sealing effect should be considered when studying gas hydrate accumulation mechanisms.

Xu, L., Shi, Y., Chen, X., Wan, C., Wang, J., 2019. Kinetic analysis of hydrocarbon generation based on saline lacustrine source rock and kerogen samples in the western Qaidam Basin, China. Carbonates and Evaporites 34, 1045-1053.

https://doi.org/10.1007/s13146-018-0462-x

Tertiary carbonate rocks from the Qaidam Basin in China are typical plateau saline lacustrine source rocks. Despite the fact that this set of source rocks has a relatively low abundance of organic matter (major frequency of total organic carbon, 0.4–0.6%), the organic matter has a high hydrocarbon conversion rate and commonly forms low-maturity oil. In this study, a comparative analysis was conducted on Tertiary source rock and kerogen samples from the Qaidam Basin using a kinetic experiment of hydrocarbon generation. The objectives of the study were to investigate the mechanism of hydrocarbon generation from source rock to low-maturity oil and the catalysis of kerogen pyrolysis by minerals. The results showed that both the source rock and kerogen samples reached a maximum liquid hydrocarbon yield during the low-maturity stage. Eighty percent of the hydrocarbons were expulsed before the Easy Ro reached 0.8%. Special algal parent materials in the saline lacustrine basin could be the primary cause that leads to generating low-maturity oil. Compared to the kerogen samples, the source rock was more prone to hydrocarbon generation via pyrolysis. The latter had a higher liquid hydrocarbon yield per unit organic matter and a lower activation energy; thus, it entered the hydrocarbon generation threshold earlier. The key factor for the aforementioned differences might be catalysis by minerals (particularly carbonate minerals) and the presence of soluble organic matter in the source rocks.



Majiagou Formation of the Lower Paleozoic in Ordos Basin is divided into three assemblages by the degree of exploration:the upper, middle and lower assemblage, respectively corresponding to the 1-4 sub-members of the 5th Member of Majiagou Formation(the upper assemblage), the 5-10 sub-members of the 5th Member of Majiagou Formation(the middle assemblage) and the 4th to the 1st Member of Majiagou Formation(the bottom assemblage). To explore the characteristics of natural gas source in the middle assemblage, this study carries out natural gas genetic identification, source rock evaluation and researches on the natural gas components, isotopes and fluid inclusions, as well as a comparative analysis with natural gas in the Upper Paleozoic and Ordovician weathering crust. The results show that:(1) In terms of composition characteristics and isotopic characteristics, the inner-type natural gas in the middle assemblage of Ordovician is different from the natural gas in the Upper Paleozoic Carboniferous-Permian and weathering crust. Through identifying based on the natural gas component data and previous experimental plates, it is believed that crude oil cracking gas exists in the internally-developed natural gas from the Ordovician middle assemblage. (2) The bitumen internally developed in the Ordovician is the thermal cracking product of liquid hydrocarbons formed in the inner source rocks. (3) Controlled by the tidal flat sedimentary system, the typical source rock stratum of the middle assemblage (the 6th sub-member of the 5th Member of Majiagou Formation) can be divided into three facies belts:argillaceous dolomitic flat belt, gypsum-containing slope, and gypsum-salt depression. (4) Source rocks in the 6th sub-member of the 5th Member of Majiagou Formation are mainly distributed in the argillaceous dolomitic flat belt, with a cumulative thickness of 8-20 m; the organic matter abundance is up to 1.75%, and Ro is 1.9% -2.7%. In the stage of thermal cracking and generation, there is a potential for hydrocarbon supply in a large scale. (5) The argillaceous dolomitic flat belt and gypsum-containing slope indicate the favorable exploration direction, and the eastern part of Wushenqi, northwest of Jingbian and Wuqi-Zhitan area are three favorable exploration zones.

Xue, C., Zhong, J., Hou, M., Li, F., Peng, C., 2019. Sedimentary facies distribution and the characteristics of transitional shale in the upper Palaeozoic in northeast Ordos basin, China. Arabian Journal of Geosciences 12, 530.

https://doi.org/10.1007/s12517-019-4669-5

The Taiyuan formation that was formed in the late Permian period of the upper Palaeozoic in the Linxing area, north-eastern of Ordos basin, China, shows the marine and continental interdepositional systems, as well as the resource potential of shale gas. Through a field outcrop, core observation, and well logging data, the Taiyuan formation can be divided into Tai1 (p1t1) and Tai2 formations (p1t2). The main depositional environments of the region in Taiyuan formation included tidal flats, swamp, and lagoon which is also a good depositional environment for high-quality shale development. During the Taiyuan formation period, the sedimentary sea level in the study area rose and fell frequently, and the barrier coastal sedimentary system is mainly developed. In addition, the shale has superior development characteristics: The Taiyuan formation shale has a considerable amount of material, with an accumulated thickness of greater than 30 m; the average organic carbon content in the Taiyuan group is 3.34%, and the content in the Tai2 formation (p1t2) is slightly higher than in the Tai1 formation (p1t1); a high thermal evolution content is developed with an average vitrinite reflectance (Ro) of 1.33%; the Kerogen type is the III model, in which gases are mainly developed; the brittle mineral content in the rock mineral components is high, and the brittleness index is generally greater than 50%, which indicates a high rate of compressibility. Therefore, the Taiyuan formation indicates a marine and continental interdeposition and has a high exploration and development potential for shale gas.

Yan, K., Zuo, Y., Yang, M., Zhou, Y., Zhang, Y., Wang, C., Song, R., Feng, R., Feng, Y., 2019. Kerogen pyrolysis experiment and hydrocarbon generation kinetics in the Dongpu depression, Bohai Bay Basin, China. Energy & Fuels 33, 8511-8521.


Recently, petroleum exploration of the Dongpu depression has become increasingly difficult, primarily because of the unclear potential and distribution of deep strata resources (specifically, the Shahejie 3 formation). A pyrolysis experiment and hydrocarbon generation kinetics can provide important parameters for hydrocarbon generation history and resource re-evaluation. Therefore, four samples of the Dongpu depression were selected for a kerogen pyrolysis experiment, and the software KINETICS 2000 was used to calculate the pre-exponential factors (A) of different components and the activation energies (E) of the reactants to further establish the kinetic parameters of different kerogens in the Dongpu depression. The hydrocarbon generation history of the sample was determined using the software BasinMod 1D based on thermal and burial histories, and the hydrocarbon generation characteristics of different sags and different types of kerogen were studied. The results show that the hydrocarbon generation potential in the northern Dongpu depression is stronger than that in the south. Moreover, the activation energy (E) distribution of type I kerogen (Well W146) is widest, followed by type II1 (Well C9) and type II2 kerogens (Well H88); and type III kerogen (Well X8) is the most concentrated. Moreover, the potential for hydrocarbon generation in the Qianliyuan the Haitongji–Liutun areas is high.

Yan, X., Dai, S., Graham, I.T., French, D., Hower, J.C., 2019. Mineralogy and geochemistry of the Palaeogene low-rank coal from the Baise Coalfield, Guangxi Province, China. International Journal of Coal Geology 214, 103282.


Some previous studies have investigated the enrichment origin of Sb and Cs in coal, but strong supportive evidence for the sources of the two elements in coal is still absent. The main aims of this study were to provide a better understanding of the geochemical and mineralogical characteristics of the Palaeogene No. 5 Coal from the Zhoujing coal mine, Baise Coalfield, Guangxi Province, southwestern China. The No. 5 Coal has a low rank (0.44% Ro,max; 46.96% volatile matter content), an average ash yield 19.37%, and a medium sulfur content (1.23% on average). The main minerals in the No. 5 Coal are kaolinite, illite, quartz, and pyrite. Bassanite (2CaSO4•(H2O)) was identified in the low-temperature ashes in varying proportions (2.7% - 37.6%). The mineralogy of the non-coal samples (partings, roof and floor strata) is similar to that of the coals but chlorite is additionally present and pyrite is largely absent in these non-coal samples. The modes of calcite occurrence in the partings indicates a terrigenous origin for this phase.

Compared with average values for world low-rank coals, the No. 5 Coal is distinctively enriched in Sb (29.12 μg/g), Cs (9.71 μg/g), and U (15.61 μg/g). Compared with the average values for world clays, the parting

and host rock samples have normal concentrations for most trace elements, with an exception of higher Sb (9.93 μg/g). The elevated Sb and Cs in the coal were derived from the detrital material shedding from the exposed middle Triassic strata, which host notable Au and Sb deposits in the surrounding region. The REY (rare earth elements and Y) distribution patterns for the coal benches, partings, roof and floor strata are generally characterized by enrichment in medium REY and positive Gd anomalies, both of which were due to acidic waters circulating within the coal basin. The mineral compositions and their association indicate that the depositional environment was weakly acidic at the early stage of peat accumulation and then changed to neutral or weakly alkaline in the later stage.



