Activated zeolite—suitable carriers for microorganisms in anaerobic digestion processes?

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BIOENERGYAND BIOFUELSActivated zeolitesuitable carriers for microorganismsin anaerobic digestion processes?S. Wei & M. Lebuhn & D. Andrade & A. Zankel &M. Cardinale & R. Birner-Gruenberger & W. Somitsch &B. J. Ueberbacher & G. M. GuebitzReceived: 12 July 2012 /Revised: 2 January 2013 /Accepted: 3 January 2013 /Published online: 23 February 2013# Springer-Verlag Berlin Heidelberg 2013Abstract Plant cell wall structures represent a barrier in thebiodegradation process to produce biogas for combustionand energy production. Consequently, approachesconcerning a more efficient de-polymerisation of celluloseand hemicellulose to monomeric sugars are required. Here,we show that natural activated zeolites (i.e. trace metalactivated zeolites) represent eminently suitable mineralmicrohabitats and potential carriers for immobilisation ofmicroorganisms responsible for anaerobic hydrolysis of bio-polymers stabilising related bacterial and methanogeniccommunities. A strategy for comprehensive analysis ofimmobilised anaerobic populations was developed thatincludes the visualisation of biofilm formation via scan-ning electron microscopy and confocal laser scanningmicroscopy, community and fingerprint analysis as wellas enzyme activity and identification analyses. UsingSDS polyacrylamide gel electrophoresis, hydrolytical ac-tive protein bands were traced by congo red staining.Liquid chromatography/mass spectroscopy revealed cellulo-lytical endo- and exoglucanase (exocellobiohydrolase) as wellas hemicellulolytical xylanase/mannase after proteolytic di-gestion. Relations to hydrolytic/fermentative zeolite colonis-ers were obtained by using single-strand conformationpolymorphism analysis (SSCP) based on amplification ofbacterial and archaeal 16S rRNA fragments. Thereby, domi-nant colonisers were affiliated to the genera Clostridium,Pseudomonas and Methanoculleus. The specific immobilisa-tion on natural zeolites with functional microbes alreadyElectronic supplementary material The online version of this article(doi:10.1007/s00253-013-4691-6) contains supplementary material,which is available to authorized users.S. Wei :M. Cardinale :G. M. GuebitzInstitute of Environmental Biotechnology,Graz University of Technology, Petersgasse 12,8010 Graz, AustriaM. Lebuhn :D. AndradeBavarian State Research Centre for Agriculture,Vttinger Strae 38,85354 Freising, GermanyA. ZankelInstitute for Electron Microscopy, Graz University of Technology,Steyrergasse 17,8010 Graz, AustriaR. Birner-GruenbergerProteomics Core Facility, Center for Medical Researchand Institute of Pathology, Medical University of Graz,Stiftingtalstrasse 24,8010 Graz, AustriaW. SomitschEngineering Consultant, Wiedner Hauptstrasse 90/2/19,1050 Vienna, AustriaB. J. UeberbacherIPUS Mineral- & Umwelttechnologie GmbH, Werksgasse 281,8786 Rottenmann, AustriaS. Wei :G. M. Guebitz (*)ACIB Austrian Centre of Industrial Biotechnology, Petersgasse 14,8010 Graz, Austriae-mail: guebitz@tugraz.atPresent Address:G. M. GuebitzDepartment of Agrobiotechnology Tulln, Institute ofEnvironmental Biotechnology, University of Natural Resourcesand Life Science, Konrad Lorenz Str. 20,3430 Tulln, AustriaAppl Microbiol Biotechnol (2013) 97:32253238DOI 10.1007/s00253-013-4691-6colonising naturally during the fermentation offers a strategyto systematically supply the biogas formation process respon-sive to population dynamics and process requirements.Keywords Biogas . Zeolites . Hemicellulases . Cellulases .Microbial community . Grass silageIntroductionIn order to stabilise and optimise biogas formation fromenergy plants several approaches were investigated to avoidunfavourable acidification, ammonia accumulation etc. de-creasing the production of methane. Adequate availability ofessential trace elements for the bacterial community wasidentified to be essential (Takashima and Speece 1989;Goodwin et al. 1990). Pobeheim et al. (2010a) showed thatthe addition of mixed trace elements increased methaneyields by up to 30 % in batch digestion of maize silage.Furthermore, effective removal of volatile solids (around73 %) has been reported for maize silage operated complete-ly stirred tank reactors (CSTR), when higher concentratedsolutions of trace metals were added (Bougrier et al. 2011).Enhancement of methane production (up to 20 %), was alsoobserved for Co and Ni addition which was corroborated byrisen cofactor F420 activities and dominance of hydrogeno-trophic Methanoculleus sp. (Pobeheim et al. 2010b). Theimportance of Co, Se and other trace metals was also ob-served for stable food waste digestion. Here, the accumula-tion of volatile fatty acids (VFAs) can only be avoided,when digesters are supplemented with a certain concentra-tion of Se, Mo, Co and W (Banks et al. 2012).Activated zeolites as used in this study combine tracemetal activation on the surface with an high ion-exchangecapacity for supplementation with cationic macro-elementssuch as Na+, K+, Mg2+ or Ca2+ and trace elements as well,that zeolites can be loaded with (Holper et al. 2005).Consequently, these materials potentially provide an excel-lent operational environment for microorganisms participat-ing either in the biomass hydrolysis or methane formationprocess. Recent studies demonstrated the capability of