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  • Aitken, C.M., Jones, D.M. and Larter, S.R. (2004) Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs. Nature 431, 291294.
  • Anderson, R.T. and Lovley, D.R. (2000) Biogeochemistry – Hexadecane decay by methanogenesis. Nature 404, 722723.
  • Asakawa, S. and Nagaoka, K. (2003) Methanoculleus bourgensis, Methanoculleus olentangyi and Methanoculleus oldenburgensis are subjective synonyms. Int J Syst Evol Microbiol 53, 15511552.
  • Baker, G.C., Smith, J.J. and Cowan, D.A. (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Meth 55, 541555.
  • Baskin, D.K. (1997) Atomic H/C ratio of kerogen as an estimate of thermal maturity and organic matter conversion. AAPG Bull 81, 14371450.
  • Behar, F., Beaumont, V. and Penteado, H.L.D. (2001) Rock-Eval 6 technology: performances and developments. Oil Gas Sci Technol 56, 111134.
  • Borsodi, A.K., Vladar, P., Cech, G., Gedeon, G., Beszteri, B., Micsinai, A., Reskone, M.N. and Marialigeti, K. (2003) Bacterial activities in the sediment of Lake Velencei, Hungary. Hydrobiologia 506, 721728.
  • Chen, S.Y., Song, L. and Dong, X.H. (2006) Sporacetigenium mesophilum gen. nov., sp nov., isolated from an anaerobic digester treating municipal solid waste and sewage. Int J Syst Evol Microbiol 56, 721725.
  • Conrad, R. (2007) Microbial ecology of methanogens and methanotrophs. In Advances in Agronomy, Vol. 96 ed. Sparks, D.L. pp. 163. Oxford, UK: Academic Press/Elsevier.
  • Dawson, K.S., Strapoc, D., Huizinga, B., Lidstrom, U., Ashby, M. and Macalady, J.L. (2012) Quantitative fluorescence in situ hybridization analysis of microbial consortia from a biogenic gas field in Alaska's Cook inlet basin. Appl Environ Microbiol 78, 35993605.
  • De Vrieze, J., Hennebel, T., Boon, N. and Verstraete, W. (2012) Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. Biores Technol 112, 19.
  • Deng, Y. and Fong, S. (2011a) Laboratory evolution and multi-platform genome re-sequencing of the cellulolytic Actinobacterium Thermobifida fusca. J Biol Chem 286, 3995839966.
  • Deng, Y. and Fong, S. (2011b) Metabolic engineering of Thermobifida fusca for direct aerobic bioconversion of untreated lignocellulosic biomass to 1-propanol. Metab Eng 13, 570577.
  • Dianou, D., Miyaki, T., Asakawa, S., Morii, H., Nagaoka, K., Oyaizu, H. and Matsumoto, S. (2001) Methanoculleus chikugoensis sp nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA–DNA hybridization among Methanoculleus species. Int J Syst Evol Microbiol 51, 16631669.
  • Durand, B. (2003) A history of organic geochemistry. Oil Gas Sci Technol 58, 203231.
  • Edwards, U., Rogall, T., Blöcker, H., Emde, M. and Böttger, E. (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17, 78437853.
  • Fredrickson, J.K., McKinley, J.P., Bjornstad, B.N., Long, P.E., Ringelberg, D.B., White, D.C., Krumholz, L.R., Suflita, J.M. et al. (1997) Pore-size constraints on the activity and survival of subsurface bacteria in a late Cretaceous shale-sandstone sequence, northwestern New Mexico. Geomicrobiol J 14, 183202.
  • Garcia, J.L., Patel, B.K.C. and Ollivier, B. (2000) Taxonomic phylogenetic and ecological diversity of methanogenic Archaea. Anaerobe 6, 205226.
  • Gieg, L.M., Duncan, K.E. and Suflita, J.M. (2008) Bioenergy production via microbial conversion of residual oil to natural gas. Appl Environ Microbiol 74, 30223029.
  • Grabowski, A., Nercessian, O., Fayolle, F., Blanchet, D. and Jeanthon, C. (2005) Microbial diversity in production waters of a low-temperature biodegraded oil reservoir. FEMS Microbiol Ecol 54, 427443.
  • Green, M.S., Flanegan, K.C. and Gilcrease, P.C. (2008) Characterization of a methanogenic consortium enriched from a coalbed methane well in the Powder River Basin, USA. Int J Coal Geol 76, 3445.
  • Grosskopf, R., Janssen, P.H. and Liesack, W. (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64, 960969.
