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References

  • Alain, K., Holler, T., Musat, F., Elvert, M., Treude, T., and Kruger, M. (2006) Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania. Environ Microbiol 8: 574590.
  • Amann, R.I., Ludwig, W., and Schleifer, K.H. (1995) Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol Rev 59: 143169.
  • Ariesyady, H.D., Ito, T., and Okabe, S. (2007) Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester. Water Res 41: 15541568.
  • Armougom, F., Henry, M., Vialettes, B., Raccah, D., and Raoult, D. (2009) Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and methanogens in anorexic patients. PLoS ONE 4: e7125. doi:7110.1371/journal.pone.0007125.
  • Banning, N., Brock, F., Fry, J.C., Parkes, R.J., Hornibrook, E.R.C., and Weightman, A.J. (2005) Investigation of the methanogen population structure and activity in a brackish lake sediment. Environ Microbiol 7: 947960.
  • Barns, S.M., Fundyga, R.E., Jeffries, M.W., and Pace, N.R. (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot-spring environment. Proc Natl Acad Sci USA 91: 16091613.
  • Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A., et al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623626.
  • Boonapatcharoen, N., Meepian, K., Chaiprasert, P., and Techkarnjanaruk, S. (2007) Molecular monitoring of microbial population dynamics during operational periods of anaerobic hybrid reactor treating cassava starch wastewater. Microb Ecol 54: 2130.
  • Bräuer, S.L., Cadillo-Quiroz, H., Yashiro, E., Yavitt, J.B., and Zinder, S.H. (2006) Isolation of a novel acidiphilic methanogen from an acidic peat bog. Nature 442: 192194.
  • Bräuer, S.L., Cadillo-Quiroz, H., Ward, R.J., Yavitt, J., and Zinder, S. (2010) Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog. Int J Syst Evol Microbiol (in press): doi:10.1099/ijs.1090.021782-021780.
  • Brazelton, W.J., Ludwig, K.A., Sogin, M.L., Andreishcheva, E.N., Kelley, D.S., Shen, C.C., et al. (2010a) Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys. Proc Natl Acad Sci USA 107: 16121617.
  • Brazelton, W.J., Sogin, M.L., and Baross, J.A. (2010b) Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms. Environ Microbiol Rep 2: 236242.
  • Cadillo-Quiroz, H., Yavitt, J.B., and Zinder, S.H. (2009) Methanosphaerula palustris gen. nov., sp nov., a hydrogenotrophic methanogen isolated from a minerotrophic fen peatland. Int J Syst Evol Microbiol 59: 928935.
  • Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335336.
  • Casamayor, E.O., Muyzer, G., and Pedros-Alio, C. (2001) Composition and temporal dynamics of planktonic archaeal assemblages from anaerobic sulfurous environments studied by 16S rDNA denaturing gradient gel electrophoresis and sequencing. Aquat Microb Ecol 25: 237246.
  • Casamayor, E.O., Massana, R., Benlloch, S., Ovreas, L., Diez, B., Goddard, V.J., et al. (2002) Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environ Microbiol 4: 338348.
  • Castro, H., Ogram, A., and Reddy, K.R. (2004) Phylogenetic characterization of methanogenic assemblages in eutrophic and oligotrophic areas of the Florida Everglades. Appl Environ Microbiol 70: 65596568.
  • Chen, C.L., Wu, J.H., Tseng, I.C., Liang, T.M., and Liu, W.T. (2009) Characterization of active microbes in a full-scale anaerobic fluidized bed reactor treating phenolic wastewater. Microbes Environ 24: 144153.
  • Chouari, R., Le Paslier, D., Daegelen, P., Ginestet, P., Weissenbach, J., and Sghir, A. (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ Microbiol 7: 11041115.
  • Colwell, F.S., Boyd, S., Delwiche, M.E., Reed, D.W., Phelps, T.J., and Newby, D.T. (2008) Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia margin. Appl Environ Microbiol 74: 34443452.
  • Conrad, R., Erkel, C., and Liesack, W. (2006) Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil. Curr Opin Biotechnol 17: 262267.
  • Crocetti, G., Murto, M., and Bjornsson, L. (2006) An update and optimisation of oligonucleotide probes targeting methanogenic Archaea for use in fluorescence in situ hybridisation (FISH). J Microbiol Methods 65: 194201.