Marine-continental transitional (hereinafter referred to as transitional) Permian shales are the important targets for shale gas in China. However, the nature and formation of organic matter (OM)-hosted pores in this shale facies have not yet been studied in detail from the perspectives of organic petrology and geochemistry. In this paper, we selected typical transitional shale samples from the Permian Longtan Formation in the northwestern Guizhou province to investigate the development of OM-hosted pores mainly through organic petrographic analysis, gas adsorption, and X-ray diffraction (XRD) measurements. Petrographic observations under an optical microscope and a scanning electron microscope (SEM) reveal that the OM in the Longtan shale is composed predominantly of type III kerogens (vitrinite and inertinite), with minor amounts of amorphous solid bitumen. SEM imaging reveals that secondary OM pores (as a result of devolatilization of gaseous hydrocarbons) were very rare in Longtan shale, being only occasionally observed in individual type III kerogens with a bubble-like morphology. This phenomenon is most likely attributed to the chemical-inert body of type III kerogens that cannot depolymerize during thermal degradation. On the other hand, the high methane adsorption values and their strong linear correlation with total organic carbon contents in the Longtan shale indicate that the type III kerogens contain numerous SEM-invisible micropores (<2 nm). By virtue of the combined N2 and CO2 adsorption on the type III kerogens separated from the bulk Longtan shale, we demonstrated the existence of SEM-invisible OM micropores (distributed at 0.34–0.36 nm) and quantified their contribution to the surface area and pore volume of OM as 87 and 13%, respectively. XRD further correlated these micropores to the spacing between the aromatic rings of type III kerogens. As such, the interlayer pores distributed among the aromatic rings are responsible for the sorptive capacity of type III kerogens and the bulk Longtan shale. Overall, the revelation of OM-hosted pores in the transitional shales provides a further understanding of shale gas generation and its occurrence in China.

Yao, J., Xiao, Z., Liu, G., Han, M., 2019. Source of crude oil in Chang-8 member of Wuqi oil-field, Ordos Basin, China. Petroleum Science and Technology 37, 2288-2294.

https://doi.org/10.1080/10916466.2019.1646282

There are three sets of source rocks in the lower assemblage of Yanchang formation in Wuqi area of Ordos Basin, and the source of Chang-8 crude oil is unknown. Through analysis of geochemical indexes of Chang-7, Chang-8, and Chang-9 source rocks and Chang-8 reservoir extracts, it is found that the relative abundance of δ13C, Pr/Ph and hopanoid compounds (C30H-C30DiaH-Ts) can well distinguish between them. The oil-source correlation results show that the geochemical characteristics of Chang-8 reservoir extracts is more similar to that of Chang-7 source rocks, indicating that Chang-8 crude oil is supplied by Chang-7 source rocks.



China is undergoing unprecedented rapid urbanization, which is accompanied by the formation of more than 2000 black and odorous urban rivers. Dissolved organic matter (DOM) is an essential component in aquatic ecosystems and regulates the carbon and nutrient cycle, but its characteristics in highly polluted urban rivers are still not well understood. Here, water samples from the mainstream, tributaries, ponds, and reservoirs within the highly urbanized Maozhou River watershed (Shenzhen, China) were analyzed using absorption and fluorescence spectroscopy, stable carbon isotope analysis, and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to explore the impact of urbanization on DOM characteristics. The results showed elevated dissolved organic carbon concentrations in the disturbed waters (mainstream, tributary, and pond) compared to those in the reservoir water. Results of the spectroscopic, isotopic, and FT-ICR MS analyses suggest that disturbed water DOM had lower aromaticity, average molecular weight, and plant- and soil-derived terrestrial (e.g., lignin-like) contributions but greater contributions from microbial-derived protein-like and anthropogenic sulfur-containing compounds (e.g., synthetic surfactants) than those of reservoir DOM. These characteristics were strengthened from the upper to the lower mainstream, which implies greater anthropogenic impact on downstream waters. Point-source wastewater effluent input caused increases in DOM level in the mainstream water and abrupt changes in DOM characteristics with very strong anthropogenic characteristics. The distinct chemistry of urban DOM from natural organic matter highlights a potentially strong impact of rapid urbanization on carbon and nutrient cycle in aquatic ecosystems.

Yin, J., Guo, L., Meng, J., Hao, F., Chen, X., Cao, Y., Zou, H., 2019. Environmental reconstruction and formation mechanisms for lacustrine source rocks of the third member of the Shahejie Formation in the Raoyang Sag, Bohai Bay Basin, eastern China. Australian Journal of Earth Sciences 66, 1145-1162.

https://doi.org/10.1080/08120099.2019.1611662

The third (Es3) member of the Eocene Shahejie Formation is the main hydrocarbon source rock interval in the Raoyang Sag of the Bohai Bay Basin. The lower Es3 (Es3

L) and upper Es3 (Es3U) submembers display clear

differences in source rock quality. The formation mechanisms of the source rocks are investigated via geochemical methods using 60 samples from three wells to reconstruct the paleo-environment during deposition. The major element parameters exhibit changes in paleoclimate from humid to arid. Indicators such as Sr/Ba, B/Ga, the gammacerane index and isotopic data suggest fresh–brackish and hydrological open lakes with unstable water column stratification likely occurred during deposition of the Es3

L submember and saline and hydrologically closed lakes with stable water column stratification likely during deposition of the Es3

U submember. Carbon isotope values of organic matter, trace elements and biomarker parameters suggest that the Es3

L submember had moderate productivity, with a significant contribution from terrigenous organic matter whereas the Es3

U submember had slightly enhanced productivity, with no or minor contributions from terrigenous organic matter. Furthermore, the pristane/phytane ratio and the enrichment of Mo and U indicate that the euxinic bottom-water conditions (sulfidic) of the lakes during deposition of the Es3

U submember were best for preserving organic matter. Comparison of the models of source rock deposition of the Es3

L and Es3U

submembers indicates that the redox conditions play an important role in the formation of organic-rich source rocks in the Raoyang Sag.

Yin, Y., Wang, R., Cai, Y., Wang, Z., Zhu, Z.-J., 2019. DecoMetDIA: Deconvolution of multiplexed MS/MS spectra for metabolite identification in SWATH-MS-based untargeted metabolomics. Analytical Chemistry 91, 11897-11904.


SWATH-MS-based data-independent acquisition mass spectrometry (DIA-MS) technology has been recently developed for untargeted metabolomics due to its capability to acquire all MS2 spectra with high quantitative accuracy. However, software tools for deconvolving multiplexed MS/MS spectra from SWATH-MS with high efficiency and high quality are still lacking in untargeted metabolomics. Here, we developed a new software tool, namely, DecoMetDIA, to deconvolve multiplexed MS/MS spectra for metabolite identification and support the SWATH-based untargeted metabolomics. In DecoMetDIA, multiple model peaks are selected to model the coeluted and unresolved chromatographic peaks of fragment ions in multiplexed spectra and

decompose them into a linear combination of the model peaks. DecoMetDIA enabled us to reconstruct the MS2 spectra of metabolites from a variety of different biological samples with high coverages. We also demonstrated that the deconvolved MS2 spectra from DecoMetDIA were of high accuracy through comparison to the experimental MS2 spectra from data-dependent acquisition (DDA). Finally, about 90% of deconvolved MS2 spectra in various biological samples were successfully annotated using software tools such as MetDNA and Sirius. The results demonstrated that the deconvolved MS2 spectra obtained from DecoMetDIA were accurate and valid for metabolite identification and structural elucidation. The comparison of DecoMetDIA to other deconvolution software such as MS-DIAL demonstrated that it performs very well for small polar metabolites. DecoMetDIA software is freely available at https://github.com/ZhuMSLab/DecoMetDIA.

Yu, K., Qiu, L., Cao, Y., Sun, P., Qu, C., Yang, Y., 2019. Hydrothermal origin of early Permian saddle dolomites in the Junggar Basin, NW China. Journal of Asian Earth Sciences 184, 103990.


Hydrothermal-related saddle dolomites widely exist in the lower Permian Fengcheng Formation in the northwestern Junggar Basin, and this formation is a set of carbonate-rich deposits in an alkaline saline basin. Core and thin section observations, cathodoluminescence (CL) imaging, and carbon and oxygen isotope composition analyses have been used to study the origins of saddle dolomites with various occurrences. Hydrothermal fluids include Si-rich and Si-poor fluids, and saddle dolomites occur, along with siliceous bands, as debris and assemblages in fragmented rocks and as cements filling pores and microfractures. Different types of dolomites in the Fengcheng Formation have similar δ13C values, while the δ18O values differed from each other, which demonstrated that the dolomites originated from the same primary carbonates and underwent multiple stages of recrystallization. The δ18O values were extremely negative, which was caused by fractionation at high temperatures from hydrothermal fluids. Dolomites are directly or indirectly affected by hydrothermal diagenetic fluids. According to the diagenetic stages, the types of migration paths for hydrothermal fluids, and the patterns of hydrothermal fluids acting on the dolomites, a model was proposed to illustrate the origins and evolution of the dolomites, and three paths were utilized. Path I occurred during the contemporaneous diagenetic stage, when the carbonate particles were still free and could be captured by high-density bottom hydrothermal flows and distorted. Path II occurred during the long diagenetic history after the carbonate-bearing sediments had consolidated. Saddle dolomite assemblages and saddle dolomite debris occurred with the aid of compressive tectonic forces. Path III also occurred in the long diagenetic history, and the host rocks were not fragmented. The saddle dolomites reprecipitated as cements in the pores, stylolites, fractures/microfractures or laminated seams.