thesezeolites to be colonised by certain microbial populationsduring anaerobic batch-wise operation and laboratory-scaled mono-grass silage or vinasses operated bioreactors(Wei et al. 2011; Fernndez et al. 2007). Furthermore, itwas shown that microorganisms acting on biomass asdegraders, obtained by selective cultivation, can be immo-bilised on zeolite surfaces. These populations can provide aspecific enzymatic activity as addition to the natural consor-tium activities, e.g. hydrolytic activity to increase recalci-trant biomass degradation (plant cell walls) and thus resultin higher methane yields in batch-culture experiments asdemonstrated before (Wei et al. 2010). This effect couldnot be seen with enzymatic treatment alone as reported byBruni et al. (2010) applying commercially available laccasesor mixture of cellulases and hemicellulases to digested bio-fibres. Consequently, there is strong need to identify zeoliteimmobilised organisms and their enzymes in order to exploitthis unique system to improve biogas formation. Here, weshow that a combination of sophisticated microscopic [con-focal laser scanning microscopy (CLSM)-fluorescence insitu hybridization (FISH), scanning electron microscopy(SEM)], genetic [(single-strand conformation polymor-phism analysis (SSCP)] and biochemical [liquid chromatog-raphy/mass spectroscopy (LC-MS) protein identification]methods can lead to a comprehensive mechanistic under-standing of the function of zeolite immobilised anaerobicpopulations.Materials and methodsSemi-continuous fermentation and analogue batch operationThe activated zeolites used (IPUS GmbH, Rottenmann,Austria) consisted of a natural zeolitic tuff containing >85 %clinoptilolite, which was crushed to a grain size below2.5 mm. The material was loaded with Fe, Ni, Co, Mo,Se, Cu and Zn as trace metal elements to enhancemicrobial activity (Holper et al. 2005). Powderous par-ticles of carried out in mineral salt medium, which had the followingcomposition (in milligramme per litre): MgSO47H2O, 9.4;CaSO42H2O, 4.7; Na2HPO42H2O, 752; KH2PO4, 63.92;NH4CL, 18.8. After mixing, 0.47-ml trace element solutionwas added and pH adjusted to 7.2 by using 1 M HCl. Traceelement solution was composed of (in milligramme per litre):Na2EDTA2H2O, 2,740; ZnSO47H2O, 100; MnCl24H2O,25.6; H3BO3, 300; CoCl26H2O, 200; CuCl22H2O, 10;NiCl22H2O, 20; Na2MO42H2O, 900; Na2SeO35H2O, 30.4;FeSO47H2O, 1,000. In order to induce production of hydro-lytic enzymes, the following model substrate was added fed-batch-wise to the mineral salt medium in a concentration of1%DM (w/v): microcrystalline cellulose (Fluka), 30%; xylanfrom Birchwood (Roth, Karlsruhe, Germany), 50 %; ligninwith low sulfonate content (Sigma-Aldrich, St. Louis, MO,USA), 14.5 %; pectin C (Roth), 0.5 % and starch (Roth), 5 %.The re-activation experiment was carried out over a totalperiod of 55 days at temperatures according to the formerbatch-fermentation experiments, i.e. 35 and 45 C respective-ly. Samples were taken as duplicates at regular intervals.PCR-based SSCP and sequencing analysisThe total bacterial community DNAwas extracted by usinga DNA extraction kit for soil samples (FastDNA Spin Kitfor Soil, MP Biomedicals, Solon, OH, USA) following themanufacturers recommendations. To collect zeolite-immobilised microorganisms, 0.1 g of zeolite was rinsedthree times with 500 l of 1 PBS (pH8.0) before applyingthe DNA extraction procedure. Free microorganisms werecollected from sample supernatants (1.0 ml) representing thetotal sludge inoculation phase. Samples were centrifuged for15 min at 16,750g to collect the cells. Amplification ofbacterial 16S rRNA gene fragments was carried out usingthe bacterial primer pair Com-1 (5-CAG CAG CCG CGGTAA TAC-3) (Schwieger and Tebbe 1998) and Unibac-II-927rP (5-CCC GTC AAT TYM TTT GAG TT-3) for anamplicon size of 412 bp according to Lieber et al. (2002).Amplification of archaeal 16S rRNA gene fragments wasperformed using the primer pair ARC-787f (5-ATTAGATACC CSBGT AGTCC-3) and ARC-1059r (5-GCCATGCACC WCCTC T-3) for an amplicon size of 273 bpfollowing Yu et al. (2005), using a Biometra T personal/gradient system (Biometra, Gttingen, Germany). After pu-rification of PCR-generated DNA products using the GeneClean Turbo Kit (Qbiogene, Heidelberg, Germany) follow-ing the manufacturers recommendations, DNA-content wasdetermined before SSCP analysis. Therefore, 1 l of puri-fied PCR-products were analysed using a micro-volumespectrophotometer for nucleic acid and protein quantitation(NanoDrop 2000, Thermo Fisher Scientific, Wilmington,DE, USA). SSCP analysis of amplified bacterial and archae-al rrs (16S rRNA gene) fragments was carried out accordingto Schwieger and Tebbe (1998). For single-strand forma-tion, 10 l of purified PCR products containing 150 ng ofdsDNA were used to generate comparable bacterial andarchaeal fingerprints after -exonuclease digestion.Individual bands of fingerprint patterns were excised forDNA elution through several incubation steps in sterile elutionbuffer pH8.0 (5 M ammonium acetate, 10 mM magnesiumacetate, 1 mM Na2EDTA, 0.1 % SDS): (1) 15 min at 70 C,(2) thawed for 5 min at 50 C, (3) heated for 5 min at 90 C,(4) incubated for 3 h at 37 C and (5) stored at 20 C for atleast 3 days before DNA precipitation using ethanol (70 %)was carried out. Similar PA-gel band positions were combinedin order to increase DNA amounts for re-amplification