  • Dahllof, I. (2002) Molecular community analysis of microbial diversity. Curr Opin Biotechnol 13: 213217.
  • Denman, S.E., Tomkins, N., and McSweeney, C.S. (2007) Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol Ecol 62: 313322.
  • Dhillon, A., Lever, M., Lloyd, K.G., Albert, D.B., Sogin, M.L., and Teske, A. (2005) Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Appl Environ Microbiol 71: 45924601.
  • Doerfert, S.N., Reichlen, M., Iyer, P., Wang, M.Y., and Ferry, J.G. (2009) Methanolobus zinderi sp nov., a methylotrophic methanogen isolated from a deep subsurface coal seam. Int J Syst Evol Microbiol 59: 10641069.
  • Dojka, M.A., Hugenholtz, P., Haack, S.K., and Pace, N.R. (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64: 38693877.
  • Embley, T.M., Finlay, B.J., Thomas, R.H., and Dyal, P.L. (1992) The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont. J Gen Microbiol 138: 14791487.
  • Falz, K.Z., Holliger, C., Grosskopf, R., Liesack, W., Nozhevnikova, A.N., Muller, B., et al. (1999) Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland). Appl Environ Microbiol 65: 24022408.
  • Franke-Whittle, I.H., Goberna, M., and Insam, H. (2009a) Design and testing of real-time PCR primers for the quantification of Methanoculleus, Methanosarcina, Methanothermobacter, and a group of uncultured methanogens. Can J Microbiol 55: 611616.
  • Franke-Whittle, I.H., Goberna, M., Pfister, V., and Insam, H. (2009b) Design and development of the ANAEROCHIP microarray for investigation of methanogenic communities. J Microbiol Methods 79: 279288.
  • Frey, J.C., Pell, A.N., Berthiaume, R., Lapierre, H., Lee, S., Ha, J.K., et al. (2009) Comparative studies of microbial populations in the rumen, duodenum, ileum and faeces of lactating dairy cows. J Appl Microbiol 108: 19821993.
  • Friedrich, M.W. (2005) Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea. Methods Enzymol 397: 428442.
  • Galand, P.E., Saarnio, S., Fritze, H., and Yrjala, K. (2002) Depth related diversity of methanogen Archaea in Finnish oligotrophic fen. FEMS Microbiol Ecol 42: 441449.
  • Galand, P.E., Juottonen, H., Fritze, H., and Yrjala, K. (2005) Methanogen communities in a drained bog: effect of ash fertilization. Microbial Ecol 49: 209217.
  • Garrity, G.M., and Holt, J.G. (2001) Phylum AII. Euryarchaeota phy. nov. In Berrgey's Manual, 2nd edn. Boone, D.R., Castenholz, R.W., and Garrity, G.M. (eds). New York, NY, USA: Springer-Verlag, pp. 211355.
  • Garrity, G.M., Lilburn, T.G., Cole, J.R., Harrison, S.H., Euzeby, J., and Tindall, B.J. (2007) Part 1 – The‘Archaea’, Phyla ‘Crenarchaeota’ and ‘Euryarchaeota’[WWW document]. URL http://www.taxonomicoutline.org/index.php/toba/article/view/178/210.
  • Griffin, M.E., McMahon, K.D., Mackie, R.I., and Raskin, L. (1998) Methanogenic population dynamics during start-up of anaerobic digesters treating municipal solid waste and biosolids. Biotechnol Bioeng 57: 342355.
  • 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.
  • Hales, B.A., Edwards, C., Ritchie, D.A., Hall, G., Pickup, R.W., and Saunders, J.R. (1996) Isolation and identification of methanogen-specific DNA from blanket bog feat by PCR amplification and sequence analysis. Appl Environ Microbiol 62: 668675.
  • Harmsen, H.J.M., Kengen, K.M.P., Akkermans, A.D.L., and Stams, A.J.M. (1995) Phylogenetic analysis of two syntrophic propionate-oxidizing bacteria in enrichments cultures. Syst Appl Microbiol 18: 6773.
