Evans PN, Boyd JA, Leu AO, Woodcroft BJ, Parks DH, Hugenholtz P, et al. An evolving view of methane metabolism in the Archaea. Nat Rev Microbiol. 2019;17:219–32.
Google Scholar
Reeburgh WS. Oceanic methane biogeochemistry. Chem Rev. 2007;107:486–513.
Google Scholar
Timmers PHA, Welte CU, Koehorst JJ, Plugge CM, Jetten MSM, Stams AJM. Reverse methanogenesis and respiration in methanotrophic Archaea. Archaea. 2017;2017:1–22.
Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, et al. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science. 2004;305:1457–62.
Google Scholar
Knittel K, Boetius A. Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol. 2009;63:311–34.
Google Scholar
Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, et al. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol. 2016;1:16170.
Google Scholar
McKay LJ, Dlakić M, Fields MW, Delmont TO, Eren AM, Jay ZJ, et al. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nat Microbiol. 2019;4:614–22.
Google Scholar
Wang Y, Wegener G, Hou J, Wang F, Xiao X. Expanding anaerobic alkane metabolism in the domain of Archaea. Nat Microbiol. 2019;4:595–602.
Google Scholar
Wang Y, Wegener G, Ruff SE, Wang F. Methyl/alkyl‐coenzyme M reductase‐based anaerobic alkane oxidation in archaea. Environ Microbiol. 2021;23:530–41.
Google Scholar
Bertram S, Blumenberg M, Michaelis W, Siegert M, Krüger M, Seifert R. Methanogenic capabilities of ANME‐archaea deduced from 13C‐labelling approaches. Environ Microbiol. 2013;15:2384–93.
Google Scholar
Sousa DZ, Smidt H, Alves MM, Stams AJM. Syntrophomonas zehnderi sp. nov., an anaerobe that degrades long-chain fatty acids in co-culture with Methanobacterium formicicum. Int J Syst Evol Micr. 2007;57:609–15.
Google Scholar
Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, et al. Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Micr. 2006;56:1331–40.
Google Scholar
Yamada T, Sekiguchi Y, Imachi H, Kamagata Y, Ohashi A, Harada H. Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl Environ Microb. 2005;71:7493–503.
Google Scholar
Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B. Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB). Stand Genomic Sci. 2016;11:80.
Google Scholar
Engelhardt T, Sahlberg M, Cypionka H, Engelen B. Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments. ISME J. 2013;7:199–209.
Google Scholar
Nölling J, Groffen A, de Vos WM. φ F1 and φF3, two novel virulent, archaeal phages infecting different thermophilic strains of the genus. Methanobacterium Microbiol. 1993;139:2511–6.
Meile L, Jenal U, Studer D, Jordan M, Leisinger T. Characterization of ψM1, a virulent phage of Methanobacterium thermoautotrophicum Marburg. Arch Microbiol. 1989;152:105–10.
Google Scholar
Weidenbach K, Nickel L, Neve H, Alkhnbashi OS, Künzel S, Kupczok A, et al. Methanosarcina spherical virus, a novel archaeal lytic virus targeting Methanosarcina strains. J Virol. 2017;91:e00955–17.
Google Scholar
Molnár J, Magyar B, Schneider G, Laczi K, Valappil SK, Kovács ÁL, et al. Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples. PLOS ONE. 2020;15:e0231864.
Google Scholar
Paul BG, Bagby SC, Czornyj E, Arambula D, Handa S, Sczyrba A, et al. Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nat Commun. 2015;6:6585.
Google Scholar
Pourcel C, Touchon M, Villeriot N, Vernadet J-P, Couvin D, Toffano-Nioche C, et al. CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. Nucleic Acids Res. 2019;48:D535–D544.
Google Scholar
Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus–host interactions resolved from publicly available microbial genomes. eLife. 2015;4:e08490.
Google Scholar
Lever MA, Teske AP. Diversity of methane-cycling Archaea in hydrothermal sediment investigated by general and group-specific PCR primers. Appl Environ Microb. 2015;81:1426–41.
Jian H, Yi Y, Wang J, Hao Y, Zhang M, Wang S, et al. Diversity and distribution of viruses inhabiting the deepest ocean on Earth. ISME J. 2021;15:3094–110.
Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC. Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nature Protoc. 2017;12:1673–82.
Google Scholar
Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015;3:e985.
Google Scholar
Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, Li Y, et al. Identifying viruses from metagenomic data using deep learning. Quant Biol. 2020;8:64–77.
Google Scholar
Roux S, Páez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, et al. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. Nucleic Acids Res. 2020;49:D764–D775.
Google Scholar
Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol. 2021;39:578–85.
