Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

Abram, 2011, A metaproteomic approach gives functional insights into anaerobic digestion, J Appl Microbiol, 110, 1550, 10.1111/j.1365-2672.2011.05011.x

Bayer, 2008, From cellulosomes to cellulosomics, Chem Rec, 8, 364, 10.1002/tcr.20160

Beganovic, 2010, Characterization of the insoluble proteome of Lactococcus lactis by SDS-PAGE LC-MS/MS leads to the identification of new markers of adaptation of the bacteria to the mouse digestive tract, J Proteome Res, 9, 677, 10.1021/pr9000866

Bhaya, 2011, CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation, Annu Rev Genet, 45, 273, 10.1146/annurev-genet-110410-132430

Cai, 2011, Proceeding of the International Conference on Bioinformatics and Computational Biology BIOCOMP’11, 18

Cantarel, 2009, The carbohydrate-active enzymes database (CAZy): an expert resource for glycogenomics, Nucleic Acids Res, 37, D233, 10.1093/nar/gkn663

Chen, 2008, Inhibition of anaerobic digestion process: a review, Biores Technol, 99, 4044, 10.1016/j.biortech.2007.01.057

Chouari, 2005, Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester, Environ Microbiol, 7, 1104, 10.1111/j.1462-2920.2005.00795.x

Conrad, 2005, Quantification of methanogenic pathways using stable carbon isotopic signatures: a review and a proposal, Org Geochem, 36, 739, 10.1016/j.orggeochem.2004.09.006

Denef, 2007, Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis, J Proteome Res, 6, 3152, 10.1021/pr0701005

Duquesne, 2007, Microcins, gene-encoded antibacterial peptides from enterobacteria, Nat Prod Rep, 24, 708, 10.1039/b516237h

Ellis, 2012, Closing the carbon balance for fermentation by Clostridium thermocellum (ATCC 27405), Biores Technol, 103, 293, 10.1016/j.biortech.2011.09.128

Etchebehere, 1998, Coprothermobacter platensis sp. nov., a new anaerobic proteolytic thermophilic bacterium isolated from an anaerobic mesophilic sludge, Int J Syst Bacteriol, 48, 1297, 10.1099/00207713-48-4-1297

Ganidi, 2009, Anaerobic digestion foaming causes—a review, Biores Technol, 100, 5546, 10.1016/j.biortech.2009.06.024

Gold, 2007, Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis, J Bacteriol, 189, 6787, 10.1128/JB.00882-07

Hamilton-Brehm, 2010, Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park, Appl Environ Microbiol, 76, 1014, 10.1128/AEM.01903-09

Hanreich, 2012, Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass, Can J Microbiol, 58, 917, 10.1139/w2012-058

Hattori, 2008, Syntrophic acetate-oxidizing microbes in methanogenic environments, Microbes Environ, 23, 118, 10.1264/jsme2.23.118

Holm-Nielsen, 2009, The future of anaerobic digestion and biogas utilization, Biores Technol, 100, 5478, 10.1016/j.biortech.2008.12.046

Imachi, 2002, Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium, Int J Syst Evol Microbiol, 52, 1729

Jaenicke, 2011, Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing, PLoS One, 6, e14519, 10.1371/journal.pone.0014519

Kersters, 1994, Isolation of Coprothermobacter proteolyticus from an anaerobic digest and further characterization of the species, Sys Appl Microbiol, 17, 289, 10.1016/S0723-2020(11)80021-4

Konstantinidis, 2007, Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead, Curr Opin Microbiol, 10, 504, 10.1016/j.mib.2007.08.006

Krause, 2008, Taxonomic composition and gene content of a methane producing microbial community isolated from a biogas reactor, J Biotechnol, 136, 91, 10.1016/j.jbiotec.2008.06.003

Kröber, 2009, Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing, J Biotechnol, 142, 38, 10.1016/j.jbiotec.2009.02.010

Li, 2009, Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions, Environ Microbiol, 11, 889, 10.1111/j.1462-2920.2008.01810.x

Liu, 2002, Extraction of extracellular polymeric substances (EPS) of sludges, J Biotechnol, 95, 249, 10.1016/S0168-1656(02)00025-1

Lochner, 2011, Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass, J Proteome Res, 10, 5302, 10.1021/pr200536j

Maki, 2009, The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass, Int J Biol Sci, 5, 500, 10.7150/ijbs.5.500

