Brussow H, Canchaya C, Hardt WD. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev. 2004;68:560–602.
Bondy-Denomy J, Davidson AR. When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. J Microbiol. 2014;52:235–42.
Paul JH. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2008;2:579–89.
Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brussow H. Phage as agents of lateral gene transfer. Curr Opin Microbiol. 2003;6:417–24.
Feiner R, Argov T, Rabinovich L, Sigal N, Borovok I, Herskovits AA. A new perspective on lysogeny: prophages as active regulatory switches of bacteria. Nat Rev Microbiol. 2015;13:641–50.
Nanda AM, Thormann K, Frunzke J. Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions. J Bacteriol. 2015;197:410–9.
Touchon M, Bernheim A, Rocha EPC. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J. 2016;10:2744–54.
Fortier LC, Sekulovic O. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence. 2013;4:354–65.
Helfrich S, Pfeifer E, Kramer C, Sachs CC, Wiechert W, Kohlheyer D, et al. Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations. Mol Microbiol. 2015;98:636–50.
Pennington JM, Rosenberg SM. Spontaneous DNA breakage in single living Escherichia coli cells. Nat Genet. 2007;39:797–802.
Simmons LA, Goranov AI, Kobayashi H, Davies BW, Yuan DS, Grossman AD, et al. Comparison of responses to double-strand breaks double-strand breaks between Escherichia coli and Bacillus subtilis reveals different requirements for SOS inductions. J Bacteriol. 2009;191:1152.
Kamenšek S, Podlesek Z, Gillor O, Zgur-Bertok D. Genes regulated by the Escherichia coli SOS repressor LexA exhibit heterogeneous expression. BMC Microbiol. 2010;10:283.
Nanda AM, Heyer A, Krämer C, Grünberger A, Kohlheyer D, Frunzke J. Analysis of SOS-induced spontaneous prophage induction in Corynebacterium glutamicum at the single-cell level. J Bacteriol. 2014;196:180.
Harrison E, Brockhurst MA. Ecological and evolutionary benefits of temperate phage: what does or doesn’t kill you makes you stronger. BioEssays. 2017;39:1700112.
Leitet C, Riemann L, Hagstrom A. Plasmids and prophages in Baltic Sea bacterioplankton isolates. J Mar Biol Assoc UK. 2006;86:567–75.
Stopar D, Cerne A, Zigman M, Poljsak-Prijatelj M, Turk V. Viral abundance and a high proportion of lysogens suggest that viruses are important members of the microbial community in the Gulf of Trieste. Microb Ecol. 2004;47:1–8.
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;111:10714–9.
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.
Brum JR, Hurwitz BL, Schofield O, Ducklow HW, Sullivan MB. Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics. ISME J. 2016;10:437–49.
Payet JP, Suttle CA. To kill or not to kill: the balance between lytic and lysogenic viral infection is driven by trophic status. Limnol Oceanogr. 2013;58:465–74.
Williamson SJ, Houchin LA, McDaniel L, Paul JH. Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida. Appl Environ Microbiol. 2002;68:4307–14.
Jiang SC, Paul JH. Significance of lysogeny in the marine environment: Studies with isolates and a model of lysogenic phage production. Microb Ecol. 1998;35:235–43.
Weinbauer MG, Suttle CA. Lysogeny and prophage induction in coastal and offshore bacterial communities. Aquat Microb Ecol. 1999;18:217–25.
Thingstad TF, Lignell R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat Microb Ecol. 1997;13:19–27.
Luo E, Aylward FO, Mende DR, DeLong EF. Bacteriophage distributions and temporal variability in the Ocean’s Interior. Mbio. 2017;8:1–13.
Giovannoni S, Temperton B, Zhao YL. SAR11 viruses and defensive host strains reply. Nature. 2013;499:E4–5.
Knowles B, Silveira CB, Bailey BA, Barott K, Cantu VA, Cobian-Guemes AG, et al. Lytic to temperate switching of viral communities. Nature. 2016;531:466–70.
Weitz JS, Beckett SJ, Brum JR, Cael BB, Dushoff J. Lysis, lysogeny and virus-microbe ratios. Nature. 2017;549:E1–3.
Knowles B, Rohwer F. Knowles & Rohwer reply. Nature. 2017;549:E3–4.
Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel HA, Brinkhoff T, et al. Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nat Microbiol. 2016;1:1–8.
