Suttle CA. Marine viruses-major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12.
Google Scholar
Fuhrman JA. Marine viruses and their biogeochemical and ecological effects. Nature 1999;399:541–8.
Google Scholar
Rohwer F, Thurber RV. Viruses manipulate the marine environment. Nature 2009;459:207–12.
Google Scholar
Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66.
Google Scholar
Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, et al. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol. 2020;18:21–34.
Google Scholar
Rosenwasser S, Ziv C, Creveld SGV, Vardi A. Virocell metabolism: metabolic innovations during host-virus interactions in the ocean. Trends Microbiol. 2016;24:821–32.
Google Scholar
Fuchsman CA, Carlson MCG, Garcia Prieto D, Hays MD, Rocap G. Cyanophage host-derived genes reflect contrasting selective pressures with depth in the oxic and anoxic water column of the Eastern Tropical North Pacific. Environ Microbiol. 2021;23:2782–2800.
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
Gregory AC, Zayed AA, Conceição-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.
Google Scholar
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, et al. Patterns and ecological drivers of ocean viral communities. Science 2015;348:1261498.
Google Scholar
Dion MB, Oechslin F, Moineau S. Phage diversity, genomics and phylogeny. Nat Rev Microbiol. 2020;18:125–38.
Google Scholar
Sullivan MB, Waterbury JB, Chisholm SW. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 2003;424:1047–51.
Google Scholar
Mann NH. Phages of the marine cyanobacterial picophytoplankton. FEMS Microbiol Rev. 2003;27:17–34.
Google Scholar
Ni T, Zeng Q. Diel infection of cyanobacteria by cyanophages. Front Mar Sci. 2016;2:123.
Flombaum P, Gallegos JL, Gordillo RA, Rincon J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci USA 2013;110:9824–9.
Google Scholar
Biller SJ, Berube PM, Lindell D, Chisholm SW. Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol 2015;13:13–27.
Google Scholar
Proctor LM, Fuhrman JA. Viral mortality of marine-bacteria and cyanobacteria. Nature 1990;343:60–62.
Carlson MCG, Ribalet F, Maidanik I, Durham BP, Hulata Y, Ferron S, et al. Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean. Nat Microbiol 2022;7:570–80.
Google Scholar
Matteson AR, Loar SN, Pickmere S, DeBruyn JM, Ellwood MJ, Boyd PW, et al. Production of viruses during a spring phytoplankton bloom in the South Pacific Ocean near of New Zealand. FEMS Microbiol Ecol 2012;79:709–19.
Google Scholar
Ribalet F, Swalwell J, Clayton S, Jimenez V, Sudek S, Lin Y, et al. Light-driven synchrony of Prochlorococcus growth and mortality in the subtropical Pacific gyre. Proc Natl Acad Sci USA. 2015;112:8008–12.
Google Scholar
Demory D, Liu R, Chen Y, Zhao F, Coenen AR, Zeng Q, et al. Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage. mSystems 2020;5:e00586–19.
Google Scholar
Avrani S, Wurtzel O, Sharon I, Sorek R, Lindell D. Genomic island variability facilitates Prochlorococcus-virus coexistence. Nature 2011;474:604–8.
Google Scholar
Marston MF, Pierciey FJ Jr, Shepard A, Gearin G, Qi J, Yandava C, et al. Rapid diversification of coevolving marine Synechococcus and a virus. Proc Natl Acad Sci USA 2012;109:4544–9.
Google Scholar
Xiao X, Guo W, Li X, Wang C, Chen X, Lin X, et al. Viral lysis alters the optical properties and biological availability of dissolved organic matter derived from Prochlorococcus picocyanobacteria. Appl Environ Microbiol. 2021;87:e02271–20.
Google Scholar
Xiao X, Zeng Q, Zhang R, Jiao N. Prochlorococcus viruses—From biodiversity to biogeochemical cycles. Sci China Earth Sci. 2018;61:1728–36.
Jover LF, Effler TC, Buchan A, Wilhelm SW, Weitz JS. The elemental composition of virus particles: implications for marine biogeochemical cycles. Nat Rev Microbiol. 2014;12:519–28.
Google Scholar
Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Viruses inhibit CO2 fixation in the most abundant phototrophs on earth. Curr Biol 2016;26:1585–9.
Google Scholar
Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, et al. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME J. 2015;9:1352–64.
Google Scholar
Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol. 2005;3:e144.
Google Scholar
Sullivan MB, Krastins B, Hughes JL, Kelly L, Chase M, Sarracino D, et al. The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’. Environ Microbiol. 2009;11:2935–51.
Google Scholar
Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, et al. Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environ Microbiol. 2010;12:3035–56.
Google Scholar
Sabehi G, Shaulov L, Silver DH, Yanai I, Harel A, Lindell D. A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans. Proc Natl Acad Sci USA 2012;109:2037–42.
Google Scholar
Huang S, Wang K, Jiao N, Chen F. Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges. Environ Microbiol. 2012;14:540–58.
