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References

  • [1]
    Prinn, R.G. (1994) Global atmospheric-biospheric chemistry. In: Global Atmospheric–Biospheric Chemistry (Prinn, R.G., Ed.), pp. 1–18. Plenum, New York.
  • [2]
    Ponnamperuma, F.N. (1972) The chemistry of submerged soils. Adv. Agron. 24, 2996.
  • [3]
    Conrad, R. (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O and NO). Microbiol. Rev. 60, 609640.
  • [4]
    Roy, R., Klüber, H.D., Conrad, R. (1997) Early initiation of methane production in anoxic rice soil despite the presence of oxidants. FEMS Microbiol. Ecol. 24, 311320.
  • [5]
    Yao, H., Conrad, R. (1999) Thermodynamics of methane production in different rice paddy soils from China, the Philippines and Italy. Soil Biol. Biochem. 31, 463473.
  • [6]
    Paul, E.A. and Clark, F.E. (1996) Soil Microbiology and Biochemistry. Academic Press, San Diego, CA.
  • [7]
    Fenchel, T., King, G.M. and Blackburn, T.H. (1998) Bacterial Biogeochemistry. The Ecophysiology of Mineral Cycling. Academic Press, San Diego.
  • [8]
    Mayer, H.P., Conrad, R. (1990) Factors influencing the population of methanogenic bacteria and the initiation of methane production upon flooding of paddy soil. FEMS Microbiol. Ecol. 73, 103112.
  • [9]
    Asakawa, S., Hayano, K. (1995) Populations of methanogenic bacteria in paddy field soil under double cropping conditions (rice-wheat). Biol. Fertil. Soils 20, 113117.
  • [10]
    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.
  • [11]
    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.
  • [12]
    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.
  • [13]
    Chin, K.J., Lukow, T., Stubner, S., Conrad, R. (1999) Structure and function of the methanogenic archaeal community in stable cellulose-degrading enrichment cultures at two different temperatures (15 and 30°C). FEMS Microbiol. Ecol. 30, 313326.
  • [14]
    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.
  • [15]
    Horz, H.P. (1997) Vergleichende Molekularbiologische Charakterisierung methanogener Populationen an Wurzeln verschiedener Reisvarietäten. Diploma thesis, University of Marburg, Marburg.
  • [16]
    Rouviere, P.E., Mandelco, L.C. and Woese, C.R. (1991) Phylogenetic analysis of methanogenic bacteria. In: Microbiology and Biochemistry of Strict Anaerobes involved in Interspecies Hydrogen Transfer (Belaich, J.P., Bruschi, M. and Garcia, J.L., Eds.), p. 467. Plenum, New York.
  • [17]
    Fraser, D.G., Doran, J.W., Sahs, W.W., Lesoing, G.W. (1988) Soil microbial populations and activities under conventional and organic management. J. Environ. Qual. 17, 585590.
  • [18]
    Kirchner, M.J. A.F. Wollum II King, L.D. (1993) Soil microbial populations and activities in reduced chemical input agroecosystems. Soil Sci. Soc. Am. J. 57, 12891295.
  • [19]
    Bossio, D.A., Scow, K.M., Gunapala, N., Graham, K.J. (1998) Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microb. Ecol. 36, 112.
  • [20]
    Fisk, A.C., Murphy, S.L. R.L. Tate III (1999) Microscopic observations of bacterial sorption in soil cores. Biol. Fertil. Soils 28, 111116.
  • [21]
    Tisdall, J.M., Oades, J.M. (1982) Organic matter and water-stable aggregates in soils. J. Soil Sci. 33, 141163.
  • [22]
    Kemper, W.D. and Rosenau, R.C. (1986) Aggregate stability and size distribution. In: Methods of Soil Analysis, Vol. 1 (Klute, A., Ed.), pp. 425–442. American Society of Agronomy, Madison, WI.
  • [23]
    Liu, W.T., Marsh, T.L., Cheng, H., Forney, L.J. (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63, 45164522.
  • [24]
    Lüdemeann, H., Arth, I., Liesack, W. (2000) Changes in the bacterial community structure along the vertical oxygen gradient in flooded paddy soil cores, as revealed by T-RFLP analysis of 16S rRNA and their encoding genes. Appl. Environ. Microbiol. 66, 754762.
  • [25]
    Lueders, T. and Friedrich, M. (2000) Archaeal population dynamics during sequential reduction processes in rice field soil. Appl. Environ. Microbiol. (in press).
  • [26]
    Holzapfel-Pschorn, A., Conrad, R., Seiler, W. (1986) Effects of vegetation on the emission of methane from submerged paddy soil. Plant Soil 92, 223233.
