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Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

Nature Microbiology volume 2, Article number: 17081 (2017) Cite this article

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Abstract

Methanogenic archaea are major players in the global carbon cycle and in the biotechnology of anaerobic digestion. The phylum Euryarchaeota includes diverse groups of methanogens that are interspersed with non-methanogenic lineages. So far, methanogens inhabiting hypersaline environments have been identified only within the order Methanosarcinales. We report the discovery of a deep phylogenetic lineage of extremophilic methanogens in hypersaline lakes and present analysis of two nearly complete genomes from this group. Within the phylum Euryarchaeota, these isolates form a separate, class-level lineage ‘Methanonatronarchaeia’ that is most closely related to the class Halobacteria. Similar to the Halobacteria, ‘Methanonatronarchaeia’ are extremely halophilic and do not accumulate organic osmoprotectants. The high intracellular concentration of potassium implies that ‘Methanonatronarchaeia’ employ the ‘salt-in’ osmoprotection strategy. These methanogens are heterotrophic methyl-reducers that use C1-methylated compounds as electron acceptors and formate or hydrogen as electron donors. The genomes contain an incomplete and apparently inactivated set of genes encoding the upper branch of methyl group oxidation to CO2 as well as membrane-bound heterodisulfide reductase and cytochromes. These features differentiate ‘Methanonatronarchaeia’ from all known methyl-reducing methanogens. The discovery of extremely halophilic, methyl-reducing methanogens related to haloarchaea provides insights into the origin of methanogenesis and shows that the strategies employed by methanogens to thrive in salt-saturating conditions are not limited to the classical methylotrophic pathway.

Methanogenesis is one of the key terminal anaerobic processes of the biogeochemical carbon cycle, both in natural ecosystems and in industrial biogas production plants1,2. Biomethane is a major contributor to global warming3. Methanogens comprise four classes—‘Methanomicrobia’, Methanobacteria, Methanopyri and Methanococci—and part of the class Thermoplasmata, within the archaeal phylum Euryarchaeota4–7. The recent metagenomic discovery of putative methyl-reducing methanogens in the candidate phyla ‘Bathyarchaeota’8 and ‘Verstaraetearchaeota’9 indicates that methanogenesis might not be limited to Euryarchaeota.

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Figure 1: Cell morphology of methyl-reducing methanogens from hypersaline soda and salt lakes.
Figure 2: Growth and activity of methyl-reducing methanogens from hypersaline soda lakes.
Figure 3: Effect of hydrotroilite (FeS × nH2O) on growth and methanogenic activity of washed and exhausted cells of the AMET1 strain.
Figure 4: Phylogenetic analysis of ‘Methanonatronarchaeia’ (AMET1 and HMET1).
Figure 5: Comparative genomic analysis and reconstruction of gene losses and gains.
Figure 6: Reconstruction of the central metabolic pathways shared by ‘Methanonatronarchaeia’.

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Acknowledgements

D.Y.S. was supported by STW (project no. 12226), the Gravitation-SIAM Program (grant no. 24002002 from the Dutch Ministry of Education and Science) and by RFBR (grant no. 16-04-00035). K.S.M., Y.I.W. and E.V.K. are supported by the intramural programme of the US Department of Health and Human Services (to the National Library of Medicine). The proteomic analysis was performed in the Proteomics Facility of The Spanish National Center for Biotechnology (CNB-CSIC), which belongs to ProteoRed (PRB2-ISCIII), supported by grant no. PT13/0001. This project received funding from the European Union's Horizon 2020 research and innovation programme (Blue Growth: Unlocking the potential of Seas and Oceans) under grant agreement no. 634486. This work was further funded by grant no. BIO2014-54494-R from the Spanish Ministry of Economy, Industry and Competitiveness.

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Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Centre for Biotechnology, Russian Academy of Sciences, Moscow, Russia

    Dimitry Y. Sorokin & Alexander Y. Merkel

  2. Department of Biotechnology, Delft University of Technology, Delft, The Netherlands

    Dimitry Y. Sorokin, Ben Abbas & Mark C. M. van Loosdrecht

  3. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, Maryland, USA

    Kira S. Makarova, Yuri I. Wolf & Eugene V. Koonin

  4. Institute of Catalysis, CSIC, Madrid, Spain

    Manuel Ferrer

  5. School of Biological Sciences, Bangor University, Gwynedd, LL57 2UW, UK

    Peter N. Golyshin

  6. Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms University, Bonn, Germany

    Erwin A. Galinski

  7. Proteomics Facility, Centro Nacional de Biotecnología, CSIC, Madrid, Spain

    Sergio Ciordia & María Carmen Mena

Authors
  1. Dimitry Y. Sorokin
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Contributions

D.Y.S. performed the fieldwork, the sediment activity incubations, enrichment and isolation of pure cultures and microbiological investigation of enriched and pure cultures. B.A. and A.Y.M. analysed the mcrA and 16S rRNA genes in sediments and methanogenic cultures. M.F., P.N.G., S.C. and M.C.M.v.L. were responsible for the proteomic analysis. E.A.G. analysed compatible solutes. K.S.M., Y.I.W. and E.V.K. performed genomic analysis and evolutionary reconstructions. D.Y.S., K.S.M. and E.V.K. wrote the paper. M.C.M.v.L. oversaw the project and participated in the data interpretation and discussion.

Corresponding authors

Correspondence to Dimitry Y. Sorokin or Eugene V. Koonin.

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Supplementary information

Supplementary information

Supplementary Figures 1–10; Supplementary Tables 1 and 2; Supplementary Data 1–4. (PDF 17605 kb)

Supplementary Table 3

Comparative genomic analysis based on arCOG assignments. (XLSX 6009 kb)

Supplementary Table 4

Reconstruction of gene gain and loss. (XLSX 434 kb)

Supplementary Table 5

Isoelectric point calculation data. (XLSX 25 kb)

Supplementary Table 6

Proteomic analysis for AMET1. (XLSX 121 kb)

Supplementary Table 7

Proteomic analysis for HMET1. (XLSX 179 kb)

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Sorokin, D., Makarova, K., Abbas, B. et al. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat Microbiol 2, 17081 (2017). https://doi.org/10.1038/nmicrobiol.2017.81

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