• [1]
    Garrity G.M., Bell, J.A., Lilburn, T.G. Taxonomic Outline of the Prokaryotes Bergey’ s Manual of Systematic Bacteriology 2nd edn. 2003, Springer, New York Release 4.0
  • [2]
    D.R. Boone W.B. Whitman P.E. Rouviere Diversity and Taxonomy of Methanogens J.G. Ferry Methanogenesis 1993 Chapman & Hall New York 35 80.
  • [3]
    W.B. Whitman T.L. Bowen D.R. Boone The Methanogenic Bacteria A. Balows H.G. Truper M. Dworkin W. Harder K.J. Schleifer The Prokaryotes 1991 Springer New York 719 767.
  • [4]
    Großkopf, R., Janssen, P.H., 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.
  • [5]
    Großkopf, R., Stubner, S., Liesack, W. (1998) Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol. 64, 49834989.
  • [6]
    Lehmann-Richter, S., Großkopf, R., Liesack, W., Frenzel, P., Conrad, R. (1999) Methanogenic archaea and CO2-dependent methanogenesis on washed rice roots. Environ. Microbiol. 1, 159166.
  • [7]
    Ramakrishnan, B., Lueders, T., Dunfield, P.F., Conrad, R., 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.
  • [8]
    Basiliko, N., Yavitt, J.B., Dees, P.M., Merkel, S.M. (2004) Methane biogeochemistry and methanogen communities in two northern peatland ecosystems, New York State. Geomicrobiol. J. 20, 563577.
  • [9]
    Galand, P.E., Saarnio, S., Fritze, H., Yrjälä, K. (2002) Depth related diversity of methanogen Archaea in Finnish oligotrophic fen. FEMS Microbiol. Ecol. 42, 441449.
  • [10]
    Sizova, M.V., Panikov, N.S., Tourova, T.P., Flanagan, P.W. (2003) Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog. FEMS Microbiol. Ecol. 45, 301315.
  • [11]
    Jurgens, G., Glöckner, F.O., Amann, R., Saano, A., Montonen, L., Likolammi, M., Münster, U. (2000) Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol. Ecol. 34, 4556.
  • [12]
    Zepp Falz, K., Holliger, C., Grosskopf, R., Liesack, W., Nozhevnikova, A.N., Muller, B., Wehrli, B., Hahn, D. (1999) Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland). Appl. Environ. Microbiol. 65, 24022408.
  • [13]
    Dojka, M.A., Hugenholtz, P., Haack, S.K., Pace, N.R. (1998) Microbial diversity in a hydrocarbon- and chlorinated-solventcontaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64, 38693877.
  • [14]
    Watanabe, K., Kodama, Y., Hamamura, N., Kaku, N. (2002) Diversity, abundance, and activity of archaeal populations in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Appl. Environ. Microbiol. 68, 38993907.
  • [15]
    Lueders, T., Chin, K.-J., Conrad, R., Friedrich, M. (2001) Molecular analyses of methyl-coenzyme M reductase α-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ. Microbiol. 3, 194204.
  • [16]
    Chin, K.-J., Rainey, F.A., Janssen, P.H., Conrad, R. (1998) Methanogenic degradation of polysaccharides and the characterization of polysaccharolytic clostridia from anoxic rice field soil. Syst. Appl. Microbiol. 21, 185200.
  • [17]
    Tschech, A., Pfennig, N. (1984) Growth-yield increase linked to caffeate reduction in Acetobacterium woodii. Arch. Microbiol. 137, 163167.
  • [18]
    Conrad, R., Mayer, H.P., Wüst, M. (1989) Temporal change of gas metabolism by hydrogen-syntrophic methanogenic bacterial associations in anoxic paddy soil. FEMS Microbiol. Ecol. 62, 265274.
  • [19]
    Krumböck, M., Conrad, R. (1991) Metabolism of position-labelled glucose in anoxic methanogenic paddy soil and lake sediment. FEMS Microbiol. Ecol. 85, 247256.
  • [20]
    Stubner, S. (2002) Enumeration of 16S rDNA of Desulfotomaculum lineage 1 in rice field soil by real-time PCR with SybrGreen™ detection. J. Microbiol. Meth. 50, 155164.
  • [21]
    D.J. Lane 16S/23S rRNA Sequencing E. Stackebrandt M. Goodfellow Nucleic Acid Techniques in Bacterial Systematics 1991 Wiley Chichester, UK 115 175.
  • [22]
    Weisburg, W.G., Barns, S.M., Pelletier, D.A., Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 679703.
  • [23]
    Springer, E., Sachs, M.S., Woese, C.R., 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.
  • [24]
    Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H. Yadhukumar Buchner A., Lai, T., Steppi, S., Jobb, G., Foerster, W., Brettske, I., Gerber, S., Ginhart, A.W., Gross, O., Grumann, S., Hermann, S., Jost, R., Koenig, A., Liss, T., Lueßmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuickmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., Schleifer, K.-H. (2004) ARB: a software environment for sequence data. Nucleic Acids Res. 32, 13631371.
  • [25]
    Kolb, S., Knief, C., Stubner, S., Conrad, R. (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time pCR assays. Appl. Environ. Microbiol. 69, 24232429.