  • Harmsen, H.J.M., Kengen, H.M.P., Akkermans, A.D.L., Stams, A.J.M., and deVos, W.M. (1996) Detection and localization of syntrophic propionate-oxidizing bacteria in granular sludge by in situ hybridization using 16S rRNA-based oligonucleotide probes. Appl Environ Microbiol 62: 16561663.
  • Hook, S.E., Northwood, K.S., Wright, A.D.G., and McBride, B.W. (2009) Long-term monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow. Appl Environ Microbiol 75: 374380.
  • Hori, T., Haruta, S., Ueno, Y., Ishii, M., and Igarashi, Y. (2006) Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester. Appl Environ Microbiol 72: 16231630.
  • Horn, M.A., Matthies, C., Kusel, K., Schramm, A., and Drake, H.L. (2003) Hydrogenotrophic methanogenesis by moderately acid-tolerant methanogens of a methane-emitting acidic peat. Appl Environ Microbiol 69: 7483.
  • Huang, W.E., Stoecker, K., Griffiths, R., Newbold, L., Daims, H., Whiteley, A.S., and Wagner, M. (2007) Raman-FISH: combining stable-isotope raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 9: 18781889.
  • Huang, W.E., Ferguson, A., Singer, A.C., Lawson, K., Thompson, I.P., Kalin, R.M., et al. (2009) Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization. Appl Environ Microbiol 75: 234241.
  • Hugenholtz, P. (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3: REVIEWS0003.
  • Iino, T., Mori, K., and Suzuki, K. (2010) Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and the emendation of the genus Methanospirillum and Methanospirillum hungatei. Int J Syst Evol Microbiol 60: 25632566.
  • Imachi, H., Sekiguchi, Y., Kamagata, Y., Ohashi, A., and Harada, H. (2000) Cultivation and in situ detection of a thermophilic bacterium capable of oxidizing propionate in syntrophic association with hydrogenotrophic methanogens in a thermophilic methanogenic granular sludge. Appl Environ Microbiol 66: 36083615.
  • Imachi, H., Sakai, S., Sekiguchi, Y., Hanada, S., Kamagata, Y., Ohashi, A., and Harada, H. (2008) Methanolinea tarda gen. nov., sp nov., a methane-producing archaeon isolated from a methanogenic digester sludge. Int J Syst Evol Microbiol 58: 294301.
  • Imachi, H., Sakai, S., Nagai, H., Yamaguchi, T., and Takai, K. (2009) Methanofollis ethanolicus sp nov., an ethanol-utilizing methanogen isolated from a lotus field. Int J Syst Evol Microbiol 59: 800805.
  • Inagaki, F., Tsunogai, U., Suzuki, M., Kosaka, A., Machiyama, H., Takai, K., et al. (2004) Characterization of C-1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 70: 74457455.
  • Jerman, V., Metje, M., Mandic-Mulec, I., and Frenzel, P. (2009) Wetland restoration and methanogenesis: the activity of microbial populations and competition for substrates at different temperatures. Biogeosciences 6: 11271138.
  • Juottonen, H., Galand, P.E., Tuittila, E.S., Laine, J., Fritze, H., and Yrjala, K. (2005) Methanogen communities and Bacteria along an ecohydrological gradient in a northern raised bog complex. Environ Microbiol 7: 15471557.
  • Juottonen, H., Galand, P.E., and Yrjala, K. (2006) Detection of methanogenic Archaea in peat: comparison of PCR primers targeting the mcrA gene. Res Microbiol 157: 914921.
  • Kalyuzhnaya, M.G., Lapidus, A., Ivanova, N., Copeland, A.C., McHardy, A.C., Szeto, E., et al. (2008) High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 26: 10291034.
  • Kawakami, S., Kubota, K., Imachi, H., Yamaguchi, T., Harada, H., and Ohashi, A. (2010) Detection of single copy genes by two-pass tyramide signal amplification fluorescence in situ hybridization (two-pass TSA-FISH) with single oligonucleotide probes. Microbes Environ 25: 1521.
  • Kemnitz, D., Chin, K.J., Bodelier, P., and Conrad, R. (2004) Community analysis of methanogenic archaea within a riparian flooding gradient. Environ Microbiol 6: 449461.