The aim of this work was to study the molecular compositional changes of dissolved organic matter (DOM) during hyperthermophilic composting (HTC) using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry. Our results reveal that DOM in hyperthermophilic compost mainly consisted of lignins/carboxylic-rich alicyclic molecules (72%) with relatively lower H/C (1.24), and the higher double bound equivalent (5.98) and aromaticity index (0.22) when compared with the DOM in composting materials, suggesting that HTC led to an increase in carboxyl-rich, unsaturated, and aromatic compounds. Profiles of the DOM’s transformation indicated that low O/C (O/C<0.3) and high H/C (H/C<1.5) compounds were preferentially decomposed in the hyperthermophilic phase of HTC. Abundant produced intermediates, such as lignin phenols and amino sugars, were further transformed to refractory humic substances. This investigation extends the current understanding of the molecular mechanisms on humification of HTC, and reveals further applications for hyperthermophilic compost.



Waste activated sludge (WAS) can be used as carbon sources to support biological nutrient removal (BNR). In this study, thermal-alkaline (THALK), ozonation (OZN), electrolysis (EC) and NaClO-promoted electrolysis (EC-AOP) were investigated to facilitate WAS solubilization and production of volatile fatty acids (VFAs). EEMF-PARAFAC and FT-ICR-MS were employed to characterize the transformation of dissolved organic matter (DOM) in WAS fermentation liquors at molecular level. THALK achieved the highest fluorescence intensity of C1 protein after pretreatment. Proteins and lipids were the dominant DOM in the pretreated WAS, while the DOM shifted towards substances with higher H/C and lower O/C after fermentation. The BNR results showed that THALK (100%) and EC-AOP (96.9%) outperformed other groups (78.9 – 90.3%) in terms of NO3-N removal, indicating the significant impact of DOM compositions. Overall, these results demonstrated that THALK and EC-AOP effectively enhanced release of VFAs and DOM, which subsequently improved NO3-N removal efficiency.

Zamansani, N., Rajabzadeh, M.A., Littke, R., Zieger, L., Baniasad, A., 2019. Organic petrology and geochemistry of Triassic and Jurassic coals of the Tabas Basin, Northeastern/Central Iran. International Journal of Coal Science & Technology 6, 354-371.

https://doi.org/10.1007/s40789-019-0260-7

Jurassic and Triassic coals and organic matter-rich shales of the Tabas Basin, Iran, were investigated with respect to their thermal maturation and petrographic composition. The Triassic coals of the Parvadeh coal field range in vitrinite reflectance between 1.17% and 1.37% and the Jurassic coals of the Mazino coal field between 2.08% and 2.29% VRr. Maceral analysis revealed a predominance of vitrinite in all samples, with slightly higher percentages of inertinite in the Jurassic samples. Rock–Eval analyses confirm the presence of type III kerogen in the Triassic coals, while the Jurassic coals contain strongly carbonized residual kerogen. The range of sulfur contents for coals from the Parvadeh coal field (0.37% to 4.64%) and Mazino coal field (0.45% to 2.92%) is related to the effect of marine water in peat. The studied samples are characterized by the predominance of short- over long-chained n-alkanes. The relatively high Pr/Ph ratios indicate predominance of terrestrial organic matter whereas Pr/n-C17 and Ph/n-C18 ratios prove oxic conditions during deposition. In addition, the DBT/Phen ratio shows that these coals formed in fluvial/deltaic environments. Molecular geochemical parameters such as carbon preference index (CPI, 0.99–1.04), methyl phenanthrene index (MPI, 1.20–1.60), methyl naphthalene ratio (MNR, 1.61–3.45), and ethyl naphthalene ratio (ENR, 4–6.78) confirm the high maturity of the samples. Burial and thermal history reconstruction indicates necessity of an erosional thickness of about 4000 m in the Parvadeh area. Towards the Mazino area, a higher basal heat flow up to 80 mW m−2 is assumed for the Paleogene leading to higher maturities.



Abstract: Astronomical calculations reveal the Solar System’s dynamical evolution, including its chaoticity, and represent the backbone of cyclostratigraphy and astrochronology. An absolute, fully calibrated astronomical time scale has hitherto been hampered beyond ~50 million years before the present (Ma) because orbital calculations disagree before that age. Here, we present geologic data and a new astronomical solution (ZB18a) showing exceptional agreement from ~58 to 53 Ma. We provide a new absolute astrochronology up to 58 Ma and a new Paleocene–Eocene boundary age (56.01 ± 0.05 Ma). We show that the Paleocene–Eocene Thermal Maximum (PETM) onset occurred near a 405-thousand-year (kyr) eccentricity maximum, suggesting an orbital trigger. We also provide an independent PETM duration (170 ± 30 kyr) from onset to recovery inflection. Our

astronomical solution requires a chaotic resonance transition at ~50 Ma in the Solar System’s fundamental frequencies.

Editor's Summary: Filling a dating hole. The periodic nature of Earth's orbit around the Sun produces cycles of insolation reflected in climate records. Conversely, these climate records can be used to infer changes in the dynamics of the Solar System, which is inherently chaotic and not always similarly periodic. A particular obstacle is the lack of well-defined planetary orbital constraints between 50 and 60 million years ago. Zeebe and Lourens found an astronomical solution for that interval showing that the Solar System experienced a specific resonance transition pattern. These data provide a measure of the duration of the Paleocene-Eocene Thermal Maximum.

Zeng, L., Chen, Y., Hossain, M.M., Saeedi, A., Xie, Q., 2019. Wettability alteration induced water uptake in shale oil reservoirs: A geochemical interpretation for oil-brine-OM interaction during hydraulic fracturing. International Journal of Coal Geology 213, 103277.


Multi-stage hydraulic fracturing is an indispensable approach to enable shale oil available and affordable. However, a low flowback water recovery (usually <30%) after fracking has been widely observed, triggering both technical and environmental concerns. While it has been confirmed that water uptake is a complex function of physicochemical processes in particular capillary forces, there have been few direct investigations on the characterization of the wettability of oil-brine-shale from the geochemical perspective, especially organic matter (OM), which impedes to better manage and predict flowback water recovery. To gain a deeper understanding of the system wettability, we hypothesized the hydraulic fracturing fluid (usually slick water with low salinity <5000 ppm) increases the hydrophilicity of oil-brine-OM system thereby contributing water uptake in shale. To be more specific, lowering salinity particularly in Ca2+ and Mg2+ increases oil and organic matter surface potentials and facilitates electrical double layer expansion, and thus triggers the hydrophilicity. To test our hypothesis, we conducted a geochemical simulation using literature data to account for the incremental oil recovery from shale oil rocks in low salinity brines. We computed surface species and surface potential of oil and organic matters as a function of pH for different brine salinity (280,000, 140,000 and 28,000 ppm of formation brine and 20,000 ppm of KCl) at different temperature (25 °C, 60 °C and 100 °C). We also examined the disjoining pressure between the interfaces of brine-oil and brine-OM.

Surface complexation modelling results show that the oil-brine-OM system wettability is primarily controlled by in-situ salinity and secondarily affected by pH and temperature. At a given pH, decreasing salinity triggers a greater positive surface potential for both oil and OM surfaces, implying a greater electrical double layer expansion thus hydrophilicity. Moreover, the surface potential for oil and OM decreases with increasing pH, which even would be shifted from positive to negative in the presence of low salinity water. Furthermore, the surface potential of both oil and OM decreases with increasing temperature at in-situ pH (from 3.5 to 7). The disjoining pressure results show that saturating sample from high salinity formation brine into the low salinity KCl solution will shift the disjoining pressure from negative values (attraction) to positive values (repulsion). Our results support the hypothesis that lowering salinity increases hydrophilicity of oil-brine-OM, which likely contributes to water uptake by shale. We also argue that geochemical modelling would be an effective tool to characterize the interaction of oil-brine-OM, providing insights into water uptake and enhanced oil recovery in shales.

Zeng, L., Chen, Y., Lu, Y., Lau, H.C., Hossain, M.M., Saeedi, A., Xie, Q., 2019. Interpreting water uptake by shale with ion exchange, surface complexation, and disjoining pressure. Energy & Fuels 33, 8250-8258.


Multi-stage hydraulic fracturing is a commonly used method to maximize production from shale gas reservoirs. However, the recovery of flowback water after hydraulic fracturing is relatively low, which gives rise to technical and environmental concerns. Although it is widely accepted that the water uptake is due to physicochemical fluid–shale interactions caused by the capillary forces, much of the studies up to now are just

descriptive in nature and little attention has been paid to quantitatively characterize the fluid–shale interactions and, thus, surface forces from a geochemical perspective. In this study, we performed geochemical modeling to explain the results of spontaneous imbibition experiments by published work. We calculated the surface potential of organic matter, quartz, and calcite in the presence of 0.1–20 wt % NaCl. Moreover, we predicted the local pH using PHREEQC with consideration of ion exchange and mineral dissolution. We also computed the disjoining pressure under constant charge conditions. Results show that a low salinity drives the surface potential of organic matter and inorganic minerals to strongly negative at in situ pH. The disjoining pressure isotherm shows that air–brine–organic matter and air–brine–calcite systems give positive disjoining pressure regardless of salinity, implying a water-wet system. Moreover, a low salinity shifts the disjoining pressure to be more positive for organic matter, suggesting a wettability alteration process. However, the change of disjoining pressure on the calcite surface is negligible as a function of salinity. Our results confirm that capillary forces at least partially contribute to the water uptake, and the presence of organic matter likely further facilitates the water uptake as a result of wettability alteration. This explains in part why a low salinity causes shale expansion and microfracture generation in organic-rich reservoirs.