Ollivier, 1985, Emendation of the genus Thermobacteroides—Thermobacteroides-Proteolyticus sp-nov, a proteolytic acetogen from a methanogenic enrichment, Int J Syst Bacteriol, 35, 425, 10.1099/00207713-35-4-425

O’Sullivan, 2007, A survey of the relative abundance of specific groups of cellulose degrading bacteria in anaerobic environments using fluorescence in situ hybridization, J Appl Microbiol, 103, 1332, 10.1111/j.1365-2672.2007.03362.x

Petersen, 2011, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nat Methods, 8, 785, 10.1038/nmeth.1701

Pierce, 2008, The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum), Environ Microbiol, 10, 2550, 10.1111/j.1462-2920.2008.01679.x

Plugge, 2002, Gelria glutamica gen. nov., sp. nov., a thermophilic, obligately syntrophic, glutamate-degrading anaerobe, Int J Syst Evol Microbiol, 52, 401, 10.1099/00207713-52-2-401

Qu, 2009, Combined monitoring of changes in delta13CH4 and archaeal community structure during mesophilic methanization of municipal solid waste, FEMS Microbiol Ecol, 68, 236, 10.1111/j.1574-6941.2009.00661.x

Rademacher, 2012, Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing, FEMS Microbiol Ecol, 79, 785, 10.1111/j.1574-6941.2011.01265.x

Rawlings, 2012, MEROPS: the database of proteolytic enzymes, their substrates and inhibitors, Nucleic Acids Res, 40, D343, 10.1093/nar/gkr987

Riviere, 2009, Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge, ISME J, 3, 700, 10.1038/ismej.2009.2

Sasaki, 2007, Microbial population in the biomass adhering to supporting material in a packed-bed reactor degrading organic solid waste, Appl Microbiol Biotechnol, 75, 941, 10.1007/s00253-007-0888-x

Sasaki, 2011, Syntrophic degradation of proteinaceous materials by the thermophilic strains Coprothermobacter proteolyticus and Methanothermobacter thermautotrophicus, J Biosci Bioeng, 112, 469, 10.1016/j.jbiosc.2011.07.003

Schink, 1997, Energetics of syntrophic cooperation in methanogenic degradation, Microbiol Mol Biol Rev, 61, 262

Schlüter, 2008, The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology, J Biotechnol, 136, 77, 10.1016/j.jbiotec.2008.05.008

Schneider, 2010, Environmental proteomics: analysis of structure and function of microbial communities, Proteomics, 10, 785, 10.1002/pmic.200900450

Sokolova, 2004, Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park, Int J Syst Evol Microbiol, 54, 2353, 10.1099/ijs.0.63186-0

Thauer, 2008, Methanogenic archaea: ecologically relevant differences in energy conservation, Nat Rev Micro, 6, 579, 10.1038/nrmicro1931

van de Werken, 2008, Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus, Appl Environ Microbiol, 74, 6720, 10.1128/AEM.00968-08

van Lier, 2001, New perspectives in anaerobic digestion, Water Sci Technol, 43, 1, 10.2166/wst.2001.0001

VanFossen, 2009, Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences, Appl Environ Microbiol, 75, 7718, 10.1128/AEM.01959-09

Ward, 2008, Optimisation of the anaerobic digestion of agricultural resources, Biores Technol, 99, 7928, 10.1016/j.biortech.2008.02.044

Westerholm, 2011, Quantification of syntrophic acetate-oxidising microbial communities in biogas processes, Environ Microbiol Rep, 3, 500, 10.1111/j.1758-2229.2011.00249.x

Wilmes, 2004, The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms, Environ Microbiol, 6, 911, 10.1111/j.1462-2920.2004.00687.x

Wilmes, 2009, Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth’s biogeochemical cycles, Curr Opin Microbiol, 12, 310, 10.1016/j.mib.2009.03.004

Wu, 2005, Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901, PLoS Genet, 1, e65, 10.1371/journal.pgen.0010065

Yang, 2009, Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe ‘Anaerocellum thermophilum’ DSM 6725, Appl Environ Microbiol, 75, 4762, 10.1128/AEM.00236-09

Zakrzewski, 2012, Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing, J Biotechnol, 158, 248, 10.1016/j.jbiotec.2012.01.020

Zaneveld, 2010, Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives, Nucleic Acids Res, 38, 3869, 10.1093/nar/gkq066