geobiological pattern formation at yellowstone’s hot...
TRANSCRIPT
![Page 1: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/1.jpg)
Geobiological Pattern Formation atYellowstone’s Hot Springs
Nigel Goldenfeld
Department of Physics
University of Illinoisat Urbana-Champaign
![Page 2: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/2.jpg)
Geology and Microbiology•Bruce Fouke•George Bonheyo•Jorge Frias-Lopez
Physics•Hector Garcia Martin•John Veysey
Undergraduates•Tracey Van Gundey•Joannah Metz
Work funded by the National Science Foundation
Acknowledgements
![Page 3: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/3.jpg)
Outline
• What is Geobiology?– Biocomplexity - and what physicists can contribute
• A virtual tour of Yellowstone’s hot springs– Facies concept
• Possible role of microbes in pattern formation– Biotic vs. abiotic formation
• Microbial ecology: microbes track facies!
• Laboratory work at Illinois– Stromatolites
– Modelling
![Page 4: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/4.jpg)
Biocomplexity
![Page 5: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/5.jpg)
Biocomplexity• What is “complexity”?
– Complexity = structure + large fluctuations
• The big idea: research on the individual componentsof complex systems provides only limited informationabout the behavior of the systems themselves
• Complexity arising from interplay of biological,physical and even social systems
![Page 6: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/6.jpg)
What is biocomplexity?
– “Biocomplexity arises from dynamics spanning several levelswithin a system, between systems, and/or across multiplespatial (microns to thousands of kilometers) and temporal(nanoseconds to eons) scales.
– This special competition will specifically support ResearchProjects which directly explore nonlinearities, chaotic behavior,emergent phenomena or feedbacks within and between systemsand/or integrate across multiple components or scales of timeand space in order to better understand and predict the dynamicbehavior of systems.”
NSF Solicitation 00-22
![Page 7: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/7.jpg)
Who cares?
DIRECTORATE FOR BIOLOGICAL SCIENCES
DIRECTORATE FOR COMPUTER AND INFORMATION SCIENCE ANDENGINEERING
DIRECTORATE FOR ENGINEERING
DIRECTORATE FOR GEOSCIENCES
DIRECTORATE FOR MATHEMATICAL AND PHYSICAL SCIENCES
DIRECTORATE FOR SOCIAL, BEHAVIORAL AND ECONOMICSCIENCES
OFFICE OF POLAR PROGRAMS
![Page 8: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/8.jpg)
Why do they care?
• Steven Jay Gould, New York Times, Feb 19, 2001• “Homo sapiens possesses between 30,000 and 40,000 genes... In
other words, our bodies develop under the directing influence ofonly half again as many genes as the tiny roundworm ....”
• “The collapse of the doctrine of one gene for one protein, and onedirection of causal flow from basic codes to elaborate totality, marksthe failure of reductionism for the complex system that we callbiology.”
• “First, the key to complexity is not more genes, but morecombinations and interactions generated by fewer units of code —and many of these interactions (as emergent properties, to use thetechnical jargon) must be explained at the level of their appearance,for they cannot be predicted from the separate underlying partsalone.”
![Page 9: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/9.jpg)
Why do they care?
“Major questions about biocomplexity remainunanswered. How does complexity among biological,physical and social systems within the environment ariseand change? How do emergent properties develop? Howdo systems with living components, including those thatare human based, respond and adapt to stress? How doesinformation and material move within and across levelsin systems? Are adaptation and change predictable? Howdo humans influence and respond to biocomplexity innatural systems?”
![Page 10: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/10.jpg)
How much do they care?
• NSF Priority Area. Others are:• Nanoscale Science and Engineering,
• Information Technology Research,
• Learning for the 21st Century.
• Program disbursed $136M over last 3 years.
• Examples with physics PIs:• Geobiology and emergence of terraced architecture (UIUC)
• Gene expression and multicellular organization inDictyostelium (UCSD, Cornell)
• Multiscale simulation of avian limb development (NotreDame)
![Page 11: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/11.jpg)
Biocomplexity studies conducted in a geological context thatpermits results of studies in modern environments to be applied toancient environments in deep geological time
Geobiology
What is the interactionbetween purely physicalgeological processes andbiological processes?
![Page 12: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/12.jpg)
Travertine terraces at hot springs
![Page 13: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/13.jpg)
Travertine terraces at hot springs
![Page 14: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/14.jpg)
Travertine terraces at hot springs
![Page 15: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/15.jpg)
Travertine terraces at hot springs
![Page 16: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/16.jpg)
![Page 17: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/17.jpg)
Angel Terrace (Nov 2002)
![Page 18: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/18.jpg)
Pond Features
Variety of tem peratures(30°-62°C)
Occur on m any scales
High deposition rates, upto m illim eters/day
Aragonite needle shrubsform at higher tem ps
Calcite Ice sheets oftencollapse and settle to bottom
Calcified air bubbles
Ridged networks ofcalcite/aragonite at lower tem ps
![Page 19: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/19.jpg)
Ponds
![Page 20: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/20.jpg)
Calcite
“Ice” Sheets
![Page 21: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/21.jpg)
Pond Lip
Shrubs
![Page 22: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/22.jpg)
Microterracetteson edge of ponds.
