A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea

Abstract

The Roseobacter clade is abundant and widespread in marine environments and plays an important role in oceanic biogeochemical cycling. In this present study, a lytic siphophage (labeled vB_DshS-R5C) infecting the strain type of Dinoroseobacter shibae named DFL12T, which is part of the Roseobacter clade, was isolated from the oligotrophic South China Sea. Phage R5C showed a narrow host range, short latent period and low burst size. The genome length of phage R5C was 77, 874 bp with a G+C content of 61.5%. Genomic comparisons detected no genome matches in the GenBank database and phylogenetic analysis based on DNA polymerase I revealed phylogenetic features that were distinct to other phages, suggesting the novelty of R5C. Several auxiliary metabolic genes (e.g., phoH gene, heat shock protein and queuosine biosynthesis genes) were identified in the R5C genome that may be beneficial to the host and/or offer a competitive advantage for the phage. Among siphophages infecting the Roseobacter clade (roseosiphophages), four gene transfer agent-like genes were commonly located with close proximity to structural genes, suggesting that their function may be related to the tail of siphoviruses. The isolation and characterization of R5C demonstrated the high genomic and physiological diversity of roseophages as well as improved our understanding of host–phage interactions and the ecology of the marine Roseobacter.

Bacteriophages that infect marine roseobacters: genomics and ecology

“…Roseophages seem to have a narrow host range and the majority of them can only infect their original isolation hosts (Zhang and Jiao, ; Zhao et al ., ; Li et al ., ; Zhan et al ., ; Yang et al ., ). A SIO1‐like phage (SBRSIO67‐2001) and three N4‐like roseophages (DS‐1410Ws‐06, RD‐1410 W1‐01 and RD‐1410Ws‐07) have broad host ranges and are able to infect other roseobacters in addition to their original hosts (Angly et al ., ; Li et al ., ).…”

“…Genomic analysis revealed that these roseophages are related to phages within the Chivirus genus (Ahern et al ., ). Recently, phage vB_DshS‐R5C, which infects Dinoroseobacter shibae DFL12, was isolated from the South China Sea (Yang et al ., ). Genomic analysis revealed that this roseophage does not cluster with any known roseophages (Fig.…”

“…Moreover, a CRISPR/Cas‐associated protein was recognized in both RDJLΦ1 and RDJLΦ2 phages, although CRISPR is not common in roseobacters and has not been found in the host genome, R. denitrificans OCh114 (Liang et al ., ). Several auxiliary metabolic genes, especially genes related to queuosine biosynthesis, have also been characterized in the vB_DshS‐R5C genome (Yang et al ., ).…”

“…Currently, almost all marine roseophages in the Siphoviridae family encode at least four genes that are homologous to genes 12, 13, 14 and 15 in RcGTA, with the exception of Chi‐like roseophages (Huang et al ., ; Liang et al ., ; Zhan et al ., ; Yang et al ., ). These four genes are involved in tail morphogenesis and host recognition.…”

Characterisation of a newly detected bacteriophage infecting Bordetella bronchiseptica in swine

“…The phages' genomic DNA was extracted using the phenolchloroform protocol [11]. Briefly, purified phages were lysed by the addition of proteinase K (100 mg/ml), SDS (10%, wt/ vol) and EDTA (0.5 mM, pH 8.0) and incubation at 56 °C in water for 2 h. The digested sample was mixed with an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1) centrifuged at 12,000× g (4 °C) for 10 min to remove any debris.…”