  • Kleikemper, J., Pombo, S.A., Schroth, M.H., Sigler, W.V., Pesaro, M., and Zeyer, J. (2005) Activity and diversity of methanogens in a petroleum hydrocarbon-contaminated aquifer. Appl Environ Microbiol 71: 149158.
  • Krivushin, K.V., Shcherbakova, V.A., Petrovskaya, L.E., and Rivkina, E.M. (2010) Methanobacterium veterum sp nov., from ancient Siberian permafrost. Int J Syst Evol Microbiol 60: 455459.
  • Kubota, K., Ohashi, A., Imachi, H., and Harada, H. (2006) Visualization of mcr mRNA in a methanogen by fluorescence in situ hybridization with an oligonucleotide probe and two-pass tyramide signal amplification (two-pass TSA-FISH). J Microbiol Methods 66: 521528.
  • Kubota, K., Imachi, H., Kawakami, S., Nakamura, K., Harada, H., and Ohashi, A. (2008) Evaluation of enzymatic cell treatments for application of CARD-FISH to methanogens. J Microbiol Methods 72: 5459.
  • Laloui-Carpentier, W., Li, T., Vigneron, V., Mazeas, L., and Bouchez, T. (2006) Methanogenic diversity and activity in municipal solid waste landfill leachates. Antonie Van Leeuwenhoek 89: 423434.
  • Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E., and Goodfellow, M. (eds). Chichester, UK: John Wiley & Sons, pp. 115175.
  • Lehmann-Richter, S., Grosskopf, R., Liesack, W., Frenzel, P., and Conrad, R. (1999) Methanogenic archaea and CO2-dependent methanogenesis on washed rice roots. Environ Microbiol 1: 159166.
  • Li, T.L., Mazeas, L., Sghir, A., Leblon, G., and Bouchez, T. (2009) Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions. Environ Microbiol 11: 889904.
  • Liu, W.T., Chan, O.C., and Fang, H.H.P. (2002) Microbial community dynamics during start-up of acidogenic anaerobic reactors. Water Res 36: 32033210.
  • Liu, Y.C., and Whitman, W.B. (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125: 171189.
  • Lu, Y.H., and Conrad, R. (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309: 10881090.
  • Lu, Y.H., Lueders, T., Friedrich, M.W., and Conrad, R. (2005) Detecting active methanogenic populations on rice roots using stable isotope probing. Environ Microbiol 7: 326336.
  • Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 13631371.
  • 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.
  • Lueders, T., Pommerenke, B., and Friedrich, M.W. (2004) Stable-isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil. Appl Environ Microbiol 70: 57785786.
  • 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.
  • McMahon, K.D., Zheng, D.D., Stams, A.J.M., Mackie, R.I., and Raskin, L. (2004) Microbial population dynamics during start-up and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge. Biotechnol Bioeng 87: 823834.
  • Manefield, M., Whiteley, A.S., Griffiths, R.I., and Bailey, M.J. (2002) RNA stable isotope probing, a novel means of linking microbial community function to Phylogeny. Appl Environ Microbiol 68: 53675373.
  • Marchesi, J.R., Weightman, A.J., Cragg, B.A., Parkes, R.J., and Fry, J.C. (2001) Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol Ecol 34: 221228.
  • Mochimaru, H., Yoshioka, H., Tamaki, H., Nakamura, K., Kaneko, N., Sakata, S., et al. (2007) Microbial diversity and methanogenic potential in a high temperature natural gas field in Japan. Extremophiles 11: 453461.
  • Mochimaru, H., Tamaki, H., Hanada, S., Imachi, H., Nakamura, K., Sakata, S., and Kamagata, Y. (2009) Methanolobus profundi sp nov., a methylotrophic methanogen isolated from deep subsurface sediments in a natural gas field. Int J Syst Evol Microbiol 59: 714718.
  • Nakamura, K., Terada, T., Sekiguchi, Y., Shinzato, N., Meng, X.Y., Enoki, M., and Kamagata, Y. (2006) Application of pseudomurein endoisopeptidase to fluorescence in situ hybridization of methanogens within the family Methanobacteliaceae. Appl Environ Microbiol 72: 69076913.
