• [1]
    IPCC (2001). Climate Change 2001: The scientific basis. Contribution of the working group I to the third assessment report of the Intergovernmental panel on climate change, 881 pp. Cambridge University Press, Cambridge
  • [2]
    LeMer, J., Roger, P. (2001) Production, oxidation, emission and consumption of methane by soils: a review. Eur. J. Soil Biol. 37, 2550.
  • [3]
    Hanson, R.S., Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol. Rev. 60, 439471.
  • [4]
    Frenzel, P. Plant-associated methane oxidation in rice fields and wetlands
  • [5]
    Bowman, J. The Methanotrophs – The Families Methylococcaceae and Methylocystaceae Dworkin, M., Ed. The Prokaryotes 2000, Springer, New York.
  • [6]
    Eller, G., Frenzel, P. (2001) Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. Appl. Environ. Microbiol. 67, 23952403.
  • [7]
    Dedysh, S.N., Dunfield, P.F., Derakshani, M., Stubner, S., Heyer, J., Liesack, W. (2003) Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes. FEMS Microbiol. Ecol. 43, 299308.
  • [8]
    Bodelier, P.L.E., Roslev, P., Henckel, T., Frenzel, P. (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403, 421424.
  • [9]
    Nold, S.C., Boschker, H.T.S., Pel, R., Laanbroek, H.J. (1999) Ammonium addition inhibits 13C-methane incorporation into methanotroph membrane lipids in a freshwater sediment. FEMS Microbiol. Ecol. 29, 8189.
  • [10]
    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.
  • [11]
    Holmes, A.J., Roslev, P., McDonald, I.R., Iversen, N., Henriksen, K., Murrell, J.C. (1999) Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl. Environ. Microbiol. 65, 33123318.
  • [12]
    Horz, H.P., Yimga, M.T., Liesack, W. (2001) Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl. Environ. Microbiol. 67, 41774185.
  • [13]
    Henckel, T., Roslev, P., Conrad, R. (2000) Effects of O2 and CH4 on presence and activity of the indigenous methanotrophic community in rice field soil. Environ. Microbiol. 2, 666679.
  • [14]
    Bodrossy, L., Stralis-Pavese, N., Murrell, J.C., Radajewski, S., Weilharter, A., Sessitsch, A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 5, 566582.
  • [15]
    Muyzer, G. (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2, 317322.
  • [16]
    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.
  • [17]
    Henckel, T., Jackel, U., Schnell, S., Conrad, R. (2000) Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane. Appl. Environ. Microbiol. 66, 18011808.
  • [18]
    Hoffmann, T., Horz, H.P., Kemnitz, D., Conrad, R. (2002) Diversity of the particulate methane monooxygenase gene in methanotrophic samples from different rice field soils in China and the Philippines. Syst. Appl. Microbiol. 25, 267274.
  • [19]
    Yimga, M.T., Dunfield, P.F., Ricke, P., Heyer, H., Liesack, W. (2003) Wide distribution of a novel pmoA-like gene copy among type II methanotrophs, and its expression in Methylocystis strain SC2. Appl. Environ. Microbiol. 69, 55935602.
  • [20]
    Tsien, H.C., Bratina, B.J., Tsuji, K., Hanson, R.S. (1990) Use of oligodeoxynucleotide signature probes for identification of physiological groups of methylotrophic bacteria. Appl. Environ. Microbiol. 56, 28582865.
  • [21]
    Wise, M.G., McArthur, J.V., Shimkets, L.J. (1999) Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis. Appl. Environ. Microbiol. 65, 48874897.
  • [22]
    Carini, S.A., Orcutt, B.N., Joye, S.B. (2003) Interactions between methane oxidation and nitrification in coastal sediments. Geomicrobiol. J. 20, 355374.
  • [23]
    Wartiainen, I., Hestnes, A.G., Svenning, M.M. (2003) Methanotrophic diversity in high arctic wetlands on the islands of svalbard (Norway)-denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures. Can. J. Microbiol. 49, 602612.
  • [24]
    Heyer, J., Galchenko, V.F., Dunfield, P.F. (2002) Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments. Microbiology-(UK) 148, 28312846.
  • [25]
    Brock, TH.C.M., VanderVelde, G., VandeSteeg, H.M. (1987) The effects of extreme water level fluctuations on the wetland vegetation of a nymphaeid-dominated oxbow lake in the Netherlands. Arch. Hydrobiol. Beih. Ergebn. Limnol. 27, 5773.
  • [26]
    Kemnitz, D., Chin, K.J., Bodelier, P., Conrad, R. (2004) Community analysis of methanogenic archaea within a riparian flooding gradient. Environ. Microbiol. 6, 449461.
  • [27]
    P.L.E. P. Frenzel, Contribution of methanotrophic and nitrifying bacteria to CH4 and inline image oxidation in the rhizosphere of rice plants as determined by new methods of discrimination, Appl. Environ. Microbiol., 65. 1999, 1826-1833.
  • [28]
    Rowe R, T.R., Waide, J. (1977) Microtechnique for most-probable-number analysis. Appl. Environ. Microbiol. 33, 676680.
  • [29]
    Muyzer, G., Dewaal, E.C., Uitterlinden, A.G. (1993) Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16s ribosomal-RNA. Appl. Environ. Microbiol. 59, 695700.
  • [30]
    Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H. Yadhukumar Buchner A., Lai, T., Steppi, S., Jobb, G., Forster, W., Brettske, I., Gerber, S., Ginhart, A.W., Gross, O., Grumann, S., Hermann, S., Jost, R., Konig, A., Liss, T., Lussmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, 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.
  • [31]
    Vandepeer, Y., Dewachter, R. (1994) Treecon for Windows – a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10, 569570.
  • [32]
    Gulledge, J., Ahmad, A., Steudler, P.A., Pomerantz, W.J., Cavanaugh, C.M. (2001) Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria. Appl. Environ. Microbiol. 67, 47264733.
  • [33]
    Omelchenko, M.V., Vasileva, L.V., Zavarzin, G.A., Saveleva, N.D., Lysenko, A.M., Mityushina, L.L., Kamelenina, V.N., Trotsenko, Y.A. (1996) A novel psychrophilic methanotroph of the genus Methylobacter. Microbiology 65, 339343.
  • [34]
    Newby, D.T., Reed, D.W., Petzke, L.M., Igoe, A.L., Delwiche, M.E., Roberto, F.F., McKinley, J.P., Whiticar, M.J., Colwell, F.S. (2004) Diversity of methanotroph communities in a basalt aquifer. FEMS Microbiol. Ecol. 48, 333344.
  • [35]
    Pester, M., Friedrich, M.W., Schink, B., Brune, A. (2004) pmoA-Based analysis of methanotrophs in a, littoral lake sediment reveals a diverse and stable community in a dynamic environment. Appl. Environ. Microbiol. 70, 31383142.
  • [36]
    Adamczyk, J., Hesselsoe, M., Iversen, N., Horn, M., Lehner, A., Nielsen, P.H., Schloter, M., Roslev, P., Wagner, M. (2003) The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 69, 68756887.
  • [37]
    Edwards, U., Rogall, T., Blocker, H., Emde, M., Bottger, E.C. (1989) Isolation and direct complete nucleotide determination of entire genes – characterization of a gene coding for 16s-ribosomal RNA. Nucleic Acids Res. 17, 78437853.
  • [38]
    Weisburg, W.G., Barns, S.M., Pelletier, D.A., Lane, D.J. (1991) 16s ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697703.