Zeng, Z., Zhou, W., Hu, N., Zou, L., Bai, B., Wang, H., 2019. Comparison of using two different labeling reagents for rapid analysis of triterpenic acids by pre-column derivatization with RP-HPLC-FLD and application to plant samples. Analytical Methods 11, 4354-4361.

http://dx.doi.org/10.1039/C9AY01357A

Triterpenic acids (TAs) commonly found in the plant kingdom are one of the most important natural ingredients owing to their various pharmacological activities. However, the determination of TAs through a rapid and efficient analysis method still remains a significant challenge because their isomers coexist in many plant samples. Herein we established a quick and sensitive determination approach for five TAs by pre-column derivatization coupled with HPLC-fluorescence detection, using 2-(5H-benzo[a]-carbazol-11(6H)-yl) ethyl hydrazine-carboxylate (BCEHC) as the labeling reagent. In addition, the relationship between the labeling reagent and the separation of TAs was further investigated by using another labeling reagent 2-(12-benzo[b]acridin-5-(12H)-yl)-acetohydrazide (BAAH) as a reference. The results of the method validations showed that both BCEHC and BAAH had good linearity with R2 ≥ 0.9907 and R2 ≥ 0.9998, exhibiting their own advantages at the same time. For five TA standards, BCEHC had lower limits of detection (0.42–1.35 μg L−1) while BAAH had a shorter retention time. Both labeling reagents can favorably satisfy the requirement of rapid determination of TAs. BCEHC was also applied to detect TAs in Caragana korshinskii Kom. (CK) exhibiting reliable outcomes. It has been verified that there are some TAs in the flowers, leaves and bark of CK. Moreover, asiatic acid and oleanolic acid are the only TAs that exist in every part of it.

Zhang, G., Wang, D., Zeng, Q., Yang, H., Li, Z., Zhao, Z., Guo, S., 2019. Characteristics of coal-measure source rock and gas accumulation belts in marine-continental transitional facies fault basins: A case study of the Oligocene deposits in the Qiongdongnan Basin located in the northern region of the South China Sea. Energy Exploration & Exploitation 37, 1752-1778.

https://doi.org/10.1177/0144598719867478

This study carried out the development and distribution prediction research on coal-formed gas accumulation belts from the perspectives of the development and distribution of the coal measure source rock and the thermal evolution degrees of those rock masses in marine-continental transitional facies fault basins. The purpose of the current study was to improve the accuracy of gas reservoir explorations in the sea areas. The methods used in this study were based on the systematic analyses of the drilling, logging, geochemistry, and seismic data of the Oligocene deposits in the Qiongdongnan Basin of the northern region of the South China Sea. It had been previously established that the sedimentary processes of the fault basin were mainly controlled by faulting, and (fan) deltas had often developed in the fault bending sections, tectonic transformation sections, and fault ends. The distribution along the fault zone was observed to be beaded. During the early Oligocene period of the Qiongdongnan Basin, there were strong extensional actions, and the marine and continental transitional facies strata had developed forming the northern fault depression and the central fault depression. Three (fan) delta

belts were formed in the slope belt in the northern fault depression and also in the slope belts located in the north and south of the central fault depression. Due to the superposition of the humid and hot climate during that period, the majority of the coal measure source rocks were developed in each (fan) delta. Also, three macroscopic coal measure source rock belts were formed. The types of source rock had mainly included autochthonous coal, allochthonous coal, and terrigenous marine mudstone, with terrigenous higher plant organic matter accounting for more than 50%. After the deposition of the lower Oligocene period, the basin continued to sink, and the coal measure source rock masses continued to be heated. During that period, the maturity of the organic matter had continued to rise. In the northern slope belt of the northern fault depression, the maturity of the organic matter in the coal measure source rock belt were low and the gas generation abilities were weak, which was advantageous to the formation of potential gas accumulation belts. The coal measure source rock belt on the northern side of the central fault depression had a high maturity of organic matter and strong gas generation ability, forming a macroscopic gas accumulation belt. In addition, the Yacheng 13–1 large coal-formed gas field had been discovered. The maturity of the organic matter had varied greatly in the coal measure source rock belt on the southern side of the central fault depression. The coal measure source rock masses with high maturity had strong gas generation abilities and had also formed a macroscopic gas accumulation belt, and three large and medium-sized coal-formed gas fields (such as Lingshui 17–2) had been discovered. The gas accumulation belts on the southern and northern sides of the central fault depression were favorable areas for coal-formed gas explorations. Furthermore, the trap zones in and near the coal measure source rock belts with mature thermal evolution were determined to be the most favorable areas for coal-formed gas explorations.


https://doi.org/10.1007/s12517-019-4684-6

The size of pore throats in tight oil reservoirs varies from a few tens of nanometers to several hundred micrometers. This complex and diverse microscopic pore throat structure restricts the exploration and development process, affecting the recovery rate. Size, shape, and spatial distribution of pore throats in tight oil reservoirs are revealed in this paper via a scanning electron microscope (SEM), casting thin-sections, high-pressure mercury injection, and Nano-CT. Results show that the pore type of the Chang 7 tight oil reservoir in the Xin’anbian area is mainly divided into three categories: intergranular pores, dissolution pores, and microfractures. Numerous nanoscale pore throats have developed in this area, which greatly contributes to reservoir capacity and seepage. Pore throat distribution on capillary pressure curves of different samples shows that when the threshold pressure is less than 1 Mpa, there are many micron-sized pores with good connectivity and pore throats form a large tubular shape with a throat radius between 3.6 and 1064 nm. When the threshold pressure ranges from 1 to 3 MPa, there are many nanoscale pores with good local connectivity, intragranular dissolution pores develop, and pore throats are in tube bundles and spherical in shape with the throat radius between 3.6−657 nm. When the threshold pressure is greater than 3 MPa, nanoscale microfractures develop and are connected to neighboring small spherical pores, small spherical nanopore spaces become isolated, vertical connectivity is poor, and the throat radius is between 3.6−242 nm.



Variations in pore types, the complexity of pore structures, and strong heterogeneity complicate the thorough characterization of pore networks in marine–continental shales. In this study, a novel 2D image processing method was proposed, expounded, and verified to clarify the geometrical morphologies, formation mechanisms, the size distributions, proportions and the fractal characteristics of different types of pores in marine–continental shales. Six types of pores (inter-particle, intra-particle, organic matter (OM), inter-crystalline, dissolved pores, and micro-fractures) were classified and morphologically characterized. The different types of shale pores had

distinct relatively restricted morphologies, formation mechanisms, and size ranges. Nano- and micron-sized pores were controlled by OM pores and micro-fractures, with the size ranging of 6–80 nm and 200–350 nm and 6–10 μm, respectively. Furthermore, the fractal dimension characteristics were investigated on the basis of the 2D binary images, and the results were verified by the fractal findings obtained from the N2 adsorption data. These fracture dimension results demonstrated that the Longtan shale pore structures had strong complexity and heterogeneity, which was strongly and positively controlled by micro-fractures, inter-crystalline and OM pores. In addition, the total organic carbon content strongly and positively influences the development and anisotropy of the nanoscopic pores, which were dominated by OM pores; while the clay minerals content has a minor effect on the total pore development and heterogeneity of shales but a significant effect on the dissolved pore development of shales, whereas brittle minerals inhibit total pore development and heterogeneity of shales but contribute greatly to the development of the inter-crystalline pores.



The transport properties of fluids in nanopores are a fundamental scientific issue in the development of tight reservoirs such as shale gas. The flow of gas in nanosized pores is affected by a size effect, therefore, the conventional fluid mechanics theory cannot be applied. Based on the molecular dynamics theory, the transport process of methane in carbon nanopores was studied, including simulation of the arrangement of the wall atoms, slip and transitional flow of methane in the supercritical state and application of different driving forces. The research of this paper revealed that the configuration of the wall carbon atoms, at the microscale, has a greater influence on the density distribution and velocity distribution of methane molecules in the pores, while the change in the driving force has a greater impact on the slippage of methane at the boundary. Particularly, the theoretical model we proposed can predict the transport properties in carbon nanopores, demonstrating the sensitivity of driving force, pore configuration and the state of flow for methane gas transport, which can provide the characteristic parameters for the establishment of the seepage mathematical model.

Zhang, J., Wei, C., Vandeginste, V., Ju, W., Qin, Z., Quan, F., Soh Tamehe, L., 2019. Experimental simulation study on water migration and methane depressurizing desorption based on nuclear magnetic resonance technology: A case study of middle-rank coals from the Panguan Syncline in the western Guizhou Region. Energy & Fuels 33, 7993-8006.