  • Hatamoto, M., Imachi, H., Ohashi, A. and Harada, H. (2007) Identification and cultivation of anaerobic, syntrophic long-chain fatty acid-degrading microbes from mesophilic and thermophilic methanogenic sludges. Appl Environ Microbiol 73, 13321340.
  • Head, I.M., Jones, D.M. and Larter, S.R. (2003) Biological activity in the deep subsurface and the origin of heavy oil. Nature 426, 344352.
  • Hoogerheide, J.C. and Kocholaty, W. (1938) Metabolism of the strict anaerobes (genus: Clostridium) II. Reduction of amino-acids with gaseous hydrogen by suspensions of Cl. sporogenes. Biochem J 32, 949957.
  • Izquierdo, J., Sizova, M. and Lynd, L. (2010) Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost. Appl Environ Microbiol 76, 35453553.
  • Jones, E.J.P., Voytek, M.A., Warwick, P.D., Corum, M.D., Cohn, A., Bunnell, J.E., Clark, A.C. and Orem, W.H. (2008) Bioassay for estimating the biogenic methane-generating potential of coal samples. Int J Coal Geol 76, 138150.
  • Jones, E.J.P., Voytek, M.A., Corum, M.D. and Orem, W.H. (2010) Stimulation of methane generation from nonproductive coal by addition of nutrients or a microbial consortium. Appl Environ Microbiol 76, 70137022.
  • Klemme, H.D. and Ulmishek, G.F. (1991) Effective petroleum source rocks of the world. AAPG Bull 75, 18091851.
  • Krumholz, L.R., McKinley, J.P., Ulrich, F.A. and Suflita, J.M. (1997) Confined subsurface microbial communities in Cretaceous rock. Nature 386, 6466.
  • Lueders, T., Chin, K.J., Conrad, R. and Friedrich, M. (2001) Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3, 194204.
  • Luton, P.E., Wayne, J.M., Sharp, R.J. and Riley, P.W. (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148, 35213530.
  • Magot, M., Ollivier, B. and Patel, B.K.C. (2000) Microbiology of petroleum reservoirs. Anton Leeuw Int J Gen Mol Microbiol 77, 103116.
  • Martini, A.M., Budai, J.M., Walter, L.M. and Schoell, M. (1996) Microbial generation of economic accumulations of methane within a shallow organic-rich shale. Nature 383, 155158.
  • Martini, A.M., Walter, L.M., Ku, T.C.W., Budai, J.M., McIntosh, J.C. and Schoell, M. (2003) Microbial production and modification of gases in sedimentary basins: a geochemical case study from a Devonian shale gas play, Michigan basin. AAPG Bull 87, 13551375.
  • Martini, A.M., Walter, L.M. and McIntosh, J.C. (2008) Identification of microbial and thermogenic gas components from Upper Devonian black shale cores, Illinois and Michigan basins. AAPG Bull 92, 327339.
  • McIntosh, J., Martini, A., Petsch, S., Huang, R. and Nuesslein, K. (2008) Biogeochemistry of the Forest City Basin coalbed methane play. Int J Coal Geol 76, 111118.
  • Mikucki, J.A., Liu, Y.T., Delwiche, M., Colwell, F.S. and Boone, D.R. (2003) Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp nov. Appl Environ Microbiol 69, 33113316.
  • Ng, T.K., Weimer, P.J. and Zeikus, J.G. (1977) Cellulolytic and physiological properties of Clostridium thermocellum. Arch Microbiol 114, 17.
  • Pallud, C., Dechesne, A., Gaudet, J.P., Debouzie, D. and Grundmann, G.L. (2004) Modification of spatial distribution of 2,4-dichloro-phenoxyacetic acid degrader microhabitats during growth in soil columns. Appl Environ Microbiol 70, 27092716.
  • Penner, T.J., Foght, J.M. and Budwill, K. (2010) Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures. Int J Coal Geol 82, 8193.
  • Porteous, L.A., Seidler, R.J. and Watrud, L.S. (1997) An improved method for purifying DNA from soil for polymerase chain reaction amplification and molecular ecology applications. Mol Ecol 6, 787791.
  • Reeve, J.N., Nolling, J., Morgan, R.M. and Smith, D.R. (1997) Methanogenesis: genes, genomes, and who's on first? J Bacteriol 179, 59755986.
  • Rice, D.D. and Claypool, G.E. (1981) Generation, accumulation and resource potential of biogenic gas. AAPG Bull 65, 525.
  • Roling, W.F.M., Head, I.M. and Larter, S.R. (2003) The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects. Res Microbiol 154, 321328.
