Fuhrman JA. Marine viruses and their biogeochemical and ecological effects. Nature. 1999;399:541–8.
Google Scholar
Suttle CA. Viruses in the sea. Nature. 2005;437:356–61.
Google Scholar
Breitbart M. Marine viruses: truth or dare. Ann Rev Mar Sci. 2012;4:425–48.
Google Scholar
Brum JR, Sullivan MB. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol. 2015;13:147–59.
Breitbart M, Thompson L, Suttle C, Sullivan M. Exploring the vast diversity of marine viruses. Oceanography. 2007;20:135–9.
Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. Photosynth Res. 2015;126:71–97.
Sharon I, Tzahor S, Williamson S, Shmoish M, Man-Aharonovich D, Rusch DB, et al. Viral photosynthetic reaction center genes and transcripts in the marine environment. ISME J. 2007;1:492–501.
Google Scholar
Roux S, Hawley AK, Torres Beltran M, Scofield M, Schwientek P, Stepanauskas R, et al. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. Elife. 2014;3:e03125.
Trubl G, Jang H Bin, Roux S, Emerson JB, Solonenko N, Vik DR, et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems. 2018;3:e00076–18.
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
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.
Google Scholar
Gazitúa MC, Vik DR, Roux S, Gregory AC, Bolduc B, Widner B, et al. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. ISME J. 2021;15:981–98.
Google Scholar
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, et al. Ocean plankton. Patterns and ecological drivers of ocean viral communities. Science. 2015;348:1261498.
Google Scholar
Cassman N, Prieto-Davó A, Walsh K, Silva GGZ, Angly F, Akhter S, et al. Oxygen minimum zones harbour novel viral communities with low diversity. Environ Microbiol. 2012;14:3043–65.
Google Scholar
Vik D, Gazitúa MC, Sun CL, Zayed AA, Aldunate M, Mulholland MR, et al. Genome-resolved viral ecology in a marine oxygen minimum zone. Environ Microbiol. 2021;23:2858–74.
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
Tiano L, Garcia-Robledo E, Dalsgaard T, Devol AH, Ward BB, Ulloa O, et al. Oxygen distribution and aerobic respiration in the north and south eastern tropical Pacific oxygen minimum zones. Deep Res Part I Oceanogr Res Pap. 2014;94:173–83.
Google Scholar
Schmidtko S, Stramma L, Visbeck M. Decline in global oceanic oxygen content during the past five decades. Nature. 2017;542:335–9.
Google Scholar
Paulmier A, Ruiz-Pino D. Oxygen minimum zones (OMZs) in the modern ocean. Prog Oceanogr. 2009;80:113–28.
Wright JJ, Konwar KM, Hallam SJ. Microbial ecology of expanding oxygen minimum zones. Nat Rev Microbiol. 2012;10:381–94.
Google Scholar
Bertagnolli AD, Stewart FJ. Microbial niches in marine oxygen minimum zones. Nat Rev Microbiol. 2018;1:723–9.
Codispoti LA, Friedrich GE, Packard TT, Glover HE, Kelly PJ, Spinrad RW, et al. High nitrite levels off northern Peru: a signal of instability in the marine denitrification rate. Science. 1986;233:1200 LP–1202.
Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, Delong EF, et al. A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science. 2010;330:1375–8.
Google Scholar
Hurwitz BL, Westveld AH, Brum JR, Sullivan MB. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. Proc Natl Acad Sci USA. 2014;111:10714 LP–10719.
Garcia-Robledo E, Padilla CC, Aldunate M, Stewart FJ, Ulloa O, Paulmier A, et al. Cryptic oxygen cycling in anoxic marine zones. Proc Natl Acad Sci USA. 2017;114:8319–24.
Google Scholar
Lavin P, González B, Santibáñez JF, Scanlan DJ, Ulloa O. Novel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific. Environ Microbiol Rep. 2010;2:728–38.
Google Scholar
Ulloa O, Canfield DE, DeLong EF, Letelier RM, Stewart FJ. Microbial oceanography of anoxic oxygen minimum zones. Proc Natl Acad Sci USA. 2012;109:15996–6003.