Water migration and methane desorption characteristics directly affect the performance of coalbed methane wells. In this paper, migration and desorption variability of methane and water in adsorption pores, seepage pores, and fractures were studied by laboratory simulation using an improved nuclear magnetic resonance displacement device. The results are as follows: Both adsorbed and bulk methane decreased logarithmically with the increase of the desorption time under the condition of one-stop desorption. The desorption process can be divided into the early rapid decline stage and the later slow desorption stage. In comparison to one-stop desorption, step-by-step depressurizing desorption can effectively increase the loss rate of the methane amount. For the two desorption modes, the variation rate of bulk methane is much higher than that of adsorbed methane at the same desorption time. The sensitivity of large pores to displacement nitrogen pressure is stronger than that of adsorption pores. In the process of methane displacement by water, the variation of bulk methane is larger than that of adsorbed methane, whereas the variation of adsorbed methane is more sensitive to injecting water pressure than that of bulk methane. The above results indicate that the quantity of water injected into the coal seam and the water drainage rate have an effect on methane desorption in the adsorption pore. Therefore, the parameters of depressurization value should be fully considered in the drainage system setting of coalbed methane wells.

Zhang, J., Xie, L., Huang, X., Liang, Z., Liu, B., Han, N., Xing, F., Deng, X., 2019. Enhanced calcite precipitation for crack healing by bacteria isolated under low-nitrogen conditions. Applied Microbiology and Biotechnology 103, 7971-7982.

https://doi.org/10.1007/s00253-019-10066-z

A nitrogen-starving isolation strategy was developed for the first time to screen bacteria with high calcium-precipitating activity (CPA) for bioremediation of damage in porous media. Meanwhile, a novel mini-tube method based on the detection of insoluble Ca2+ was established to evaluate the CPA of the isolates. A low-nitrogen-demanding strain B6, identified as Bacillus sp., was screened to exhibit the highest CPA (55 mM insoluble Ca2+). Furthermore, the effects of environmental factors and nutrient availability on B6-induced calcium precipitation were evaluated. The results show that nitrate and starch are the best nitrogen source and carbon source with optimal concentration being 4 and 2 g L−1, respectively. The suitable pH range for B6 to precipitate calcium is from 8.5 to 10.5. B6 can maintain the highest CPA at an initial spore concentration of 1.0 × 108 spores·mL−1. The optimal CaO2 dosage is 10 g L−1. Finally, the calcite precipitation is confirmed by ESEM, EDS, and XRD analysis.

Zhang, J., Xu, H., Zhou, Z., Ren, P., Guo, J., Wang, Q., 2019. Geological characteristics of shale gas reservoir in Yichang area, western Hubei. Acta Petrolei Sinica 40, 887-899.


Through analyzing the geological characteristics of shale gas, this paper discussed the controlling factors of shale gas accumulation in Yichang area of western Hubei. Based on the tectonic evolution characteristics of Huangling uplift, the evolution of Yichang area could be divided into three stages:formation of rigid basement, sedimentation of overlying strata and transformation by uplifting. Under the control of tectonic evolution, three sets of shale, i.e., Sinian Doushantuo Formation, Cambrian Niutitang Formation and Upper Ordovician Wufeng Formation-Lower Silurian Longmaxi Formation in Yichang area, mainly developed in relatively deep water sedimentary environment and had the same depositional setting and composition characteristics with Doushantuo Formation, Qiongzhusi Formation and Longmaxi Formation in Sichuan Basin and material conditions for shale gas formation. Further, based on analyzing the discovered shale gas reservoir, this paper investigated the key control role of Huangling uplift in shale gas accumulation in Yichang area of western Hubei from the aspects of preservation conditions and thermal evolution process. In Yichang area of western Hubei, the ancient blind rigid basement had the characteristics of early formation, wide distribution, strong compression resistance, late and long-duration uplifting, and the ancient shale in the overlying Cambrian, Sinian and Upper Ordovician-Lower Silurian strata had short buried time, relatively low degree of thermal evolution, stable tectonic structure and good preservation condition, which provided favorable geological conditions for shale gas accumulation.


https://doi.org/10.1080/01490451.2019.1641772

How microbes respond to substantial and increasing anthropogenic disturbance remains an open question in river systems. We tested the hypothesis that the source and distribution of anthropogenic organic matter (OM) were significant factors affecting the spatial variation of the microbial community composition of the Yangtze River sediments. Bulk geochemical proxies and lignin phenols suggested a general decrease of terrestrial C3 plants or soil OM input from the middle to the lower reaches. Fecal sterols inferred higher sewage contamination levels in the middle reaches. Polycyclic aromatic hydrocarbons (PAHs) distribution indicated a dominant biomass and coal combustion signal in the middle reaches, whereas a mixed source including petroleum combustion in the lower reaches. Phylogenetic analysis revealed a large portion of Methanobacteria and Verrucomicrobia enriched in the middle reaches, whereas OM-degrading bacteria, including Flavobacteria, Acidobacteria, and Alphaproteobacteria were dominant in the lower reaches. Quantitative PCR analyses and

multivariate analysis further demonstrated that sources and distribution of OM had combined effects in shaping alpha and beta-diversity of sediment microbial communities. Sewage discharge and incomplete OM combustion, respectively, were associated with Methylococcaceae, Chloroflexi, and Bacteroidetes groups. This study provides a foundation for further understanding of the river sediment microbial composition, considering the continued increase of anthropogenic influences.

Zhang, S., Liu, H., Liu, Y., Wang, Y., Wang, M., Bao, Y., Hu, Q., Li, Z., Zhang, S., Yao, S., Wang, Y., Xiong, W., Liu, P., Fang, Z., 2020. Main controls and geological sweet spot types in Paleogene shale oil rich areas of the Jiyang Depression, Bohai Bay basin, China. Marine and Petroleum Geology 111, 576-587.


The shale oil wells drilled in the early stage of the Jiyang Depression have achieved industrial-scale flow, but the oil production in special exploration wells has been less than ideal. The area of continental shale oil and gas accumulations has not been properly controlled, and geological sweet sections and sweet areas need to be systematically studied. In this study, shale reservoir characteristics are analyzed in detail based on thin sections, field emission scanning electron microscopy (FE-SEM) observations and mercury injection experiments of well core samples combined with X-ray diffraction (XRD) and geochemical indicators. Key factors related to a high yield of shale oil are determined in addition to the shale oil production capacity, and the types of shale oil sweet spots are classified, while the sweet spot distribution pattern is determined. The results show that the Paleogene shale in the Jiyang Depression is rich in carbonate minerals (mainly calcite and ferrocalcite, followed by dolomite and ferrodolomite) and has a low clastic content, high organic carbon content (2.0–7.0 wt%), and medium maturity (Ro = 0.51%–1.1%). An effective reservoir space assemblage usually has a three-tier intercommunication form within the porosity-fracture network. Laminar lithofacies that are rich in carbonates are the most favorable for containing continental shale oil reservoirs. Shale oil geological sweet spots can be roughly divided into matrix shale oil, fracture shale oil, interlayer shale oil, and compound shale oil types. The key focus in locating shale oil wells is to find geological sweet spots that have an appropriate organic matter (OM) content, interlayer development, light oil, and high pressure. This study demonstrates that favorable sweet spots are found to have the following conditions: a shale formation pressure coefficient of >1.2, shale total organic carbon content of >2%, organic-rich laminar lithofacies (including interlayer and single-interlayer thicknesses of >2 cm), burial depth of >3200 m, middle diagenetic stage B (Ro > 0.7%), and crude oil density of <0.89 g/cm3.

Zhang, S., Song, W., Wemheuer, B., Reveillaud, J., Webster, N., Thomas, T., 2019. Comparative genomics reveals ecological and evolutionary insights into sponge-associated Thaumarchaeota. mSystems 4, e00288-19.

http://msystems.asm.org/content/4/4/e00288-19.abstract

Abstract: Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis. Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names “Candidatus UNitrosopumilus hexadellus,” “Candidatus UNitrosopumilus detritiferus,” and “Candidatus UCenporiarchaeum stylissum” (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that “Ca. UCenporiarchaeum stylissum” has been exclusively detected in sponges and can hence be classified as a specialist, while “Ca. UNitrosopumilus detritiferus” and “Ca. UNitrosopumilus hexadellus” are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study

therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.

Importance: Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.

Zhang, W., Williams-Jones, A.E., Leng, C.-B., Zhang, X.-C., Chen, W.T., Qin, C.-J., Su, W.-C., Yan, J.-H., 2019. The origin of CH4-rich fluids in reduced porphyry–skarn Cu–Mo–Au systems. Ore Geology Reviews 114, 103135.


Although most of the methane on Earth is of biogenic origin, significant abiogenic methane has been identified in a variety of geological environments. Moreover, the presence of methane has been reported recently in fluid inclusions from a number of reduced porphyry deposits. The genesis of this methane, however, remains poorly understood. Here, we present results of a study of magma-exsolved CH4-rich aqueous fluid inclusions in the Seleteguole reduced porphyry–skarn Cu–Mo–Au deposit, NW China. Four types of fluid inclusions, namely intermediate-density two-phase aqueous inclusions, low-density vapor inclusions, brine inclusions and aqueous liquid inclusions, have been distinguished on the basis of the phases present at room temperature. The intermediate-density inclusions were trapped as a single phase and contain 3.8–10.4 mol/kg CH4, corresponding to an oxygen fugacity between ΔFMQ − 1 and ΔFMQ − 0.5. This attests to the remarkably reduced nature of the fluid. The δ13C value of the CH4-hosted fluid inclusions ranges from –29.4‰ to –19.1‰ (PDB), which distinguishes this methane from biogenic methane. Indeed, the high homogenization temperature of the CH4-rich inclusions (~400 °C) implies that the CH4 was exsolved directly from the magma. Given the environment in which the magma was likely generated, i.e., at or immediately above a subducting plate, we propose that the methane was produced by reactions involving organic matter-bearing carbonate rocks in the subduction zone. Although Cu, Mo and Au in most porphyry systems are interpreted to have been transported under oxidizing conditions, our results indicate that reduced aqueous liquids and vapors are also capable of transporting appreciable concentrations of these metals.

