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Methanotrophy below pH 1 by a new Verrucomicrobia species

Abstract

Mud volcanoes, mudpots and fumaroles are remarkable geological features characterized by the emission of gas, water and/or semi-liquid mud matrices1 with significant methane fluxes to the atmosphere (10-1 to 103 t y-1)2,3,4. Environmental conditions in these areas vary from ambient temperature and neutral pH to high temperatures and low pH. Although there are strong indications for biological methane consumption in mud volcanoes4,5, no methanotrophic bacteria are known that would thrive in the hostile conditions of fumaroles (temperatures up to 70 °C and pH down to 1.8)2. The first step in aerobic methane oxidation is performed by a soluble or membrane-bound methane mono-oxygenase. Here we report that pmoA (encoding the β-subunit of membrane-bound methane mono-oxygenase) clone libraries, made by using DNA extracted from the Solfatara volcano mudpot and surrounding bare soil near the fumaroles, showed clusters of novel and distant pmoA genes. After methanotrophic enrichment at 50 °C and pH 2.0 the most distant cluster, sharing less than 50% identity with any other described pmoA gene, was represented in the culture. Finally we isolated an acidiphilic methanotrophic bacterium Acidimethylosilex fumarolicum SolV belonging to the Planctomycetes/Verrucomicrobia/Chlamydiae superphylum6, ‘outside’ the subphyla of the Alpha- and Gammaproteobacteria containing the established methanotrophs. This bacterium grows under oxygen limitation on methane as the sole source of energy, down to pH 0.8—far below the pH optimum of any previously described methanotroph. A. fumarolicum SolV has three different pmoA genes, with two that are very similar to sequences retrieved from the mudpot. Highly homologous environmental 16S rRNA gene sequences from Yellowstone Park show that this new type of methanotrophic bacteria may be a common inhabitant of extreme environments. This is the first time that a representative of the widely distributed Verrucomicrobia phylum, of which most members remain uncultivated6, is coupled to a geochemically relevant reaction.

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Figure 1: Phylogenetic relationship among deduced PmoA and AmoA proteins.
Figure 2: Growth characteristics of strain SolV.
Figure 3: Phylogenetic relationship between the 16S rRNA gene sequence of strain SolV and representatives of the Planctomycetes/Verrucomicrobia/Chlamydiae superphylum.

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Acknowledgements

The authors thank M. Strous and S. Castaldi for critical reading and discussion, L. van Niftrik and G.-J. Janssen for technical assistance with electron microscopy, M. Schmid for assistance with FISH microscopy and phylogenetic analyses, and H. A. Mohammadi and M. Gerrits for technical assistance in cultivation. H. Lunstroo is acknowledged for allowing access to the 454-sequencing technology, and G. Angarano for allowing access to the Solfatara and P. Mariani for assistance during sampling. The nucleotide sequence data have been deposited in GenBank under accession numbers EF591085 (pmo_1), EF591086 (pmo_2), EF591087 (pmo_3) and EF591088 (16S rRNA).

Author Contributions A.P. and D.T. performed the sampling; A.P. did the enrichment and isolation; K.H. and A.P. carried out the physiological experiments; K.H. and H.R.H. were responsible for the molecular analysis; A.P. and H.J.M.O.d.C. performed phylogenetic analyses, alignments and probe design. The research was conceived by A.P., M.S.M.J. and H.J.M.O.d.C. and was based on observations made by D.T. A.P., M.S.M.J., D.T. and H.J.M.O.d.C. contributed to interpreting the data and writing the paper.

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Correspondence to Mike S. M. Jetten or Huub J. M. Op den Camp.

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Supplementary information

Supplementary Information

The file contains Supplementary Notes with the etymological description of Acidimethylosilex fumarolicum solV and Supplementary Figures S1-S5 with Legends (PDF 2141 kb)

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Pol, A., Heijmans, K., Harhangi, H. et al. Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450, 874–878 (2007). https://doi.org/10.1038/nature06222

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