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Genome of a Member of the Candidate Archaeal Phylum Verstraetearchaeota from a Subsurface Thermal Aquifer Revealed Pathways of Methyl-Reducing Methanogenesis and Fermentative Metabolism

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Abstract—

Methanogenesis is the main source of biogenic methane in the atmosphere and therefore plays an important role in climate change. While all methanogens known until recently belonged to the phylum Euryarchaeota, potential methanogens were recently found among two uncultured archaeal phyla, Bathyarchaeota and Verstraetearchaeota. Analysis of the genomes of several members of Verstraetearchaeota revealed their ability to use methylated compounds for methanogenesis; however, all these genomes were incomplete, which prevents an unequivocal reconstruction of their metabolic pathways. The present work reports the complete genome of a new member of Verstraetearchaeota from the metagenome of the microbial community of a deep subsurface reservoir of thermal waters in Western Siberia. Phylogenetic analysis revealed the new archaeon to belong to a new species of the genus ‘Candidatus Methanosuratus’, for which the name ‘Candidatus Methanosuratus subterraneum’ was proposed. The possibility of methyl-reducing methanogenesis was indicated by the presence of the methyl coenzyme M reductase complex and of the genes required for methane production using methanol as the methyl group donor, while the genes required for the oxidation of methyl group to CO2 were missing. Genome analysis showed that ‘Ca. Methanosuratus subterraneum’ has the metabolic pathways required for growth by fermentation of proteinaceous substrates. Analysis of the global distribution of ‘Ca. Methanosuratus’ revealed the 16S rRNA gene sequences assigned to this genus in hot springs, underground waters, and oil reservoirs, which makes it possible to consider this genus as a representative of the subsurface biosphere.

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ACKNOWLEDGMENTS

The authors are grateful to D.Yu. Sorokin for his help in analysis of the metabolic pathways.

The work was carried out using the equipment of the Core Research Facility ‘Bioengineering’.

Funding

The work was supported by the Russian Foundation for Basic Research, project no. 16-34-60124 and by the Ministry of Science and Higher Education of the Russian Federation.

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Authors and Affiliations

  1. Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    V. V. Kadnikov, A. V. Mardanov, A. V. Beletsky & N. V. Ravin

  2. Faculty of Biology, Moscow State University, 119192, Moscow, Russia

    V. V. Kadnikov & N. V. Ravin

  3. Tomsk State University, 634050, Tomsk, Russia

    Y. A. Frank & O. V. Karnachuk

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  1. V. V. Kadnikov
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Correspondence to V. V. Kadnikov.

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Translated by P. Sigalevich

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Kadnikov, V.V., Mardanov, A.V., Beletsky, A.V. et al. Genome of a Member of the Candidate Archaeal Phylum Verstraetearchaeota from a Subsurface Thermal Aquifer Revealed Pathways of Methyl-Reducing Methanogenesis and Fermentative Metabolism. Microbiology 88, 316–323 (2019). https://doi.org/10.1134/S0026261719030068

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