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

Abstract

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.

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

“…This has been shown recently with previously unknown groups of viruses isolated on Pelagibacter ubique (Zhao et al, 2013), a bacterium of SAR116 clade (Kang et al, 2013) and Cellulophaga baltica (Holmfeldt et al, 2013). Similarly, most cyanophages have been isolated using a few strains of Synechococcus spp.…”

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

“…When only one or a handful of affiliated isolate genomes were included in the VC and lacked genus-level classification, a candidate name was derived from the isolate (if several isolates, from the first one isolated). This was the case for VC_5 (Cbaphi381virus 67 ), VC_12 (P12024virus 68 ), VC_14 (MED4-117virus), VC_19 (HMO-2011virus 69 ), VC_31 (RM378virus 70 ), VC_36 (GBK2virus 71 ), VC_47 (Cbaphi142virus 67 ) , and VC_277 (vB_RglS_P106Bvirus 72 ). Otherwise, VCs were considered as "new VCs".…”

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

“…The 'core' and 'flexible' genomic repertoire documented here in the Pacific Ocean offers new biological insight into spatial patterns of viralencoded, niche-defining functions that are fundamental to viral and host ecology. Linking nichedefining AMGs identified in these 'gene ecology' observations to their viral 'owners' will help in elucidating which viruses drive specific metabolic pathways in the sunlit and dark oceans, and can be accomplished through screening for particular AMGs in large-insert fosmid libraries (Beja et al, 2000;Mizuno et al, 2013), novel model phage-host systems (for example, phages for the abundant bacterial phyla SAR11 (Zhao et al, 2013), SAR116 (Kang et al, 2013) and Bacteriodetes (Holmfeldt et al, 2012)) or simplified/enriched viral metagenomes (Brum et al, 2013a;Deng et al, 2014). With such a refined toolkit in-hand and a metagenomeinferred roadmap of hypotheses to test, we can now more comprehensively develop experiments to untangle viral-host interactions in nature.…”