usingthe same primer pairs as for the initial PCR. PCR productswere then used for sequencing analysis after adjusting the totalDNA concentration to 2 ngl1. Sequencing analyses wereperformed by Eurofins MWG Operon (Ebersberg, Germany).To identify similar sequences that are available in the NCBIGenbank, sequences were used in BLASTn searches(Altschul et al. 1997; hits with minimum 95 % sequence identity and acoverage cut off of 90 % were considered for discussion.Accession numbers for primary nucleotide sequence datadetermined during 16S rRNA gene fragment-based commu-nity analyses were submitted to the NCBI GenBank database(reference code: BankIt1555395) representing band numbers1 to 17 from SSCP-generated fingerprint patterns: (1)JX436456, (3) JX436455, (4) JX436459, (7) JX436458, (8)JX436457, (9) JX436454 and (17) JX436453. According tothe guidelines of the database, SSCP sequence lengths werenot less than 150 bp, and quality of the data was granted byclipping.Enzyme activity assayEnzyme activity, i.e. cellulase, pectinase and xylanase weremeasured using a 3-amino,5-nitrosalicylic acid (DNS) assaywhich is based on the quantification of reducing sugarsreleased with DNS according to Bailey et al. (1992).Samples were collected at two different sample sites: (1)liquid phase, for determination of extracellular enzymes asample volume of 1 ml was centrifuged (13,000g for5 min) and supernatants used; (2) pellet, for determinationof cell-bound enzymes of zeolite-immobilised microorgan-isms a sample volume of 1 ml was centrifuged, the pelletcollected and two times rinsed with 1x PBS, before it wasresuspended in 500 l of 1 PBS (pH8.0). The resuspensionwas achieved by gently using the pipet tip (a) or treating thepellet with glass beads (0.15 to 2.00 m) for 40 s. using aFastPrep Instrument (Qbiogene, Heidelberg, Germany) toensure complete detachment of zeolite-immobilised bacteriacells (b). The different sample fractions were then incubatedat 50 C for 10 min in the presence of a substrate solutionAppl Microbiol Biotechnol (2013) 97:32253238 3227containing 1 % (w/v) carboxymethylcellulose (Fluka, St.Gallen, Switzerland), polygalacturonic acid (Fluka) or xylanfrom birchwood (Roth) in an adjusted pH range of 6.0 to 6.5by using potassium phosphate buffer. The photometricabsorption was determined at 530/540 nm in 96-wellplates (Greiner, Frickenhausen, Germany) using a platereader (Tecan Infinite 200 M, Mnnedorf, Switzerland).Enzyme activity is given as units of enzyme activity perlitre (Ul1). An enzyme unit is defined as conversion of1 mol reduced sugar (D-glucose, or D-xylose) per minuteunder the given conditions above. One unit corresponds to16.67 nkat.SDS-PA-Gel analysisFor protein separation SDS-PAGE was performed in 10 %polyacrylamide slab gels according to Laemmli (1970). Theseparating gel composition (5 ml) contained: 1.25 ml acryl-amide (40 %), 1.25 ml Tris (1.5 M, pH8.8), 50 l sodiumdodecyl sulphate (SDS; 10 %), 25 l ammonium persulfate(APS; 10 %), 6 lN,N,N,N-tetramethylethylenediamine(TEMED), 2.4 ml dH2O. The stacking gel (5 ml) wascomposed of: 0.5 ml acrylamide (40 %), 1.25 ml Tris(0.5 M, pH6.8), 50 l SDS (10 %), 25 l APS, 6 lTEMED, 3.2 ml dH2O. For activity staining, polymericsubstrate, i.e. carboxymethylcellulose (Fluka, St. Gallen,Switzerland), lichenan (Megazyme, Wicklow, Ireland) orxylan (Roth, Karlsruhe, Germany) was incorporated intothe separating gel in a concentration of 0.5 % (w/v) priorto the addition of APS according to Zverlov et al. (2010).Protein samples were mixed with loading dye (1:1) contain-ing 2.2 % SDS and applied directly to the polymerised gelafter determination of the protein concentration followingLowry et al. (1951) using the Roti-Nanoquant proteinquantitation assay (Roth, Karlsruhe, Germany). The runningbuffer contained the following components: 1 g SDS, 3 gTris, 14 g glycine (Roth). Electrophoresis was performed onice at a conduction current of 30 mA (60 V) until theloading dye front reached the bottom of the slab gel (23 h). Gels were then put between cellulosic filter papers(Schleicher and Schuell, Dassel, Germany) soaked with0.1 M succinate buffer (pH4.5) and incubated for 120 minat 50 C for renaturation. Protein bands were optionallydetected by staining with Coomassie blue R-250 followingKang et al. (2002). After destaining with 10 % ethanolsolution containing 2 % (v/v) o-phosphoric acid, Congored (Sigma-Aldrich, St. Louis, MO, USA) was appliedto detect catalytically active bands by staining the poly-meric gel matrix. Therefore gels were submersed inCongo red solution (0.02 %) for 15 min at room tem-perature (20 C). After destaining with 1 M NaCl,halo zones in the red-stained background revealed thedegradation of the matrix incorporated biopolymer,which were therefore chosen for further characterisationvia LC-MS/MSLC-MS/MS analysisProtein identification and internal sequence information wasreceived from LC-MS/MS. Protein bands were excised fromgels and reduced, alkylated and digested with Promega-modified trypsin according to the method of Shevchenkoet al. (1996). Digests were separated by nano-HPLC(Agilent 1200 system, Vienna, Austria) equipped with aZorbax 300SB-C18 enrichment column (5 m, 50.3 mm)and a Zorbax 300SB-C18 nanocolumn (3.5 m, 1500.075 mm). Forty microlitres of sample were injected andconcentrated on the enrichment column for 6 min using0.1 % formic acid as