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Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

Abstract

Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea (‘Candidatus Methanoliparia’). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.

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Fig. 1: Placement of nine MAGs described in this study in the reference phylogeny of Archaea.
Fig. 2: Phylogeny of the MCR/MCR-like complex and conservation of important positions in the catalytic site.
Fig. 3: Predicted methane and short-chain alkane metabolism of the MAGs described in this study, with the exception of NM1, which is presented in Fig. 4, and NM2, which has a low completeness.
Fig. 4: Predicted methane, short-chain alkane and long/medium-chain fatty acid metabolism of the two MAGs NM1a (‘Ca. Methanoliparum thermophilum’ completeness of 92.5%) and NM1b (‘Ca. Methanolliviera hydrocarbonicum’ completeness of 90.2%) belonging to the candidate class ‘Ca. Methanoliparia’.

Data availability

MAG sequences are available in the BioProject PRJNA472146 and Biosamples SAMN10387997, SAMN10390728, SAMN10390732, SAMN10390733, SAMN10390735, SAMN10390736, SAMN10390737, SAMN10390738, SAMN10390739. NM2 sequences corresponding to markers reported in Table 2 are deposited under MK202738 to MK202758.

References

  1. 1.

    Demirel, B. & Scherer, P. The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review. Rev. Environ. Sci. Biotechnol. 7, 173–190 (2008).

    CAS  Article  Google Scholar 

  2. 2.

    Schink, B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262–280 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Ueno, Y., Yamada, K., Yoshida, N., Maruyama, S. & Isozaki, Y. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440, 516–519 (2006).

    CAS  Article  Google Scholar 

  4. 4.

    Sousa, F. L. et al. Early bioenergetic evolution.Philos. Trans. R Soc. Lond. B 368, 20130088 (2013).

    Article  Google Scholar 

  5. 5.

    Kasting, J. F. & Siefert, J. L. Life and the evolution of Earth’s atmosphere. Science 296, 1066–1068 (2002).

    CAS  Article  Google Scholar 

  6. 6.

    Bapteste, E., Brochier, C. & Boucher, Y. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea. 1, 353–363 (2005).

    CAS  Article  Google Scholar 

  7. 7.

    Whitman, W. B., Bowen, T. L. & Boone, D. R. The Methanogenic Bacteria. Prokaryotes Vol. 3 (Springer, New York, 2006); https://doi.org/10.1007/0-387-30743-5_9

    Chapter  Google Scholar 

  8. 8.

    Kendall, M. M. & Boone, D. R. in The Prokaryotes 244–256 (Springer, New York, 2006); https://doi.org/10.1007/0-387-30743-5_12

    Chapter  Google Scholar 

  9. 9.

    Oren, A. in The Prokaryotes: Other Major Lineages of Bacteria and The Archaea (eds Rosenberg, E. et al.) 165–193 (Springer, New York, 2014).

  10. 10.

    Borrel, G., Adam, P. S. & Gribaldo, S. Methanogenesis and the Wood-Ljungdahl pathway: an ancient, versatile, and fragile association. Genome Biol. Evol. 8, 1706–1711 (2016).

    CAS  Article  Google Scholar 

  11. 11.

    Timmers, P. H. A. et al. Reverse methanogenesis and respiration in Methanotrophic Archaea. Archaea 2017, 1654237 (2017).

    Article  Google Scholar 

  12. 12.

    Scheller, S., Ermler, U. & Shima, S. in Anaerobic Utilization of Hydrocarbons, Oils, and Lipids (ed. Bool, M.) 1–29 (Springer, Chamonix, 2017); https://doi.org/10.1007/978-3-319-33598-8_3-1.

    Google Scholar 

  13. 13.

    Hallam, S. J. et al. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305, 1457–1462 (2004).

    CAS  Article  Google Scholar 

  14. 14.

    Adam, P. S., Borrel, G., Brochier-Armanet, C. & Gribaldo, S. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME. J. 11, 2407–2425 (2017).

    Article  Google Scholar 

  15. 15.

    Spang, A., Caceres, E. F. & Ettema, T. J. G. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357, pii: eaaf3883 (2017).

    Article  Google Scholar 

  16. 16.

    Borrel, G. et al. Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol. Evol. 5, 1769–1780 (2013).

    CAS  Article  Google Scholar 

  17. 17.

    Nobu, M. K., Narihiro, T., Kuroda, K., Mei, R. & Liu, W.-T. Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME. J. 10, 2478–2487 (2016).

    CAS  Article  Google Scholar 

  18. 18.

