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Isolating a methanotrophic Verrucomicrobia

methanotrophic Verrucomicrobia

In a recent article published in Nature (1), we describe the isolation of an acidophilic Verrucomicrobia that oxidises methane at acidities as low as pH 1.0. Methane is the second most important greenhouse gas and is considered, when comparing an equal number of molecules, to be between 20-25x more harmful to the atmosphere than of CO2(2-3). Methane consuming bacteria, known as methanotrophs utilise methane diffusing through soils and sediments. These microbes act as biofilters and reduce the quantity of methane reaching the atmosphere. Methanotrophs utilise methane as their sole source of carbon and energy, converting methane to carbon dioxide via the following reaction:

CH4 + 2O2 → CO2 + 2H2O

The majority of cultured (laboratory grown) methanotrophs operate under neutral or slightly acidic or alkaline conditions. Yet many environments that have an active methane cycles, such as geothermal fields, peat bogs and Sphagnum wetlands are highly acidic (pH's 3-5). Scientists have long known that methane was being consumed in these environments, yet have never before isolated an extremely acidophilic methanotroph(4-6). Our acidophilic Verrucomicrobia (known as V4) obligately grows on methane as low as pH 1.0(1) and provides the first proof for microbial methane oxidation under truly acidic conditions.


methanotrophic Verrucomicrobia figure 2

V4 was enriched from steam-affected soil (Figure 1) at Hell's Gate (Tikitere), New Zealand. The bacterium was the dominant bacterial species within a soil layer where geothermally sourced methane was being oxidised prior to reaching the soil surface (Figure 2). The bacterium was enriched and isolated on solid medium in a 25% (v/v) methane atmosphere. It grows optimally between pH 2.0-2.5 and 60ºC. Two phylogenetically similar acidophilic methanotrophic Verrucomicrobia species have also been isolated from geothermal fields in Italy and Russia(7,8).

Unlike, all known methanotrophs, V4(1) and other recent isolates(7,8) are not from the bacterial phylum Proteobacteria, rather from a widespread phylum of soil bacteria known as Verrucomicrobia, and represent the first non-proteobacterial methanotrophs ever isolated. The V4 isolate also possesses three distinct copies of the methane oxidising enzyme, particulate methane monooxygenase (pMMO). Phylogenetic characterisation of the pmoA genes suggests that the V4 pMMO forms a distinct evolutionary lineage to that of proteobacterial methanotrophs (Figure 3).

methanotrophic Verrucomicrobia figure 3

The genome of V4 has been sequenced and a draft annotation completed. Continuing analysis of the genome is allowing scientists to gain an understanding of the bacteria's unique metabolism, methane oxidation pathways and growth strategies. Our future work is aimed at identifying the distribution of methane oxidising Verrucomicrobia and similar microorganisms across a broad spectrum of environments, to further investigate novel aspects of the V4 genome, and to understand the V4's methanotrophic evolution as compared to other methanotrophs.

This work, in particular the sequencing of the V4 genome was a result of a collaboration between GNS, the Dunfield Laboratory at the University of Calgary, and the Alam Laboratory at the University of Hawaii.


  1. Dunfield, P.F., Yuryev, A., Senin, P., Smirnova, A.V., Stott, M.B., Hou, S., Ly, B., Saw, J.H., Zhou, Z., Ren, Y., Wang, J., Mountain, B.W., Crowe, M.A., Weatherby, T.M., Bodelier, P.L.E., Liesack, W., Feng, L., Wang, L. & Alam, M. 2007. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature, 450(7171), 879-882.
  2.  Lelieveld, J., Crutzen, P.J. & Dentener, F.J. 1998. Changing concentration, lifetime and climate forcing of atmospheric methane.
     Tellus, Series B: Chemical and Physical Meteorology,50(2), 128-150.
  3.  Kvenvolden, K.A. & Rogers, B.W. 2005. Gaia's breath - Global methane exhalations. Marine and Petroleum Geology, 22(4), 579-590.
  4. Segers, R. 1998. Methane production and methane consumption: A review of processes underlying wetland methane fluxes. Biogeochemistry, 41(1), 23-51.
  5. Krumholz, L.R. 1995. Methanogenesis and methanotrophy within a Sphagnum peatland. FEMS Microbiology Ecology, 18(3), 215-224.
  6. McDonald, I.R. & Murrell, J.C. 1997. The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs. FEMS Microbiology Letters, 156(2), 205-210.
  7. Pol, A., Heijmans, K., Harhangi, H.R., Tedesco, D., Jetten, M.S.M. & Op Den Camp, H.J.M. 2007. Methanotrophy below pH 1 by a new Verrucomicrobia species. 2007. Nature, 450(7171), 874-878.
  8. Islam, T., Jensen, S., Reigstad, L.J., Larsen, Ø. & Birkeland, N.-K. 2008. Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proceedings of the National Academy of Sciences of the United States of America. 105(1), 300-304.