Google Scholar
Bettarel Y, Sime-Ngando T, Amblard C, Dolan J. Viral activity in two contrasting lake ecosystems. Appl Environ Microbiol. 2004;70:2941–51.
Google Scholar
Weinbauer MG, Brettar I, Höfle MG. Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters. Limnol Oceanogr. 2003;48:1457–65.
Heldal M, Bratbak G. Production and decay of viruses in aquatic environments. Mar Ecol Prog Ser. 1991;72:205–12.
Proctor LM, Fuhrman JA. Viral mortality of marine bacteria and cyanobacteria. Nature. 1990;343:60–62.
Brum JR, Morris J, Décima M, Stukel M. Mortality in the oceans: causes and consequences. In Eco-DAS IX Symposium Proceedings. Association for the Sciences of Limnology and Oceanography; 2014.
Colombet J, Sime-Ngando T. Seasonal depth-related gradients in virioplankton: lytic activity and comparison with protistan grazing potential in Lake Pavin (France). Micro Ecol. 2012;64:67–78.
Colombet J, Sime-Ngando T, Cauchie HM, Fonty G, Hoffmann L, Demeure G. Depth-related gradients of viral activity in Lake Pavin. Appl Environ Microbiol. 2006;72:4440–5.
Google Scholar
Brum J, Steward G, Jiang S, Jellison R. Spatial and temporal variability of prokaryotes, viruses, and viral infections of prokaryotes in an alkaline, hypersaline lake. Aquat Micro Ecol. 2005;41:247–60.
Brum JR, Schenck RO, Sullivan MB. Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. ISME J. 2013;7:1738–51.
Google Scholar
Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, et al. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature. 2018;554:118–22.
Google Scholar
Székely AJ, Breitbart M. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology. FEMS Microbiol Lett. 2016;363:27.
Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: Mining viral signal from microbial genomic data. PeerJ. 2015;2015:e985.
Hurwitz BL, Sullivan MB. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 2013;8:e57355.
Google Scholar
Aldunate M, Henríquez-Castillo C, Ji Q, Lueders-Dumont J, Mulholland MR, Ward BB, et al. Nitrogen assimilation in picocyanobacteria inhabiting the oxygen-deficient waters of the eastern tropical North and South Pacific. Limnol Oceanogr. 2020;65:437–53.
Google Scholar
Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, et al. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genom. 2013;14:320.
Google Scholar
Duhaime MB, Deng L, Poulos BT, Sullivan MB. Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environ Microbiol. 2012;14:2526–37.
Google Scholar
Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ. Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone. ISME J. 2015;9:2682–96.
Google Scholar
Allen LZ, Allen EE, Badger JH, McCrow JP, Paulsen IT, Elbourne LD, et al. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J. 2012;6:1403–14.
Google Scholar
Hurwitz BL, U’Ren JM. Viral metabolic reprogramming in marine ecosystems. Curr Opin Microbiol. 2016;31:161–8.
Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol. 2018;3:754–66.
Google Scholar
Ignacio-Espinoza JC, Sullivan MB. Phylogenomics of T4 cyanophages: lateral gene transfer in the ‘core’ and origins of host genes. Environ Microbiol. 2012;14:2113–26.
Google Scholar
Crummett LT, Puxty RJ, Weihe C, Marston MF, Martiny JBH. The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses. Virology. 2016;499:219–29.
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:e234.
Google Scholar
Bragg JG, Chisholm SW. Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene. PLoS One. 2008;3:e3550.
Google Scholar
Puxty RJ, Evans DJ, Millard AD, Scanlan DJ. Energy limitation of cyanophage development: implications for marine carbon cycling. ISME J. 2018;12:1273–86.
Google Scholar
White AE, Foster RA, Benitez-Nelson CR, Masqué P, Verdeny E, Popp BN, et al. Nitrogen fixation in the Gulf of California and the Eastern Tropical North Pacific. Prog Oceanogr. 2013;109:1–17.
Jayakumar A, Chang BX, Widner B, Bernhardt P, Mulholland MR, Ward BB. Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean. ISME J. 2017;11:2356–67.
Google Scholar
Fuchsman CA, Devol AH, Saunders JK, McKay C, Rocap G. Niche partitioning of the N cycling microbial community of an offshore oxygen deficient zone. Front Microbiol. 2017;8:2384.
