Suess E. Marine cold seeps and their manifestations: geological control, biogeochemical criteria and environmental conditions. Int J Earth Sci. 2014;103:1889–916.
Joye SB. The geology and biogeochemistry of hydrocarbon seeps. Annu Rev Earth Planet Sci. 2020;48:205–31.
Etiope G, Panieri G, Fattorini D, Regoli F, Vannoli P, Italiano F, et al. A thermogenic hydrocarbon seep in shallow Adriatic Sea (Italy): Gas origin, sediment contamination and benthic foraminifera. Mar Pet Geol. 2014;57:283–93.
Kennicutt, MC Habitats and biota of the Gulf of Mexico: before the deepwater horizon oil spill. Ward CH, editor. New York, NY: Springer New York; 2017. p. 275–358.
Ruppel CD, Kessler JD. The interaction of climate change and methane hydrates. Rev Geophys. 2017;55:126–68.
Kniemeyer O, Musat F, Sievert SM, Knittel K, Wilkes H, Blumenberg M, et al. Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature. 2007;449:898–901.
Jaekel U, Musat N, Adam B, Kuypers M, Grundmann O, Musat F. Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps. ISME J. 2013;7:885–95.
Teske A, Carvalho V. Marine hydrocarbon seeps: microbiology and biogeochemistry of a global marine habitat. Cham, Switzerland: Springer Nature; 2020.
Kellogg CA. Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico. Deep Sea Res Part II Top Stud Oceanogr. 2010;57:2002–7.
Bryson SJ, Thurber AR, Correa AM, Orphan VJ, Vega Thurber R. A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments. Environ Microbiol. 2015;17:3708–21.
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.
Pan D, Morono Y, Inagaki F, Takai K. An improved method for extracting viruses from sediment: detection of far more viruses in the subseafloor than previously reported. Front Microbiol. 2019;10:878.
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.
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.
Labbe M, Girard C, Vincent WF, Culley AI. Extreme viral partitioning in a marine-derived high arctic lake. mSphere. 2020;5:e00334–00320.
Okazaki Y, Nishimura Y, Yoshida T, Ogata H, Nakano SI. Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake. Environ Microbiol. 2019;21:4740–54.
Backstrom D, Yutin N, Jorgensen SL, Dharamshi J, Homa F, Zaremba-Niedwiedzka K, et al. Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism. mBio. 2019;10:e02497–02418.
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.
Daly RA, Borton MA, Wilkins MJ, Hoyt DW, Kountz DJ, Wolfe RA, et al. Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales. Nat Microbiol. 2016;1:16146.
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.
Gregory AC, Zayed AA, Conceicao-Neto N, Temperton B, Bolduc B, Alberti A, et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell. 2019;177:1109–23.
Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, et al. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nat Commun. 2017;8:15955.
Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66.
Chen LX, Meheust R, Crits-Christoph A, McMahon KD, Nelson TC, Slater GF, et al. Large freshwater phages with the potential to augment aerobic methane oxidation. Nat Microbiol. 2020;5:1504–15.
Cai L, Jorgensen BB, Suttle CA, He M, Cragg BA, Jiao N, et al. Active and diverse viruses persist in the deep sub-seafloor sediments over thousands of years. ISME J. 2019;13:1857–64.
Danovaro R, Dell’Anno A, Corinaldesi C, Magagnini M, Noble R, Tamburini C, et al. Major viral impact on the functioning of benthic deep-sea ecosystems. Nature. 2008;454:1084–7.
Middelboe M, Glud RN, Wenzhöfer F, Oguri K, Kitazato H. Spatial distribution and activity of viruses in the deep-sea sediments of Sagami Bay. Jpn Deep Sea Res Part 1 Oceanogr Res Pap. 2006;53:1–13.
Danovaro R, Serresi M. Viral density and virus-to-bacterium ratio in deep-sea sediments of the Eastern Mediterranean. Appl Environ Microbiol. 2000;66:1857–61.
Hewson I, Fuhrman JA. Viriobenthos production and virioplankton sorptive scavenging by suspended sediment particles in coastal and pelagic waters. Micro Ecol. 2003;46:337–47.
Corinaldesi C, Dell’Anno A, Danovaro R. Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems. Limnol Oceanogr. 2007;52:508–16.
Dong X, Greening C, Rattray JE, Chakraborty A, Chuvochina M, Mayumi D, et al. Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nat Commun. 2019;10:1816.
Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo O, et al. Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nat Commun. 2020;11:5825.
Gruber-Vodicka HR, Seah BKB, Pruesse E. phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems. 2020;5:e00920–00920.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6:158.
Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, et al. MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3–11.
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.
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2019;36:1925–7.
Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;38:1079–86.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Federhen S. The NCBI taxonomy database. Nucleic Acids Res. 2012;40:D136–43.
Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015;3:e985.
Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome. 2017;5:69.
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.
Marquet M, Hölzer M, Pletz MW, Viehweger A, Makarewicz O, Ehricht R, et al. What the phage: a scalable workflow for the identification and analysis of phage sequences. 2020. https://www.biorxiv.org/content/10.1101/2020.07.24.219899v1.
Kieft K, Zhou Z, Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 2020;8:90.
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. 2020. https://doi.org/10.1101/2020.1105.1106.081778.
Dalcin Martins P, Danczak RE, Roux S, Frank J, Borton MA, Wolfe RA, et al. Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems. Microbiome. 2018;6:138.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.
Bin Jang H, 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.
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.
Roux S, Paez-Espino D, Chen IA, 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:D764–75.
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus genome (MIUViG). Nat Biotechnol. 2019;37:29–37.
Castelan-Sanchez HG, Lopez-Rosas I, Garcia-Suastegui WA, Peralta R, Dobson ADW, Batista-Garcia RA, et al. Extremophile deep-sea viral communities from hydrothermal vents: structural and functional analysis. Mar Genom. 2019;46:16–28.
Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007;17:377–86.
Tominaga K, Morimoto D, Nishimura Y, Ogata H, Yoshida T. In silico prediction of virus-host interactions for marine bacteroidetes with the use of metagenome-assembled genomes. Front Microbiol. 2020;11:738.
Ahlgren NA, Ren J, Lu YY, Fuhrman JA, Sun F. Alignment-free d2*oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic Acids Res. 2017;45:39–53.
Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004;32:11–16.
Skennerton CT, Imelfort M, Tyson GW. Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Res. 2013;41:e105.
Dong X, Strous M. An integrated pipeline for annotation and visualization of metagenomic contigs. Front Genet. 2019;10:999.
Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K, Cowley ES, et al. METABOLIC: a scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes. 2020. https://www.biorxiv.org/content/10.1101/761643v1.
Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 2004;5:113.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9.
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.
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.
Vik D, Gazitua MC, Sun CL, Zayed AA, Aldunate M, Mulholland MR et al. Genome-resolved viral ecology in a marine oxygen minimum zone. Environ Microbiol. 2020. https://doi.org/10.1111/1462-2920.15313.
ter Horst AM, Santos-Medellin C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, et al. Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. 2020. https://www.biorxiv.org/content/10.1101/2020.12.15.422944v1.full.
Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 2020;48:D265–8.
Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10:845–58.
Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14:927–30.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.
Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.
Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, et al. Clades of huge phages from across Earth’s ecosystems. Nature. 2020;578:425–31.
Ruff SE, Biddle JF, Teske AP, Knittel K, Boetius A, Ramette A. Global dispersion and local diversification of the methane seep microbiome. Proc Natl Acad Sci USA. 2015;112:4015–20.
Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems. 2018;3:e00076–00018.
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.
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.
Castelle CJ, Brown CT, Anantharaman K, Probst AJ, Huang RH, Banfield JF. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol. 2018;16:629–45.
Jarett JK, Dzunkova M, Schulz F, Roux S, Paez-Espino D, Eloe-Fadrosh E, et al. Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. ISME J. 2020;14:2527–41.
Orsi WD. Ecology and evolution of seafloor and subseafloor microbial communities. Nat Rev Microbiol. 2018;16:671–83.
Hurwitz BL, Brum JR, Sullivan MB. Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome. ISME J. 2015;9:472–84.
Brum JR, Sullivan MB. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol. 2015;13:147–59.
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.
Anderson CL, Sullivan MB, Fernando SC. Dietary energy drives the dynamic response of bovine rumen viral communities. Microbiome. 2017;5:155.
Gao SM, Schippers A, Chen N, Yuan Y, Zhang MM, Li Q, et al. Depth-related variability in viral communities in highly stratified sulfidic mine tailings. Microbiome. 2020;8:89.
Zhao R, Summers ZM, Christman GD, Yoshimura KM, Biddle JF. Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico. Sci Rep. 2020;10:5772.
Dekas AE, Poretsky RS, Orphan VJ. Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science. 2009;326:422–6.
Zheng, X, Liu, W, Dai, X, Zhu, Y, Wang, J, Zhu, Y et al. Extraordinary diversity of viruses in deep-sea sediments as revealed by metagenomics without prior virion separation. Environ Microbiol. 2020. https://doi.org/10.1111/1462-2920.15154.
Source: Ecology - nature.com