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A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment

Nature Microbiology volume 8, pages 2170–2182 (2023)Cite this article

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Abstract

Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.

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Fig. 1: Discovery of methanogenic viruses and other mobile genetic elements.
Fig. 2: Diversity and relationships of viruses of methanogenic archaea.
Fig. 3: Genome maps of the identified (pro)viruses, with one example given for each order of methanogens.
Fig. 4: Proteomic tree of Methanobacteriales viral species (vOTUs).
Fig. 5: Ig-like domains and DGRs in viruses of methanogens.

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Data availability

All nucleotide and protein sequences of identified (pro)viruses and plasmids, spacers from the CRISPR database and MAGs of methanogenic archaea from animal gut are deposited in Mendeley Data (https://doi.org/10.17632/wdyjgcdgbm) and provided as Supplementary Data. Viral sequences assembled from metagenomic data are available in the third-party annotation (TPA) section of the DDBJ/ENA/GenBank databases under the accession numbers: BK063666–BK063680. Phrogs database of viral protein families can be found at https://phrogs.lmge.uca.fr/. The IMG/VR database is available at https://img.jgi.doe.gov/cgi-bin/vr/main.cgi.

Code availability

No custom code was used. Commands are provided in GitHub at https://github.com/Smedvede/methanoviruses.

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Acknowledgements

This work was supported by the French National Agency for Research Grants Viromet (ANR-20-CE20-009-01 to S.G. and M.K.) and Methevol (ANR-19-CE02-0005-01 to G.B.), and by the French Government’s Investissement d’Avenir programme, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant no. ANR-10-LABX-62-IBEID to S.G.). We thank the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur, Paris.

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Authors and Affiliations

  1. Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France

    Sofia Medvedeva, Guillaume Borrel & Simonetta Gribaldo

  2. Institut Pasteur, Université Paris Cité, Unit Archaeal Virology, Paris, France

    Mart Krupovic

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  1. Sofia Medvedeva
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  2. Guillaume Borrel
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Contributions

S.M. carried out all analysis. G.B., M.K. and S.G. conceived and supervised the study. All authors wrote the paper.

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Correspondence to Guillaume Borrel, Mart Krupovic or Simonetta Gribaldo.

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Extended data

Extended Data Fig. 1 Capsid-forming PICI elements (cf-PICI) of Methanothrix (Methanosarcinales) archaea.

Capsid-forming PICI elements (cf-PICI) associated with Methanothrix (Methanosarcinales) archaea and potential helper virus also infecting Methanothrix. Protein identity is shown in green (for the same oriented proteins) and in brown (for proteins encoded on different strands).

Extended Data Fig. 2 Diversity of plasmids (and viruses with unknown capsid proteins) associated with methanogenic archaea.

vConTACT2 network showing proteome-based similarities between plasmids of methanogens. Connections between plasmids indicate sharing 20% or more protein clusters. The color of the node correspond to the host, which was defined by targeting of CRISPR spacers. The color scheme is the same as in Fig. 2b in the main text.

Extended Data Fig. 3 Two mobile genetic elements of Methanopyrales archaea.

The first MGE (36 kbp) encode viral hallmark genes – lysis protein (in green), glycosyl transferases (in violet). No MCP was predicted.

Extended Data Fig. 4 Potential conjugation systems in MGEs of Methanosarcinales.

Genome maps of plasmids and head-tailed viruses of Methanosarcina and ANME-3 archaea, showing three conjugation-related proteins (red), as well as clusters of genes involved in head assembly (yellow), tail assembly (orange), integration and recombination (green), and replication (blue).

Extended Data Fig. 5 Diverse architectures of endolysins of Methanobacteriales viruses.

Alpha-fold 2 structural predictions of PPG-binding modules are shown on the left. The diversity of pPG-cleaving enzymes (endolysins) and the number of viruses associated with each type are shown on the right. pPG-cleaving domains are shown in shades of red, and pPG-recognition modules are shown in shades of blue.

Extended Data Fig. 6 Phylogenetic tree of reverse transcriptase proteins (RTs) from diversity generating retroelements (DGRs).

Branches with bootstrap support >0.95 are marked with dots, branches with bootstrap support less than 0.8 are collapsed. The tree is rooted at midpoint. Reverse transcriptases (RTs) from viruses of methanogens are shown with bold, colored font. The symbol next to leaf ID for RTs from methanogens shows the morphology of the virus.

Supplementary information

Supplementary Information

Supplementary text and Figs. 7–9.

Reporting Summary

Supplementary Table 1

Supplementary Tables 1–14.

Supplementary Data 1

Nucleotide sequences of viruses of methanogens.

Supplementary Data 2

Nucleotide sequences of plasmids of methanogens.

Supplementary Data 3

Collection of CRISPR spacers of methanogens.

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Medvedeva, S., Borrel, G., Krupovic, M. et al. A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment. Nat Microbiol 8, 2170–2182 (2023). https://doi.org/10.1038/s41564-023-01485-w

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