Wallenius, A. J., Dalcin Martins, P., Slomp, C. P. & Jetten, M. S. M. Anthropogenic and environmental constraints on the microbial methane cycle in coastal sediments. Front. Microbiol. 12, 631621 (2021).
Thauer, R. K., Kaster, A.-K., Seedorf, H., Buckel, W. & Hedderich, R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6, 579–591 (2008).
Hanson, R. S. & Hanson, T. E. Methanotrophic bacteria. Microbiol. Rev. 60, 439–471 (1996).
Boetius, A. et al. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623–626 (2000).
Hallam, S. J., Girguis, P. R., Preston, C. M., Richardson, P. M. & DeLong, E. F. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl. Environ. Microbiol. 69, 5483–5491 (2003).
Leu, A. O. et al. Lateral gene transfer drives metabolic fFlexibility in the anaerobic methane-oxidizing archaeal family Methanoperedenaceae. mBio 11, e01325-20 (2020).
Ettwig, K. F. et al. Archaea catalyze iron-dependent anaerobic oxidation of methane. Proc. Natl Acad. Sci. USA 113, 12792–12796 (2016).
Lee, S. et al. Methane-derived carbon flow through host-virus trophic networks in soil. Preprint at bioRxiv https://doi.org/10.1101/2020.12.16.423115 (2021).
Chen, L.-X. et al. Large freshwater phages with the potential to augment aerobic methane oxidation. Nat. Microbiol. 5, 1504–1515 (2020).
Ng, W. V. et al. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome? Genome Res. 8, 1131–1141 (1998).
Ausiannikava, D. et al. Evolution of genome architecture in Archaea: spontaneous generation of a new chromosome in Haloferax volcanii. Mol. Biol. Evol. 35, 1855–1868 (2018).
Wang, H., Peng, N., Shah, S. A., Huang, L. & She, Q. Archaeal extrachromosomal genetic elements. Microbiol. Mol. Biol. Rev. 79, 117–152 (2015).
Lindell, D. et al. Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc. Natl Acad. Sci. USA 101, 11013–11018 (2004).
Anantharaman, K. et al. Sulfur oxidation genes in diverse deep-sea viruses. Science 344, 757–760 (2014).
Hug, L. A. et al. Aquifer environment selects for microbial species cohorts in sediment and groundwater. ISME J. 9, 1846–1856 (2015).
Lawrence, J. G. & Ochman, H. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44, 383–397 (1997).
Hua, Z.-S. et al. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nat. Commun. 10, 4574 (2019).
DasSarma, S., Capes, M. & DasSarma, P. in Microbial Megaplasmids (ed. Schwartz, E.) 3–30 (Springer Berlin Heidelberg, 2009).
Al-Shayeb, B. et al. Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020).
Schoelmerich, M. C. et al. A widespread group of large plasmids in methanotrophic Methanoperedens archaea. Preprint at bioRxiv https://doi.org/10.1101/2022.02.01.478723 (2022).
Hall, J. P. J., Botelho, J., Cazares, A. & Baltrus, D. A. What makes a megaplasmid? Phil. Trans. R. Soc. B 377, 20200472 (2022).
Medema, M. H. et al. The sequence of a 1.8-Mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol. Evol. 2, 212–224 (2010).
Wagenknecht, M. et al. Structural peculiarities of linear megaplasmid, pLMA1, from Micrococcus luteus interfere with pyrosequencing reads assembly. Biotechnol. Lett. 32, 1853–1862 (2010).
Liu, Z. et al. Domain-centric dissection and classification of prokaryotic poly(3-hydroxyalkanoate) synthases. Preprint at bioRxiv https://doi.org/10.1101/693432 (2019).
Berger, W., Steiner, E., Grusch, M., Elbling, L. & Micksche, M. Vaults and the major vault protein: novel roles in signal pathway regulation and immunity. Cell. Mol. Life Sci. 66, 43–61 (2009).
Cai, C. et al. A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. ISME J. 12, 1929–1939 (2018).
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).
Scheller, S., Yu, H., Chadwick, G. L., McGlynn, S. E. & Orphan, V. J. Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction. Science 351, 703–707 (2016).
Lindell, D., Jaffe, J. D., Johnson, Z. I., Church, G. M. & Chisholm, S. W. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438, 86–89 (2005).
Heider, J., Szaleniec, M., Sünwoldt, K. & Boll, M. Ethylbenzene dehydrogenase and related molybdenum enzymes involved in oxygen-independent alkyl chain hydroxylation. J. Mol. Microbiol. Biotechnol. 26, 45–62 (2016).
Wang, Q. et al. Aerobic bacterial methane synthesis. Proc. Natl Acad. Sci. USA 118, e2019229118 (2021).
Boyd, J. A. et al. Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. ISME J. 13, 1269–1279 (2019).
Bushnell, B. BBTools software package. http://sourceforge.net/projects/bbmap (Source Forge, 2014).
Joshi, N. & Fass, J. N. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. GitHub https://github.com/najoshi/sickle (2011).
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).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).
Brown, C. T., Olm, M. R., Thomas, B. C. & Banfield, J. F. Measurement of bacterial replication rates in microbial communities. Nat. Biotechnol. 34, 1256–1263 (2016).
Darling, A. E., Mau, B. & Perna, N. T.progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5, e11147 (2010).
Bushnell, B. BBMap: A fast, accurate, splice-aware aligner. OSTI.gov https://www.osti.gov/biblio/1241166 (2014).
Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).
Biswas, A., Staals, R. H. J., Morales, S. E., Fineran, P. C. & Brown, C. M. CRISPRDetect: a flexible algorithm to define CRISPR arrays. BMC Genomics 17, 356 (2016).
Makarova, K. S. et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2020).
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
McWilliam, H. et al. Analysis Tool Web Services from the EMBL-EBI. Nucleic Acids Res. 41, W597–W600 (2013).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Huang, Y., Niu, B., Gao, Y., Fu, L. & Li, W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26, 680–682 (2010).
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).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007).
Darling, A. C. E., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403 (2004).
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