  • Narihiro, T., and Sekiguchi, Y. (2007) Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update. Curr Opin Biotechnol 18: 273278.
  • Narihiro, T., Terada, T., Kikuchi, K., Iguchi, A., Ikeda, M., Yamauchi, T., et al. (2009a) Comparative analysis of bacterial and archaeal communities in methanogenic sludge granules from upflow anaerobic sludge blanket reactors treating various food-processing, high-strength organic wastewaters. Microbes Environ 24: 8896.
  • Narihiro, T., Terada, T., Ohashi, A., Wu, J.H., Liu, W.T., Araki, N., et al. (2009b) Quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rRNA cleavage method. ISME J 3: 522535.
  • Nercessian, D., Upton, M., Lloyd, D., and Edwards, C. (1999) Phylogenetic analysis of peat bog methanogen populations. FEMS Microbiol Lett 173: 425429.
  • Nercessian, O., Prokofeva, M., Lebedinski, A., L'Haridon, S., Cary, C., Prieur, D., and Jeanthon, C. (2004) Design of 16S rRNA-targeted oligonucleotide probes for detecting cultured and uncultured archaeal lineages in high-temperature environments. Environ Microbiol 6: 170182.
  • Nercessian, O., Bienvenu, N., Moreira, D., Prieur, D., and Jeanthon, C. (2005) Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments. Environ Microbiol 7: 118132.
  • Neu, T.R., Kuhlicke, U., and Lawrence, J.R. (2002) Assessment of fluorochromes for two-photon laser scanning microscopy of biofilms. Appl Environ Microbiol 68: 901909.
  • Nunoura, T., Oida, H., Toki, T., Ashi, J., Takai, K., and Horikoshi, K. (2006) Quantification of mcrA by quantitative fluorescent PCR in sediments from methane seep of the Nankai Trough. FEMS Microbiol Ecol 57: 149157.
  • Nunoura, T., Oida, H., Miyazaki, J., Miyashita, A., Imachi, H., and Takai, K. (2008) Quantification of mcrA by fluorescent PCR in methanogenic and methanotrophic microbial communities. FEMS Microbiol Ecol 64: 240247.
  • Orphan, V.J., House, C.H., Hinrichs, K.U., McKeegan, K.D., and DeLong, E.F. (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293: 484487.
  • Ottesen, E.A., Hong, J.W., Quake, S.R., and Leadbetter, J.R. (2006) Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314: 14641467.
  • Ovreas, L., Forney, L., Daae, F.L., and Torsvik, V. (1997) Distribution of bacterioplankton in meromictic lake Saelenvanner, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63: 33673373.
  • Penning, H., Claus, P., Casper, P., and Conrad, R. (2006) Carbon isotope fractionation during acetoclastic methanogenesis by Methanosaeta concilii in culture and a lake sediment. Appl Environ Microbiol 72: 56485652.
  • Plumb, J.J., Bell, J., and Stuckey, D.C. (2001) Microbial populations associated with treatment of an industrial dye effluent in an anaerobic baffled reactor. Appl Environ Microbiol 67: 32263235.
  • Poulsen, L.K., Ballard, G., and Stahl, D.A. (1993) Use of ribosomal-RNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol 59: 13541360.
  • Radajewski, S., Ineson, P., Parekh, N.R., and Murrell, J.C. (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646649.
  • Ramakrishnan, B., Lueders, T., Dunfield, P.F., Conrad, R., and Friedrich, M.W. (2001) Archaeal community structures in rice soils from different geographical regions before and after initiation of methane production. FEMS Microbiol Ecol 37: 175186.
  • Raskin, L., Poulsen, L.K., Noguera, D.R., Rittmann, B.E., and Stahl, D.A. (1994a) Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl Environ Microbiol 60: 12411248.
  • Raskin, L., Stromley, J.M., Rittmann, B.E., and Stahl, D.A. (1994b) Group-specific 16S ribosomal-RNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol 60: 12321240.
  • Raskin, L., Zheng, D.D., Griffin, M.E., Stroot, P.G., and Misra, P. (1995) Characterization of microbial communities in anaerobic bioreactors using molecular probes. Antonie Van Leeuwenhoek 68: 297308.