  • [26]
    Chin, K.-J., Lukow, T., Conrad, R. (1999) Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil. Appl. Environ. Microbiol. 65, 23412349.
  • [27]
    Lukow, T., Dunfield, P.F., Liesack, W. (2000) Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol. Ecol. 32, 241247.
  • [28]
    Dedysh, S.N., Derakshani, M., Liesack, W. (2001) Detection and enumeration of methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris. Appl. Environ. Microbiol. 67, 48504857.
  • [29]
    Amann, R.I., Krumholz, L., Stahl, D.A. (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172, 762770.
  • [30]
    Raskin, L., Stromley, J.M., Rittmann, B.E., Stahl, D.A. (1994) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60, 12321240.
  • [31]
    Ricke, P., Erkel, C., Kube, M., Reinhardt, R., Liesack, W. (2004) Comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from Methylocystis strain SC2. Appl. Environ. Microbiol. 70, 30553063.
  • [32]
    Rabus, R., Kube, M., Beck, A., Widdel, F., Reinhardt, R. (2002) Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch. Microbiol. 178, 506516.
  • [33]
    Olsen, G.J., Matsuda, H., Hagstrom, R., Overbeek, R. (1994) FastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10, 4148.
  • [34]
    Altschult, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403410.
  • [35]
    Adachi, J. and Hasegawa, M. (1996) Molphy Version 2.3, Programs for Molecular Phylogenetics Based on Maximum Likelihood. Technical Report, The Institute of Statistical Mathematics, Tokyo
  • [36]
    Frishman, D., Mironov, A., Mewes, H.-W., Gelfand, M. (1998) Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res. 26, 29412947.
  • [37]
    Collins, M.D., Lawson, P.A., Willems, A., Cordoba, J.J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H., Farrow, J.A. (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44, 812826.
  • [38]
    Rivera, M.C., Jain, R., Moore, J.E., Lake, J.A. (1998) Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. USA 95, 62396244.
  • [39]
    Matte-Tailliez, O., Brochier, C., Forterre, P., Philippe, H. (2002) Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol. 19, 631639.
  • [40]
    Brochier, C., Forterre, P., Gribaldo, S. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol. 5, 2004, R17.
  • [41]
    Schönheit, P., Moll, J., Thauer, R.K. (1980) Growth parameters (KS, μmax, YS) of Methanobacterium thermoautotrophicum. Arch. Microbiol. 127, 5965.
  • [42]
    Fey, A., Chin, K.-J., Conrad, R. (2001) Thermophilic methanogens in rice field soil. Environ. Microbiol. 3, 295303.
  • [43]
    Liesack, W., Schnell, S., Revsbech, N.P. (2000) Microbiology of flooded rice paddies. FEMS Microbiol. Ecol. 24, 625645.
  • [44]
    Klappenbach, J.A., Dunbar, J.M., Schmidt, T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66, 13281333.
  • [45]
    Slobodkin, A., Reysenbach, A.-L., Struntz, N., Dreier, M., Wiegel, J. (1997) Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring. Int. J. Syst. Bacteriol. 47, 541547.
  • [46]
    Plugge, C.M., Balk, M., Zoetendal, E.G., Stams, A.J.M. (2002) Gelria glutamica gen. nov., sp. nov., a thermophilic, obligately syntrophic, glutamate-degrading anaerobe. Int. J. Syst. Bacteriol. 52, 401407.
  • [47]
    Guertler, V., Stanisich, V.A. (1996) New approaches to typing and identification of bacteria using the 16S–23S rDNA spacer. Microbiology 142, 316.
  • [48]
    Klappenbach, J.A., Saxman, P.R., Cole, J.T., Schmidt, T.M. (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 29, 181184.
  • [49]
    Neumann, H., Gierl, A., Tu, J., Leibrock, J., Staiger, D., Zillig, W. (1983) Organization of the genes for ribosomal RNA in archaebacteria. Mol. Gen. Genet. 192, 6672.
  • [50]
    Peterson, J.D., Umayam, L.A., Dickinson, T., Hickey, E.K., White, O. (2001) The comprehensive microbial resource. Nucleic Acids Res. 29, 123125.
  • [51]
    Makarova, K.S., Aravind, L., Galperin, M.Y., Grishin, N.V., Tatusov, R.L., Wolf, Y.I., Koonin, E.V. (1999) Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9, 608628.
  • [52]
    Jain, R., Rivera, M.C., Lake, J.A. (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96, 38013806.
  • [53]
    Nesbø, C.L., Boucher, Y., Doolittle, W.F. (2001) Defining the core of nontransferable prokaryotic genes: the euryarchaeal core. J. Mol. Evol. 53, 340350.
  • [54]
    Daubin, V., Moran, N.A., Ochman, H. (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301, 829832.
  • [55]
    Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, L., Nelson, K.E., Nelson, W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, O., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.H., Smith, H.O. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 6674.
  • [56]
    Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., Solovyev, V.V., Rubin, E.M., Rokhsar, D.S., Banfield, J.F. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 3743.
  • [57]
    Hallin, P.F., Ussery, D.W. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics. 20, 2004.