isocratic solvent at a flow rate of 20 lmin1. The column was then switched in the nanoflow circuit,and the sample was loaded on the nanocolumn at a flow rate of300 nlmin1. Separation was carried out using the followinggradient, where solvent A is 0.3 % formic acid in water andsolvent B is a mixture of acetonitrile and water (4:1) contain-ing 0.3 % formic acid: 06 min, 13 % B; 663 min, 1328 %B; 6388 min, 2850 % B; 8889 min, 50100 % B; 89100 min, 100 % B; 100101 min, 10013 % B; 101120 min,re-equilibration at 13 % B. The sample was ionized in thenanospray source equipped with nanospray tips (PicoTipTMStock# FS360-75-15-D-20, Coating: 1P4P, 15+/ 1 mEmitter, New Objective, Woburn, MA, USA). It was analyzedin a Thermo LTQ-FT mass spectrometer (Thermo FisherScientific, Waltham, MA, USA) operated in positive ionmode, applying alternating full scan MS (m/z 400 to 2,000)in the ion cyclotron and MS/MS by collision induced disso-ciation of the five most intense peaks in the ion trap withdynamic exclusion enabled. The LC-MS/MS data were ana-lyzed by searching the NCBI public database with Mascot 2.2(MatrixScience, London, UK). A maximum false discoveryrate of 5% using decoy database search, an ion score cut off of20 and a minimum of two identified peptides was chosen asidentification criteria.Scanning electron microscopyFor the investigation of morphological colonisation charac-teristics of activated zeolite particles, scanning electron mi-croscopy was used (Zeiss ULTRA 55, Carl Zeiss MicroImaging GmbH, Germany). Particles of 1.0 to 2.5 mm indiameter were analysed. The biological material was imagedwith the high-efficiency in-lens SE detector using second-ary electrons (SE), which deliver topographic contrast(Goldstein et al. 2003). Additionally, imaging with an angleselective backscattered electron (AsB) detector was per-formed. It detects backscattered electrons (BSE) and deliv-ers compositional contrast, which is determined by the3228 Appl Microbiol Biotechnol (2013) 97:32253238differences in the local chemical composition of an investi-gated specimen (Goldstein et al. 2003). In the case of SEimaging, 5-kV acceleration voltage of the primary electronswas applied with the exception of one micrograph whichwas imaged simultaneously with the AsB detector at anacceleration voltage of 15 kV. Before application, freshsamples were fixed in glutaraldehyde (2.5 % in 0.1 Mphosphate puffer, pH7.2), dehydrated in a graded ethanolseries with a final step in propylene oxide and ultimately driedby lyophilisation (Labconco Freeze Dry System FreeZone4.5, Kansas City, MO, USA) or critical point drying (CO2;Bal-Tec CPD, Balzers, Frstentum Liechtenstein). For obser-vation, prepared samples were mounted on aluminum stubsusing double-sided carbon tape and moreover a carbon filmwas applied onto the specimens surfaces by high-vacuumevaporation.Confocal laser-scanning microscopy and fluorescencein situ hybridizationTo investigate taxonomic groups embedded in biofilms ongrass silage fibres and activated zeolite particles reactors of a model substrate for grass silage (Fig. 3c, d). Here,bacteria were seen both on the surface and deep inside theclefts of zeolites. Bacterial colonisation was less pronouncedwhen compared to grass silage, however, still approximatelyFig. 1 SEM images ofactivated zeolite particles (80 %.Highest band pattern similarity value (>88 %) was found forfingerprints from semi-continuous digestion of grass silageforming a third major cluster, which revealed no significantdifferences between zeolite surface and total sludge originatedpatterns. Populations in the liquid phase and on the surfaceFig. 3 a Bright field total viewof washed zeolite particleswere probably foremost equally abundant, but within themajor cluster, two more distinct ones were found for activatedzeolite surfaces from bioreactor I2 (after in sacco incubationfrom days 7 to 21) and I3 (days 21 to 84) with simi-larities of 88 and 90 % respectively. Sequence analysesof zeolite surface samples collected from semi-continuously and batch-operated fermentation of grasssilage and model substrate indicated affiliations to two bacte-rial orders, i.e. Pseudomonadales and Clostridiales, and onearchaeal order, i.e. Methanomicrobiales. Within the familyPseudomonadaceae, affiliations to cellulases and pectinasesproducing Pseudomonas fluorescens (Pseudomonas cellu-losa) and Pseudomonas putida were indicated, when colon-ised zeolites from batch fermentation of model substrate at35 C were analysed (Fig. 4, band spot 17). Correspondingbands were also observed when samples from semi-continuously operated fermentation approaches at 45 C wereapplied to the SSCP analysis. In contrast, affiliations to thefamily Clostridiaceae were only present in samples frombatch and semi-continuously operated fermentations of grasssilage (Fig. 4, band spot 9). Within the archaeal domain,affiliations to the order Methanomicrobiales, i.e. thegenus Methanoculleus spp. was indicated during thetotal observation period of semi-continuously operatedfermentation of grass silage analysing colonised zeolites.Data on the community composition of zeolite-associatedmicroorganisms (archaea and bacteria) are summarised in-cluding indications to affiliations below the family level(Table 1).Role of zeolite-associated populations in biomassdegradationIn order to analyse the role of microorganisms colonisingactivated zeolites on biomass degradation, hydrolytic en-zyme activities were determined. Therefore, washed colon-ised activated zeolites were re-incubated in buffer onsubstrate according to their pre-incubation, i.e. model sub-strate or grass silage. Then, cellulase and xylanase activitieswere measured after certain time points throughout the re-incubation (Fig. 6). Highest hydrolytic enzyme activities(2.8 kUl1) were observed for colonized zeolite samplestaken from model substrate fermentations after 8 days ofre-incubation at 35 C. When increased temperature (45 C)was applied, an individual maximum was reached (1.9 kUl1). Re-incubation in the presence of grass silage at 35 Cled to 2.2 kUl1 on average. As for model substrate, in-creased incubation temperature decreased hydrolyticalFig. 