  • Reysenbach, A.-L., and Pace, N.R. (1995) Thermophiles. In Archaea: A Laboratory Manual. Robb, F.T., and Place, A.R. (eds). Cold Spring Harbor, NY, USA: Cold Spring Harbour Press, pp. 101107.
  • Rocheleau, S., Greer, C.W., Lawrence, J.R., Cantin, C., Laramee, L., and Guiot, S.R. (1999) Differentiation of Methanosaeta concilii and Methanosarcina barkeri in anaerobic mesophilic granular sludge by fluorescent in situ hybridization and confocal scanning laser microscopy. Appl Environ Microbiol 65: 22222229.
  • Sakai, S., Imachi, H., Hanada, S., Ohashi, A., Harada, H., and Kamagata, Y. (2008) Methanocella paludicola gen. nov., sp nov., a methane-producing archaeon, the first isolate of the lineage ‘Rice Cluster I’, and proposal of the new archaeal order Methanocellales ord. nov. Int J Syst Evol Microbiol 58: 929936.
  • Sakai, S., Imachi, H., Sekiguchi, Y., Ohashi, A., Harada, H., and Kamagata, Y. (2007) Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster rice cluster I. Appl Environ Microbiol 73: 43264331.
  • Sakai, S., Conrad, R., Liesack, W., and Imachi, H. (2010) Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen, isolated from Italian rice field soil. Int J Syst Evol Microbiol 60: 29182923.
  • Sawayama, S., Tada, C., Tsukahara, K., and Yagishita, T. (2004) Effect of ammonium addition on methanogenic community in a fluidized bed anaerobic digestion. J Biosci Bioeng 97: 6570.
  • Sawayama, S., Tsukahara, K., and Yagishita, T. (2006) Phylogenetic description of immobilized methanogenic community using real-time PCR in a fixed-bed anaerobic digester. Bioresour Technol 97: 6976.
  • Scanlan, P.D., Shanahan, F., and Marchesi, J.R. (2008) Human methanogen diversity and incidence in healthy and diseased colonic group using mcrA gene analysis. BMC Microbiol 8: 79.
  • Schink, B. (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61: 262280.
  • Sekiguchi, Y. (2006) Yet-to-be cultured microorganisms relevant to methane fermentation processes. Microbes Environ 21: 115.
  • Sekiguchi, Y., and Kamagata, Y. (2004) Microbial community structure and functions in methane fermentation technology for wastewater treatment. In Strict and Facultative Anaerobes: Medical and Environmental Aspects. Nakano, M.M., and Zuber, P. (eds). Norfolk, UK: Horizon Bioscience, pp. 361384.
  • Sekiguchi, Y., Kamagata, Y., Nakamura, K., Ohashi, A., and Harada, H. (1999) Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Appl Environ Microbiol 65: 12801288.
  • Sekiguchi, Y., Uyeno, Y., Sunaga, A., Yoshida, H., and Kamagata, Y. (2005) Sequence-specific cleavage of 16S rRNA for rapid and quantitative detection of particular groups of anaerobes in bioreactors. Water Sci Technol 52: 107113.
  • Shcherbakova, V.A., Rivkina, E.M., Pecheritsyna, S., Laurinavichuis, K., Suzina, N.E., and Gilichinsky, D. (2010) Methanobacterium arcticum sp.nov., methanogenic archaeon from Holocene Arctic permafrost. Int J Syst Evol Microbiol (in press): doi: 10.1099/ijs.1090.021311-021310.
  • Shigematsu, T., Tang, Y.Q., Kawaguchi, H., Ninomiya, K., Kijima, J., Kobayashi, T., et al. (2003) Effect of dilution rate on structure of a mesophilic acetate-degrading methanogenic community during continuous cultivation. J Biosci Bioeng 96: 547558.
  • Shigematsu, T., Tang, Y.Q., Kobayashi, T., Kawaguchi, H., Morimura, S., and Kida, K. (2004) Effect of dilution rate on metabolic pathway shift between aceticlastic and nonaceticlastic methanogenesis in chemostat cultivation. Appl Environ Microbiol 70: 40484052.
  • Shinzato, N., Watanabe, I., Meng, X.Y., Sekiguchi, Y., Tamaki, H., Matsui, T., and Kamagata, Y. (2007) Phylogenetic analysis and fluorescence in situ hybridization detection of archaeal and bacterial endosymbionts in the anaerobic ciliate Trimyema compressum. Microb Ecol 54: 627636.
  • Skillman, L.C., Evans, P.N., Naylor, G.E., Morvan, B., Jarvis, G.N., and Joblin, K.N. (2004) 16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs. Anaerobe 10: 277285.
  • Smith, J.M., Green, S.J., Kelley, C.A., Prufert-Bebout, L., and Bebout, B.M. (2008) Shifts in methanogen community structure and function associated with long-term manipulation of sulfate and salinity in a hypersaline microbial mat. Environ Microbiol 10: 386394.
  • Sorensen, A.H., and Ahring, B.K. (1997) An improved enzyme-linked immunosorbent assay for whole-cell determination of methanogens in samples from anaerobic reactors. Appl Environ Microbiol 63: 20012006.
  • Springer, E., Sachs, M.S., Woese, C.R., and Boone, D.R. (1995) Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. Int J Syst Bacteriol 45: 554559.
  • Stahl, D.A., and Amann, R. (1991) Development and application of nucleic acid probes. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E., and Goodfellow, M. (eds). Chichester, UK: Wiley, pp. 205248.
  • Stahl, D.A., Flesher, B., Mansfield, H.R., and Montgomery, L. (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl Environ Microbiol 54: 10791084.
  • Steinberg, L.M., and Regan, J.M. (2008) Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge. Appl Environ Microbiol 74: 66636671.
  • Steinberg, L.M., and Regan, J.M. (2009) mcrA-targeted real-time quantitative PCR method to examine methanogen communities. Appl Environ Microbiol 75: 44354442.
  • Strapoc, D., Picardal, F.W., Turich, C., Schaperdoth, I., Macalady, J.L., Lipp, J.S., et al. (2008) Methane-producing microbial community in a coal bed of the Illinois Basin. Appl Environ Microbiol 74: 24242432.
  • Sul, W.J., Park, J., Quensen, J.F., Rodrigues, J.L.M., Seliger, L., Tsoi, T.V., et al. (2009) DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75: 55015506.
  • Tabatabaei, M., Rahim, R.A., Abdullah, N., Wright, A.-D.G., Shirai, Y., Sakai, K., et al. (2010) Importance of the methanogenic archaea populations in anaerobic wastewater treatments. Process Biochem 45: 12141225.
  • Takai, K., Nakamura, K., Toki, T., Tsunogai, U., Miyazaki, M., Miyazaki, J., et al. (2008) Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proc Natl Acad Sci USA 105: 1094910954.
  • Talbot, G., Topp, E., Palin, M.F., and Masse, D.I. (2008) Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. Water Res 42: 513537.
  • Tang, Y.Q., Shigematsu, T., Morimura, S., and Kida, K. (2005) Microbial community analysis of mesophilic anaerobic protein degradation process using bovine serum albumin (BSA)-fed continuous cultivation. J Biosci Bioeng 99: 150164.
  • Tatsuoka, N., Mohammed, N., Mitsumori, M., Hara, K., Kurihara, M., and Itabashi, H. (2004) Phylogenetic analysis of methyl coenzyme-M reductase detected from the bovine rumen. Lett Appl Microbiol 39: 257260.
  • Thauer, R.K. (1998) Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology 144: 23772406.
  • Thauer, R.K., and Shima, S. (2008) Methane as fuel for anaerobic microorganisms. Ann N Y Acad Sci 1125: 158170.
  • Tringe, S.G., and Hugenholtz, P. (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11: 442446.
  • Tung, H.C., Bramall, N.E., and Price, P.B. (2005) Microbial origin of excess methane in glacial ice and implications for life on Mars. Proc Natl Acad Sci USA 102: 1829218296.
  • Ufnar, J.A., Ufnar, D.F., Wang, S.Y., and Ellender, R.D. (2007) Development of a swine-specific fecal pollution marker based on host differences in methanogen mcrA genes. Appl Environ Microbiol 73: 52095217.
