Nature：王磊等—极端微生物研究

Nature advance online publication 14 November 2007 | doi:10.1038/nature06411; Received 13 August 2007; Accepted 24 October 2007; Published online 14 November 2007

Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia

Peter F. Dunfield1,9, Anton Yuryev2, Pavel Senin3,4, Angela V. Smirnova1, Matthew B. Stott1, Shaobin Hou3,4, Binh Ly3,4, Jimmy H. Saw3, Zhemin Zhou5, Yan Ren5, Jianmei Wang5, Bruce W. Mountain1, Michelle A. Crowe1, Tina M. Weatherby6, Paul L. E. Bodelier7, Werner Liesack8, Lu Feng5, Lei Wang5 & Maqsudul Alam3,4

Correspondence to: Peter F. Dunfield1,9Lei Wang5Maqsudul Alam3,4 Correspondence and requests for materials should be addressed to P.D. (Email: p.dunfield@gns.cri.nz), M.A. (Email: alam@hawaii.edu) or L.W. (Email: wanglei@nankai.edu.cn).

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.