Bergh O, Borsheim KY, Bratbak G, Heldal M. High abundance of viruses found in aquatic environments. Nature. 1989;340(6233):467–8.
Article
CAS
PubMed
Google Scholar
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A. 2002;99(22):14250–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, Salamon P, Rohwer F. Diversity and population structure of a near-shore marine-sediment viral community. Proc Biol Sci. 2004;271(1539):565–74.
Article
PubMed
PubMed Central
Google Scholar
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, et al. The marine viromes of four oceanic regions. PLoS Biol. 2006;4(11):e368.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ge X, Wu Y, Wang M, Wang J, Wu L, Yang X, Zhang Y, Shi Z. Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China. Virol Sin. 2013;28(5):280–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lopez-Bueno A, Tamames J, Velazquez D, Moya A, Quesada A, Alcami A. High diversity of the viral community from an Antarctic lake. Science. 2009;326(5954):858–61.
Article
CAS
PubMed
Google Scholar
Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, Haynes M, Liu H, Furlan M, Wegley L, Chau B, et al. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature. 2008;452(7185):340–3.
Article
CAS
PubMed
Google Scholar
Yoshida M, Takaki Y, Eitoku M, Nunoura T, Takai K. Metagenomic analysis of viral communities in (hado) pelagic sediments. PLoS One. 2013;8(2):e57271.
Article
CAS
PubMed
PubMed Central
Google Scholar
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33(17):5691–702.
Article
CAS
PubMed
PubMed Central
Google Scholar
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2014;42(D1):D206–14.
Article
CAS
PubMed
Google Scholar
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Ostell J, Pruitt KD, Sayers EW. GenBank. Nucleic Acids Res. 2018;46(D1):D41–7.
Article
CAS
PubMed
Google Scholar
Van Etten JL. Another really, Really Big Virus. Viruses. 2011;3(1):32–46.
Article
PubMed
PubMed Central
CAS
Google Scholar
Brum JR, Sullivan MB. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol. 2015;13(3):147–59.
Article
CAS
PubMed
Google Scholar
Gong Z, Liang Y, Wang M, Jiang Y, Yang Q, Xia J, Zhou X, You S, Gao C, Wang J, et al. Viral diversity and its relationship with environmental factors at the surface and Deep Sea of Prydz Bay, Antarctica. Front Microbiol. 2018;9:2981.
Article
PubMed
PubMed Central
Google Scholar
Garin-Fernandez A, Pereira-Flores E, Glockner FO, Wichels A. The North Sea goes viral: occurrence and distribution of North Sea bacteriophages. Mar Genomics. 2018;41:31–41.
Article
PubMed
Google Scholar
Taboada B, Isa P, Gutierrez-Escolano AL, Del Angel RM, Ludert JE, Vazquez N, Tapia-Palacios MA, Chavez P, Garrido E, Espinosa AC, et al. The Geographic Structure of Viruses in the Cuatro Cienegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale. Appl Environ Microbiol. 2018;84(11).
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, et al. Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science (New York, NY). 2015;348(6237):1261498.
Article
CAS
Google Scholar
Cai L, Zhang R, He Y, Feng X, Jiao N. Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China. Viruses. 2016;8(2).
Yan Q, Wang M, Bai X, Sun J, Liang Y, Wang F, Yang L, Liu G, Lu L. New phylogenetically distinct cyanophages found in the coastal Yellow Sea by Qingdao. Acta Virol. 2010;54(4):255–60.
Article
CAS
PubMed
Google Scholar
Zheng Q, Jiao N, Zhang R, Wei J, Zhang F. The evolutionary divergence of psbA gene in Synechococcus and their myoviruses in the East China Sea. PLoS One. 2014;9(1):e86644.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liang Y, Wang L, Wang Z, Zhao J, Yang Q, Wang M, Yang K, Zhang L, Jiao N, Zhang Y. Metagenomic analysis of the diversity of DNA viruses in the surface and deep-sea of the South China Sea. Front Microbiol. 2019;10:1951.
Article
PubMed
PubMed Central
Google Scholar
Li W, Wang M, Pan H, Burgaud G, Liang S, Guo J, Luo T, Li Z, Zhang S, Cai L. Highlighting patterns of fungal diversity and composition shaped by ocean currents using the East China Sea as a model. Mol Ecol. 2018;27(2):564–76.
