COMMENTARY Insight into the unknown marine virus majority Alexander I. Culley1,2 understanding of viral ecology is the isolation Department of Oceanography, Center for Microbial Oceanography: Research and Education, and characterization of viruses that infect University of Hawai‘i at Manoa, Honolulu, HI 96822 hosts who play important roles in the en- vironment. In PNAS, Kang et al. (6) make fi fi Viruses of marine bacteria (bacteriophage) viruses influence the community dynamics asigni cant contribution to the eld with a report describing the isolation and char- have been characterized since the mid-20th and evolution of their hosts and ultimately acterization of a bacteriophage, HMO- century (1). However, it took several addi- the role viruses play in biogeochemical cycling. 2011, which infects a member of the tional decades before electron micrographs Critical to the understanding of viral ecology is SAR116 clade, a group of marine bacteria fi of seawater revealed that particles of virus-like the identi cation of the constituents of the that are abundant and ubiquitous in the morphology could exceed concentrations of 1 viral community and whom they infect. This surface ocean (7, 8). The isolation of a million per milliliter of seawater (2, 3), and is a formidable challenge because there are phage that lyses a SAR116 strain demon- that phage infection could cause substantial thousands of different types of viruses in every strates that viruses are an additional source mortality in marine bacterial communities (4). liter of seawater (5) that are mostly distantly of mortality for these organisms, and anal- Subsequent research in the field of marine vi- related to the catalog of known viruses, and yses based on the sequence of the HMO- ral ecology has focused on the characterization whose morphology and genotype do not iden- 2011 genome suggest that viruses related to of the diversity of the virioplankton (commu- tify the host that they infect. A clear, albeit this phage comprise a substantial fraction nity of extracellular viruses), elucidating how challenging, path forward to gaining a greater of the virioplankton. The isolation of a virus–host system from the marine environment can be a demand- SEAWATER SAMPLE EXTRACTED METAGENOMIC ing process; nevertheless, the payoff for this CONTAINING GENOMES SEQUENCES FROM AGGC AG often frustrating and exacting work has UNKNOWN PHAGES FROM SAMPLE SAMPLE G ACGTTAC been substantial. The characterization of C CTGAACC AGAACTA A the modest number of cultivated marine COMPARE THESE WITH CTCACT phage–host systems has resulted in data DATABASE OF IDENTIFIED GENOMES critical in the modeling of marine viral dy- namics, understanding the extent of gene transfer between virus and host, and the compilation of a reference database crucial to the interpretation of sequences generated from ostensibly cultivation-independent ap- BEFORE SAR PHAGE GENOMES AFTER SAR PHAGE GENOMES proaches. An excellent example of the ben- efit of cultivation-based research is the line REFERENCE METAGENOMEIC REFERENCE METAGENOMEIC of investigation founded on the isolation of DATABASE SEQUENCE FROM DATABASE SEQUENCE FROM viruses that infect the cyanobacterium Pro- SAMPLE SAMPLE chlorococcus (9), the most abundant primary ? ID ? ID producer in the largest regions of the ocean ? ? (10). One highlight was the discovery that ? ? ? ID these viruses encode genes that form the core ? ? ID ID components of the cyanobacterial photosyn- ? ? ? ? thetic apparatus (11). These genes may enable ? ? the virus to coax more energy from the host cell to complete its replication cycle, even as 10% OF SAMPLE 30% MORE OF the virus is simultaneously destroying the cell IDENTIFIED SAMPLE IDENTIFIED Fig. 1. A simplified depiction of how the addition of the SAR116 and SAR11 phages to the catalog of known viruses results in the identification of substantially more of the marine phage community. A seawater sample containing Author contributions: A.I.C. wrote the paper. a community of viruses is harvested from the ocean, the viral genomes are extracted, and a metagenome is generated The author declares no conflict of interest. through random sequencing. To identify the viruses in the sample, the metagenomic sequences are compared with See companion article on page 12343. a reference library of known viruses. The identification of these viruses is ultimately dependent on their similarity to 1 ́ viruses in the reference database. The addition of the SAR phages results in the identification of ∼30% more met- Present address: De partement de biochimie, de microbiologie, et ́ agenomic sequences (6). In the reference database, the orange, light green, and pink circles represent known, de bio-informatique, Faculté des sciences et de génie, Universite SAR116, and SAR11 phages, respectively. A question mark next to a row of sequences indicates the sequences remain Laval, Québec, QC, Canada G1V 0A6. unidentified, and an ID indicates the sequences are known. Graphics by Amanda Toperoff. 2E-mail: [email protected]. 