1. Falkowski PG, Fenchel T, Delong EF. 2008. The microbial engines that drive Earth’s biogeochemical cycles. Science 320:1034–1039. https://doi.org/10.1126/science.1153213.
2. Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P, Tara Oceans Coordinators. 2015. Structure and func- tion of the global ocean microbiome. Science 348:1261359. https://doi .org/10.1126/science.1261359.
3. Pommier T, Canbäck B, Riemann L, Boström KH, Simu K, Lundberg P, Tunlid A, Hagström A. 2007. Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16:867–880. https://doi .org/10.1111/j.1365-294X.2006.03189.x.
4. Suttle CA. 2007. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol 5:801–812. https://doi.org/10.1038/nrmicro1750.
5. Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, Kassabgy M, Huang S, Mann AJ, Waldmann J, Weber M, Klindworth A, Otto A, Lange J, Bernhardt J, Reinsch C, Hecker M, Peplies J, Bockelmann FD, Callies U, Gerdts G, Wichels A, Wiltshire KH, Glockner FO, Schweder T, Amann R. 2012. Substrate-controlled succession of marine bacterio- plankton populations induced by a phytoplankton bloom. Science 336: 608–611. https://doi.org/10.1126/science.1218344.
6. Needham DM, Fuhrman JA, Cram JA, Fuhrman JA, Sun F. 2016. Pro- nounced daily succession of phytoplankton, archaea and bacteria fol- lowing a spring bloom. Nat Microbiol 1:16005. https://doi.org/10.1038/ nmicrobiol.2016.5.
7. Needham DM, Sachdeva R, Fuhrman JA. 2017. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. ISME J 11:1614–1629. https://doi.org/10 .1038/ismej.2017.29.
8. Chafee M, Fernàndez-Guerra A, Buttigieg PL, Gerdts G, Eren AM, Teeling H, Amann RI. 2018. Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME J 12:237–252. https://doi.org/10.1038/ ismej.2017.165.
9. Tikhonov M, Leach RW, Wingreen NS. 2015. Interpreting 16S metage- nomic data without clustering to achieve sub-OTU resolution. ISME J 9: 68–80. https://doi.org/10.1038/ismej.2014.117.
10. Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML. 2013. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol 4:1111–1119. https:// doi.org/10.1111/2041-210X.12114.
11. Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. 2015. Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J 9:968–979. https://doi.org/10.1038/ismej.2014.195.
12. Suttle CA. 2005. Viruses in the sea. Nature 437:356–361. https://doi.org/ 10.1038/nature04160.
13. Breitbart M, Bonnain C, Malki K, Sawaya NA. 2018. Phage puppet masters of the marine microbial realm. Nat Microbiol 3:754–766. https://doi.org/ 10.1038/s41564-018-0166-y.
14. Fuhrman J, Suttle C. 1993. Viruses in marine planktonic systems. Ocean- ography 6:51–63. https://doi.org/10.5670/oceanog.1993.14.
15. Winter C, Bouvier T, Weinbauer MG, Thingstad TF. 2010. Trade-offs between competition and defense specialists among unicellular plank- tonic organisms: the “killing the winner” hypothesis revisited. Microbiol Mol Biol Rev 74:42–57. https://doi.org/10.1128/MMBR.00034-09.
16. Rodriguez-Valera F, Martin-Cuadrado A-B, Rodriguez-Brito B, Pasi´c L, Thingstad TF, Rohwer F, Mira A. 2009. Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7:828–836. https:// doi.org/10.1038/nrmicro2235.
17. Thingstad TF. 2000. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol Oceanogr 45:1320–1328. https://doi.org/10 .4319/lo.2000.45.6.1320.
18. Våge S, Storesund JE, Thingstad TF. 2013. Adding a cost of resistance description extends the ability of virus-host model to explain observed patterns in structure and function of pelagic microbial communities. En- viron Microbiol 15:1842–1852. https://doi.org/10.1111/1462-2920.12077.
19. Zhao Y, Temperton B, Thrash JC, Schwalbach MS, Vergin KL, Landry ZC, Ellisman M, Deerinck T, Sullivan MB, Giovannoni SJ. 2013. Abundant SAR11 viruses in the ocean. Nature 494:357–360. https://doi.org/10.1038/ nature11921.
20. Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, Anton J, Gasol JM, Rosselli R, Rodriguez-Valera F, Sullivan MB, Acinas SG, Martinez-Garcia M. 2017. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun 8: 15892. https://doi.org/10.1038/ncomms15892.