Google Scholar
Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, et al. Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environ Microbiol. 2013;15:1356–76.
Google Scholar
Dekel-Bird NP, Avrani S, Sabehi G, Pekarsky I, Marston MF, Kirzner S, et al. Diversity and evolutionary relationships of T7-like podoviruses infecting marine cyanobacteria. Environ Microbiol. 2013;15:1476–91.
Google Scholar
Huang S, Wilhelm SW, Jiao N, Chen F. Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences. ISME J. 2010;4:1243–51.
Google Scholar
Baran N, Goldin S, Maidanik I, Lindell D. Quantification of diverse virus populations in the environment using the polony method. Nat Microbiol. 2018;3:62–72.
Google Scholar
Chow C-ET, Suttle CA. Biogeography of viruses in the sea. Annu Rev Virol. 2015;2:41–66.
Google Scholar
Chen F, Lu JR. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl Environ Microbiol. 2002;68:2589–94.
Google Scholar
Huang S, Zhang S, Jiao N, Chen F. Comparative genomic and phylogenomic analyses reveal a conserved core genome shared by estuarine and oceanic cyanopodoviruses. PLoS One. 2015;10:e0142962.
Google Scholar
Pope WH, Weigele PR, Chang J, Pedulla ML, Ford ME, Houtz JM, et al. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: A “horned’ bacteriophage of marine Synechococcus. J Mol Biol. 2007;368:966–81.
Google Scholar
Huang S, Sun Y, Zhang S, Long L. Temporal transcriptomes of a marine cyanopodovirus and its Synechococcus host during infection. Microbiologyopen 2021;10:e1150.
Google Scholar
Wang K, Chen F. Prevalence of highly host-specific cyanophages in the estuarine environment. Environ Microbiol. 2008;10:300–12.
Google Scholar
Chen F, Wang K, Huang S, Cai H, Zhao M, Jiao N, et al. Diverse and dynamic populations of cyanobacterial podoviruses in the Chesapeake Bay unveiled through DNA polymerase gene sequences. Environ Microbiol. 2009;11:2884–92.
Google Scholar
Goldin S, Hulata Y, Baran N, Lindell D. Quantification of T4-like and T7-like cyanophages using the polony method show they are significant members of the virioplankton in the North Pacific Subtropical Gyre. Front Microbiol. 2020;11:1210.
Google Scholar
Nasko DJ, Chopyk J, Sakowski EG, Ferrell BD, Polson SW, Wommack KE. Family A DNA polymerase phylogeny uncovers diversity and replication gene organization in the virioplankton. Front Microbiol. 2018;9:3053.
Google Scholar
Dekel-Bird NP, Sabehi G, Mosevitzky B, Lindell D. Host-dependent differences in abundance, composition and host range of cyanophages from the Red Sea. Environ Microbiol. 2015;17:1286–99.
Google Scholar
Hanson CA, Marston MF, Martiny JBH. Biogeographic variation in host range phenotypes and taxonomic composition of marine cyanophage isolates. Front Microbiol. 2016;7:983.
Google Scholar
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 2003;424:1042–7.
Google Scholar
Chen B, Wang L, Song S, Huang B, Sun J, Liu H. Comparisons of picophytoplankton abundance, size, and fluorescence between summer and winter in northern South China Sea. Cont Shelf Res. 2011;31:1527–40.
Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, et al. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 2007;449:83–86.
Google Scholar
Zhao Y, Qin F, Zhang R, Giovannoni SJ, Zhang Z, Sun J, et al. Pelagiphages in the Podoviridae family integrate into host genomes. Environ Microbiol. 2019;21:1989–2001.
Google Scholar
Leptihn S, Gottschalk J, Kuhn A. T7 ejectosome assembly: A story unfolds. Bacteriophage 2016;6:e1128513.
Google Scholar
Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J, et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proc Natl Acad Sci USA 2011;108:E757–64.
Google Scholar
Zeng Q, Chisholm SW. Marine viruses exploit their host’s two-component regulatory system in response to resource limitation. Curr Biol 2012;22:124–8.
Google Scholar
Zeng Q, Bonocora RP, Shub DA. A free-standing homing endonuclease targets an intron insertion site in the psbA gene of cyanophages. Curr Biol. 2009;19:218–22.
Google Scholar
Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 2005;438:86–89.
Google Scholar
Breitbart M, Thompson LR, Suttle CA, Sullivan MB. Exploring the vast diversity of marine viruses. Oceanography. 2007;20:135–9.
Kazlauskas D, Venclovas C. Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size. Nucleic Acids Res. 2011;39:8291–305.
Google Scholar
Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, et al. Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat Struct Mol Biol. 2010;17:830–6.
Google Scholar
Dai W, Fu C, Raytcheva D, Flanagan J, Khant HA, Liu XG, et al. Visualizing virus assembly intermediates inside marine cyanobacteria. Nature 2013;502:707–10.
