, Volume 83, Issue 1–2, pp 67–76 | Cite as

Abundance and diversity of methanotrophic Gammaproteobacteria in northern wetlands

  • O. V. Danilova
  • S. N. DedyshEmail author
Experimental Articles


Numeric abundance, identity, and pH preferences of methanotrophic Gammaproteobacteria (type I methanotrophs) inhabiting the northern acidic wetlands were studied. The rates of methane oxidation by peat samples from six wetlands of European Northern Russia (pH 3.9–4.7) varied from 0.04 to 0.60 μg CH4 g−1 peat h−1. The number of cells revealed by hybridization with fluorochrome labeled probes M84 + M705 specific for type I methanotrophs was 0.05–2.16 × 105 cells g−1 dry peat, i.e., 0.4–12.5% of the total number of methanotrophs and 0.004–0.39% of the total number of bacteria. Analysis of the fragments of the pmoA gene encoding particulate methane monooxygenase revealed predominance of the genus Methylocystis (92% of the clones) in the studied sample of acidic peat, while the proportion of the pmoA sequences of type I methanotrophs was insignificant (8%). PCR amplification of the 16S rRNA gene fragments of type I methanotrophs with TypeIF-Type IR primers had low specificity, since only three sequences out of 53 analyzed belonged to methanotrophs and exhibited 93–99% similarity to those of Methylovulum, Methylomonas, and Methylobacter species. Isolates of type I methanotrophs obtained from peat (strains SH10 and 83A5) were identified as members of the species Methylomonas paludis and Methylovulum miyakonense, respectively. Only Methylomonas paludis SH10 was capable of growth in acidic media (pH range for growth 3.8–7.2 with the optimum at pH 5.8–6.2), while Methylovulum miyakonense 83A5 exhibited the typical growth characteristics of neutrophilic methanotrophs (pH range for growth 5.5–8.0 with the optimum at pH 6.5–7.5).


