A newly isolated roseophage represents a distinct member of Siphoviridae family

Abstract

BackgroundMembers of the Roseobacter lineage are a major group of marine heterotrophic bacteria because of their wide distribution, versatile lifestyles and important biogeochemical roles. Bacteriophages, the most abundant biological entities in the ocean, play important roles in shaping their hosts’ population structures and mediating genetic exchange between hosts. However, our knowledge of roseophages (bacteriophages that infect Roseobacter) is far behind that of their host counterparts, partly reflecting the need to isolate and analyze the phages associated with this ecologically important bacterial clade.MethodsvB_DshS-R4C (R4C), a novel virulent roseophage that infects Dinoroseobacter shibae DFL12T, was isolated with the double-layer agar method. The phage morphology was visualized with transmission electron microscopy. We characterized R4C in-depth with a genomic analysis and investigated the distribution of the R4C genome in different environments with a metagenomic recruitment analysis.ResultsThe double-stranded DNA genome of R4C consists of 36,291 bp with a high GC content of 66.75%. It has 49 genes with low DNA and protein homologies to those of other known phages. Morphological and phylogenetic analyses suggested that R4C is a novel member of the family Siphoviridae and is most closely related to phages in the genus Cronusvirus. However, unlike the Cronusvirus phages, R4C encodes an integrase, implying its ability to establish a lysogenic life cycle. A terminal analysis shows that, like that of λ phage, the R4C genome utilize the ‘cohesive ends’ DNA-packaging mechanism. Significantly, homologues of the R4C genes are more prevalent in coastal areas than in the open ocean.ConclusionsInformation about this newly discovered phage extends our understanding of bacteriophage diversity, evolution, and their roles in different environments.

Genome and Ecology of a NovelAlteromonasPodovirus, ZP6, Representing a New Viral Genus,Mareflavirus

“…The gaps between remaining contigs were closed using GapCloser and GapFiller, with purified genomic DNA as the template. The termini were identified by using PhageTerm ( 83 , 84 ). The reads with the maximum coverage were considered phage termini (see the supplemental material).…”

Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

“…A recently published genome of a phage isolated off the coast of China that infects D. shibae, vB_DshS-R4C (GenBank accession MK882925.1), was reported to have substantial similarities to the genomes of the RcA cluster phages (34). This same phage also was found to have the most similar major capsid and large terminase proteins through BLASTP searches with these sequences (Table 4).…”

Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18

“…A BLAST search of this assembly revealed notable sequence similarity to the recently discovered Roseobacter phage DSS3P8 ( Fig. S2), which is also of the Siphoviridae morphotype and a close relative of the CbK-like phages which infect Caulobacter crescentus (15,16). To clarify the relationship of MD18 and other phages, we performed a phylogenetic analysis encompassing MD18, DSS3P8, and six Cbk-like phages (17) using the Virus Classification and Tree Building Online Resource (VICTOR) (Fig.…”