Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia


Aerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment1. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows optimally below pH 5, but some environments with active methane cycles are very acidic2,3. Here we describe an extremely acidophilic methanotroph that grows optimally at pH 2.0–2.5. Unlike the known methanotrophs, it does not belong to the phylum Proteobacteria but rather to the Verrucomicrobia, a widespread and diverse bacterial phylum that primarily comprises uncultivated species with unknown genotypes. Analysis of its draft genome detected genes encoding particulate methane monooxygenase that were homologous to genes found in methanotrophic proteobacteria. However, known genetic modules for methanol and formaldehyde oxidation were incomplete or missing, suggesting that the bacterium uses some novel methylotrophic pathways. Phylogenetic analysis of its three pmoA genes (encoding a subunit of particulate methane monooxygenase) placed them into a distinct cluster from proteobacterial homologues. This indicates an ancient divergence of Verrucomicrobia and Proteobacteria methanotrophs rather than a recent horizontal gene transfer of methanotrophic ability. The findings show that methanotrophy in the Bacteria is more taxonomically, ecologically and genetically diverse than previously thought, and that previous studies have failed to assess the full diversity of methanotrophs in acidic environments.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Vertical profiles of methane partial pressures (open circles), O 2 partial pressures (open triangles) and temperature (filled diamonds) in a geothermal soil.
Figure 2: D 600 (open diamonds), methane consumption (open circles), and O 2 consumption (open triangles) of isolate V4 growing in liquid medium at pH 1.5 and 50 °C.
Figure 3: Growth rate constant based on D 600 (open circles) and average methane consumption rates (filled circles) of isolate V4 at a range of pH values.
Figure 4: Transmission electron micrographs of internal membrane structures observed in some cells of Verrucomicrobia isolate V4.
Figure 5: Phylogenetic tree constructed from derived PmoA and AmoA sequences (subunits of particulate methane monooxygenase or ammonia monooxygenase), showing the relative positions of the three sequences from Verrucomicrobia isolate V4.


  1. Conrad, R. Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol. Rev. 60, 609–640 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Castaldi, S. & Tedesco, D. Methane production and consumption in an active volcanic environment of southern Italy. Chemosphere 58, 131–139 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  3. Dedysh, S. N. et al. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science 282, 281–284 (1998)

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Intergovernmental Panel on Climate Change. Climate Change 2007: The Physical Science Basis. Working Group I Contribution to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (eds Solomon S. et al.) (Cambridge Univ. Press, Cambridge, 2007)

  5. Kvenvolden, K. A. & Rogers, B. W. Gaia’s breath—global methane exhalations. Mar. Petrol. Geol. 22, 579–590 (2005)

    Article  CAS  Google Scholar 

  6. Giggenbach, W. F., Sheppard, D. S., Robinson, B. W., Stewart, M. K. & Lyon, G. L. Geochemical structure and position of the Waiotapu geothermal field, New Zealand. Geothermics 23, 599–644 (1994)

    Article  CAS  Google Scholar 

  7. Dedysh, S. N. Methanotrophic bacteria of acidic Sphagnum peat bogs. Microbiology (Russia) 71, 638–650 (2002)

    CAS  Google Scholar 

  8. Theisen, A. R. et al. Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2. Mol. Microbiol. 58, 682–692 (2005)

    Article  CAS  PubMed  Google Scholar 

  9. Dumont, M. G. & Murrell, J. C. Community-level analysis: key genes of aerobic methane oxidation. Methods Enzymol. 397, 413–427 (2005)

    Article  CAS  PubMed  Google Scholar 

  10. Knief, C., Lipski, A. & Dunfield, P. F. Diversity and activity of methanotrophic bacteria in different upland soils. Appl. Environ. Microbiol. 69, 6703–6714 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Hou, S. et al. Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc. Natl Acad. Sci. USA 101, 18036–18041 (2004)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ward, N. et al. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol. 2, E303 (2004)

    Article  PubMed  PubMed Central  Google Scholar 

  13. Gilbert, B. et al. Molecular analysis of the pmo (particulate methane monooxygenase) operons from two type II methanotrophs. Appl. Environ. Microbiol. 66, 966–975 (2000)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Ricke, P., Erkel, C., Kube, M., Reinhardt, R. & Liesack, W. Comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from Methylocystis strain SC2. Appl. Environ. Microbiol. 70, 3055–3063 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Holmes, A. J. et al. Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl. Environ. Microbiol. 65, 3312–3318 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Chistoserdova, L., Chen, S. W., Lapidus, A. & Lidstrom, M. L. Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J. Bacteriol. 185, 2980–2987 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Chistoserdova, L. et al. Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J. Bacteriol. 189, 4020–4027 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kane, S. R. et al. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J. Bacteriol. 189, 1931–1945 (2007)