Article
CAS
PubMed
Google Scholar
Wang H, Wu S, Li K, Pan Y, Yan S, Wang Y. Metagenomic analysis of ssDNA viruses in surface seawater of Yangshan deep-Water Harbor, Shanghai, China. Mar Genomics. 2018;41:4.
Article
Google Scholar
Roux S, Emerson JB, Eloe-Fadrosh EA, Sullivan MB. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. Peer J. 2017;5:e3817.
Article
PubMed
PubMed Central
Google Scholar
Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a web browser. BMC Bioinformatics. 2011;12:385.
Article
PubMed
PubMed Central
Google Scholar
Chow CE, Winget DM, White RA 3rd, Hallam SJ, Suttle CA. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions. Front Microbiol. 2015;6:265.
PubMed
PubMed Central
Google Scholar
Philosof A, Yutin N, Flores-Uribe J, Sharon I, Koonin EV, Beja O. Novel abundant oceanic viruses of uncultured marine group II Euryarchaeota. Curr Biol. 2017;27(9):1362–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bagci C, Beier S, Gorska A, Huson DH. Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN. Methods Mol Biol (Clifton, NJ). 2019;1910:591–604.
Article
CAS
Google Scholar
Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol. 2006;4(8):e234.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roux S, Krupovic M, Debroas D, Forterre P, Enault F. Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences. Open Biol. 2013;3(12):130160.
Article
PubMed
PubMed Central
CAS
Google Scholar
Koonin EV, Dolja VV, Krupovic M. Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology. 2015;479:2–25.
Article
PubMed
CAS
Google Scholar
La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, et al. The virophage as a unique parasite of the giant mimivirus. Nature. 2008;455(7209):100–4.
Article
PubMed
CAS
Google Scholar
Gong C, Zhang W, Zhou X, Wang H, Sun G, Xiao J, Pan Y, Yan S, Wang Y. Novel Virophages discovered in a freshwater Lake in China. Front Microbiol. 2016;7:5.
PubMed
PubMed Central
Google Scholar
Zhou J, Sun D, Childers A, McDermott TR, Wang Y, Liles MR. Three novel virophage genomes discovered from Yellowstone Lake metagenomes. J Virol. 2015;89(2):1278–85.
Article
PubMed
CAS
Google Scholar
Zhou J, Zhang W, Yan S, Xiao J, Zhang Y, Li B, Pan Y, Wang Y. Diversity of virophages in metagenomic data sets. J Virol. 2013;87(8):4225–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Labonte JM, Reid KE, Suttle CA. Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences. Appl Environ Microbiol. 2009;75(11):3634–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Giovannoni SJ. SAR11 Bacteria: the Most abundant plankton in the oceans. Annu Rev Mar Sci. 2017;9:231–55.
Article
Google Scholar
Zhao X, Schwartz CL, Pierson J, Giovannoni SJ, McIntosh JR, Nicastro D. Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium “Candidatus Pelagibacter ubique”. Appl Environ Microbiol. 2017;83(3).
Pennekamp F, Pontarp M, Tabi A, Altermatt F, Alther R, Choffat Y, Fronhofer EA, Ganesanandamoorthy P, Garnier A, Griffiths JI, et al. Biodiversity increases and decreases ecosystem stability. Nature. 2018;563(7729):109–12.
Article
CAS
PubMed
Google Scholar
Colombet J, Billard H, Viguès B, Balor S, Boulé C, Geay L, Benzerara K, Menguy N, Ilango G, Fuster M. Discovery of high abundances of aster-like nanoparticles in pelagic environments: characterization and dynamics. Front Microbiol. 2019;10:2376.
Article
PubMed
PubMed Central
Google Scholar
Prangishvili D, Bamford DH, Forterre P, Iranzo J, Koonin EV, Krupovic M. The enigmatic archaeal virosphere. Nat Rev Microbiol. 2017;15(12):724–39.
Article
CAS
PubMed
Google Scholar
Abergel C, Legendre M, Claverie JM. The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus. FEMS Microbiol Rev. 2015;39(6):779–96.