  • Sakamoto, M. and Benno, Y. (2006) Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov and Parabacteroides merdae comb. nov. Int J Syst Evol Microbiol 56, 15991605.
  • Sakamoto, M., Kitahara, M. and Benno, Y. (2007) Parabacteroides johnsonii sp nov., isolated from human faeces. Int J Syst Evol Microbiol 57, 293296.
  • Schink, B. (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61, 262280.
  • Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B. et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75, 75377541.
  • Schnurer, A., Schink, B. and Svensson, B.H. (1996) Clostridium ultunense sp nov, a mesophilic bacterium oxidizing acetate in syntrophic association with a hydrogenotrophic methanogenic bacterium. Int J Syst Evol Microbiol 46, 11451152.
  • Schulz, H.-M., Horsefield, B. and Sachsenhofer, R.F. (2010) Shale gas in Europe: a regional overview and current research activities. In Petroleum Geology: From Mature Basins to New Frontiers – Proceedings of the 7th Petroleum Geology Conference eds Vinning, B.A. and Pickering, S.C. pp. 10791085. London: Geological Society.
  • Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D., Huse, S.M., Neal, P.R., Arrieta, J.M. and Herndl, G.J. (2006) Microbial diversity in the deep sea and the underexplored ‘rare biosphere’. Proc Natl Acad Sci USA 103, 1211512120.
  • Stams, A.J.M. and Plugge, C.M. (2009) Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 7, 568577.
  • Stieb, M. and Schink, B. (1985) Anaerobic oxidation of fatty-acids by Clostridium bryantii sp nov, a sporeforming, obligately syntrophic bacterium. Arch Microbiol 140, 387390.
  • Strapoc, D., Picardal, F.W., Turich, C., Schaperdoth, I., Macalady, J.L., Lipp, J.S., Lin, Y.-S., Ertefai, T.F. et al. (2008) Methane-producing microbial community in a coal bed of the Illinois Basin. Appl Environ Microbiol 74, 24242432.
  • Suflita, J.M., Davidova, I.A., Gieg, L.M., Nanny, M. and Prince, R.C. (2004) Anaerobic hydrocarbon biodegradation and the prospects for microbial enhanced energy production. In Petroleum Biotechnology: Developments and Perspectives ed. Vaquez-Duhalt, R. and Quintero-Ramirez, R. pp. 283305. Oxford, UK: Academic Press/Elsevier.
  • Takai, K., Mormile, M.R., McKinley, J.P., Brockman, F.J., Holben, W.E., Kovacik, W.P. and Fredrickson, J.K. (2003) Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock. Environ Microbiol 5, 309320.
  • Tissot, B., Durand, B., Espitali, J. and Combaz, A. (1974) Influence of nature and diagenesis of organic-matter in formation of petroleum. AAPG Bull 58, 499506.
  • Townsend, G.T., Prince, R.C. and Suflita, J.M. (2003) Anaerobic oxidation of crude oil hydrocarbons by the resident microorganisms of a contaminated anoxic aquifer. Environ Sci Technol 37, 52135218.
  • Uroz, S., Buee, M., Murat, C., Frey-Klett, P. and Martin, F. (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2, 281288.
  • Vandenbroucke, M. and Largeau, C. (2007) Kerogen origin, evolution and structure. Org Geochem 38, 719833.
  • Voordouw, G. (2011) Production-related petroleum microbiology: progress and prospects. Curr Opin Biotechnol 22, 401405.
  • Warwick, P.D., Breland, F.C. Jr and Hackley, P.C. (2008) Biogenic origin of coalbed gas in the northern Gulf of Mexico Coastal Plain, USA. Int J Coal Geol 76, 119137.
  • Watson, R.J. and Blackwell, B. (2000) Purification and characterization of a common soil component which inhibits the polymerase chain reaction. Can J Microbiol 46, 633642.
  • Wawrik, B., Mendivelso, M., Parisi, V.A., Suflita, J.M., Davidova, I.A., Marks, C.R., Van Nostrand, J.D., Liang, Y. et al. (2012) Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microbiol Ecol 81, 2642.
  • Wolin, E., Wolin, M. and Wolfe, R. (1963) Formation of methane by bacterial extracts. J Biol Chem 238, 28822886.
  • Zakrzewski, M., Goesmann, A., Jaenicke, S., Juenemann, S., Eikmeyer, F., Szczepanowski, R., Abu Al-Soud, W., Sorensen, S. et al. (2012) Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol 158, 248258.
  • Zengler, K., Richnow, H.H., Rossello-Mora, R., Michaelis, W. and Widdel, F. (1999) Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401, 266269.