Buchan A, Gonzalez JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol. 2005;71:5665–77.
Slightom RN, Buchan A. Surface colonization by marine Roseobacters: integrating genotype and phenotype. Appl Environ Microbiol. 2009;75:6027–37.
Zhao YL, Wang K, Ackermann HW, Halden RU, Jiao NZ, Chen F. Searching for a “Hidden” prophage in a Marine Bacterium. Appl Environ Microbiol. 2010;76:589–95.
Chen F, Wang K, Stewart J, Belas R. Induction of multiple prophages from a marine bacterium: a genomic approach. Appl Environ Microbiol. 2006;72:4995–5001.
Ankrah NYD, Budinoff CR, Wilson WH, Wilhelm SW, Buchan A. Genome sequences of two temperate phages, ΦCB2047-A and ΦCB2047-C, infecting Sulfitobacter sp. Strain 2047. Genome Announc. 2014;2:1–2.
Ankrah NYD, Lane T, Budinoff CR, Hadden MK, Buchan A. Draft genome sequence of Sulfitobacter sp. CB2047, a member of the roseobacter clade of marine bacteria, isolated from an Emiliania huxleyi Bloom. Genome Announc. 2014;2:1–2.
Budinoff CR, Hollibaugh JT. Ecophysiology of a mono lake picocyanobacterium. Limnol Oceanogr. 2007;52:2484–95.
Ankrah NYD. Elucidating the impact of roseophage on roseobacter metabolism and marine nutrient cycles [Doctoral dissertation]. Knoxville: The University of Tennessee; 2015.
Kropinski AM, Mazzocco A, Waddell TE, Lingohr E, Johnson RP. Enumeration of bacteriophages by double agar overlay plaque assay. In: Clokie MRJ, Kropinski AM, editors. Bacteriophages: methods and protocols, Volume 1: isolation, characterization, and interactions. Totowa, NJ: Humana Press; 2009. p. 69–76.
Nieto PA, Covarrubias PC, Jedlicki E, Holmes DS, Quatrini R. Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans. BMC Mol Biol. 2009;10:63.
Green MR. In: Sambrook J, editor. Molecular cloning: a laboratory manual. 4th ed. Cold Spring Harbor Laboratory Press: NY; 2012.
Cude WN, Prevatte CW, Hadden MK, May AL, Smith RT, Swain CL, et al. Phaeobacter sp strain Y4I utilizes two separate cell-to-cell communication systems to regulate production of the antimicrobial indigoidine. Appl Environ Microbiol. 2015;81:1417–25.
Pagarete A, Le Corguille G, Tiwari B, Ogata H, de Vargas C, Wilson WH, et al. Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiol Ecol. 2011;78:555–64.
Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007;8:R19.
Mahadevan P, King JF, Seto D. CGUG: in silico proteome and genome parsing tool for the determination of “core” and unique genes in the analysis of genomes up to ca. 1.9 Mb. BMC Res Notes. 2009;2:168.
Fouts DE. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 2006;34:5839–51.
Fuhrman JA. Marine viruses and their biogeochemical and ecological effects. Nature. 1999;399:541–8.
Weinbauer MG. Ecology of prokaryotic viruses. FEMS Microbiol Rev. 2004;28:127–81.
Dorscht J, Klumpp J, Bielmann R, Schmelcher M, Born Y, Zimmer M, et al. Comparative Genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site. J Bacteriol. 2009;191:7206.
Randall-Hazelbauer L, Schwartz M. Isolation of the bacteriophage lambda receptor from Escherichia coli. J Bacteriol. 1973;116:1436–46.
Wang J, Hofnung M, Charbit A. The C-terminal portion of the tail fiber protein of bacteriophage lambda is responsible for binding to LamB, its receptor at the surface of Escherichia coli K-12. J Bacteriol. 2000;182:508.
Mavrich TN, Hatfull GF. Evolution of superinfection immunity in cluster A mycobacteriophages. mBio. 2019;10:e00971–19.
Degnan PH, Michalowski CB, Babić AC, Cordes MHJ, Little JW. Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage λ. Mol Microbiol. 2007;64:232–44.
Berngruber TW, Weissing FJ, Gandon S. Inhibition of superinfection and the evolution of viral latency. J Virol. 2010;84:10200.