5 cm
![Page 23: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/23.jpg)
![Page 24: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/24.jpg)
Pond lip
![Page 25: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/25.jpg)
Apron channel - fingers ofmicrobes, encrusted with aragonite
![Page 26: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/26.jpg)
Fouke et al. (2000)
Travertine Facies Model
Constructed independent of microbial analyses
![Page 27: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/27.jpg)
Section through shrubs
![Page 28: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/28.jpg)
1 - 5 mm/day“Living Geology”
![Page 29: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/29.jpg)
![Page 30: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/30.jpg)
Physical•Water Temperature
•Pressure•Flow rate/velocity
•Seasonal differences•Diurnal differences
•Weather
TimeGeological
• Sediment(s) composition• Stratigraphy• Geochemistry
• Crystal structure• Porosity / Induration
• Precipitation rates• Diagenesis
Microbiological• Population(s) constituency
• Colonization and succession• Biochemistry / gene expression
• Colony macrostructure• Transport/ Mobility
• Growth rates• Evolution
![Page 31: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/31.jpg)
• Role of microbes versus the environment?– Can microbes locally alter CO2 concentration, driving the large-scale
crystallization and geomorphology?
– Microbial cells act as passive or active nucleation sites?
• Dynamics of landscape evolution?– Fluid flow + crystallization (universal stochastic dynamics?)
– Statistical characterization of geomorphology
– Biological terra-forming (globally important deposits)
• Identification of ancient microfossils?– Bacteria as sensitive indicators of paleoenvironments?
Key Scientific Questions
![Page 32: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/32.jpg)
Water chemistry primarilydetermined by CO2
degassing.
C13 content followstheoretical predictions forthe different facies
Water chemistry
![Page 33: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/33.jpg)
C13 concentration as afunction of temperatureindicates anomalouslylow level.
Biologically drivendisequilibrium?
Disequilibrium in isotopicfractionation
![Page 34: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/34.jpg)
Normalised ion activityproduct shows degree ofsaturation at differentfacies.
Undersaturation abovepond facies correlatedwith bacteria changingfrom autotrophic toheterotrophicmetabolism?
Saturation state at each facies
![Page 35: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/35.jpg)
Analysis of microbial biodiversity
Goal: spatial arrangement of microbial species?
![Page 36: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/36.jpg)
Problem: “Species” based solely on gene sequences iscontroversial and inconsistent
Problem: ~ 98+% of the microbes at Mammoth HotSprings have not been (can not be?) cultured
Solution:- define an Operational Taxonomic Unit (OTU)- based on % similarity of 16S rRNA gene sequences- OTU analyses at 3%, 1%, and 0.5% differences
“Species” or OTU Definition
![Page 37: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/37.jpg)
16S rRNA Gene BChromosome B Chromosome BEnvironmental Chromosomal DNA
PCRAmplification
16S rRNA Gene B
(Millions of copies)
16S rRNA Gene AChromosome A Chromosome A
16S rRNA Gene A
Isolate each gene(isolate = clone)
andSequence genes
Simplified Molecular Biological Analysis
![Page 38: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/38.jpg)
162 bp
= area of broad range sequence conservation (sequence is virtually the same in all bacteria)
= area between primers (not including the primer sequences)
16S rRNA Gene Sequence Primers
Bact 519R
= location of primer sequence and its orientation
Primer E. coli Primer: Primer Sequence: Length PositionBact 343 F 5’ TAC GGR AGG CAG CAG 15-mer 343 - 357Bact519 R 5’ GWA TTA CCG CGG CKG CTG 18-mer 536 - 519
= section of the 16S rRNA sequence that is highly variable between different bacterialdivisions, conservation exists only between closely related species
3’5’
Bact 343 F Univ Bact RUniv Bact F
~1470 bp
![Page 39: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/39.jpg)
90% partitioned within facies
Two occur in all 5 faciesAquificales pBBOPB30 ββββ-Proteobacteria
![Page 40: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/40.jpg)
0.5% O.T.U.
V AC P PS DSV 23 2 3 5 2
AC 24 2 3 2P 167 17 10
PS 114 8DS 40
1.0% O.T.U.
V AC P PS DSV 15 3 2 3 2
AC 21 2 4 3P 118 14 7
PS 84 6DS 29
3.0% O.T.U.
V AC P PS DSV 6 3 2 2 2
AC 20 5 6 4P 99 14 8
PS 71 6DS 28
Decrease in OTU % definition•increases # OTUs•overlap unchanged
•Conclusion: extreme partitioningof microbial species between facies
Overlap between facies
![Page 41: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/41.jpg)
Estimation of abundance
• How do we know that we have sampled all themicrobes present in a given facies?– Incomplete sampling may cause us to conclude that species are
partitioned when in fact they are actually present in more thanone facies.
• Test convergence of sampling– How does the number of OTUs scale with number of samples
of microbes? Do we observe saturation indicatingconvergence?