21. Martinez-Hernandez F, Fornas Ò, Lluesma Gomez M, Garcia-Heredia I, Maestre-Carballa L, López-Pérez M, Haro-Moreno JM, Rodriguez-Valera F, Martinez-Garcia M. 2018. Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral pop- ulation in the ocean. ISME J 13:232–236. https://doi.org/10.1038/s41396 -018-0278-7.
22. Fuhrman JA, Cram JA, Needham DM. 2015. Marine microbial community dynamics and their ecological interpretation. Nat Rev Microbiol 13: 133–146. https://doi.org/10.1038/nrmicro3417.
23. Bunse C, Pinhassi J. 2017. Marine bacterioplankton seasonal succession dynamics. Trends Microbiol 25:494–505. https://doi.org/10.1016/j.tim .2016.12.013.
24. Pagarete A, Chow C-ET, Johannessen T, Fuhrman JA, Thingstad TF, Sandaa RA. 2013. Strong seasonality and interannual recurrence in ma- rine myovirus communities. Appl Environ Microbiol 79:6253–6259. https://doi.org/10.1128/AEM.01075-13.
25. Chow CET, Fuhrman JA. 2012. Seasonality and monthly dynamics of ma- rine myovirus communities. Environ Microbiol 14:2171–2183. https://doi .org/10.1111/j.1462-2920.2012.02744.x.
26. Ignacio-Espinoza JC, Ahlgren NA, Fuhrman JA. 2020. Long-term stability and Red Queen-like strain dynamics in marine viruses. Nat Microbiol 5: 265–271. https://doi.org/10.1038/s41564-019-0628-x.
27. Hwang J, Park SY, Park M, Lee S, Lee T-K. 2017. Seasonal dynamics and metagenomic characterization of marine viruses in Goseong Bay, Korea. PLoS One 12:e0169841. https://doi.org/10.1371/journal.pone.0169841.
28. Hevroni G, Flores-Uribe J, Béjà O, Philosof A. 2020. Seasonal and diel pat- terns of abundance and activity of viruses in the Red Sea. Proc Natl Acad Sci U S A 117:29738–29747. https://doi.org/10.1073/pnas.2010783117.
29. Ahlgren NA, Perelman JN, Yeh Y, Fuhrman JA. 2019. Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors. Environ Microbiol 21:2948–2963. https://doi.org/10.1111/1462-2920.14687.
30. Brum JR, Sullivan MB. 2015. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol 13:147–159. https://doi.org/10.1038/nrmicro3404.
31. Ozaki K, Uye S-I, Kusumoto T, Hagino T. 2004. Interannual variability of the ecosystem of the Kii Channel, the Inland Sea of Japan, as influenced by bottom intrusion of cold and nutrient-rich water from the Pacific Ocean, and a recent trend of warming and oligotrophication. Fish Oce- anogr 13:65–79. https://doi.org/10.1046/j.1365-2419.2003.00274.x.
32. Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O’Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, et al. 2015. The ocean sampling day con- sortium. GigaScience 4:27. https://doi.org/10.1186/s13742-015-0066-5.
33. Nishimura Y, Watai H, Honda T, Mihara T, Omae K, Roux S, Blanc-Mathieu R, Yamamoto K, Hingamp P, Sako Y, Sullivan MB, Goto S, Ogata H, Yoshida T. 2017. Environmental viral genomes shed new light on virus- host interactions in the ocean. mSphere 2:e00359-16. https://doi.org/10 .1128/mSphere.00359-16.
34. Yoshida T, Nishimura Y, Watai H, Haruki N, Morimoto D, Kaneko H, Honda T, Yamamoto K, Hingamp P, Sako Y, Goto S, Ogata H. 2018. Local- ity and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan. ISME J 12:1287–1295. https://doi.org/10.1038/s41396-018-0052-x.
35. Martinez-Hernandez F, Luo E, Tominaga K, Ogata H, Yoshida T, DeLong EF, Martinez-Garcia M. 2020. Diel cycling of the cosmopolitan abundant Pela- gibacter virus 37-F6: one of the most abundant viruses on earth. Environ Microbiol Rep 12:214–219. https://doi.org/10.1111/1758-2229.12825.
36. Coenen AR, Weitz JS. 2018. Limitations of correlation-based inference in complex virus-microbe communities. mSystems 3:e00084-18. https://doi .org/10.1128/mSystems.00084-18.
37. Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, et al. 2019. Minimum information about an uncultivated virus genome (MIUVIG). Nat Biotechnol 37:29–37. https:// doi.org/10.1038/nbt.4306.
