Host–virus interactions structure microbial communities, drive biogeochemical cycles and enhance genetic diversity in nature1,2. Hypotheses proposed to explain the range of interactions that mediate these processes often invoke lysogeny3,4,5,6, a latent infection strategy used by temperate bacterial viruses to replicate in host cells until an induction event triggers the production and lytic release of free viruses. Most cultured bacteria harbour temperate viruses in their genomes (prophage)7. The absence of prophages in cultures of the dominant lineages of marine bacteria has contributed to an ongoing debate over the ecological significance of lysogeny and other viral life strategies in nature6,8,9,10,11,12,13,14,15. Here, we report the discovery of prophages in cultured SAR11, the ocean’s most abundant clade of heterotrophic bacteria16,17. We show the concurrent production of cells and viruses, with enhanced virus production under carbon-limiting growth conditions. Evidence that related prophages are broadly distributed in the oceans suggests that similar interactions have contributed to the evolutionary success of SAR11 in nutrient-limited systems.
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Ca. P. giovannonii strain NP1 and associated data have been deposited under GenBank accession number CP038852 and BioProject number PRJNA531001. The strain NP1 16S rRNA sequence has been deposited under GenBank accession number MH923014. Original negative-stain micrographs will be made available on request. Ca. P. giovannonii strain NP1 cultures have unique growth requirements and cannot be maintained in standard culture collections. Requests for bacterial cultures or DNA from the University of Washington Culture Collection should be addressed to the corresponding author. On receiving a request for materials, we will assist the requesting institution in completing a Uniform Biological Material Transfer Agreement. There is no transmittal fee for academic institutions.
Rohwer, F. & Thurber, R. V. Viruses manipulate the marine environment. Nature 459, 207–212 (2009).
Breitbart, M., Bonnain, C., Malki, K. & Sawaya, N. A. Phage puppet masters of the marine microbial realm. Nat. Microbiol. 3, 754–766 (2018).
Stewart, F. M. & Levin, B. R. The population biology of bacterial viruses: why be temperate. Theor. Popul. Biol. 26, 93–117 (1984).
Jiang, S. & Paul, J. Significance of lysogeny in the marine environment: studies with isolates and a model of lysogenic phage production. Microb. Ecol. 35, 235–243 (1998).
Howard-Varona, C., Hargreaves, K. R., Abedon, S. T. & Sullivan, M. B. Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 11, 1511–1520 (2017).
Knowles, B. et al. Lytic to temperate switching of viral communities. Nature 531, 466–470 (2016).
Kang, H. S. et al. Prophage genomics reveals patterns in phage genome organization and replication. Preprint at bioRxiv https://doi.org/10.1101/114819 (2017).
Zhao, Y. et al. Abundant SAR11 viruses in the ocean. Nature 494, 357–360 (2013).
Våge, S., Storesund, J. E. & Thingstad, T. F. SAR11 viruses and defensive host strains. Nature 499, E3–E4 (2013).
Giovannoni, S., Temperton, B. & Zhao, Y. Giovannoni et al. reply. Nature 499, E4–E5 (2013).
Thingstad, T. F. & Bratbak, G. Microbial oceanography: viral strategies at sea. Nature 531, 454–455 (2016).
Wigington, C. H. et al. Re-examination of the relationship between marine virus and microbial cell abundances. Nat. Microbiol. 1, 15024 (2016).
Parikka, K. J., Le Romancer, M., Wauters, N. & Jacquet, S. Deciphering the virus‐to‐prokaryote ratio (VPR): insights into virus–host relationships in a variety of ecosystems. Biol. Rev. 92, 1081–1100 (2017).
Knowles, B. & Rohwer, F. Knowles & Rohwer reply. Nature 549, E3–E4 (2017).
Weitz, J. S., Beckett, S. J., Brum, J. R., Cael, B. & Dushoff, J. Lysis, lysogeny and virus–microbe ratios. Nature 549, E1–E3 (2017).
Morris, R. M. et al. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420, 806–810 (2002).
Giovannoni, S. J. SAR11 bacteria: the most abundant plankton in the oceans. Annu. Rev. Mar. Sci. 9, 231–255 (2017).
Jiang, S. C. & Paul, J. H. Seasonal and diel abundance of viruses and occurrence of lysogeny/bacteriocinogeny in the marine environment. Mar. Ecol. Prog. Ser. 104, 163–172 (1994).
Jiang, S. C. & Paul, J. H. Occurrence of lysogenic bacteria in marine microbial communities as determined by prophage induction. Mar. Ecol. Prog. Ser. 142, 27–38 (1996).
Leitet, C., Riemann, L. & Hagström, Å. Plasmids and prophages in Baltic Sea bacterioplankton isolates. J. Mar. Biol. Assoc. UK 86, 567–575 (2006).
Paul, J. H. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2, 579–589 (2008).
Durham, B. P. et al. Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nat. Microbiol. 4, 1706–1715 (2019).
Rappe, M. S., Connon, S. A., Vergin, K. L. & Giovannoni, S. J. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630–633 (2002).
Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60–63 (1990).
Giovannoni, S. J. et al. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438, 82–85 (2005).
Giovannoni, S. J. et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309, 1242–1245 (2005).
Fogg, P. C., Colloms, S., Rosser, S., Stark, M. & Smith, M. C. New applications for phage integrases. J. Mol. Biol. 426, 2703–2716 (2014).
Ptashne, M. Principles of a switch. Nat. Chem. Biol. 7, 484–487 (2011).
Owen, S. V. et al. Characterization of the prophage repertoire of African Salmonella Typhimurium ST313 reveals high levels of spontaneous induction of novel phage BTP1. Front. Microbiol. 8, 235 (2017).