4 Non-denaturating polyacrylamide gel from the SSCP analysisbased on (a) archaeal rrs (16S rDNA gene) fragments and (b) bacterialrrs (16S rDNA gene) fragments of (a) semi-continuously operatedmono-grass silage fermentation exposed zeolites (IS2/3),corresponding total sludge samples (I13) and of (b) batch-culturesfed with grass silage (GS) or model substrate (MS). (M: 1 kb DNA-ladder marker lanes; sample-identity: IS2/3=bioreactors (in sacco sam-ple); MS/GS=batch-substrate, 35/45=fermentation temperature in (indegree Celsius), 7353=fermentation time in (in day)3232 Appl Microbiol Biotechnol (2013) 97:32253238enzyme activities (1.8 kUl1 at day27). The overall maxi-mum was found for re-incubation on model substrate (35 C) at day27 with 3.2 kUl1 on average. Assessing xylanaseand cellulase activities individually, highest xylanase activ-ities (around 1.5 to 1.6 kUl1) were found for both sub-strates (at day8 for model substrate and day27 for grasssilage) at 45 C incubation temperature. In contrast, maxi-mum cellulase activities occurred during incubation at 35 Cranging from 1.3 kUl1 upon grass silage to 1.9 kUl1 uponmodel substrate at days8 and 27, respectively. As a result,cellulase activities pushed the maximum value of totalhydrolytical enzyme activity towards the lower incubationtemperature condition. During incubation, pH was adjustedto 6.0 to 6.5 initially and at each sampling point. This pHrange was not exceeded, except for batches re-incubated onmodel substrate at 45 C. Here, pH values were around 7.5from days8 to 27, which suggests that decreased hydrolyticenzyme activities from day8 on where due to unstable pHconditions, possibly exceeding the optimal pH range forhydrolytic enzymes. Further feedings of model substrate orgrass silage after day27 could not provoke additionalincreases of enzyme activities (data not shown).Overall, bacteria immobilised on activated zeolites,washed and stored for more than 20 months, started produc-tion of hydrolytic enzymes after only a few days upon re-incubation. These results clearly demonstrated that zeolite-habituating functional microorganisms endure or gain along-term revitalisation ability throughout immobilisationon zeolites. Thus, bacteria cells are able to immediately starthydrolytic enzyme production when re-incubated in synthet-ic medium with model substrate at 35 C or grass silage at45 C fermentation temperature.For further characterisation of enzymes associated withzeolite surfaces involved in the degradation of grass silage,identification was realised through LC-MS peptide sequenc-ing analysis and protein database searches. Hydrolyticalactive proteins secreted by zeolite immobilised microorgan-isms after re-incubation were preselected by separation viagel electrophoresis on polyacrylamide gel matrix incorpo-rating compounds of plant cell wall biopolymers. All threesimilarity [%]10095908580757065605550.............................surfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfacesurfaceGS1.35.17GS2.35.17GS3.35.17GS2.45.17GS3.45.17GS1.45.17MS1.45.17MS2.45.17MS3.45.17MS1.35.17MS3.35.17MS2.35.17I2.45.285I3.45.285IS2.45.84IS2.45.42I2.45.264IS3.45.21IS3.45.42IS3.45.84I3.45.264I1.45.285IS3.45.7I1.45.264I3.45.353IS3.45.14IS2.45.14IS2.45.21IS2.45.7I II IIIzeolite surfacebzeolite surfaceaIIIIIIFig. 5 Clustering analysis generated dendrogram using band-basedcomparison (DICE; 1 % tolerance, 1 % optimisation, grouped byUPGMA) of anaerobic populations on activated zeolite surfaces(highlighted in grey) taken from batch-cultures (zeolite surface b)and semi-continuous operated bioreactors [zeolite surface a andtotal sludge samples (highlighted in white)]. Sample-identity: I2/3=bioreactors (IS=in sacco sample); MS/GS=batch-substrate, 35/45=fermentation temperature in (in degree Celsius), 7353=fermentationtime [in days])Appl Microbiol Biotechnol (2013) 97:32253238 3233substrates for cellulases/hemicellulases were useful fordetecting active enzymes, although CMC delivered thesharpest protein bands compared to lichenan and was there-fore preferred for enzyme separation. Samples were collect-ed from batch-cultivated activated zeolite inhabitinganaerobic populations during re-incubation in syntheticmineral medium on model substrate or grass silage(Table 2). Sampling points were coordinated with positiveenzyme activity findings. When lichenan was used, onlyexocellobiohydrolase II ( and amylase ( identified throughout the total re-incubation periodupon model substrate at 35 C. At day1, several positivematches for grass silage fed batch-cultures re-incubated at35 C appeared, i.e. cellulases (exocellobiohydrolases),hemicellulase (1,4--mannanohydrolase) and a sugar-hydrolysing enzyme with molecular weights ranging from47 to 149 kD exclusively related to Paenibacillus polymyxastrains from the division Firmicutes. At day8 of re-incubation, where highest enzyme activities in batch-cultures fed with model substrate (at 35/45 C) and grassTable 1 Identified clinoptilolite-associated microorganisms separatedby SSCP analysis and direct sequencing from bioreactors semi-continuously operated with grass silage; sample-identity: I2/3=bio-reactors (IS=in sacco sample); fermentation temperature during thesampling period: 45 C; 784=days of fermentation, when appearan-ces were observed; band numbers are in accordance with band selec-tion marked in Fig. 4 (see above)Fermentation BLASTacc. no.Indicated organism Family Querycoverage (%)Maximumidentity (%)Mode Time (day) BandContinuous I3 7, 21 4 AY196674.1 Methanoculleus bourgensis Methanomicrobiaceae 90 98Continuous I3 7, 21 EF118904.1 Methanoculleus thermophilus Methanomicrobiaceae 90 98Continuous I3 7, 21 DQ787476.1 Methanoculleus receptaculi strain ZC-2,3 Methanomicrobiaceae 90 98Continuous I3 7, 2142 7 AF107104 Methanoculleus sp. MAB2 Methanomicrobiaceae 92 99Continuous I3 7, 2142 AY196674 Methanoculleus bourgensis Methanomicrobiaceae 92 99Continuous I3 7, 2142 DQ787476.1 Methanoculleus receptaculi strain ZC-2,3 Methanomicrobiaceae 92 98Continuous I3 7, 2142 NR_028253.1 Methanoculleus palmolei DSM 4273 Methanomicrobiaceae 92 97Continuous I3 7, 2142 AJ862839.1 Methanoculleus thermophilus Methanomicrobiaceae 92 97Continuous I3 7, 2142 AF095270.1 Methanoculleus olentangyi Methanomicrobiaceae 92 96Continuous I3 7, 2142 8 AF107103.1 Methanoculleus sp. MAB1 Methanomicrobiaceae 96 99Continuous I3 7, 2142 AY196674 Methanoculleus bourgensis Methanomicrobiaceae 96 99Continuous I3 7, 2142 DQ787476.1 Methanoculleus receptaculi strain ZC-2,3 Methanomicrobiaceae 96 98Continuous I3 7, 2142 NR_028253.1 Methanoculleus palmolei DSM 4273 Methanomicrobiaceae 96 97Continuous I3 7, 2142 NR_028163.1 Methanolinea tarda NOBI-1 Methanomicrobiaceae 96 96Continuous I2 4284 1 AY196674 Methanoculleus bourgensis Methanomicrobiaceae 90 99Continuous I2 4284 EF118904 Methanoculleus thermophilus strain JB-1 Methanomicrobiaceae 90 98Continuous I2 4284 DQ787476 Methanoculleus receptaculi Methanomicrobiaceae 90 98Continuous I2 4284 EU722338.1 Methanoculleus marisnigri Methanomicrobiaceae 90 98Continuous I2 4284 NR_028856 Methanoculleus submarinus strain Nankai-1 Methanomicrobiaceae 90 98Continuous I2 4284 NR_028152.1 Methanoculleus chikugoensis MG62 Methanomicrobiaceae 90 98Continuous I2 4284 NR_028253.1 Methanoculleus palmolei DSM 4273 Methanomicrobiaceae 90 98Continuous I2 784 3 AY196674 Methanoculleus bourgensis Methanomicrobiaceae 90 98Continuous I2 784 EF118904 Methanoculleus thermophilus strain JB-1 Methanomicrobiaceae 90 98Continuous I2 784 DQ787476 Methanoculleus receptaculi Methanomicrobiaceae 90 98Continuous I2 784 EU722338.1 Methanoculleus marisnigri Methanomicrobiaceae 90 98Continuous I2 784 NR_028856 Methanoculleus submarinus strain Nankai-1 Methanomicrobiaceae 90 98Continuous I2 784 NR_028152.1 Methanoculleus chikugoensis MG62 Methanomicrobiaceae 90 98Continuous I2 784 NR_028253.1 Methanoculleus palmolei DSM 4273 Methanomicrobiaceae 90 98Continuous I2,3 784 9 FJ808611 Clostridium sp. Clostridiaceae 96 92Continuous I2,3 784 17 JF432053 Pseudomonas sp. Pseudomonadaceae 100 100Continuous I2,3 784 JF756250.1 Pseudomonas lundensis strain MFPB42A12-09 Pseudomonadaceae 100 100Continuous I2,3 784 HM854252.1 Pseudomonas pelagia strain KTT-14 Pseudomonadaceae 100 100Continuous I2,3 784 HM031486.1 Pseudomonas pertucinogena strain mol25 Pseudomonadaceae 100 100Continuous I2,3 784 FJ232608 Pseudomonas fluorescens Pseudomonadaceae 100 100Continuous I2,3 784 AF173970 Pseudomonas putida Pseudomonadaceae 100 1003234 Appl Microbiol Biotechnol (2013) 97:32253238silage (at 35 C) were measured, mainly cellulolytic endo-1,4-/1,3--D-glucanohydrolase was identified (foremost re-lated to Paenibacillus spp.). At day16, endoglucanase fromPaenibacillus sp. was present in batch-cultures re-incubatedat 45 C. Furthermore, endo-1,4--glucanase affiliated toSymbiobacterium thermophilum and isomerases ofThermoanaerobacter pseudethanolicus and Fusobacteriumnucleatum were present. At day27, xylose isomerases andglycoside hydrolase related to three genera from within theorder Bacillales were identified, possibly indicating a shifttowards carbohydrate conversion in succession to the for-mer degradation of plant cell wall biopolymers. Besidespositive matches for recalcitrant biomass degradingenzymes, flagellin of P. fluorescens was found with highestscore and sequence coverage (23 %) from day28 on to theend of the observation period at day84 of the semi-continuously operated bioreactor experiment. These findingconfirmed the positive identification of Pseudomonadaceaein the course of the community analysis.DiscussionScanning electron and confocal laser scanning microscopyusing FISH gave optical evidence of microbes preferringactivated zeolite surfaces as operational environment.Thereby, colonisation was not only observed on the surfaceof zeolite particles, it also took place inside the porousframework as well. Observed cell morphologies and piliformations on surfaces did match with findings of Jarrellet al. (2011), who reported that Flagella