38. Luo E, Aylward FO, Mende DR, DeLong EF. 2017. Bacteriophage distribu- tions and temporal variability in the ocean’s interior. mBio 8:e01903-17. https://doi.org/10.1128/mBio.01903-17.
39. Prodinger F, Endo H, Takano Y, Li Y, Tominaga K, Isozaki T, Blanc-Mathieu R, Gotoh Y, Hayashi T, Taniguchi E, Nagasaki K, Yoshida T, Ogata H. 2021. Year-round dynamics of amplicon sequence variant communities differ among eukaryotes, Imitervirales and prokaryotes in a coastal ecosystem. FEMS Microbiol Ecol 97:fiab167. https://doi.org/10.1093/femsec/fiab167.
40. Cram JA, Chow C-ET, Sachdeva R, Needham DM, Parada AE, Steele JA, Fuhrman JA. 2015. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME J 9:563–580. https://doi.org/10.1038/ismej.2014.153.
41. Yeh Y-C, Fuhrman JA. 2022. Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time. ISME Commun 2:36. https://doi.org/10.1038/s43705-022-00121-8.
42. Tominaga K, Morimoto D, Nishimura Y, Ogata H, Yoshida T. 2020. In silico prediction of virus-host interactions for marine Bacteroidetes with the use of metagenome-assembled genomes. Front Microbiol 11:738. https://doi.org/10.3389/fmicb.2020.00738.
43. Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay J´E, Vik D, Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, de Vargas C, Follows M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Not F, Ogata H, Poulton N, Raes J, Sardet C, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Culley AI, Tara Oceans Coordinators, et al. 2019. Marine DNA viral macro- and microdiversity from pole to pole. Cell 177:1109–1123. https://doi.org/10 .1016/j.cell.2019.03.040.
44. Mizuno CM, Ghai R, Saghaï A, López-García P, Rodriguez-Valeraa F. 2016. Genomes of abundant and widespread viruses from the deep ocean. mBio 7:e00805-16. https://doi.org/10.1128/mBio.00805-16.
45. Tully BJ, Graham ED, Heidelberg JF. 2018. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci Data 5:170203. https://doi.org/10.1038/sdata.2017.203.
46. Tully BJ, Sachdeva R, Graham ED, Heidelberg JF. 2017. 290 metagenome- assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PeerJ 5:e3558. https://doi.org/10.7717/peerj.3558.
47. Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. 2018. Nitrogen-fixing populations of Planctomy- cetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol 3:804–813. https://doi.org/10.1038/s41564-018-0176-9.
48. Krüger K, Chafee M, Ben Francis T, Glavina del Rio T, Becher D, Schweder T, Amann RI, Teeling H. 2019. In marine Bacteroidetes the bulk of glycan degra- dation during algae blooms is mediated by few clades using a restricted set of genes. ISME J 13:2800–2816. https://doi.org/10.1038/s41396-019-0476-y.
49. Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, Poulton NJ, Burkart MD, La Clair JJ, Chisholm SW, Stepanauskas R. 2019. Charting the complexity of the marine microbiome through single-cell genomics. Cell 179:1623–1635. https://doi.org/10.1016/j.cell.2019.11.017.
50. Parada V, Herndl GJ, Weinbauer MG. 2006. Viral burst size of heterotro- phic prokaryotes in aquatic systems. J Mar Biolog Assoc U K 86:613–621. https://doi.org/10.1017/S002531540601352X.
51. Morris RM, Cain KR, Hvorecny KL, Kollman JM. 2020. Lysogenic host-virus interactions in SAR11 marine bacteria. Nat Microbiol 5:1011–1015. https://doi.org/10.1038/s41564-020-0725-x.
52. Needham DM, Chow C-ET, Cram JA, Sachdeva R, Parada A, Fuhrman JA. 2013. Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. ISME J 7:1274–1285. https://doi.org/ 10.1038/ismej.2013.19.
53. Sullivan MB, Waterbury JB, Chisholm SW. 2003. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 424:1047–1051. https://doi.org/10.1038/nature01929.
54. Waterbury JB, Valois FW. 1993. Resistance to co-occurring phages ena- bles marine Synechococcus communities to coexist with cyanophages abundant in seawater. Appl Environ Microbiol 59:3393–3399. https://doi .org/10.1128/aem.59.10.3393-3399.1993.
55. Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. 2005. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol 3:e144. https://doi.org/10.1371/journal.pbio .0030144.
56. Suttle CA, Chan AM. 1993. Marine cyanophages infecting oceanic and coastal strains of Synechococcus: abundance, morphology, cross-infectiv- ity and growth characteristics. Mar Ecol Prog Ser 92:99–109. https://doi .org/10.3354/meps092099.