Google Scholar
Zhang Y, Pohlmann EL, Halbleib CM, Ludden PW, Roberts GP. Effect of P(II) and its homolog GlnK on reversible ADP-ribosylation of dinitrogenase reductase by heterologous expression of the Rhodospirillum rubrum dinitrogenase reductase ADP-ribosyl transferase-dinitrogenase reductase-activating glycohydrolase regula. J Bacteriol. 2001;183:1610–20.
Google Scholar
Tong W-H. Distinct iron-sulfur cluster assembly complexes exist in the cytosol and mitochondria of human cells. EMBO J. 2000;19:5692–5700.
Google Scholar
Py B, Barras F. Building Feg-S proteins: bacterial strategies. Nat Rev Microbiol. 2010;8:436–46.
Eichhorn E, van der Ploeg JR, Kertesz MA, Leisinger T. Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. J Biol Chem. 1997;272:23031–6.
Google Scholar
Friedrich CG, Bardischewsky F, Rother D, Quentmeier A, Fischer J. Prokaryotic sulfur oxidation. Curr Opin Microbiol. 2005;8:253–9.
Anantharaman K, Duhaime MB, Breier JA, Wendt KA, Toner BM, Dick GJ. Sulfur oxidation genes in diverse deep-sea viruses. Science. 2014;344:757 LP–760.
Callbeck CM, Lavik G, Ferdelman TG, Fuchs B, Gruber-Vodicka HR, Hach PF, et al. Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria. Nat Commun. 2018;9:1729.
Google Scholar
Carolan MT, Smith JM, Beman JM. Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone. Front Microbiol. 2015;6:334.
Google Scholar
Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, et al. Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. ISME J. 2018;1:2706–22.
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
Lill R, Dutkiewicz R, Elsässer HP, Hausmann A, Netz DJA, Pierik AJ, et al. Mechanisms of iron-sulfur protein maturation in mitochondria, cytosol and nucleus of eukaryotes. Biochim Biophys Acta Mol Cell Res. 2006;1763:652–67.
Fontecave M. Iron-sulfur clusters: ever-expanding roles. Nat Chem Biol. 2006;2:171–4.
Google Scholar
Roche B, Aussel L, Ezraty B, Mandin P, Py B, Barras F. Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. Biochim Biophys Acta Bioenerg. 2013;1827:455–69.
Google Scholar
Xu XM, Møller SG. Iron-sulfur clusters: Biogenesis, molecular mechanisms, and their functional significance. Antioxid Redox Signal. 2011;15:271–307.
Google Scholar
Miller HK, Auerbuch V. Bacterial iron-sulfur cluster sensors in mammalian pathogens. Metallomics. 2015;7:943–56.
Google Scholar
Sharon I, Battchikova N, Aro E-M, Giglione C, Meinnel T, Glaser F, et al. Comparative metagenomics of microbial traits within oceanic viral communities. ISME J. 2011;5:1178–90.
Google Scholar
Loiseau L, Ollagnier-de-Choudens S, Nachin L, Fontecave M, Barras F. Biogenesis of Fe-S cluster by the bacterial suf system. SufS and SufE form a new type of cysteine desulfurase. J Biol Chem. 2003;278:38352–9.
Google Scholar
Outten FW, Wood MJ, Muñoz FM, Storz G. The SufE protein and the SufBCD complex enhance SufS cysteine desulfurase activity as part of a sulfur transfer pathway for Fe-S cluster assembly in Escherichia coli. J Biol Chem. 2003;278:45713–9.
Google Scholar
Ayala-Castro C, Saini A, Outten FW. Fe-S cluster assembly pathways in bacteria. Microbiol Mol Biol Rev. 2008;72:110–25.
Google Scholar
Shepard EM, Boyd ES, Broderick JB, Peters JW. Biosynthesis of complex iron-sulfur enzymes. Curr Opin Chem Biol. 2011;15:319–27.
Lill R. Function and biogenesis of iron–sulphur proteins. Nature. 2009;460:831–8.
Google Scholar
Seidler A, Jaschkowitz K, Wollenberg M. Incorporation of iron-sulphur clusters in membrane-bound proteins. Biochem Soc Trans. 2001;29:418–21.