and pili ofMethanococcus maripaludis have a second and first role insurface attachment besides motility and cell-connectingfunctions and that those cells lacking such surfaceappendages were unable to attach efficiently to any surfaces.Bacterial biomass degraders in anaerobic processes areknown to produce multi-enzyme complexes, i.e. cellulo-somes for efficient cellulose and hemicellulose degradation(Schwarz 2001; Karita et al. 1997). Here, the attachment tosubstrate surfaces, e.g. fibres of microcrystalline cellulose isrealised by protuberances with dimensions up to 550 nm inlength and between 50 and 300 nm in width (Bayer et al.1998) that were also observed in our study. Furthermore,FISH-labeling confirmed dense biofilm formation on andinside zeolite particles by bacteria exclusively. Althougharchaeal colonisers were detected during community analy-sis and methane production during the colonisation processwas observed (Fig. S1), archaea-specific probing did notlead to corresponding detection signals, which is most likelydue to the lower threshold detection level of the in situhybridization technique compared to PCR-based methods,than real evidence for the absence of methanogens.Cluster and sequencing analyses were useful tools for theverification of microbial populations associated with zeolitesurfaces. Amongst them, affiliations to the familyClostridiaceae were observed, representing a group of obli-gate anaerobes involving several species from the genusClostridium producing hemicellulolytic and cellulolytic en-zyme activities (Van Gylswyk and van der Toorn 1986).Furthermore, affiliations to the family Pseudomonadaceaewere found amongst zeolite colonisers. These gram-negativeaerobes are involving species that produce non-complexed,cell-free cellulolytic enzymes, e.g. P. cellulosa (Dees et al.1995). Recently, Potivichayanon et al. (2011) demonstratedbiogas production enhancement by the addition ofPseudomonas aeruginosa into the anaerobic biodegradationprocess. In general, Clostridiaceae and Pseudomonadaceaerender well-known degraders of cellulose and lipids05001000150020002500300035001 8 16 27 1 8 16 27 1 8 16 27 1 8 16 27a b c dhydrolytic enzyme activity [U l-1]sample and time [d]cellulasexylanaseFig. 6 Hydrolytic enzymeactivities (cellulase [whitecolumn part]+xylanase [greycolumn part]; in units per litre)determined during batch-wiseoperated re-incubation ofwashed colonised zeolites inmineral salt medium on a mod-el substrate at 35 C, b modelsubstrate at 45 C, c grass silageat 35 C, d grass silage at 45 Cover a total time period of27 daysAppl Microbiol Biotechnol (2013) 97:32253238 3235producing monomeric sugars, fatty acids and glycerol in an-aerobic processes (Bischofsberger et al. 2004). However,since clinoptilolitezeolite possesses a nano- and micro-porous framework with an internal surface size of up to400 m2g1, it possibly provides anaerobic and aerobic zonesfor both obligate anaerobes and aerobes.Colonisers affiliated to the archaeal domain wereassigned solely to the order Methanomicrobiales. Thisgroup uses the hydrogenotrophic pathway to generate meth-ane that allows faster growth rates than acetotrophic growth,which in turn probably led to its dominant appearance onzeolite surfaces. Sequence analyses indicated the presenceof Methanoculleus sp. amongst the colonisers, a genus thathas also been reported to appear in association with in-creased methane production from model substrate for maizeupon trace metal supplementation (Pobeheim et al. 2010b).Table 2 Identification of hydrolases secreted by clinoptilolite immo-bilised microorganisms through SDS-PAGE with matrix incorporatedCMC, lichenan or xylan for activity staining. Active bands wereexcised and further analysed (LC-MS/MS, NCBI public databasesearch with Mascot). Only hits with highest score are listed (exceptfor samples collected at day8 where ID was still reliable, but highestscores not reached). Samples were collected from batch-cultivatedactivated clinoptilolite migulator inhabiting microorganisms duringre-incubation on model substrate (MS) or grass silage (GS) over atotal time period of 27 daysCultivation gi no. EC no. Enzyme Mass(kD)Related organism Score Peptides SequenceSubstrate Temp.(C)Time(day)(unique) CoverageGS 35 1 308067135 Arabinosidase ~57 Paenibacillus polymyxa E681 113 2 (2) 7GS 35 1 308071054 1,4--Mannase B ~149 Paenibacillus polymyxa E681 160 2 (2) 2GS 35 1 308067781 Exocellobiohydrolase 3 ~77 Paenibacillus polymyxa E681 775 24 (12) 18GS 35 1 308069068 Exocellobiohydrolase II ~108 Paenibacillus polymyxa E681 271 4 (4) 6GS 35 1 310640531 Exoglucanase A ~77 Paenibacillus polymyxa SC2 609 16 (10) 19GS 35 1 308071411 Pectate lyase 2 ~47 Paenibacillus polymyxa E681 190 4 (3) 12GS 35 1 308068567 Glucosidase yic I ~87 Paenibacillus polymyxa E681 103 2 (2) 3GS 35 8 146350814 Endoglucanase ~62 Paenibacillus sp. KSM-N659 120 3 (3) 5GS 35 8 4249556 Endoglucanase ~33 Humicola grisea var. Thermoidea 129 3 9GS 35 8 232219 Endoglucanase A ~77 Paenibacillus lautus 168 4 (3) 5MS 35 8 146350814 Endoglucanase ~62 Paenibacillus sp. KSM-N659 120 3 2MS 35 8 146350812 Endoglucanase ~62 Paenibacillus sp. KSM-N440 115 2 3MS 35 8 146350810 Endoglucanase ~62 Paenibacillus sp. KSM-N145 115 2 3MS 35 8 146350808 Endoglucanase ~62 Paenibacillus sp. KSM-N115 115 2 3MS 35 8 232219 Endoglucanase A ~77 Paenibacillus lautus 168 3 5MS 35 8 308069068 