57. Suttle CA, Chan AM. 1994. Dynamics and distribution of cyanophages and their effect on marine Synechococcus spp. Appl Environ Microbiol 60:3167–3174. https://doi.org/10.1128/aem.60.9.3167-3174.1994.
58. Wiggins BA, Alexander M. 1985. Minimum bacterial density for bacterio- phage replication: implications for significance of bacteriophages in natu- ral ecosystems. Appl Environ Microbiol 49:19–23. https://doi.org/10.1128/ aem.49.1.19-23.1985.
59. Weinbauer MG. 2004. Ecology of prokaryotic viruses. FEMS Microbiol Rev 28:127–181. https://doi.org/10.1016/j.femsre.2003.08.001.
60. Aylward FO, Boeuf D, Mende DR, Wood-Charlson EM, Vislova A, Eppley JM, Romano AE, DeLong EF. 2017. Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone. Proc Natl Acad Sci U S A 114: 11446–11451. https://doi.org/10.1073/pnas.1714821114.
61. Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB, Tara Oceans Coordinators. 2015. Patterns and ecological drivers of ocean viral com- munities. Science 348:1261498. https://doi.org/10.1126/science.1261498.
62. Zborowsky S, Lindell D. 2019. Resistance in marine cyanobacteria differs against specialist and generalist cyanophages. Proc Natl Acad Sci U S A 116:16899–16908. https://doi.org/10.1073/pnas.1906897116.
63. Andrews JH, Harris RF. 1986. r- and K-selection and microbial ecology, p 99–147. In Marshall KC (ed), Advances in microbial ecology. Springer, Boston, MA.
64. Kimura S, Sako Y, Yoshida T. 2013. Rapid Microcystis cyanophage gene diversification revealed by long- and short-term genetic analyses of the tail sheath gene in a natural pond. Appl Environ Microbiol 79:2789–2795. https://doi.org/10.1128/AEM.03751-12.
65. Koskella B, Brockhurst MA. 2014. Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev 38:916–931. https://doi.org/10.1111/1574-6976.12072.
66. Cohan FM, Perry EB. 2007. A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17:R373–R386. https://doi.org/10 .1016/j.cub.2007.03.032.
67. Kimura S, Uehara M, Morimoto D, Yamanaka M, Sako Y, Yoshida T. 2018. Incomplete selective sweeps of Microcystis population detected by the leader-end CRISPR fragment analysis in a natural pond. Front Microbiol 9:425. https://doi.org/10.3389/fmicb.2018.00425.
68. Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL. 2017. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nat Commun 8:15955. https://doi.org/10.1038/ncomms15955.
69. Chen F, Lu J, Binder BJ, Liu Y, Hodson RE. 2001. Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR gold. Appl Environ Microbiol 67:539–545. https://doi.org/10 .1128/AEM.67.2.539-545.2001.
70. Noble R, Fuhrman J. 1998. Use of SYBR green I for rapid epifluorescence counts of marine viruses and bacteria. Aquatic Microb Ecol 14:113–118. https://doi.org/10.3354/ame014113.
71. Takebe H, Tominaga K, Fujiwara K, Yamamoto K, Yoshida T. 2020. Differen- tial responses of a coastal prokaryotic community to phytoplanktonic or- ganic matter derived from cellular components and exudates. Microbes and Environments 35:ME20033. https://doi.org/10.1264/jsme2.ME20033.
72. Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M. 2014. Develop- ment of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing. PLoS One 9: e105592. https://doi.org/10.1371/journal.pone.0105592.
73. Rognes T, Flouri T, Nichols B, Quince C, Mahé F. 2016. VSEARCH: a versa- tile open source tool for metagenomics. PeerJ 4:e2584. https://doi.org/ 10.7717/peerj.2584.
74. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590–D596. https://doi.org/10.1093/nar/gks1219.
75. Pruesse E, Peplies J, Glöckner FO. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829. https://doi.org/10.1093/bioinformatics/bts252.
76. Whitman WB, Coleman DC, Wiebe WJ, Schwalbach MS, Brown MV, Green JL, Brown JH. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578–6583. https://doi.org/10.1073/pnas.95.12.6578.
77. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066. https://doi.org/10.1093/nar/gkf436.
78. John SG, Mendez CB, Deng L, Poulos B, Kauffman AKM, Kern S, Brum J, Polz MF, Boyle EA, Sullivan MB. 2011. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ Micro- biol Rep 3:195–202. https://doi.org/10.1111/j.1758-2229.2010.00208.x.