Google Scholar
Sandaa R, Gómez‐Consarnau L, Pinhassi J, Riemann L, Malits A, Weinbauer MG, et al. Viral control of bacterial biodiversity – evidence from a nutrient‐enriched marine mesocosm experiment. Environ Microbiol. 2009;11:2585–97.
Google Scholar
Howard-Varona C, Hargreaves KR, Abedon ST, Sullivan MB. Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 2017;11:1511–20.
Google Scholar
Li Z, Pan D, Wei G, Pi W, Zhang C, Wang J-H, et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J. 2021;15:2366–78.
Google Scholar
Krupovič M, Forterre P, Bamford DH. Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria. J Mol Biol. 2010;397:144–60.
Google Scholar
Thiroux S, Dupont S, Nesbø CL, Bienvenu N, Krupovic M, L’Haridon S, et al. The first head‐tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep‐sea archaea. Environ Microbiol. 2021;23:3614–26.
Google Scholar
Jang HB, Bolduc B, Zablocki O, Kuhn JH, Roux S, Adriaenssens EM, et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat Biotechnol. 2019;37:632–9.
Hao L, Bize A, Conteau D, Chapleur O, Courtois S, Kroff P, et al. New insights into the key microbial phylotypes of anaerobic sludge digesters under different operational conditions. Water Res. 2016;102:158–69.
Google Scholar
Bedoya K, Hoyos O, Zurek E, Cabarcas F, Alzate JF. Annual microbial community dynamics in a full-scale anaerobic sludge digester from a wastewater treatment plant in Colombia. Sci Total Environ. 2020;726:138479.
Google Scholar
Murphy KC, Fenton AC, Poteete AR. Sequence of the bacteriophage P22 Anti-RecBCD (abc) genes and properties of P22 abc region deletion mutants. Virology. 1987;160:456–64.
Google Scholar
Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, et al. Bacterial retrons function in anti-phage defense. Cell. 2020;183:1551–61.
Google Scholar
Pawluk A, Davidson AR, Maxwell KL. Anti-CRISPR: discovery, mechanism and function. Nat Rev Microbiol. 2018;16:12–7.
Google Scholar
Jonge PA, de, Nobrega FL, Brouns SJJ, Dutilh BE. Molecular and evolutionary determinants of bacteriophage host range. Trends Microbiol. 2018;27:51–63.
Google Scholar
Daly RA, Roux S, Borton MA, Morgan DM, Johnston MD, Booker AE, et al. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat Microbiol. 2019;4:352–61.
Google Scholar
Salmond GPC, Fineran PC. A century of the phage: past, present and future. Nat Rev Microbiol. 2015;13:777–86.
Google Scholar
Rastogi S, Liberles DA. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol. 2005;5:28.
Google Scholar
Petitjean C, Makarova KS, Wolf YI, Koonin EV. Extreme deviations from expected evolutionary rates in archaeal protein families. Genome Biol Evol. 2017;9:2791–811.
Google Scholar
Anderson CL, Sullivan MB, Fernando SC. Dietary energy drives the dynamic response of bovine rumen viral communities. Microbiome. 2017;5:155.
Google Scholar
Gao S-M, Schippers A, Chen N, Yuan Y, Zhang M-M, Li Q, et al. Depth-related variability in viral communities in highly stratified sulfidic mine tailings. Microbiome. 2020;8:89.
Google Scholar
Mara P, Vik D, Pachiadaki MG, Suter EA, Poulos B, Taylor GT, et al. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. ISME J. 2020;14:3079–92.
Google Scholar
Pfennig N, Widdel F, Trüper HG. The prokaryotes, A handbook on habitats, isolation, and identification of bacteria. Springer-Verlag, Berlin, Germany. 1981.
Moran MA, Durham BP. Sulfur metabolites in the pelagic ocean. Nat Rev Microbiol. 2019;17:665–78.
Google Scholar
Kumar S, Cheng X, Klimasauskas S, Sha M, Posfai J, Roberts RJ, et al. The DNA (cytosine-5) methyltransferases. Nucleic Acids Res. 1994;22:1–10.
Google Scholar
Ashcroft AE, Lago H, Macedo JMB, Horn WT, Stonehouse NJ, Stockley PG. Engineering thermal stability in RNA phage capsids via disulphide bonds. J Nanosci Nanotechno. 2005;5:2034–41.
Google Scholar
Walter M, Fiedler C, Grassl R, Biebl M, Rachel R, Hermo-Parrado XL, et al. Structure of the receptor-binding protein of bacteriophage Det7: a podoviral tail spike in a Myovirus. J Virol. 2008;82:2265–73.
Google Scholar
Shai Y. Mode of action of membrane active antimicrobial peptides. Peptide Sci. 2002;66:236–48.