Exocellobiohydrolase II ~108 Paenibacillus polymyxa E681 130 2 2MS 35 8 310641984 Glycoside hydrolase family 48 ~110 Paenibacillus polymyxa SC2 130 2 2GS 35 16 4249556 Endoglucanase ~33 Humicola grisea var. Thermoidea 170 7 (4) 15GS 35 16 16078876 Endoxylanase ~47 Bacillus subtilis 168 72 4 (2) 4MS 35 16 1170135 Cellulase ~24 Humicola insolens 87 2 9MS 35 16 146350814 Endoglucanase ~62 Paenibacillus sp. KSM-N659 292 6 9GS 45 16 51893813 Endo-1,4--glucanase ~40 Symbiobacterium thermophilum 570 8 35MS 45 16 146350812 Endoglucanase ~62 Paenibacillus sp. KSM-N440 270 4 6MS 45 16 146350810 Endoglucanase ~62 Paenibacillus sp. KSM-N145 270 4 6MS 45 16 146350808 Endoglucanase ~62 Paenibacillus sp. KSM-N115 270 4 6MS 45 16 308068047 Glucose-6-phosphate isomerase ~50 Paenibacillus polymyxa E681 116 3 7MS 45 16 167037114 Glucose-6-phosphate isomerase ~50 Thermoanaerobacter pseudethanolicusATCC 3322379 2 6MS 45 16 34763477 Glucose-6-phosphate isomerase ~42 Fusobacterium nucleatum ATCC 49256 139 3 7MS 45 16 253574746 L-Arabinose isomerase ~55 Paenibacillus sp. D14 92 2 4MS 35 27 232219 Endoglucanase A ~77 Paenibacillus lautus 619 12 (8) 19MS 35 27 310641984 Glycoside hydrolase family 48 ~110 Paenibacillus polymyxa SC2 305 10 (5) 5MS 35 27 253574413 Xylose isomerase ~49 Paenibacillus sp. D14 227 10 (4) 8MS 35 27 1750124 Xylose isomerase ~50 Bacillus subtilis 164 2 6MS 35 27 310641984 Glycoside hydrolase family 48 ~110 Paenibacillus polymyxa SC2 305 5 5MS 35 27 27227837 Xylanase 5 ~143 Paenibacillus sp. W-61 128 2 (2) 1MS 35 27 261409352 Xylose isomerase ~49 Geobacillus sp. Y412MC10 196 2 63236 Appl Microbiol Biotechnol (2013) 97:32253238Amongst coccoid methanogens, which grow on H2CO2,formate and some secondary alcohols, the presence ofMethanoculleus marisnigri was indicated, although its mor-phology could not be observed in microscopy approaches.Cells are usually 1 to 2 m in diameter and have optimumgrowth conditions at mesophilic temperatures and slightlyalkaline pH values (Maestrojun et al. 1990). All the meth-anogenic species we found were identified under mild ther-mophilic conditions.Enzyme identification complemented the community anal-ysis revealing a broad spectrum of cellulolytical enzymes andrelated organisms that belonged to the genera Bacillus sp.,Clostridium sp. and Paenibacillus sp. Generated peptidesequences via LC-MS resulted in 36 positive hits coveringup several important enzymes for the degradation of plant cellwall polymers. Additionally, a set of isomerases was foundthat was affiliated to, e.g. Thermoanaerobacter pseudethano-licus, a rod-shaped, spore-forming, carbohydrate fermentingbacterium (Onyenwoke et al. 2007) and Fusobacteriumnucleatum, that is closely related to Bacteroides sp. andFlavobacterium sp. (Bolstad et al. 1996). The conver-sion of D-glucose-6-phosphate to D-fructose-6-phosphatemediated by isomerases represents an energy-deliveringstep within the bacterial metabolism and was probablyevolved subsequent to hydrolysis of complex polysac-charides. In addition, enzyme activity tests revealed along-term revitalisation ability regarding cellulases andxylanases associated with zeolite-habituating microor-ganisms. Former experiments showed that such popula-tions can be introduced to the fermentation processresulting in significantly increased methane productivity(Wei et al. 2010). In conclusion, activated zeolites areeminently suited as natural carrier material for micro-organisms, potentially stabilising and enhancing the bio-gas production process from recalcitrant plant biomass.Acknowledgments This study was performed within the AustrianCentre of Industrial Biotechnology ACIB and has been kindly sup-ported by IPUS GmbH (Austria), the Federal Ministry of Economy,Family and Youth (BMWFJ), the Federal Ministry of Traffic, Innova-tion and Technology (bmvit), the Styrian Business Promotion AgencySFG, the Standortagentur Tirol and ZITTechnology Agency of theCity of Vienna through the COMET-Funding Program managed by theAustrian Research Promotion Agency FFG. Many thanks go to con-tributors of the collaborating organisations and institutes (FELMI-ZFE,ZMF and LfL).ReferencesAltschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W,Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a newgeneration of protein database search programs. 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Biotechnol Bioeng 89(6):670679Zheng D, Alm EW, Stahl DA, Raskin L (1996) Characterization ofuniversal small-unit rRNA hybridization probes for quantitativemolecular ecology studies. Appl Environ Microbiol 62:45044513Zverlov VV, Hiegl W, Kck DE, Kellermann J, Kllmeier T, SchwarzWH (2010) Hydrolytic bacteria in mesophilic and thermophilicdegradation of plant biomass. Eng Life Sci 10(6):5285363238 Appl Microbiol Biotechnol (2013) 97:32253238Activated zeolitesuitable carriers for microorganisms in anaerobic digestion processes?AbstractIntroductionMaterials and methodsSemi-continuous fermentation and analogue batch operationPCR-based SSCP and sequencing analysisEnzyme activity assaySDS-PA-Gel analysisLC-MS/MS analysisScanning electron microscopyConfocal laser-scanning microscopy and fluorescence in situ hybridizationResultsCommunity profile and characterisation of populations on zeolitesRole of zeolite-associated populations in biomass degradationDiscussionReferences


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