![Page 42: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/42.jpg)
Accumulation Curves
S = number of OTUsn = number of samplesSm = est. total number of OTUsK = fitted constant
S(n) = Sm(1-e-Kn)
![Page 43: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/43.jpg)
S = number of OTUsn = number of samplesSm = estimated total number of OTUsK = fitted constant
S(n) = Sm(1-e-Kn)
![Page 44: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/44.jpg)
Exponential Fit to Accumulation Curve
S = number of OTUsn = number of samplesSm = est. total number of OTUsK = fitted constant
(Number of Samples)
2 - 5 samples
![Page 45: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/45.jpg)
![Page 46: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/46.jpg)
Comparison of gene sequences
• Gene sequence identifies most of the microbes andtheir metabolic characteristics.– Vent: chemolithotropy
– Pond: phototrophy
– Distal slope: heterotrophy
• Greatest biodiversity in pond facies - the facies withthe most fluctuations in pH, temperature, water flowrate
![Page 47: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/47.jpg)
Conclusion of microbe analysis
• Microbial ecology seems to track the geological facies– this would occur if microbial activity was essential to degassing
and carbonate precipitation
– but may also just indicate microbes are passive markers ofwater chemistry
• Next step: measure absolute abundances to determinequantitatively if there are enough microbes toproduce precipitation ...
![Page 48: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/48.jpg)
Laboratory experiments
• Our goal: create a laboratory analog ofpond/terracette system without microbes– Can we reproduce gross geological features such as ponds,
terracettes, microterracettes?
• In a generic flow crystallization setting, with NaCl?
• In a simulation of YNP water chemistry?
![Page 49: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/49.jpg)
Small Scale Salt Experiment
5° Slope
Variable flow rate
H2O :
-Supersaturated with NaCl
-Heated to approx. 53°
-Recirculated
![Page 50: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/50.jpg)
Shrubs
![Page 51: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/51.jpg)
![Page 52: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/52.jpg)
Large Scale NaClExperim ent
Heated 30 gallon can-Subm erged in 55 gal drum
-Used for m ixing saltwater
Tem peratures- 60°- 65° at top of ram p
- 40°- 45° at bottom
Peristaltic Pum ps
-(flow rate = 0.67 L/m in)
Heated collection tub-for recycling water
![Page 53: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/53.jpg)
DoubleTerracette
LipsAfter 2days
![Page 54: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/54.jpg)
“Ice” sheets
Shrubs
![Page 55: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/55.jpg)
Large Scale
Calcium CarbonateExperiment
-Initial Pressure 2-3 atm
-Precipitation driven by
CO2 outgassing
CaCO 3(s) + H2O (l) + CO 2 (g) Ca2+ (aq) + CO 32-(aq) +
H2CO 3(aq)
![Page 56: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/56.jpg)
What’s Next?
• Re-run Large Scale Salt Experiment– Increase slope and flow rate– Decrease/eliminate temperature gradient– Under supersaturation– Color coding with food dye– Time-lapse photography
• Large Scale Calcium Carbonate Experiment– UV sterilization on one ramp– Vary slopes, substrates– Color coding and time lapse photography– How do patterns formed compare with those at YNP?
• Back to Yellowstone National Park– Measure fractal dimensions of ponds, look for power scaling– UV sterilization of water channeled from spring
• Examine Shrubs Closer– Preserve with epoxy and examine thin sections
![Page 57: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/57.jpg)
Connection between shrubs andStrom atolites?
strom atolite: an organosedim entary structure produced by sedim ent trapping,binding, and / or precipitation as a result of the growth and m etabolic activity ofm icroorganism s, principally cyanophytes (blue-green algae) (W alter, 1976, p.1).
From the fourth edition of the "Glossary of Geology" by Julia A Jackson:
Strom atolites in AustraliaGrotzinger, et.al.
Shrubs from LargeScale NaCl experim ent
Shrubs at YellowstoneNational Park
![Page 58: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/58.jpg)
Theoretical Interest inShrub/Stromatolite Connection
• Is shrub formation generic?– Stromatolites & YNP shrubs from under water– NaCl shrubs form above water, presumably due to capillary action
• Detailed chemistry irrelevant• Physical Ingredients of simple model
– Sedimentation– Capillary action– Diffusion
• Simple model can capture qualitative and scaling features of real phenomena
DLA plus sedimentation yields stromatoliticstructures in 2D (Grotzinger and Chan,unpublished)
![Page 59: Geobiological Pattern Formation at Yellowstone’s Hot Springsonline.itp.ucsb.edu/online/pattern_c03/goldenfeld/pdf/Goldenfeld.pdfOutline • What is Geobiology? – Biocomplexity](https://reader036.vdocuments.mx/reader036/viewer/2022070805/5f03afc17e708231d40a4655/html5/thumbnails/59.jpg)
Conclusions
• Geobiological pattern formation at hot springs showsstrong microbial partitioning, following geology andwater chemistry
• Microbial cause of carbonate precipitation stillunknown
• Indication that at least some of the geomorphology isgeneric