  • Uyeno, Y., Sekiguchi, Y., Sunaga, A., Yoshida, H., and Kamagata, Y. (2004) Sequence-specific cleavage of small-subunit (SSU) rRNA with oligonucleotides and RNase H: a rapid and simple approach to SSU rRNA-based quantitative detection of microorganisms. Appl Environ Microbiol 70: 36503663.
  • Vavilin, V.A., Qu, X., Mazeas, L., Lemunier, M., Duquennoi, C., He, P.J., and Bouchez, T. (2008) Methanosarcina as the dominant aceticlastic methanogens during mesophilic anaerobic digestion of putrescible waste. Antonie Van Leeuwenhoek 94: 593605.
  • Vianna, M.E., Holtgraewe, S., Seyfarth, I., Conrads, G., and Horz, H.P. (2008) Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease. J Bacteriol 190: 37793785.
  • Visser, F.A., van Lier, J.B., Macario, A.J.L., and de Macario, E.C. (1991) Diversity and population dynamics of methanogenic bacteria in a granular consortium. Appl Environ Microbiol 57: 17281734.
  • Wang, F.P., Zhou, H.Y., Meng, J., Peng, X.T., Jiang, L.J., Sun, P., et al. (2009) GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci USA 106: 48404845.
  • Weijers, J.W.H., Schouten, S., van der Linden, M., van Geel, B., and Damste, J.S.S. (2004) Water table related variations in the abundance of intact archaeal membrane lipids in a Swedish peat bog. FEMS Microbiol Lett 239: 5156.
  • Wright, A.D.G., and Pimm, C. (2003) Improved strategy for presumptive identification of methanogens using 16S riboprinting. J Microbiol Methods 55: 337349.
  • Wu, J.H., and Liu, W.T. (2007) Quantitative multiplexing analysis of PCR-amplified ribosomal RNA genes by hierarchical oligonucleotide primer extension reaction. Nucleic Acids Res 35: e82.
  • Yanagita, K., Kamagata, Y., Kawaharasaki, M., Suzuki, T., Nakamura, Y., and Minato, H. (2000) Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization. Biosci Biotechnol Biochem 64: 17371742.
  • Yarza, P., Richter, M., Peplies, J., Euzeby, J., Amann, R., Schleifer, K.H., et al. (2008) The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31: 241250.
  • Yashiro, Y., Sakai, S., Ehara, M., Miyazaki, M., Yamaguchi, T., and Imachi, H. (2009) Methanoregula formicica sp. nov., a novel methane-producing archaeon isolated from methanogenic sludge. Int J Syst Evol Microbiol (in press): doi: 10.1099/ijs.1090.014811-014810.
  • Yu, Y., Lee, C., Kim, J., and Hwang, S. (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89: 670679.
  • Yu, Y., Kim, J., and Hwang, S. (2006) Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures. Biotechnol Bioeng 93: 424433.
  • Yu, Z.T., Garcia-Gonzalez, R., Schanbacher, F.L., and Morrison, M. (2008) Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens denaturing by Archaea-specific PCR and gradient gel electrophoresis. Appl Environ Microbiol 74: 889893.
  • Zhang, G.S., Jiang, N., Liu, X.L., and Dong, X.Z. (2008a) Methanogenesis from methanol at low temperatures by a novel psychrophilic methanogen, ‘Methanolobus psychrophilus’ sp nov., prevalent in Zoige wetland of the Tibetan plateau. Appl Environ Microbiol 74: 61146120.
  • Zhang, G.S., Tian, J.Q., Jiang, N., Guo, X.P., Wang, Y.F., and Dong, X.Z. (2008b) Methanogen community in Zoige wetland of Tibetan plateau and phenotypic characterization of a dominant uncultured methanogen cluster ZC-I. Environ Microbiol 10: 18501860.
  • Zhang, T., and Fang, H.H.P. (2006) Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl Microbiol Biotechnol 70: 281289.
  • Zheng, D., and Raskin, L. (2000) Quantification of Methanosaeta species in anaerobic bioreactors using genus- and species-specific hybridization probes. Microbial Ecol 39: 246262.
  • Zheng, D., Angenent, L.T., and Raskin, L. (2006) Monitoring granule formation in anaerobic upflow bioreactors using oligonucleotide hybridization probes. Biotechnol Bioeng 94: 458472.