Zhang, X., Joachimski, M.M., Over, D.J., Ma, K., Huang, C., Gong, Y., 2019. Late Devonian carbon isotope chemostratigraphy: A new record from the offshore facies of South China. Global and Planetary Change 182, 103024.


We present a new biostratigraphically constrained carbon isotope record from the Lali section (South China) to document perturbations in the Late Devonian carbon cycle. Positive carbon isotope excursions (CIEs) are most important components of the Late Devonian long-term carbon isotope cycle: Frasnes (+2‰), Middlesex (+1‰), Lower Kellwasser (+3‰), Upper Kellwasser (+3‰) and Upper annulata (+1‰) events, as well as a small positive CIE (+1‰) in the Famennian expansa-aculeatus zones were recorded. It is noteworthy that no significant carbon isotope shifts are found for the Rhinestreet, Nehden, Condroz and Enkeberg events. The Late Devonian long-term carbon isotope curve from South China is in agreement with contemporaneous world-wide trends in Euramerica (Europe and North America) and Gondwana. Global data suggests a higher Famennian δ13Ccarb baseline (about +2.5 ‰) than that of the Frasnian (about +1‰). Previous studies have related the positive CIE to ocean anoxia, but its ultimate driver remains unclear. Other interpretations include the spread of land plants or increased tectonic activity, but these explanations are questionable due to the relative short durations of the CIEs compared to long-term processes of plant evolution and plant cover extension as well as tectonic movements.



To evaluate the characteristics of microorganisms and the origin of organic matter of the Wufeng Formation and Longmaxi Formation (WF-LMX) in Sichuan Basin (South China), the type and number of microorganisms were determined in this study using scanning electron microscope (SEM) microphotographs and microbial extraction. The contribution of various microorganisms to organic matter was analyzed in combination with the data of biomarkers and total organic carbon (TOC). It can be deduced from the paleogeography and pristine/phytane (Pr/Ph) ratio that the microorganisms of WF-LMX resided in 60 m–200 m deep shelf with anoxic bottom water. From SEM microphotographs and microbial microscopy analysis, it was demonstrated that the microorganisms in the WF-LMX can be divided into 3 types: planktonic algae (mainly including acritarchs and green algae), fungi, and benthic algae. Acritarchs were the most common microorganisms in the WF-LMX with the average relative content of 60.5%. The average relative contents of benthic algae, fungi, and green algae were 17.6%, 18.0% and 3.9%, respectively. Since the acritarchs and green algae in the Wufeng Formation and the Longmaxi Formation basically belong to planktonic algae, the relative content of planktonic algae in them is about 64.4%. The strata of WF-LMX can be divided into 3 sections based on the distribution characteristics of various microorganisms. The relative content of acritarchs gradually decreased upwards, while that of benthic algae gradually increased. The multiple proxies of biomarkers proved that the planktonic algae was the main source of organic matter in the WF-LMX. Combining the statistical data of microorganisms, it was considered that the organic matter in WF-LMX was mainly derived from acritarchs, which might be the components of planktonic algae. The fungi had a significant contribution to the organic matter in organic-rich layers (TOC > 2.0%) rather than in organic-poor layers, while green algae and benthic algae made little contribution to the organic matters in WF-LMX.



The very high temperature at the center of a hydrothermal system is detrimental for the deposition of organic-rich sediments. However, it's not known how the petroleum source rock develops at the boundary of a hydrothermal system where the seawater temperature was only slightly elevated. The petroleum generation potential, using pyrolysis-GC, GC-MS and FT-ICR MS techniques, of eight organic-rich Permian shale samples from Shangsi Section China were systematically investigated. Principal component analysis reveals that the quantity and quality of the organic matter in the shale is dominated by biomass productivity, the redox condition, and terrestrial organic matter input. Rare earth element distribution pattern reveals that the two samples with highest TOC contents show a slight Eu anomaly which indicates the sample was influenced by a hydrothermal system to some degree. A depositional model showing how the influences from hydrothermal event promote the development of petroleum source rock is summarized: (1) At the edge of a hydrothermal system, the seawater-temperature can be elevated by 5–10 °C which further promotes the development of phytoplankton and zooplankton. (2) An upwelling can be intrigued and chemical weathering will be accelerated which both introduce excessive nutrients and increase the biota productivity. (3) Flux with the terrestrial advanced plant can also be accelerated to the shelf area by the volcano-induced climate change. (4) The consumption of the extensive biomass induced by the hydrothermal activity would expand the oxygen minimum zone, and further enable more organic matter to be preserved in shale.

Zhao, S., Li, H., Han, W., Chan, W., Li, L., 2019. Metabolomic coverage of chemical-group-submetabolome analysis: Group classification and four-channel chemical isotope labeling LC-MS. Analytical Chemistry 91, 12108-12115.


Chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) is a powerful technique for in-depth metabolome analysis with high quantification accuracy. Unlike conventional LC-MS, it analyzes chemical-group-based submetabolomes and uses the combined results to represent the whole metabolome. Due to analysis time and cost constraint, not all submetabolomes can be profiled and thus knowledge of chemical group classification is important in guiding submetabolome selection. Herein we report a study of determining the distribution of functional groups of compounds in a database and then examine how well we can experimentally analyze the major chemical groups in two representative samples (i.e., human plasma and yeast). We developed a computer algorithm to classify chemical structures according to their functional groups. After removing lipids which are targeted molecules in lipidomic analysis, inorganic species and other molecules that are unique to drug, food, plant, and environmental origins, five groups (i.e., amine, phenol, hydroxyl, carboxyl, and carbonyl) are found to be the dominant classes. In the databases of MCID (2683 filtered metabolites), HMDB (5506), KEGG (11598), YMDB (1107), and ECMDB (1462), 94.7%, 85.7%, 86.4%, 85.7%, and 95.8% of the filtered metabolites belong to one or more of the five groups, respectively. These groups can be analyzed in four-channel CIL LC-MS where hydroxyls (H), amines and phenols (A), carboxyls (C), and carbonyls or ketones/aldehydes (K) are separately profiled as individual channels using dansyl and DmPA labeling reagents. A total of 7431 peak pairs were detected with 6109 unique-mass pairs from plasma, while 5629 pairs with 4955 unique-mass pairs were detected in yeast. Compared to group distributions of database compounds, hydroxyl-containing metabolites were severely underdetected, which might indicate that the current method is less than optimal for analyzing this group of metabolites. As a result, the overall experimental coverage is likely significantly lower than the database-derived coverage. In short, this study has shown that high metabolome coverage is theoretically attainable by analyzing only the H, A, C, and K submetabolomes and the group classification information should be helpful in guiding future analytical method development and choices of submetabolomes to be analyzed.



Dark carbon fixation (DCF) by chemolithotrophic microbes can make considerable contribution to inorganic carbon fixation in aquatic ecosystems. However, little is known about the importance and diversity of chemolithotrophic microbes in cascade reservoir sediments. In this study, we determined the potential DCF rates of sediments of three cascade reservoirs in Wujiang River basin by carbon isotopic labeling. The results showed that the DCF rates of the surface sediments ranged from 1.5 to 14.7 mmol C m−2 d−1. The ratio of DCF to mineralization rate of sediment organic matter of surface sediment was between 11.6%~60.9%. High-throughput sequencing analysis of cbbL and cbbM genes involved in Calvin Benson Cycle indicated that cbbL-carrying CO2-assimilating bacteria included diverse functional groups, while cbbM type was mostly involved in sulfur oxidation. The sediments of Hongfeng (HF) reservoir, which has much longer hydraulic residence time (HRT) and locates in most upstream of a major tributary of Wujiang River, have substantially higher DCF rates. The cbbL and cbbM communities in HF were dominated by sulfur oxidizing bacteria, and were largely different from that in the other two reservoirs. Our results suggested that chemolithotrophy plays an important role in carbon cycling of sediments in cascade reservoir. Meanwhile, HRT and relative location of cascade reservoirs are the key control factors of both DCF and composition of autotrophic microbial communities in cascade reservoir sediments.