    Sorokin, D. Y. et al. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat. Microbiol. 2, 17081 (2017).

    CAS  Article  Google Scholar 

  19. 19.

    Vanwonterghem, I. et al. Methylotrophic methanogenesis discovered in the novel archaeal phylum Verstraetearchaeota. Nat. Microbiol. 1, 16170 (2016).

    CAS  Article  Google Scholar 

  20. 20.

    Brugère, J. F. et al. Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes 5, 5–10 (2014).

    Article  Google Scholar 

  21. 21.

    Laso-Pérez, R. et al. Thermophilic Archaea activate butane via alkyl-coenzyme M formation. Nature 539, 396–401 (2016).

    Article  Google Scholar 

  22. 22.

    Evans, P. N. et al. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350, 434–438 (2015).

    CAS  Article  Google Scholar 

  23. 23.

    Dombrowski, N., Seitz, K. W., Teske, A. P. & Baker, B. J. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments.Microbiome 5, 106 (2017).

    Article  Google Scholar 

  24. 24.

    McKay, L. J., & Hatzenpichler, R., Inskeep, W. P. & Fields, M. W. Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments. Sci. Rep. 7, 7252 (2017).

    Article  Google Scholar 

  25. 25.

    Hawley, E. R. et al. Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Mar. Genomics 18, 97–99 (2014).

    Article  Google Scholar 

  26. 26.

    Seitz, K. W., Lazar, C. S., Hinrichs, K.-U., Teske, A. P. & Baker, B. J. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME. J. 10, 1696–1705 (2016).

    CAS  Article  Google Scholar 

  27. 27.

    Mckay, L. J. et al. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nat. Microbiol. https://doi.org/10.1038/s41564-019-0362-4 (2019).

    CAS  Article  Google Scholar 

  28. 28.

    Ermler, U., Grabarse, W., Shima, S., Goubeaud, M. & Thauer, R. K. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science 278, 1457–1462 (1997).

    CAS  Article  Google Scholar 

  29. 29.

    Arshad, A. et al. A metagenomics-based metabolic model of nitrate-dependent anaerobic oxidation of methane by Methanoperedens-like archaea. Front. Microbiol. 6, 1423 (2015).

    Article  Google Scholar 

  30. 30.

    Wegener, G., Krukenberg, V., Riedel, D., Tegetmeyer, H. E. & Boetius, A. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature 526, 587–590 (2015).

    CAS  Article  Google Scholar 

  31. 31.

    McGlynn, S. E., Chadwick, G. L., Kempes, C. P. & Orphan, V. J. Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature 526, 531–535 (2015).

    CAS  Article  Google Scholar 

  32. 32.

    Meyerdierks, A. et al. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ. Microbiol. 12, 422–439 (2010).

    CAS  Article  Google Scholar 

  33. 33.

    Grimaldi, S., Schoepp-Cothenet, B., Ceccaldi, P., Guigliarelli, B. & Magalon, A. The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. Biochim. Biophys. Acta Bioenerg. 1827, 1048–1085 (2013).

    CAS  Article  Google Scholar 

  34. 34.

    Jormakka, M. et al. Molecular mechanism of energy conservation in polysulfide respiration. Nat. Struct. Mol. Biol. 15, 730–737 (2008).

    CAS  Article  Google Scholar 

  35. 35.

    Hagemeier, C. H., Chistoserdova, L., Lidstrom, M. E., Thauer, R. K. & Vorholt, J. A. Characterization of a second methylene tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1. Eur. J. Biochem. 267, 3762–3769 (2000).

    CAS  Article  Google Scholar 

  36. 36.

    McInerney, M. J. et al. The genome of Syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth. Proc. Natl Acad. Sci. USA 104, 7600–7605 (2007).

    Article  Google Scholar 

  37. 37.

    Klenk, H.-P. et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364–370 (1997).

    CAS  Article  Google Scholar 

  38. 38.

    Milkov, A. V. Molecular and stable isotope compositions of natural gas hydrates: a revised global dataset and basic interpretations in the context of geological settings. Org. Geochem. 36, 681–702 (2005).

    CAS  Article  Google Scholar 

  39. 39.

    Meredith, W., Kelland, S. J. & Jones, D. M. Influence of biodegradation on crude oil acidity and carboxylic acid composition. Org. Geochem. 31, 1059–1073 (2000).

    CAS  Article  Google Scholar 

  40. 40.

    Sieber, J. R., McInerney, M. J. & Gunsalus, R. P. Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation. Annu. Rev. Microbiol. 66, 429–452 (2012).