northern bog ecosystems methanotrophic bacteria fluorescent in situ hybridization Gammapro-teobacteria Methylomonas Methylovulum 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Matthews, E. and Fung, I., Methane emissions from natural wetlands: global distribution, area, and environmental characteristics of sources, Global Biogeochem. Cycles, 1987, vol. 1, pp. 61–86.CrossRefGoogle Scholar
  2. 2.
    Dedysh, S.N., Derakshani, M., and Liesack, W., 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., 2001, vol. 67, pp. 4850–4857.PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Chen, Y., Dumont, M.G., McNamara, N.P., Chamberlain, P.M., Bodrossy, L., Stralis-Pavese, N., and Murrell, J.C., Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses, Environ. Microbiol., 2008, vol. 10, pp. 446–459.PubMedCrossRefGoogle Scholar
  4. 4.
    Dedysh, S.N., Exploring methanotroph diversity in acidic northern wetlands: molecular and cultivationbased studies, Microbiology (Moscow), 2009, vol. 78, pp. 655–669.CrossRefGoogle Scholar
  5. 5.
    Dedysh, S.N., Liesack, W., Khmelenina, V.N., Suzina, N.E., Trotsenko, Y.A., Semrau, J.D., Bares, A.M., Panikov, N.S., and Tiedje, J.M., Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs, Int. J. Syst. Evol. Microbiol., 2000, vol. 50, pp. 955–969.PubMedCrossRefGoogle Scholar
  6. 6.
    Dedysh, S.N., Khmelenina, V.N., Suzina, N.E., Trotsenko, Y.A., Semrau, J.D., Liesack, W., and Tiedje, J.M., Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, pp. 251–261.PubMedGoogle Scholar
  7. 7.
    Dedysh, S.N., Belova, S.E., Khmelenina, V.N., Chidthaisong, A., Trotsenko, Y.A., Liesack, W., and Dunfield, P.F., Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing “signature” fatty acids of type I methanotrophs, Int. J. Syst. Evol. Microbiol., 2007, vol. 57, pp. 472–479.PubMedCrossRefGoogle Scholar
  8. 8.
    Vorobev, A.V., Baani, M., Doronina, N.V., Brady, A.L., Liesack, W., Dunfield, P.F., and Dedysh, S.N., Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase, Int. J. Syst. Evol. Microbiol., 2011, vol. 61, pp. 2456–2463.PubMedCrossRefGoogle Scholar
  9. 9.
    Belova, S.E., Kulichevskaya, I.S., Bodelier, P.L.E., and Dedysh, S.N., Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al., 1970) Bowman et al. 1993, Int. J. Syst. Evol. Microbiol., 2013, vol. 63, pp. 1096–1104.PubMedCrossRefGoogle Scholar
  10. 10.
    Dedysh, S.N., Dunfield, P.F., Derakshani, M., Stubner, S., Heyer, J., and Liesack, W., Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes, FEMS Microbiol. Ecol., 2003, vol. 43, pp. 299–308.PubMedCrossRefGoogle Scholar
  11. 11.
    Morris, S.A., Radajewski, S., Willison, T.W., and Murrell, J.C., Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing, Appl. Environ. Microbiol., 2002, vol. 68, pp. 1446–1453.PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Jaatinen, K., Tuittila, E-S., Laine, J., Yrjää, K., and Fritze, H., Methane-oxidizing bacteria in a Finnish raised mire complex: effects of site fertility and drainage, Microb. Ecol., 2005, vol. 50, pp. 429–439.PubMedCrossRefGoogle Scholar
  13. 13.
    Kip, N., van Winden, J., Pan, Y., Bodrossy, L., Reichart, G.-J., Smolders, A.J.P., Jetten, M.S.M., Sinninghe Damsté, J.S., and Op den Camp, H.J.M., Global prevalence of methane oxidation by symbiotic bacteria in peat-moss ecosystems, Nature Geoscience, 2010, vol. 3, pp. 617–621.CrossRefGoogle Scholar
  14. 14.
    Kip, N., Dutilh, B.E., Pan, Y., Bodrossy, L., Neveling, K., Kwint, M.P., Jetten, M.S., and Op den Camp, H.J., Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog, Environ. Microb. Rep., 2011, vol. 3, pp. 667–673.CrossRefGoogle Scholar
  15. 15.
    Kip, N., Ouyang, W., van Winden, J., Raghoebarsing, A., van Niftrik, L., Pol, A., Pan, Y., Bodrossy, L., van Donselaar, E.G., Reichart, G.-J., Jetten, M.S.M., Sinninghe Damsté, J.S., and Op den Camp, H.J.M., Detection, isolation and characterization of acidophilic methanotrophs from Sphagnum mosses, Appl. Environ. Microbiol., 2011, vol. 77, pp. 5643–5654.PubMedCentralPubMedCrossRefGoogle Scholar
  16. 16.
    Danilova, O.V., Kulichevskaya, I.S., Rozova, O.N., Detkova, E.N., Bodelier, P.L., Trotsenko, Y.A., and Dedysh, S.N., Methylomonas paludis sp. nov., the first acid-tolerant member of the genus Methylomonas, from an acidic wetland, Int. J. Syst. Evol. Microbiol., 2013, vol. 63, pp. 2282–2289.PubMedCrossRefGoogle Scholar
  17. 17.
    Stahl, D.A. and Amann, R., Development and application of nucleic acid probes, in Nucleic Acid Techniques in Bacterial Systematics, Stackebrandt, E. and Goodfellow, M., Eds., New York: Wiley, 1991, pp. 205–248.Google Scholar
  18. 18.
    Eller, G., Stubner, S., and Frenzel, P., Group-specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridization, FEMS Microbiol. Lett., 2001, vol. 198, pp. 91–97.PubMedCrossRefGoogle Scholar
  19. 19.
    Daims, H., Brühl, A., Amann, R., Schleifer, K.-H., and Wagner, M., The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set, Syst. Appl. Microbiol., 1999, vol. 22, pp. 434–444.PubMedCrossRefGoogle Scholar
  20. 20.
    Holmes, A.J., Costello, A., Lidstrom, M.E., and Murrell, J.C., Evidence that particulate methane monooxygenase and ammonium monooxygenase may be evolutionarily related, FEMS Microbiol. Lett., 1995, vol. 132, pp. 203–208.PubMedCrossRefGoogle Scholar
  21. 21.
    Chen, Y., Dumont, M.G., Cebron, A., and Murrell, J.C., Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes, Environ. Microbiol., 2007, vol. 9, pp. 2855–2869.PubMedCrossRefGoogle Scholar
  22. 22.
    Wise, M.G., McArthur, J.V., and Shimkets, L.J., 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., 1999, vol. 65, pp. 4889–4897.Google Scholar
  23. 23.
    Gal’chenko, V.F., Metanotrofnye bakterii (Methanotrophic Bacteria), Moscow: GEOS, 2001.Google Scholar
  24. 24.
    Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J., 16S ribosomal DNA amplification for phylogenetic study, J. Bacteriol., 1991, vol. 173, pp. 697–703.PubMedCentralPubMedGoogle Scholar
  25. 25.
    Baani, M. and Liesack, W., Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2, Proc. Natl. Acad. Sci. USA, 2008, vol. 105, pp. 10203–10208.PubMedCentralPubMedCrossRefGoogle Scholar
  26. 26.
    Iguchi, H., Yurimoto, H., and Sakai, Y., Methylovulum miyakonense gen. nov., sp. nov., a type I methanotroph isolated from forest soil, Int. J. Syst. Evol. Microbiol., 2011, vol. 61, pp. 810–815.PubMedCrossRefGoogle Scholar
  27. 27.
    Bragina, A., Berg, C., Muller, H., Moser, D., and Berg, G., Insights into functional bacterial diversity and its effects on Alpine bog ecosystem functioning, Scientific Reports, 2013, vol. 3, 1955. doi: 10.1038/srep01955PubMedCrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2014

Authors and Affiliations

  1. 1.Winogradsky Institute of MicrobiologyRussian Academy of SciencesMoscowRussia

Personalised recommendations