Zhao, Y., Wang, C., Zhang, Y., Liu, Q., 2019. Experimental study of adsorption effects on shale permeability. Natural Resources Research 28, 1575-1586.

https://doi.org/10.1007/s11053-019-09476-7

CH4 adsorption plays an important role in the permeability evolution of unconventional gas reservoirs. In this paper, an experimental method for simultaneous measurement of rock adsorption and permeability has been

developed. For this experimental method, the CH4 adsorption amounts were obtained using a volumetric method. The permeability was measured by considering gas diffusion from the reference chamber to the core sample, under the pressure difference. A set of adsorption-permeability experiments were conducted on shale samples from lower Silurian Longmaxi Formation in the Sichuan Basin. The experimental results show that both the adsorption and swelling behavior of shale can be well described by the Langmuir equation. The effects of adsorption on permeability are influenced by two factors: (1) adsorption-induced storage, which causes an incremental in apparent porosity, leading to a significant error in permeability measurement if true porosity is used; and (2) adsorption-induced swelling, which potentially closes the existing natural fractures and reduces the intrinsic permeability. The adsorption storage effects are more significant at low pressure and are influenced by the experimental configurations (ratio of chamber volume to pore volume). With the increase in adsorption-induced swelling strain, the permeability declines by a cubic function during the adsorption process. Since swelling strain is linearly proportional to the amount of CH4 adsorbed, the behaviors of permeability and the amount of adsorbing gas follow similar trends.


https://doi.org/10.1038/s41396-019-0449-1

Picocyanobacteria make up half of the ocean’s primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days’ incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.

Zheng, F., Chen, Y., Tang, X., Su, J., Zhu, Y., Zhang, C., 2019. Changes in archaeal ether lipid composition in response to agriculture alternation in ancient and modern paddy soils. Organic Geochemistry 138, 103912.


Paddy soil is the consequence of human activity, which has exerted significant anthropogenic impacts on the global carbon cycle in recent earth history, particularly through the production of microbial methane from paddy soils. However, the anthropogenic impact of rice fields on the distribution of methanogenic archaea and methane emission during human history is poorly documented. Isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) are unique biomarkers for archaea, which can be used to examine changes in climate and environment during human evolution. This study aimed to reconstruct archaeal communities and evaluate how they might have been impacted by human activities during the development of two paddy soil profiles that recorded a cultivation history of over 6300 years in Zhejiang Province, southeastern China. Variations in archaeol, GDGT-0 and crenarchaeol strongly suggest that archaeal ether lipids deeply buried in the ancient paddy soil profiles are mainly fossil records rather than contemporary signals. Cluster analysis based on GDGT

compositions revealed two major groups of GDGTs corresponding to different soil types, reflecting the shift of archaeal communities from Thaumarchaeota to methanogens. The archaeal ether lipid-based proxies (MI, archaeol/crenarchaeol and GDGT-0/crenarchaeol) related to methane-producing archaea varied remarkably in different soil types associated with the anthropogenic management. These proxies had significantly higher values in the buried paddy soils than currently cultivated paddy soils, implying that the earlier anthropogenic flooding may have resulted in considerable methane emission from paddy soils in southeastern China.

Zhong, X., Li, C., Pu, H., Zhou, Y., Zhao, J.X., 2019. Increased nonionic surfactant efficiency in oil recovery by integrating with hydrophilic silica nanoparticle. Energy & Fuels 33, 8522-8529.


Nonionic surfactants are nonvolatile and benign chemicals widely used in the oil and gas industry. However, their huge loss especially under high temperature and high salinity conditions has limited their large-scale applications; thus, various additives were introduced to prepare compounded systems. This paper mainly focuses on nonionic surfactant–silica nanoparticle augmented systems. Herein, an extensive series of adsorption tests related to the adsorption of surfactant on nanoparticles and surfactant adsorption behavior change with the presence of nanoparticles was conducted, together with their combined effects on interfacial properties and their potentials in boosting oil production, trying to systematically evaluate their synergistic interactions and reveal the underlying functional mechanisms. Experimental results showed that surfactant adsorption was generally reduced with the addition of nanoparticles, and the efficiency largely depended on the adsorbents and nanoparticle size. In addition, the properties of nanofluids differ at varying surfactant/nanoparticle concentration ratios because of diverse surfactant adsorption structures, and smaller particles turned out to be better surfactant carriers. In the spontaneous imbibition tests, positive cooperative effects by integrating nanoparticles with surfactant were highlighted, where the nanoparticles efficiently improved the surfactant performance and a considerable amount of additional oil was recovered. Acknowledging the interactions and combined effects of nonionic surfactants and hydrophilic silica nanoparticles may shed light on the development and improvement of potential nanofluids for industrial practices.

Zhou, H., Luo, F., Luo, Z., Li, D., Liu, C., Li, X., 2019. Programming conventional electron microscopes for solving ultrahigh-resolution structures of small and macro-molecules. Analytical Chemistry 91, 10996-11003.


Microcrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of this technique are still limited by the special requirement for radiation-tolerated movie-mode camera and the lack of automated data collection methods. Herein, we develop a stage-camera synchronization scheme to minimize the hardware requirements and enable the use of the conventional electron cryo-microscope with a single-frame CCD camera, which ensures not only the acquisition of ultrahigh-resolution diffraction data but also low cost in practice. This method renders the structure determination of both peptide and small organic compounds at ultrahigh resolution up to ∼0.60 Å with unambiguous assignment of nearly all hydrogen atoms. The present work provides a widely applicable solution for routine structure determination of MicroED and demonstrates the capability of the low-end 120 kV microscope with a CCD camera in solving ultrahigh resolution structures of both organic compounds and biological macromolecules.



A solvent-assisted vacuum desorption method is developed and combined with gas chromatography-tandem mass spectrometry (GC-MS/MS) for quick determination of soil PAHs. With the assistance of a reduced

pressure of 0.0001 kPa and the DMSO/acetone (1:1) mixed solvent, this method allows desorption of PAHs in a moderate temperature of 160 °C. Analytes were trapped in a collection tube and eluted with n-hexan for GC-MS/MS analysis. The entire procedure can be completed within 20 min. In order to validate this method for determining soil PAHs, the solvent-assisted vacuum desorption method, Soxhlet extraction and ASE extraction were applied in different samples of real contaminated soils. Most HMW PAHs showed similar concentrations, yet LMW PAHs with solvent-assisted vacuum desorption presented significantly higher concentrations than those with conventional methods, such as NAP, ANY, ANA and FLU. Further investigation revealed that solvent-assisted vacuum desorption is capable of improving both the extractability and collection efficiency of those four LMW PAHs in real contaminated soil. This method enables desorption of HMW PAHs and provides the additional benefit of improved extractability and collection efficiency for LMW PAHs.

Zhou, Y., Chen, Q., Wu, K., Wang, X., Liu, Y., 2019. The basin and range systems and their evolution of the northwestern margin of Junggar Basin, China: Implications for the hydrocarbon accumulation. Energy Exploration & Exploitation 37, 1577-1598.

https://doi.org/10.1177/0144598719852419

Basin and range system in the northwestern margin of the Junggar Basin highly controlled the distribution of sediments and oil and gas. Detailed studies of basin and range system will be helpful in understanding the formation of hydrocarbon resources. Based on the previous studies and geophysical data, we analyze the structural characteristics and their evolution of basin and range system in this area. Although the basement of the Junggar Basin is still uncertain, high resolution of geophysical data suggests that the basement of the basin generally has lower and much stable gravity and magnetic anomalies than that in the orogenic belts around the basin and these anomalies are uneven in the basin, implying the basement may be assembled by different blocks. The amalgamation of these blocks will affect the deformation of the corresponding sedimentary cover. Detailed seismic interpretation across the basin and range system suggest that the imbricate thrust faults are dominant structural styles in this area. The Zaire-Hala’alate mountains were raised after multi-stage tectonic movement, and they started to rise in Late Carboniferous. The evolution of the western margin of the Junggar Basin can be divided into three stages, which are the initial formation stage in Late Carboniferous, the foreland basin developed stage from Permian to Jurassic and the rejuvenated foreland basin stage in Cenozoic. The coupling processes of basin and range system caused the formation, migration, and accumulation of the hydrocarbon resources both in space and time in the northwestern margin of the Junggar Basin.

Zhu, G.-y., Li, T.-t., Zhao, K., Zhang, Z.-y., Chen, W.-y., Yan, H.-h., Zhang, K.-j., Chi, L.-x., 2019. Excellent source rocks discovered in the Cryogenian interglacial deposits in South China: Geology, geochemistry, and hydrocarbon potential. Precambrian Research 333, 105455.


The Cryogenian (720–635 Ma) is characterized by the well-known Sturtian and Marinoan glaciations which plays a key role in understanding remarkable climate and sea level changes, and oxygenation events that occurred during the Neoproterozoic Era. However, less attention has been paid to the interglacial deposits. Recently, we paid great attentions to the excellent hydrocarbon source rocks (TOC > 2%) in the Cryogenian interglacial Datangpo Formation (663 ± 4 Ma–654 ± 3.8 Ma) in South China, which mainly consists of black shales with thin manganese interbeds, making the interglacial interval a new focus. To elucidate their characteristics and depositional environments, petrological and geochemical studies were conducted on fresh rock samples collected from six sections (Gucheng, Sanlian, Xiaoxi, Gaodongyuan, Xiaochayuan, Yanglizhang) in manganese mining areas at southeastern South China. Sedimentary reconstructions suggest a transition from restricted to open ocean environment during the deposition of the Datangpo Formation. And, this formation records variations from warm and humid to dry and cold climate. Black shales were deposited in its lowest member during the warm period and showed greatest thicknesses more than 20 m at depocenters. Microscopic observations of the black shale samples exhibited abundant benthic algae with great diversities, indicating a gradual recovery of the ecosystem. Biomarker analyses further reveal that these algae combined with bacterial microorganisms prosperous in low-salinity reducing environments were the dominant organic contributors to

the source rocks, which were inferred by low pristane (Pr) to phytane (Ph) ratio (Pr/Ph), low gammacerane, high tricyclic terpene and high C27 sterane contents. Trace element records combined with isotopic data suggest that the deposition of source rocks in Datangpo Formation were related to a burst in surface-water productivity due to warm climate and better preservations resulted from anoxic waters within a stratified water column. These findings indicate the Cryogenian source rocks may provide a new potential field for future explorations of shale gas and deep oil and gas.