79. Hurwitz BL, Deng L, Poulos BT, Sullivan MB. 2013. Evaluation of methods to concentrate and purify ocean virus communities through compara- tive, replicated metagenomics. Environ Microbiol 15:1428–1440. https:// doi.org/10.1111/j.1462-2920.2012.02836.x.
80. Kimura S, Yoshida T, Hosoda N, Honda T, Kuno S, Kamiji R, Hashimoto R, Sako Y. 2012. Diurnal infection patterns and impact of Microcystis cyano- phages in a Japanese pond. Appl Environ Microbiol 78:5805–5811. https:// doi.org/10.1128/AEM.00571-12.
81. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new ge- nome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021.
82. Roux S, Enault F, Hurwitz BL, Sullivan MB. 2015. VirSorter: mining viral sig- nal from microbial genomic data. PeerJ 3:e985. https://doi.org/10.7717/ peerj.985.
83. Li W, Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659. https://doi.org/10.1093/bioinformatics/btl158.
84. Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S, Kyrpides NC. 2020. CheckV assesses the quality and completeness of metagenome- assembled viral genomes. Nat Biotechnol 39:578–585. https://doi.org/10 .1038/s41587-020-00774-7.
85. Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S. 2017. ViPTree: the viral proteomic tree server. Bioinformatics 33:2379–2380. https://doi.org/10.1093/bioinformatics/btx157.
86. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bow- tie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923.
87. Mihara T, Nishimura Y, Shimizu Y, Nishiyama H, Yoshikawa G, Uehara H, Hingamp P, Goto S, Ogata H. 2016. Linking virus genomes with host tax- onomy. Viruses 8:66. https://doi.org/10.3390/v8030066.
88. Zhang Z, Qin F, Chen F, Chu X, Luo H, Zhang R, Du S, Tian Z, Zhao Y. 2020. Culturing novel and abundant pelagiphages in the ocean. Environ Microbiol 23:1145–1161. https://doi.org/10.1111/1462-2920.15272.
89. Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC. 2016. Uncovering Earth’s virome. Nature 536:425–430. https://doi.org/10.1038/nature19094.
90. Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaqué D, Bork P, Acinas SG, Wincker P, Sullivan MB, Sullivan MB, Tara Oceans Coordinators. 2016. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537:689–693. https://doi.org/ 10.1038/nature19366.
91. Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. 2016. Computational approaches to predict bacteriophage–host relationships. FEMS Microbiol Rev 40:258–272. https://doi.org/10.1093/femsre/fuv048.
92. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. 2007. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209. https://doi.org/10.1186/1471-2105-8-209.
93. Grissa I, Vergnaud G, Pourcel C. 2007. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8:172. https://doi.org/10.1186/1471-2105-8-172.
94. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST1: architecture and applications. BMC Bioinfor- matics 10:421. https://doi.org/10.1186/1471-2105-10-421.
95. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16. https://doi.org/10.1093/nar/gkh152.
96. Chan PP, Lowe TM. 2016. GtRNAdb 2.0: an expanded database of trans- fer RNA genes identified in complete and draft genomes. Nucleic Acids Res 44:D184–D189. https://doi.org/10.1093/nar/gkv1309.
97. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, Mcglinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Henry M, Stevens H, Szoecs E, Maintainer HW. 2020. vegan: community ecology package (version 2.6.2). https://github.com/vegandevs/vegan.
98. Dixon P. 2003. VEGAN, a package of R functions for community ecology. J Veg Sci 14:927–930. https://doi.org/10.1111/j.1654-1103.2003.tb02228.x.
99. Xia LC, Steele JA, Cram JA, Cardon ZG, Simmons SL, Vallino JJ, Fuhrman JA, Sun F. 2011. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst Biol 5: S15. https://doi.org/10.1186/1752-0509-5-S2-S15.
100. Xia LC, Ai D, Cram J, Fuhrman JA, Sun F. 2013. Efficient statistical signifi- cance approximation for local similarity analysis of high-throughput time series data. Bioinformatics 29:230–237. https://doi.org/10.1093/ bioinformatics/bts668.
101. Csardi G, Nepusz T. 2006. The igraph software package (version 1.3.0) for complex network research. InterJournal, Complex Systems 1695. https:// igraph.org/.
102. Tyner S, Briatte F, Hofmann H. 2017. Network visualization with ggplot2. R Journal 9:27–59.
103. Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987–2993. https://doi.org/10 .1093/bioinformatics/btr509.
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