Google Scholar
Buchanan BB, Schürmann P, Wolosiuk RA, Jacquot J-P. The ferredoxin/thioredoxin system: from discovery to molecular structures and beyond. Photosynth Res. 2002;73:215–22.
Google Scholar
Dubnau D, Losick R. Bistability in bacteria. Mol Microbiol. 2006;61:564–72.
Google Scholar
Resnekov O, Driks A, Losick R. Identification and characterization of sporulation gene spoVS from Bacillus subtilis. J Bacteriol. 1995;177:5628–35.
Google Scholar
Sonenshein AL. Bacteriophages: how bacterial spores capture and protect phage DNA. Curr Biol. 2006;16:R14–R16.
Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol. 2005;3:0790–806.
Google Scholar
Fortier L-C, Sekulovic O. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence. 2013;4:354–65.
Google Scholar
Mobberley J, Nathan Authement R, Segall AM, Edwards RA, Slepecky RA, Paul JH. Lysogeny and sporulation in Bacillus isolates from the Gulf of Mexico. Appl Environ Microbiol. 2010;76:829–42.
Google Scholar
Brüssow H, Canchaya C, Hardt W-D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev. 2004;68:560–602.
Google Scholar
Meinhart A, Alonso JC, Strater N, Saenger W. Crystal structure of the plasmid maintenance system /: functional mechanism of toxin and inactivation by 2 2 complex formation. Proc Natl Acad Sci. 2003;100:1661–6.
Google Scholar
Schuster CF, Bertram R. Toxin-antitoxin systems are ubiquitous and versatile modulators of prokaryotic cell fate. FEMS Microbiol Lett. 2013;340:73–85.
Kawano M. Divergently overlapping cis -encoded antisense RNA regulating toxin-antitoxin systems from E. coli. RNA Biol. 2012;9:1520–7.
Google Scholar
Smith MA, Bidochka MJ. Bacterial fitness and plasmid-loss: the importance of culture conditions and plasmid size. Can J Microbiol. 1998;44:351–5.
Google Scholar
Summers DK. The kinetics of plasmid loss. Trends Biotechnol. 1991;9: 273–8.
Persad AK, Williams ML, LeJeune JT. Rapid loss of a green fluorescent plasmid in Escherichia coli O157:H7. AIMS Microbiol. 2017;3:872–84.
Google Scholar
Modi SR, Lee HH, Spina CS, Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature. 2013;499:219–22.
Google Scholar
Hargreaves KR, Kropinski AM, Clokie MR. Bacteriophage behavioral ecology. Bacteriophage. 2014;4:e29866.
Google Scholar
Naught LE, Gilbert S, Imhoff R, Snook C, Beamer L, Tipton P. Allosterism and cooperativity in Pseudomonas aeruginosa GDP-mannose dehydrogenase. Biochemistry. 2002;41:9637–45.
Google Scholar
Dong C, Flecks S, Unversucht S, Haupt C, van Pee K-H, Naismith JH. Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination. Science. 2005;309:2216–9.
Google Scholar
Fouces R, Mellado E, Diez B, Barredo JL. The tylosin biosynthetic cluster from Streptomyces fradiae: genetic organization of the left region. Microbiology. 1999;145:855–68.
Google Scholar
Heacock-Kang Y, Zarzycki-Siek J, Sun Z, Poonsuk K, Bluhm AP, Cabanas D, et al. Novel dual regulators of Pseudomonas aeruginosa essential for productive biofilms and virulence. Mol Microbiol. 2018;109:401–14.
Google Scholar
Kurtov D, Kinghorn JR, Unkles SE. The Aspergillus nidulans panB gene encodes ketopantoate hydroxymethyltransferase, required for biosynthesis of pantothenate and Coenzyme A. Mol Gen Genet. 1999;262:115–20.
Google Scholar
Huisjes R, Card DJ. Methods for assessment of pantothenic acid (Vitamin B5). In: Harrington D, editor. Laboratory assessment of vitamin status. London, UK; San Diego, CA, USA; Cambridge, MA, USA; Oxford, UK : Elsevier Inc.; 2019. p. 265–299. https://doi.org/10.1038/s41396-021-01143-1.