Zhu, G., Zhang, Z., Zhou, X., Li, T., Han, J., Sun, C., 2019. The complexity, secondary geochemical process, genetic mechanism and distribution prediction of deep marine oil and gas in the Tarim Basin, China. Earth-Science Reviews 198, 102930.


Most Paleozoic marine craton basins in China are rich in natural gas except the Tarim Basin, where both oil and gas are prolific. Various hydrocarbon types have been found in this basin, including deep ultra-heavy oil, heavy oil, normal oil, volatile oil, condensate and natural gas. Petroleums with diverse types even coexist within a single reservoir. Generally, the Ordovician and Cambrian reservoirs are deeply buried (5500–8000 m) and intensively altered after initial oil and gas accumulations, bringing challenges to physical property prediction before drilling and evaluation of exploration target. Based on recent exploration discoveries and experimental data, we systematically analyzed the origin of oil and gas, demonstrated the mechanisms and processes of secondary geochemical alteration (e.g. biodegradation, gas washing fractionation, TSR and high-temperature cracking). Moreover, the preservation mechanism of ultra-deep normal oil was also clarified, and the distribution patterns of oil and gas were predicted. Tarim Basin has been uplifted and shallowly buried in the early accumulation stage, then rapidly and deeply buried in the late stage, resulting in various geochemical alteration processes at different burial stages. Through the reconstruction of complicated deep-strata oil and gas accumulation histories, the spatial distribution of deep petroleum types were predicted. This review has provided detailed assessment with case studies in the Tarim Basin, and sheds light on the preservation mechanisms and the alteration processes of deep liquid petroleums. In addition to massive gas accumulations, liquid oils still have great exploration potential in strata deeper than 8000 m in the Tarim Basin.

Zhu, J., Poulsen, C.J., Tierney, J.E., 2019. Simulation of Eocene extreme warmth and high climate sensitivity through cloud feedbacks. Science Advances 5, eaax1874.


The Early Eocene, a period of elevated atmospheric CO2 (>1000 ppmv), is considered an analog for future climate. Previous modeling attempts have been unable to reproduce major features of Eocene climate indicated by proxy data without substantial modification to the model physics. Here, we present simulations using a state-of-the-art climate model forced by proxy-estimated CO2 levels that capture the extreme surface warmth and reduced latitudinal temperature gradient of the Early Eocene and the warming of the Paleocene-Eocene Thermal Maximum. Our simulations exhibit increasing equilibrium climate sensitivity with warming and suggest an Eocene sensitivity of more than 6.6°C, much greater than the present-day value (4.2°C). This higher climate sensitivity is mainly attributable to the shortwave cloud feedback, which is linked primarily to cloud microphysical processes. Our findings highlight the role of small-scale cloud processes in determining large-scale climate changes and suggest a potential increase in climate sensitivity with future warming.

Zhu, X., Chen, J., Li, W., Pei, L., Liu, K., Chen, X., Zhang, T., 2020. Hydrocarbon generation potential of Paleogene coals and organic rich mudstones in Xihu sag, East China Sea Shelf basin, offshore eastern China. Journal of Petroleum Science and Engineering 184, 106450.


Paleogene coals and organic rich mudstones in Xihu sag, East China Sea Shelf basin in offshore eastern China were analysed to evaluate the hydrocarbon generation potential based on organic petrographic and organic

geochemical methods. The results reveal that the source rocks are dominated by Type III-II2 kerogens deposited in sub-oxic to oxic environments as coal-bearing source rocks. The total organic carbon (TOC) content values for the samples range from 0.31 wt% to 75.68 wt%, suggesting fair to excellent hydrocarbon generation potential, which is also consistent with the Hydrogen Index (HI) and extractable organic matter (EOM) content results. Thermal maturity of organic matter in Western Depression Group (WDG) area are mainly in early thermal maturity stage (Rr ranges from 0.57% to 0.76%), while Central Uplift Group (CUG) area samples have relatively higher thermal maturity (Rr ranges from 0.72% to 1.41%). The characteristics of Paleogene coal and organic rich mudstones reveal that the potential source rocks in both WDG and CUG area have fair to excellent hydrocarbon generative potential, but vary in hydrocarbon phase. WDG source rocks are expected to generate both commercial liquid hydrocarbons and gaseous hydrocarbons, which is also implied by the presence of significant liptinite and exsudatinite macerals. On the other hand, source rocks for CUG area exhibit a dominant gaseous hydrocarbon generation and some oil hydrocarbon generation potential. The data exhibited in this study illustrate source rock characteristics and provide evidence for hydrocarbon generation potential of Paleogene coal and organic rich mudstones in Xihu sag, in offshore eastern China.

Zhu, Z., Li, M., Tang, Y., Qi, L., Leng, J., Liu, X., Xiao, H., 2019. Identification of phenyldibenzothiophenes in coals and the effects of thermal maturity on their distributions based on geochemical data and theoretical calculations. Organic Geochemistry 138, 103910.


All four phenyldibenzothiophene (PhDBT) isomers were unequivocally identified in coals for the first time by the co-injection of authentic standards and comparison of the retention indices with those reported in previous studies. Based on density functional theory (DFT) calculations, the relative thermodynamic stability order of the phenyldibenzothiophene isomers (PhDBTs) was determined to be 3-PhDBT > 2-PhDBT > 4-PhDBT > 1-PhDBT. All PhDBT isomers were observed in a suite of coals from the Junggar and Ordos basins, and the effects of thermal maturity on their distributions were systematically investigated. Based on geochemical data and theoretical calculations, two phenyldibenzothiophene maturity indicators, i.e., PhDR1 (2-PhDBT/4-PhDBT) and PhDR2 ((2-PhDBT + 3-PhDBT)/4-PhDBT), are proposed. For high maturity coals (≥0.96 %Ro), PhDR1 and PhDR2 increase gradually with increasing thermal maturity. Two preliminary calibrations of these parameters against measured %Ro were made: %Rc = 0.60 × PhDR1 + 1.00 (≥1.00 %Ro) and %Rc = 0.30 × PhDR2 + 1.00 (≥1.00 %Ro). Compared to their corresponding methylated counterparts, phenyldibenzothiophenes are particularly useful as molecular markers of maturity at higher levels of thermal stress and provide a molecular assessment for sedimentary rocks containing types II and III kerogens where few biomarker parameters are available. PhDBTs in coals are likely to be generated during diagenesis/catagenesis as intermediate products in the formation of more condensed heterocyclic polycyclic aromatic compounds, such as triphenyleno[1,12-bcd]thiophene and benzobisbenzothiophenes, which were detected in the highly mature samples. This study broadens the current understanding of the occurrence, distribution, geochemical significance, and origin of phenyldibenzothiophenes in sedimentary organic matter.

Zou, J., Liao, X., Chen, Z., Zhao, X., Mu, L., Chu, H., Dong, P., Guan, C., 2019. Integrated PVT and coreflooding studies of carbonated water injection in tight oil reservoirs: A case study. Energy & Fuels 33, 8852-8863.


Carbonated water injection (CWI) is a modified CO2 flooding technique for enhanced oil recovery, which takes advantage of both CO2 flooding and water injection and has attracted much attention recently. However, the dedicated research so far has focused heavily on conventional reservoirs. The objective of this research is to investigate the performance of CWI in a tight oil reservoir. First, a set of well-designed multiple contact tests were conducted to simulate the dynamic mass transfer process of fresh carbonated water (CW) to live crude oil. In each test, CW was brought into contact with live crude oil in a high-temperature and high-pressure PVT cell. Pressure changes during the test were observed and recorded. After equilibrium, all the transferred CW was taken out of the cell and the swelled oil proceeded to the next contact. The volumes of water and liberated gas were measured. Then, the oil swelling factor could be calculated, which would verify the existence of the

moving interface between CW and live crude oil. It was observed that the system pressure built up immediately after CW was mixed with live crude oil in the PVT cell. For the first contact, the equilibrium pressure increased by 6.46 MPa, and the equilibrium pressure increased by 2.16 MPa at the last contact. This result indicates a strong interaction between CW and live crude oil, which is beneficial to maintain reservoir pressure. Because a large amount of CO2 from CW was transferred to the live crude oil, the swelling factor of 1.26 was obtained at the end of the tests. The diffusion of CO2 into the live crude oil also leads to subsequent oil viscosity reduction. In addition, a series of coreflood experiments under real reservoir conditions were carried out to evaluate the performance of CWI for improving oil recovery in core samples from a tight sandstone reservoir. Coreflood results showed that both secondary and tertiary CWI recovered additional oil compared to water flooding. Finally, a significant amount of CO2 was stored in the cores. Our experimental results clearly indicate the potential of CWI for improving oil recovery and CO2 storage capacity in tight oil reservoirs.

eaogorg.files.wordpress.com · web viewgeochemistry articles – september 2019. analytical...

Documents