Hay, I. D. & Lithgow, T. Filamentous phages: masters of a microbial sharing economy. EMBO Rep. 20, e47427 (2019).
Weitz, J. S., Li, G., Gulbudak, H., Cortez, M. H. & Whitaker, R. J. Viral invasion fitness across a continuum from lysis to latency. Virus Evol. 5, vez006 (2019).
Toyofuku, M., Nomura, N. & Eberl, L. Types and origins of bacterial membrane vesicles. Nat. Rev. Microbiol. 17, 13–24 (2019).
Biller, S. J. et al. Bacterial vesicles in marine ecosystems. Science 343, 183–186 (2014).
Biller, S. J. et al. Membrane vesicles in seawater: heterogeneous DNA content and implications for viral abundance estimates. ISME J. 11, 394–404 (2017).
Carini, P., Steindler, L., Beszteri, S. & Giovannoni, S. J. Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium. ISME J. 7, 592–602 (2013).
Bondy-Denomy, J. et al. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 10, 2854–2866 (2016).
Ofir, G. & Sorek, R. Vesicles spread susceptibility to phages. Cell 168, 13–15 (2017).
Mizuno, C. M., Rodriguez-Valera, F., Kimes, N. E. & Ghai, R. Expanding the marine virosphere using metagenomics. PLoS Genet. 9, e1003987 (2013).
Beaulaurier, J. et al. Assembly-free single-molecule nanopore sequencing recovers complete virus genomes from natural microbial communities. Genome Res. 30, 437–446 (2020).
Deschamps, P., Zivanovic, Y., Moreira, D., Rodriguez-Valera, F. & López-García, P. Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic Thaumarchaeota and Euryarchaeota. Genome Biol. Evol. 6, 1549–1563 (2014).
Chen, L. X. et al. Wide distribution of phage that infect freshwater SAR11 bacteria. mSystems 4, e00410-19 (2019).
Zhao, Y. et al. Pelagiphages in the Podoviridae family integrate into host genomes. Environ. Microbiol. 21, 1989–2001 (2019).
Chin, C. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).
Alikhan, N., Petty, N. K., Zakour, N. L. B. & Beatson, S. A. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12, 402 (2011).
Noble, R. T. & Fuhrman, J. A. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol. 14, 113–118 (1998).
This work was funded by a grant from the National Science Foundation awarded to R.M.M. and A. Ingalls (OCE-15584830). K.L.H. was supported by the National Institute of Allergy and Infectious Disease, award number F32AI14511. We thank members of the Center for Environmental Genomics at the University of Washington for their support and valuable feedback. We especially thank C. Rathwell for her valuable advice and thoughtful insights into marine virus ecology, and B. Durham and M. A. Moran for their help with experimental design leading to the cultivation of lysogenic strains of SAR11.
The authors declare no competing interests.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
A total of 5346 reads. Mean coverage is 696 with 0 missing bases.
PCR primers were designed to connect genomic contigs, to validate genomic assemblies, and to identify phage insertion sites.
a, The bacterial chromosomal sequence (attB), phage sequences (attP), and core sequences in blue, black, and red, respectively. b, PCR reactions verifying sequences associated with phage integration and excision, with bacterial (16S rRNA gene) and phage (internal) controls. All PCR products were sequenced to verify phage integration (attL and attR sites), a circular phage genome with an attachment site (attP), and phage excision from the bacterial chromosome with an attachment site (attB). PCR reactions were verified with DNA extracted from two or more cultures.
40 bp core sequences identified in PNP1 (attP) and exact matches to tRNA sequences in SAR11 (attB) or to sequences in the NCBI genomic survey database.
Extended Data Fig. 5 Ca. P. Giovannonii strain NP1 growth initiated from cultures with PNP1 virions added at different ratios.
Ratio of 1:1 (black) and 10:1 (red). Data points are the mean of n=3 biologically independent samples and the error bars are the standard deviation.
Size and sequence characteristics of PNP1 and PNP2 phage relative to other Pelagibacter phages. Measurements are the mean from 2 independent biological samples of NP1 and 1 sample of NP2. Images were acquired from n=2-3 distinct regions on n=2-3 grids. Errors are the standard deviation.
a, Image of a Ca. P. giovannonii NP1 host cell with an elongated morphology, evidence of budding, and possible virion attachment. Image acquired at 8,900x. Arrow mark budding and asterisks mark virions; not all budding and viruses have been marked. b–d, Representative images of vesicle-like particles found in strain NP1, independently acquired at 22,000x; asterisks mark virions. e, Image of strain NP2 host cell showing evidence of budding, acquired at 14,000x. Arrow marks budding. f–h, Representative images of vesicle-like particles found in strain NP2, independently acquired at 22,000x. Scale Bars: A, E = 500 nm; B-D, F-H = 100 nm. Panels A-D, images from 2 separate cultures of NP1. Panels E-H, images from 1 culture of NP2. Images for cultures were acquired from 2–3 distinct regions on 2–3 grids.
Defined media used to grow SAR11 strain NP1 and strain NP2.
a, Raw image of cells and free viruses stained, mounted, and viewed by epifluorescence microscopy. b, Cells (purple) and viruses (green) separated and enumerated by size exclusion (for example insert). All counts were determined by taking the average number of cells and viruses from 15–20 images at each time point and in biological triplicate. Direct cell and virus counts were repeated weekly on biologically independent samples and to verify continuous virus production in transfer cultures.
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Morris, R.M., Cain, K.R., Hvorecny, K.L. et al. Lysogenic host–virus interactions in SAR11 marine bacteria. Nat Microbiol 5, 1011–1015 (2020). https://doi.org/10.1038/s41564-020-0725-x
Nature Microbiology (2020)