    CAS  Article  Google Scholar 

  41. 41.

    Zengler, K., Richnow, H. H., Rosselló-Mora R., Michaelis, W. & Widdel, F. Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401, 266–269, https://doi.org/10.1038/45777 (1999).

    CAS  Article  PubMed  Google Scholar 

  42. 42.

    Stams, A. J. M., Sousa, D. Z., Kleerebezem, R. & Plugge, C. M. Role of syntrophic microbial communities in high-rate methanogenic bioreactors. Water Sci. Technol. 66, 353–363 (2012).

    Article  Google Scholar 

  43. 43.

    Gao, B. & Gupta, R. S. Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics 8, 86 (2007).

    Article  Google Scholar 

  44. 44.

    Kaster, A. K. More than 200 genes required for methane formation from H2 and CO2 and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. Archaea 2011, 973848 (2011).

    Article  Google Scholar 

  45. 45.

    Nayak, D. D., Mahanta, N., Mitchell, D. A. & Metcalf, W. W. Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic archaea. eLife 6, e29218 (2017).

    Article  Google Scholar 

  46. 46.

    Lyu, Z. et al. Mmp10 is required for post-translational methylation of arginine at the active site of methyl-coenzyme M reductase. Preprint at BioRxiv https://doi.org/10.1101/211441 (2017).

  47. 47.

    Sarmiento, F., Mrázek, J. & Whitman, W. B. Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. Proc. Natl Acad. Sci. USA 110, 4726–4731 (2013).

    CAS  Article  Google Scholar 

  48. 48.

    Wagner, T., Kahnt, J., Ermler, U. & Shima, S. Didehydroaspartate modification in methyl-coenzyme M reductase catalyzing methane formation. Angew. Chemie - Int. Ed. 55, 10630–10633 (2016).

    Google Scholar 

  49. 49.

    Borrel, G. et al. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 15, 679 (2014).

    Article  Google Scholar 

  50. 50.

    Zheng, K., Ngo, P. D., Owens, V. L., Yang, X. & Mansoorabadi, S. O. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354, 339–342 (2016).

    CAS  Article  Google Scholar 

  51. 51.

    Prakash, D., Wu, Y., Suh, S. J. & Duin, E. C. Elucidating the process of activation of methyl-coenzyme M reductase. J. Bacteriol. 196, 2491–2498 (2014).

    Article  Google Scholar 

  52. 52.

    Li, J. et al. Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus. Sci. Rep. 5, 9209 (2015).

    CAS  Article  Google Scholar 

  53. 53.

    Raymann, K., Brochier-Armanet, C. & Gribaldo, S. The two-domain tree of life is linked to a new root for the Archaea. Proc. Natl Acad. Sci. USA 112, 6670–6675 (2015).

    CAS  Article  Google Scholar 

  54. 54.

    Weiss, M. C. et al. The physiology and habitat of the last universal common ancestor. Nat. Microbiol. 1, 16116 (2016).

    CAS  Article  Google Scholar 

  55. 55.

    Adam, P. S., Borrel, G. & Gribaldo, S. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. Proc. Natl Acad. Sci. USA 115, E5837 (2018).

    Article  Google Scholar 

  56. 56.

    McGlynn, S. E. Energy metabolism during anaerobic methane oxidation in ANME Archaea. Microbes Environ. 32, 5–13 (2017).

    Article  Google Scholar 

  57. 57.

    Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    CAS  Article  Google Scholar 

  58. 58.

    Criscuolo, A. & Gribaldo, S. BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010).

    Article  Google Scholar 

  59. 59.

    Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

    CAS  Article  Google Scholar 

  60. 60.

    Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. MetaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).

    CAS  Article  Google Scholar 

  61. 61.

    Peng, Y., Leung, H. C. M., Yiu, S.-M. & Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420–1428 (2012).

    CAS  Article  Google Scholar 

  62. 62.

    Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. Peer J. 3, e1165 (2015).

    Article  Google Scholar 

  63. 63.

    Wu, Y. W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2015).

    Article  Google Scholar 

  64. 64.

    Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146 (2014).

    CAS  Article  Google Scholar 

  65. 65.

    Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy. Nat. Microbiol. 3, 836–843 (2018).

  66. 66.

    Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).

    CAS  Article  Google Scholar 

  67. 67.

    Darling, A. E. et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. Peer J. 2, e243 (2014).

    Article  Google Scholar 

  68. 68.

    Kobert, K., Salichos, L., Rokas, A. & Stamatakis, A. Computing the internode certainty and related measures from partial gene trees. Mol. Biol. Evol. 33, 1606–1617 (2016).