Leonardi R, Jackowski S. Biosynthesis of pantothenic acid and coenzyme A. EcoSal Plus. 2007;2:2.
Begley TP, Kinsland C, Strauss E. The biosynthesis of coenzyme a in bacteria. Vitam Horm. 2001;61:157–71.
Google Scholar
Cameron B, Guilhot C, Blanche F, Cauchois L, Rouyez MC, Rigault S, et al. Genetic and sequence analyses of a Pseudomonas denitrificans DNA fragment containing two cob genes. J Bacteriol. 1991;173:6058–65.
Google Scholar
Doxey AC, Kurtz DA, Lynch MD, Sauder LA, Neufeld JD. Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production. ISME J. 2015;9:461–71.
Google Scholar
Heal KR, Qin W, Amin SA, Devol AH, Moffett JW, Armbrust EV, et al. Accumulation of NO2-cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the eastern tropical North Pacific. Environ Microbiol Rep. 2018;10:453–7.
Google Scholar
Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC, et al. Putative archaeal viruses from the mesopelagic ocean. PeerJ. 2017;5:e3428.
Google Scholar
Streisinger G, Emrich J, Stahl MM. Chromosome structure in phage T4, III. Terminal redundancy and length determination. Proc Natl Acad Sci USA. 1967;57:292–5.
Google Scholar
Mahmoudabadi G, Milo R, Phillips R. Energetic cost of building a virus. Proc Natl Acad Sci USA. 2017;114:E4324–E4333.
Google Scholar
Brum J. 5m intervals of CTD profiles from R/V New Horizon cruise NH1315 in the Eastern Tropical North Pacific (ETNP) during June 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-08-31 (2020). https://doi.org/10.26008/1912/bco-dmo.822818.1.
Noble RT, Fuhrman JA. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Micro Ecol. 1998;14:113–8.
Brum J. Estimated abundances of viruses and bacteria determined in samples collected in the Eastern Tropical North Pacific (ETNP) on R/V New Horizon cruise NH1315 during June 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-09-02 (2020). https://doi.org/10.26008/1912/bco-dmo.823094.1.
Binder B. Reconsidering the relationship between vitally induced bacterial mortality and frequency of infected cells. Aquat Micro Ecol. 1999;18:207–15.
Brum J. Estimated frequency of lytic viral infection from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-09-01 (2020). https://doi.org/10.26008/1912/bco-dmo.822914.1.
Abramoff MD, Magalhaes PJ, Ram SJ. Image processing with ImageJ. Biophotonics Int 2004;11:36–42.
Brum J. Morphotypes, capsid widths, and tail lengths of viruses from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-09-02 (2020). https://doi.org/10.26008/1912/bco-dmo.823131.1.
John SG, Mendez CB, Deng L, Poulos B, Kauffman AKM, 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
Duhaime MB, Sullivan MB. Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology. 2012;434:181–6.
Google Scholar
Brum J. Accession numbers of viral metagenomes from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-09-04 (2020) https://doi.org/10.26008/1912/bco-dmo.823295.1.
Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.
Google Scholar
Delcher AL, Salzberg SL, Phillippy AM. Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinforma. 2003; Chapter 10: Unit 10.3.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–D230.
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7:1002195.
Team RCR. A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2018.
Wickham H. ggplot2: elegant graphics for data analysis. Springer-Verlag, New York: 2016.
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB et al. vegan: Community Ecology Package. R package version 2.5-2. 2013 http://RForge.R-project.org/projects/vegan/.
Wilkinson L. venneuler: Venn and Euler diagrams. R package version 1.1-0. 2011 https://CRAN.Rproject.org/package=venneuler.
Harrell FE, With contributions from Charles Dupont and many others. Hmisc: Harrell Miscellaneous. R package version 4.3-0. 2019 https://CRAN.R-project.org/package=Hmisc.
Wei T, Simko V. R package “corrplot”: Visualization of a Correlation Matrix (Version 0.84). 2017. Available from https://github.com/taiyun/corrplot.
Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang H Bin, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat Microbiol. 2018;3:870–80.
Sturges HA. The choice of a class interval. J Am Stat Assoc. 1926;21:65–66.
Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics. 2006;22:1540–2.
Google Scholar
Source: Ecology - nature.com