Google Scholar
Liu R, Liu Y, Chen Y, Zhan Y, Zeng Q. Cyanobacterial viruses exhibit diurnal rhythms during infection. Proc Natl Acad Sci USA 2019;116:14077–82.
Google Scholar
Maidanik I, Kirzner S, Pekarski I, Arsenieff L, Tahan R, Carlson MCG, et al. Cyanophages from a less virulent clade dominate over their sister clade in global oceans. ISME J. 2022;16:2169–80.
Google Scholar
Shitrit D, Hackl T, Laurenceau R, Raho N, Carlson MCG, Sabehi G, et al. Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages. ISME J. 2022;16:488–99.
Google Scholar
Liang Y, Wang L, Wang Z, Zhao J, Yang Q, Wang M, et al. Metagenomic analysis of the diversity of DNA viruses in the surface and deep sea of the South China Sea. Front Microbiol. 2019;10:1951.
Google Scholar
Pedrós-Alió C, Potvin M, Lovejoy C. Diversity of planktonic microorganisms in the Arctic Ocean. Prog Oceanogr. 2015;139:233–43.
Luo E, Eppley JM, Romano AE, Mende DR, DeLong EF. Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column. ISME J. 2020;14:1304–15.
Google Scholar
Steidinger BS, Crowther TW, Liang J, Van Nuland ME, Werner GDA, Reich PB, et al. Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature 2019;569:404–8.
Google Scholar
Xie X, Wu T, Zhu M, Jiang G, Xu Y, Wang X, et al. Comparison of random forest and multiple linear regression models for estimation of soil extracellular enzyme activities in agricultural reclaimed coastal saline land. Ecol Indic. 2021;120:106925.
Google Scholar
Lee SJ, Richardson CC. Choreography of bacteriophage T7 DNA replication. Curr Opin Chem Biol. 2011;15:580–6.
Google Scholar
Kulczyk AW, Richardson CC. The replication system of bacteriophage T7. Enzymes. 2016;39:89–136.
Google Scholar
Benkovic SJ, Valentine AM, Salinas F. Replisome-mediated DNA replication. Annu Rev Biochem. 2001;70:181–208.
Google Scholar
Johnson A, O’Donnell M. Cellular DNA replicases: components and dynamics at the replication fork. Annu Rev Biochem. 2005;74:283–315.
Google Scholar
Seco EM, Zinder JC, Manhart CM, Lo Piano A, McHenry CS, Ayora S. Bacteriophage SPP1 DNA replication strategies promote viral and disable host replication in vitro. Nucleic Acids Res. 2013;41:1711–21.
Google Scholar
Mruwat N, Carlson MCG, Goldin S, Ribalet F, Kirzner S, Hulata Y, et al. A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances. ISME J. 2021;15:41–54.
Google Scholar
Moore LR, Rocap G, Chisholm SW. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 1998;393:464–7.
Google Scholar
Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. Photosynth Res. 2015;126:71–97.
Google Scholar
Edwards KF, Steward GF, Schvarcz CR. Making sense of virus size and the tradeoffs shaping viral fitness. Ecol Lett. 2021;24:363–73.
Google Scholar
Moore LR, Coe A, Zinser ER, Saito MA, Sullivan MB, Lindell D, et al. Culturing the marine cyanobacterium Prochlorococcus. Limnol Oceanogr Methods. 2007;5:353–62.
Google Scholar
Hyman P, Abedon ST. Bacteriophage host range and bacterial resistance. Adv Appl Microbiol. 2010;70:217–48.
Google Scholar
Fridman S, Flores-Uribe J, Larom S, Alalouf O, Liran O, Yacoby I, et al. A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells. Nat Microbiol. 2017;2:1350–7.
Google Scholar
Fang X, Liu Y, Zhao Y, Chen Y, Liu R, Qin QL, et al. Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products. Environ Microbiol. 2019;21:2015–28.
Google Scholar
John SG, Mendez CB, Deng L, Poulos B, Kauffman AK, Kern S, et al. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ Microbiol Rep. 2011;3:195–202.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–20.
Google Scholar
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011;27:863–4.
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:1–10.
Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012;28:1420–8.
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–9.
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Google Scholar
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic Inference in the genomic era. Mol Biol Evol. 2020;37:2461–2461.
Google Scholar
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35:518–22.
Google Scholar
Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Pena MJ, Martinez JM, et al. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun. 2017;8:15892.
Google Scholar
Zhang Z, Qin F, Chen F, Chu X, Luo H, Zhang R, et al. Culturing novel and abundant pelagiphages in the ocean. Environ Microbiol 2021;23:1145–61.
Google Scholar
Buchholz HH, Michelsen ML, Bolanos LM, Browne E, Allen MJ, Temperton B. Efficient dilution-to-extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria. ISME J. 2021;15:1585–98.
Google Scholar
Qin F, Du S, Zhang Z, Ying H, Wu Y, Zhao G, et al. Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group. ISME J. 2022;16:1363–75.
Google Scholar
Source: Ecology - nature.com