Article
CAS
PubMed
Google Scholar
Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, et al. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. Proc Natl Acad Sci U S A. 2015;112(38):E5327–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, et al. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci U S A. 2014;111(11):4274–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hwang J, Park SY, Lee S, Lee TK. High diversity and potential translocation of DNA viruses in ballast water. Mar Pollut Bull. 2018;137:449–55.
Article
CAS
PubMed
Google Scholar
Koonin EV, Makarova KS. Origins and evolution of CRISPR-Cas systems. Philos Trans R Soc Lond Ser B Biol Sci. 2019;374(1772):20180087.
Article
CAS
Google Scholar
Zhang J, Kasciukovic T, White MF. The CRISPR associated protein Cas4 is a 5′ to 3′ DNA exonuclease with an iron-sulfur cluster. PLoS One. 2012;7(10):e47232.
Article
CAS
PubMed
PubMed Central
Google Scholar
Amitai G, Sorek R. CRISPR-Cas adaptation: insights into the mechanism of action. Nat Rev Microbiol. 2016;14(2):67–76.
Article
CAS
PubMed
Google Scholar
Hille F, Richter H, Wong SP, Bratovic M, Ressel S, Charpentier E. The biology of CRISPR-Cas: backward and forward. Cell. 2018;172(6):1239–59.
Article
CAS
PubMed
Google Scholar
Sorek R, Lawrence CM, Wiedenheft B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem. 2013;82:237–66.
Article
CAS
PubMed
Google Scholar
Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev. 2016;40(2):258–72.
Article
CAS
PubMed
Google Scholar
Ramaswamy V, Cresence VM, Rejitha JS, Lekshmi MU, Dharsana KS, Prasad SP, Vijila HM. Listeria--review of epidemiology and pathogenesis. J Microbiol Immunol Infect. 2007;40(1):4–13.
CAS
PubMed
Google Scholar
Razin A, Sedat JW, Sinsheimer RL. In vivo methylation of replicating bacteriophage phi chi174 DNA. J Mol Biol. 1973;78(3):417–25.
Article
CAS
PubMed
Google Scholar
Magrini V, Salmi D, Thomas D, Herbert SK, Hartzell PL, Youderian P. Temperate Myxococcus xanthus phage Mx8 encodes a DNA adenine methylase, Mox. J Bacteriol. 1997;179(13):4254–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature. 2020;577(7789):244–8.
Article
CAS
PubMed
Google Scholar
Koonin EV, Krupovic M. Phages build anti-defence barriers. Nat Microbiol. 2020;5(1):8–9.
Article
CAS
PubMed
Google Scholar
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature. 2016;537(7622):689–93.
Article
CAS
PubMed
Google Scholar
Wen K, Ortmann AC, Suttle CA. Accurate estimation of viral abundance by epifluorescence microscopy. Appl Environ Microbiol. 2004;70(7):3862–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA. Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR green I. Nat Protoc. 2007;2(2):269.
Article
CAS
PubMed
Google Scholar
Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protoc. 2009;4(4):470–83.
Article
CAS
PubMed
Google Scholar
Sun G, Xiao J, Wang H, Gong C, Pan Y, Yan S, Wang Y. Efficient purification and concentration of viruses from a large body of high turbidity seawater. MethodsX. 2014;1:197–206.
Article
PubMed
PubMed Central
Google Scholar
Niu B, Fu L, Sun S, Li W. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC bioinformatics. 2010;11(1):187.
Article
PubMed
PubMed Central
CAS
Google Scholar
Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007;17(3):377–86.
Article
CAS
PubMed
PubMed Central
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 Bioinformatics. 2010;11(1):119.
Article
PubMed
PubMed Central
CAS
Google Scholar
Angly FE, Willner D, Prieto-Davo A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, et al. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009;5(12):e1000593.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–9.
Article
CAS
PubMed
Google Scholar
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P. Fast genome-wide functional annotation through Orthology assignment by eggNOG-mapper. Mol Biol Evol. 2017;34(8):2115–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44(D1):D286–93.
Article
CAS
PubMed
Google Scholar
Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017;45(D1):D200–3.
Article
CAS
PubMed
Google Scholar
Shmakov SA, Sitnik V, Makarova KS, Wolf YI, Severinov KV, Koonin EV. The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes. MBio. 2017;8(5).