    CAS  Article  Google Scholar 

  69. 69.

    Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690 (2006).

    CAS  Article  Google Scholar 

  70. 70.

    Lartillot, N., Lepage, T. & Blanquart, S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288 (2009).

    CAS  Article  Google Scholar 

  71. 71.

    Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).

    Article  Google Scholar 

  72. 72.

    Aziz, R. K. et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).

    Article  Google Scholar 

  73. 73.

    Oberto, J. SyntTax: a web server linking synteny to prokaryotic taxonomy. BMC Bioinformatics 14, 4 (2013).

    Article  Google Scholar 

  74. 74.

    Marchler-Bauer, A. et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res. 43, D222–D226 (2015).

    CAS  Article  Google Scholar 

  75. 75.

    Abby, S. S., Néron, B., Ménager, H., Touchon, M. & Rocha, E. P. A. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.PLoS One 9, e110726(2014).

    Article  Google Scholar 

  76. 76.

    Kahnt, J. et al. Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea. FEBS. J. 274, 4913–4921 (2007).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank R. Thauer for feedback on an earlier version of the manuscript. G.B. acknowledges support from the Institut Pasteur through a Roux-Cantarini fellowship. P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme ‘Frontières du Vivant (FdV)-Programme Bettencourt’. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (No. ANR-16-CE02-0005-01). This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris. S.J.H. acknowledges support from the US Department of Energy (DOE) JGI supported by the Office of Science of US DOE Contract No. DE-AC02–05CH11231, the Natural Sciences and Engineering Research Council (NSERC) of Canada, Genome British Columbia, Genome Canada, Canada Foundation for Innovation (CFI) and the Tula Foundation. I.N.S.-G. and V.M.d.O. are grateful to São Paulo Research Foundation—FAPESP (process Nos. 2011/14501-6 and 2013/20436-8) and Petrobras for financial support and to N. Gray and I. Head from the School of Civil Engineering and Geosciences at Newcastle University for lab facilities. W-J.L. was supported by Key Projects of Ministry of Science and Technology (MOST) (Nos. 2013DFA31980 and 2015FY110100). G.M. was supported by the ERC Advanced Grant PARASOL (No. 322551). L.J.M. appreciates funding from the NASA Postdoctoral Programme through the NASA Astrobiology Institute and W.P.I. was supported by the Montana Agricultural Experiment Station (Project No. 911300).

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Contributions

G.B. and S.G. conceived the study. L.J.M., L-X.C., I.N.S.-G., C.M.K.S., G.L.A., W.-J.L., S.J. H., G.M., V.M.d.O., W.P.I. and J.F.B. sequenced and assembled the metagenomes. G.B. screened the IMG database for McrA and identified these metagenomes. Q.L., A.G. and G.B. developed the pipeline Let-it-bin. G.B. performed the contig binning of NM1a, NM1b, NM2, NM3, NM4, Verst-YHS, and Mnatro-ASL MAGs. L-X.C. carried out the contig binning of ANME-1-THS MAG and C.M.K.S. those of GoM-Arc1-GOS and ANME-2c MAGs. G.B. inferred the metabolism associated to each MAG and performed all phylogenetic analyses. P.S.A. performed the congruence tests. G.B. and S.G. wrote the manuscript. All authors read and commented on the manuscript.

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Correspondence to Guillaume Borrel or Simonetta Gribaldo.

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Supplementary information

Supplementary Information

Supplementary Discussion, Supplementary References, Legends for Supplementary Tables, Supplementary Table 2, Supplementary Table 4, Supplementary Table 5, and Supplementary Figures 1–13.

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Supplementary Table 1

Presence/absence of genes involved in specific substrate utilization, energy metabolism, cofactor biosynthesis, secretion, sulfate assimilation, N2 fixation, dissimilatory reduction of inorganic compounds and motility. Pathways and systems are subdivided into different spreadsheets. In each spreadsheet and for each metagenome-assembled genome, protein accession numbers with the same colour indicate co-localized genes.

Supplementary Table 3

Occurrence in archaea of 38 genes previously suggested to be methanogenesis markers.

Supplementary Table 6

Genomes used to build the archaea reference tree (Fig. 1). The first spreadsheet shows the number of genomes available and selected for the phylogeny, and the second spreadsheet gives the NCBI accession numbers (if any) of the selected genomes.

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Borrel, G., Adam, P.S., McKay, L.J. et al. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat Microbiol 4, 603–613 (2019). https://doi.org/10.1038/s41564-019-0363-3

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