Butala M, Žgur-Bertok D, Busby SJW. The bacterial LexA transcriptional repressor. Cell Mol Life Sci. 2008;66:82.
Campoy S, Hervàs A, Busquets N, Erill I, Teixidó L, Barbé J. Induction of the SOS response by bacteriophage lytic development in Salmonella enterica. Virology. 2006;351:360–7.
Cirz RT, O’Neill BM, Hammond JA, Head SR, Romesberg FE. Defining the Pseudomonas aeruginosa SOS response and its role in the global response to the antibiotic ciprofloxacin. J Bacteriol. 2006;188:7101–10.
Campos J, Martinez E, Suzarte E, Rodriguez BL, Marrero K, Silva Y, et al. VGJ phi, a novel filamentous phage of Vibrio cholerae, integrates into the same chromosomal site as CTX phi. J Bacteriol. 2003;185:5685–96.
Espeland EM, Lipp EK, Huq A, Colwell RR. Polylysogeny and prophage induction by secondary infection in Vibrio cholerae. Environ Microbiol. 2004;6:760–3.
Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, et al. Communication between viruses guides lysis-lysogeny decisions. Nature. 2017;541:488–93.
Clark AJ, Inwood W, Cloutier T, Dhillon TS. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages1 1 (Edited by) M Gottesman. J Mol Biol. 2001;311:657–79.
De Paepe M, Hutinet G, Son O, Amarir-Bouhram J, Schbath S, Petit M-A. Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases. PLoS Genet. 2014;10:e1004181.
Bouchard JD, Moineau S. Homologous recombination between a lactococcal bacteriophage and the chromosome of its host strain. Virology. 2000;270:65–75.
Broussard GW, Oldfield LM, Villanueva VM, Lunt BL, Shine EE, Hatfull GF. Integration-dependent bacteriophage immunity provides insights into the evolution of genetic switches. Mol Cell. 2013;49:237–48.
Howard-Varona C, Roux S, Dore H, Solonenko NE, Holmfeldt K, Markillie LM, et al. Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus. ISME J. 2017;11:284–95.
Carrolo M, Frias MJ, Pinto FR, Melo-Cristino J, Ramirez M. Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae. PLoS ONE. 2010;5:1–10.
Bossi L, Fuentes JA, Mora G, Figueroa-Bossi N. Prophage contribution to bacterial population dynamics. J Bacteriol. 2003;185:6467–71.
Stewart FM, Levin BR. The population biology of bacterial viruses: why be temperate. Theor Popul Biol. 1984;26:93–117.
Cortes MG, Krog J, Balázsi G. Optimality of the spontaneous prophage induction rate. J Theor Biol. 2019;483:110005.
Davies EV, James CE, Kukavica-Ibrulj I, Levesque RC, Brockhurst MA, Winstanley C. Temperate phages enhance pathogen fitness in chronic lung infection. ISME J. 2016;10:2553–5.
Gama JA, Reis AM, Domingues I, Mendes-Soares H, Matos AM, Dionisio F. Temperate bacterial viruses as double-edged swords in bacterial warfare. PLoS ONE. 2013;8:1–9.
Li XY, Lachnit T, Fraune S, Bosch TCG, Traulsen A, Sieber M. Temperate phages as self-replicating weapons in bacterial competition. J R Soc Interface. 2017;14:1–7.
Buchan A, LeCleir GR, Gulvik CA, Gonzalez JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol. 2014;12:686–98.
LeCleir GR, DeBruyn JM, Maas EW, Boyd PW, Wilhelm SW. Temporal changes in particle-associated microbial communities after interception by nonlethal sediment traps. FEMS Microbiol Ecol. 2014;87:153–63.
Budinoff CR. Diversity and activity of roseobacters and roseophage [Doctoral dissertation]. Knoxville: The University of Tennessee; 2012.
Lederberg J, Iino T. Phase variation in Salmonella. Genetics. 1956;41:743–57.
Wang XX, Kim Y, Ma Q, Hong SH, Pokusaeva K, Sturino JM, et al. Cryptic prophages help bacteria cope with adverse environments. Nat Commun. 2010;1:1–9.
Terzi M, Levinthal C. Effects of λ-phage infection on bacterial synthesis. J Mol Biol. 1967;26:525–35.
Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, et al. Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton. ISME J. 2015;9:2386–99.
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.
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