Google Scholar
Thevissen K, Ferket KKA, François IEJA, Cammue BPA. Interactions of antifungal plant defensins with fungal membrane components. Peptides. 2003;24:1705–12.
Google Scholar
Broderick JB, Duffus BR, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev. 2014;114:4229–317.
Google Scholar
Wildschutte H, Preheim SP, Hernandez Y, Polz MF. O‐antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates. Environ Microbiol. 2010;12:2977–87.
Google Scholar
Samuel G, Reeves P. Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly. Carbohyd Res. 2003;338:2503–19.
Google Scholar
Polz MF, Alm EJ, Hanage WP. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet. 2013;29:170–5.
Google Scholar
Markine-Goriaynoff N, Gillet L, Etten JLV, Korres H, Verma N, Vanderplasschen A. Glycosyltransferases encoded by viruses. J Gen Virol. 2004;85:2741–54.
Google Scholar
Clifford JC, Rapicavoli JN, Roper MC. A rhamnose-rich O-antigen mediates adhesion, virulence, and host colonization for the xylem-limited phytopathogen Xylella fastidiosa. Mol Plant-microbe Interac. 2013;26:676–85.
Google Scholar
Trueba G, Zapata S, Madrid K, Cullen P, Haake D. Cell aggregation: a mechanism of pathogenic Leptospira to survive in fresh water. Int Microbiol Official J Span Soc Microbiol. 2004;7:35–40.
Trunk T, Khalil HS, Leo JC. Norway BCSG Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslb,. Bacterial autoaggregation. Aims Microbiol. 2018;4:140–164.
Google Scholar
Guan S, Bastin DA, Verma NK. Functional analysis of the O antigen glucosylation gene cluster of Shigella flexneri bacteriophage SfX. Microbiology. 1999;145:1263–73.
Google Scholar
Rakhuba DV, Kolomiets EI, Dey ES, Novik GI. Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Pol J Microbiol. 2010;59:145–55.
Google Scholar
Silva JB, Storms Z, Sauvageau D. Host receptors for bacteriophage adsorption. FEMS Microbiol Lett. 2016;363:fnw002.
Tsuzuki K, Kimura K, Fujii N, Yokosawa N, Oguma K. The complete nucleotide sequence of the gene coding for the nontoxic-nonhemagglutinin component of Clostridium botulinum type C progenitor toxin. Biochem Bioph Res Co. 1992;183:1273–9.
Google Scholar
Enav H, Mandel-Gutfreund Y, Béjà O. Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis. Microbiome. 2014;2:9.
Google Scholar
Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat Microbiol. 2018;3:870–80.
Google Scholar
Jin M, Guo X, Zhang R, Qu W, Gao B, Zeng R. Diversities and potential biogeochemical impacts of mangrove soil viruses. Microbiome. 2019;7:58.
Google Scholar
Anderson RE, Reveillaud J, Reddington E, Delmont TO, Eren AM, McDermott JM, et al. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat Commun. 2017;8:1114.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Google Scholar
Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–7.
Google Scholar
Lu J, Salzberg SL. Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2. Microbiome. 2020;8:124.
Google Scholar
Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: estimating species abundance in metagenomics data. Peerj Comput Sci. 2017;3:e104.
Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 2021;10:e65088.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat methods. 2012;9:357–9.
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Google Scholar
Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.
Google Scholar
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. Peerj. 2019;7:e7359.
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;3:1043–55.
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8.
Google Scholar
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;6:1925–7.
Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9:37.
Google Scholar
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 2016;537:689–93.
Google Scholar
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. Uncovering Earth’s virome. Nature. 2016;536:425–30.
Google Scholar
Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018;46:W246–W251.
Google Scholar
Lowe TM, Eddy SR. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Res. 1997;25:955–64.
Google Scholar
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
Google Scholar
Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2019;36:2251–52.
Google Scholar
Mistry J, Bateman A, Finn RD. Predicting active site residue annotations in the Pfam database. BMC Bioinform. 2007;8:298.
Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 2020;48:8883–900.
Google Scholar
Pratama AA, Bolduc B, Zayed AA, Zhong Z-P, Guo J, Vik DR, et al. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. Peerj. 2021;9:e11447.
Google Scholar
Zimmermann L, Stephens A, Nam S-Z, Rau D, Kübler J, Lozajic M, et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol. 2018;430:2237–43.
Google Scholar
Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10:845–58.
Google Scholar
Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinform Oxf Engl. 2011;27:1009–10.
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Google Scholar
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Haeseler Avon, et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4.
Google Scholar
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:gkab301-.
Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, et al. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 2009;10:R85–R85.
Google Scholar
Source: Ecology - nature.com