From the Cover: Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans

The abundance, genetic diversity, and crucial ecological and evolutionary roles of marine phages have prompted a large number of metagenomic studies. However, obtaining a thorough understanding of marine phages has been hampered by the low number of phage isolates infecting major bacterial groups other than cyanophages and pelagiphages. Therefore, there is an urgent requirement for the isolation of phages that infect abundant marine bacterial groups. In this study, we isolated and characterized HMO-2011, a phage infecting a bacterium of the SAR116 clade, one of the most abundant marine bacterial lineages. HMO-2011, which infects “Candidatus Puniceispirillum marinum” strain IMCC1322, has an ∼55-kb dsDNA genome that harbors many genes with novel features rarely found in cultured organisms, including genes encoding a DNA polymerase with a partial DnaJ central domain and an atypical methanesulfonate monooxygenase. Furthermore, homologs of nearly all HMO-2011 genes were predominantly found in marine metagenomes rather than cultured organisms, suggesting the novelty of HMO-2011 and the prevalence of this phage type in the oceans. A significant number of the viral metagenome sequences obtained from the ocean surface were best assigned to the HMO-2011 genome. The number of reads assigned to HMO-2011 accounted for 10.3%–25.3% of the total reads assigned to viruses in seven viromes from the Pacific and Indian Oceans, making the HMO-2011 genome the most or second-most frequently assigned viral genome. Given its ability to infect the abundant SAR116 clade and its widespread distribution, Puniceispirillum phage HMO-2011 could be an important resource for marine virus research.Viruses are the most abundant biological entities in diverse marine environments, as revealed by electron microscopy, epifluorescence microscopy, and flow cytometry studies (1–3). The average number of virus-like particles in surface seawater is ∼10⁷ per mL, and it typically exceeds the number of prokaryotes by an order of magnitude. Marine viruses play an important role in nutrient cycles by mediating a significant proportion of bacterial mortality. This so-called “viral shunt” diverts organic matter from particulate forms to dissolved forms, influencing the overall biogeochemistry of various elements (4). Viruses affect the community composition and genetic diversity of marine organisms by selectively infecting susceptible hosts (5, 6), which also increases the genetic diversity of the viruses themselves through mechanisms such as antagonistic coevolution (6, 7).Recent metagenomic studies of the oceans have revealed the numerous novel genetic repertoires of marine viromes (8–14). However, most genome fragments in these viromes cannot be categorized into any known viral group (8, 9, 13, 14). Because most marine viruses are believed to be phages (15), a more thorough understanding of the ecological and evolutionary roles of marine viruses and a better interpretation of the rapidly increasing virome sequences require the isolation and genomic analysis of individual viruses, especially phages infecting diverse marine bacterioplankton.The importance of phage isolation is exemplified by studies on marine cyanophages and pelagiphages. The isolation and characterization of cyanophages have shown that they have auxiliary metabolic genes (16), including photosynthesis-related genes that are expressed during infection and modulate host metabolism toward successful infection (17–21). Cyanophages are important in the diversification of hosts and horizontal gene transfer and are extensively used to interpret marine metagenome sequences (6, 22, 23). Very recently, four pelagiphages, viruses infecting the SAR11 clade, were isolated (24). Pelagiphage genome sequences have been found to be crucial for the interpretation of viromes from the Pacific Ocean (24). However, there are many abundant marine bacterial groups, including SAR86, SAR116, and Bacteroidetes, for which few phages have been isolated or characterized. Given the poor assignment of virome sequences into specific viral groups and the presence of difficult-to-cultivate or unculturable bacterial groups in the ocean, cultivating these bacteria and isolating the phages infecting them are prerequisites for understanding phage diversity.The SAR116 clade is one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. Since its initial discovery through the cloning of 16S rRNA genes from the Sargasso Sea (25), many culture-independent studies have shown that the SAR116 clade contributes significantly—more than 10% in some cases—to the bacterial assemblages of the marine euphotic zone (26–33). The genome sequences of two bacteria in this clade, HIMB100 and “Candidatus Puniceispirillum marinum” IMCC1322, have recently been reported (34, 35). Both strains have genes for proteorhodopsin-based photoheterotrophy, carbon monoxide dehydrogenase, and dimethylsulfoniopropionate demethylase, suggesting the diverse metabolic potential and biogeochemical importance of the SAR116 clade. Considering the widespread distribution and ecologically meaningful genome characteristics of this clade, their phages are likely to be abundant in marine environments and may provide useful references for functional and phylogenetic annotation of marine viromes.Here, we report the isolation and genomic characterization of HMO-2011, a phage that infects strain IMCC1322 of the SAR116 clade. The HMO-2011 genome harbors many novel genes, such as a gene encoding a DNA polymerase with a DnaJ central domain. The genome of HMO-2011 was a notable resource for the identification of unknown marine viral gene fragments, as HMO-2011 accounted for 10.3%–25.3% of viral metagenome reads assigned to viruses.