  • [27]
    Klüber, H.D., Conrad, R. (1998) Effects of nitrate, nitrite, NO and N2O on methanogenesis and other redox processes in anoxic rice field soil. FEMS Microbiol. Ecol. 25, 301318.
  • [28]
    Schnell, S., Ratering, S., Jansen, K.H. (1998) Simultaneous determination of iron(III), iron(II), and manganese(II) in environmental samples by ion chromatography. Environ. Sci. Technol. 32, 15301537.
  • [29]
    Bak, F., Scheff, G., Jansen, K.H. (1991) A rapid and sensitive ion chromatographic technique for the determination of sulfate and sulfate reduction rates in freshwater lake sediments. FEMS Microbiol. Ecol. 85, 2330.
  • [30]
    Dannenberg, S., Wudler, J., Conrad, R. (1997) Agitation of anoxic paddy soil slurries affects the performance of the methanogenic microbial community. FEMS Microbiol. Ecol. 22, 257263.
  • [31]
    Conrad, R., Schütz, H., Babbel, M. (1987) Temperature limitation of hydrogen turnover and methanogenesis in anoxic paddy soil. FEMS Microbiol. Ecol. 45, 281289.
  • [32]
    Krumböck, M., Conrad, R. (1991) Metabolism of position-labelled glucose in anoxic methanogenic paddy soil and lake sediment. FEMS Microbiol. Ecol. 85, 247256.
  • [33]
    Moré, M.I., Herrick, J.B., Silva, M.C., Ghiorse, W.C., Madsen, E.L. (1994) Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60, 15721580.
  • [34]
    Henckel, T., Friedrich, M., Conrad, R. (1999) Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl. Environ. Microbiol. 65, 19801990.
  • [35]
    Berthelet, M., Whyte, L.G., Greer, C.W. (1996) Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol. Lett. 138, 1722.
  • [36]
    Suzuki, M., Rappe, M.S., Giovannoni, S.J. (1998) Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64, 45224529.
  • [37]
    Strunk, O. and Ludwig, W. (2000) Technische Universität München, Germany. ARB software package version 2.5b (http://www.biol.chemie.tu-muenchen.de/pub/ARB/; last access: 28 Jan. 2000).
  • [38]
    Tiessen, H., Stewart, J.W.B. (1988) Light and electron microscopy of stained microaggregates: the role of organic matter and microbes in soil aggregation. Biogeochem. 5, 312322.
  • [39]
    Elliott, E.T. (1986) Aggregate structure and carbon, nitrogen and phosphorus in native and cultivated soils. Soil Sci. Soc. Am. J. 50, 627633.
  • [40]
    Sandaa, R.A., Enger, O., Torsvik, V. (1998) Rapid method for fluorometric quantification of DNA in soil. Soil Biol. Biochem. 30, 265268.
  • [41]
    Brunk, C.F., Avaniss-Aghajani, E., Brunk, C.A. (1996) A computer analysis of primer and probe hybridization potential with bacterial small-subunit rRNA sequences. Appl. Environ. Microbiol. 62, 872879.
  • [42]
    Ninet, B., Monod, M., Emler, S., Pawlowski, J., Metral, C., Rohner, P., Auckenthaler, R., Hirschel, B. (1996) Two different 16S rRNA genes in a mycobacterial strain. J. Clin. Microbiol. 34, 25312536.
  • [43]
    Clement, B.G., Kehl, L.E., DeBord, K.L., Kitts, C.L. (1998) Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Methods 31, 135142.
  • [44]
    Frostegård, A., Courtois, S., Ramisse, V., Clerc, S., Bernillon, D., Le Gall, F., Jeannin, P., Nesme, X., Simonet, P. (1999) Quantification of bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65, 54095420.
  • [45]
    Dell’Anno, A., Fabiano, M., Duineveld, G.C.A., Kok, A., Danovaro, R. (1998) Nucleic acid (DNA, RNA) quantification and RNA/DNA ratio determination in marine sediments- comparison of spectrophotometric, fluorometric, and high-performance liquid chromatography methods and estimation of detrital DNA. Appl. Environ. Microbiol. 64, 32383245.
  • [46]
    Bintrim, S.B., Donohue, T.J., Handelsman, J., Roberts, G.P., Goodman, R.M. (1997) Molecular phylogeny of archaea from soil. Proc. Natl. Acad. Sci. USA 94, 277282.
  • [47]
    Jurgens, G., Saano, A. (1999) Diversity of soil archaea in boreal forest before, and after clear-cutting and prescribed burning. FEMS Microbiol. Ecol. 29, 205213.
  • [48]
    Buckley, D.H., Graber, J.R., Schmidt, T.M. (1998) Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Appl. Environ. Microbiol. 64, 43334339.