12166–12167 | PNAS | July 23, 2013 | vol. 110 | no. 30 www.pnas.org/cgi/doi/10.1073/pnas.1310671110 Downloaded by guest on September 29, 2021 fi from within. The HMO-2011 genome con- must be con rmed independently. Beyond the virioplankton, diverse communities of COMMENTARY tains genes that suggest that the virus is ca- providing greater insight into the un- largely uncharacterized viruses with single- pable of altering its host’smetabolismaswell known viral majority, the SAR phages should stranded (ss)DNA (16), ssRNA and dsRNA (6), raising the possibility that future re- provide excellent model systems to better genomes are present as well (17). In fact, – search based on this virus host system there are data that suggest that at times the may bear similar fruit. Analyses based on the abundance of RNA viruses can exceed that Bringing thousands of marine prokaryotes sequence of the of dsDNA phage (18). Moreover sequences and tens of thousands of viruses into culture HMO-2011 genome closely related to a group of viruses with mas- to produce an accurate assessment of the fi composition of a virus community is pres- suggest that viruses sive dsDNA genomes have been identi ed in ently intractable. Therefore, a cultivation- marine microbial metagenomic libraries (19), independent, metagenomic approach has been related to this phage suggesting that these viruses are also persistent the most commonly used method to charac- comprise a substantial constituents of the virus community. Inte- terizing diversity (e.g., ref. 12). In this method, fraction of the grating the diverse and complex groups that the genomes from a community of viruses are comprise the virioplankton into a cohesive extracted from seawater, sequenced in toto, virioplankton. ecological picture presents a substantial chal- and analyzed (Fig. 1). Of the billions of nu- lenge. Fortunately, increased sequencing ca- understand the influence of viruses on these cleotide sequences generated from metage- pabilities, advances in analytical tools, more nomic studies of the marine virus commu- key groups of organisms in the ocean. fi refined modeling efforts, and innovative new nity, often 90% of the sequences have no Although these exciting ndings rep- methodologies promise to expedite this pro- similarity to reference databases that include resent substantial progress toward iden- tifying the dominant marine viruses, the cess. Nevertheless, the importance of culti- the genome sequences of known viruses fi (13). These results are particularly problem- virioplankton appears to be more diverse vation, as exempli ed in the work of Kang atic because they indicate that the identity of than previously appreciated. Whereas dsDNA et al. (6), is incontrovertible. Expanding this asignificant majority of the virioplankton phage are undoubtedly major contributors to collection is of paramount importance. (and therefore their hosts) remains unknown. However, one of the remarkable findings of the research by Kang et al. (6) is that when 1 Spencer R (1960) Indigenous marine bacteriophages. J Bacteriol 10 Chisholm SW, et al. (1988) A novel free-living prochlorophyte the genome sequence from HMO-2011, as 79(4):614. abundant in the oceanic euphotic zone. Nature 334(6154):340–343. 2 Torrella F, Morita RY (1979) Evidence by electron micrographs for 11 Mann NH, Cook A, Millard A, Bailey S, Clokie M (2003) Marine well as four recently described phages that a high incidence of bacteriophage particles in the waters of Yaquina ecosystems: Bacterial photosynthesis genes in a virus. Nature infect a strain of SAR11 (14) (another impor- Bay, Oregon: Ecological and taxonomical implications. Appl Environ 424(6950):741. tant group of marine bacteria), are included Microbiol 37(4):774–778. 12 Breitbart M, et al. (2002) Genomic analysis of uncultured 3 Bergh Ø, Børsheim KY, Bratbak G, Heldal M (1989) High marine viral communities. Proc Natl Acad Sci USA 99(22): in similarity searches with sequences from – abundance of viruses found in aquatic environments. Nature 14250 14255. fi viral metagenomes generated from the Indian 340(6233):467–468. 13 Hurwitz BL, Sullivan MB (2013) The Paci c Ocean virome (POV): fi 4 Proctor L, Fuhrman J (1990) Viral mortality of marine bacteria and A marine viral metagenomic dataset and associated protein clusters and Paci c Ocean, an average of 30% more of for quantitative viral ecology. PLoS ONE 8(2):e57355. cyanobacteria. Nature 343(6253):60–62. the total sequences assigned to viruses are 14 Zhao Y, et al. (2013) Abundant SAR11 viruses in the ocean. 5 Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev Nature 494(7437):357–360. identified than if these phages were not in- Microbiol 3(6):504–510. 15 Hendrix RW, Smith MCM, Burns RN, Ford ME, Hatfull GF (1999) 6 Kang I, Oh H-M, Kang D, Cho J-C (2013) Genome of a SAR116 cluded (Fig. 1). These results suggest that Evolutionary relationships among diverse bacteriophages and bacteriophage shows the prevalence of this phage type in the viruses related to SAR phages comprise a sub- prophages: All the world’s a phage.