    Article  CAS  PubMed  Google Scholar 

  19. Chistoserdova, L. et al. The enigmatic Planctomycetes may hold a key to the origins of methanogenesis and methylotrophy. Mol. Biol. Evol. 21, 1234–1241 (2004)

    Article  CAS  PubMed  Google Scholar 

  20. Trotsenko, Y. Metabolic features of methane- and methanol-utilizing bacteria. Acta Biotechnol. 3, 269–277 (2004)

    Article  Google Scholar 

  21. Kelly, D. P., Anthony, C. & Murrell, J. C. Insights from the complete genome sequence of the obligate methanotroph, Methylococcus capsulatus . Trends Microbiol. 13, 195–198 (2005)

    Article  CAS  PubMed  Google Scholar 

  22. Janssen, P. H. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72, 1719–1728 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Bryant, D. A. et al. Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium . Science 317, 523–526 (2007)

    Article  ADS  CAS  PubMed  Google Scholar 

  24. Morris, S. A., Radajewski, S., Willison, T. W. & Murrell, J. C. Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl. Environ. Microbiol. 68, 1446–1453 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Lin, J. L. et al. Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potentially active populations by stable isotope probing. Environ. Microbiol. 6, 1049–1060 (2004)

    Article  CAS  PubMed  Google Scholar 

  26. Dedysh, S. N. et al. Methylocystis heyerii sp. nov., a novel type II methanotrophic bacterium possessing the ‘signature’ fatty acid of type I methanotrophs. Int. J. Syst. Evol. Microbiol. 57, 472–479 (2007)

    Article  CAS  PubMed  Google Scholar 

  27. Weatherby, T. M. & Lenz, P. H. Mechanoreceptors in calanoid copepods: Designed for high sensitivity. Arthropod Struct. Dev. 29, 275–288 (2000)

    Article  CAS  PubMed  Google Scholar 

  28. Ispolatov, I., Yuryev, A., Mazo, I. & Maslov, S. Binding properties and evolution of homodimers in protein–protein interaction networks. Nucleic Acids Res. 33, 3629–3635 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502–504 (2002)

    Article  CAS  PubMed  Google Scholar 

Download references


We thank S. Dedysh, J. C. Murrell and J. Euzéby for comments; A. Malahoff for supporting this research programme; and the Tikitere Trust for permission to sample at Hell’s Gate. This work was supported in part by the Wairakei Environmental Mitigation Charitable Trust (P.D.). The genome analysis was funded by the US Department of Defense (M.A.). Gene sequences referenced in this paper are deposited DDBJ/EMBL/GenBank under accession numbers AM900833–AM900834 and EU223838–EU223931.

Author Contributions P.F.D., B.W.M., M.A.C. and M.B.S. performed field sampling, methane measurement and molecular 16S rRNA analyses. P.F.D. and M.B.S. isolated and characterized the culture. S.H., B.L., J.H.S., Z.Z., Y.R., J.W., L.F., M.B.S., L.W., W.L. and M.A. conducted genome sequencing. P.F.D., P.S., A.Y., A.V.S., J.S., P.S. and M.A. conducted genome analyses. T.M.W. and M.B.S. performed electron microscopy. P.B. undertook phospholipid fatty-acid analysis.

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Peter F. Dunfield, Lei Wang or Maqsudul Alam.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figure 1 with Legend and Supplementary Tables 1-3. The Supplementary Figure 1 shows phylogenetic 16S rRNA gene tree showing the position of isolate V4 relative to other members of the phylum Verrucomicrobia and to proteobacterial methanotrophs. The Supplementary Table 1 illustrates putative genes involved in one-carbon metabolism in Verrucomicrobia isolate V4. The Supplementary Table 2 illustrates identities of partial segments (165 amino acids) of derived PmoA sequences in isolate V4 to PmoA and AmoA sequences of selected bacterial nitrifiers and methanotrophs, and the occurrence of proposed "signature" amino acid residues for either PmoA or AmoA. The Supplementary Table 3 illustrates phospholipid fatty acid profile of isolate V4. (PDF 479 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dunfield, P., Yuryev, A., Senin, P. et al. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450, 879–882 (2007).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing