A novel roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents

Abstract

Bacteria in the Roseobacter lineage have been studied extensively due to their significant biogeochemical roles in the marine ecosystem. However, our knowledge on bacteriophage which infects the Roseobacter clade is still very limited. Here, we report a new bacteriophage, phage DSS3Φ8, which infects marine roseobacter Ruegeria pomeroyi DSS-3. DSS3Φ8 is a lytic siphovirus. Genomic analysis showed that DSS3Φ8 is most closely related to a group of siphoviruses, CbK-like phages, which infect freshwater bacterium Caulobacter crescentus. DSS3Φ8 contains a smaller capsid and has a reduced genome size (146 kb) compared to the CbK-like phages (205-279 kb). DSS3Φ8 contains the DNA polymerase gene which is closely related to T7-like podoviruses. DSS3Φ8 also contains the integrase and repressor genes, indicating its potential to involve in lysogenic cycle. In addition, four GTA (gene transfer agent) genes were identified in the DSS3Φ8 genome. Genomic analysis suggests that DSS3Φ8 is a highly mosaic phage that inherits the genetic features from siphoviruses, podoviruses, prophages and GTAs. This is the first report of CbK-like phages infecting marine bacteria. We believe phage isolation is still a powerful tool that can lead to discovery of new phages and help interpret the overwhelming unknown sequences in the viral metagenomics.

Figure 1

(A) Transmission electron microscopy image of roseophage DSS3Φ8. Scale bar = 200 nm. (B) One-step growth curve of roseophage DSS3Φ8.

Figure 2. Genome map of roseophage DSS3Φ8.

Gene features (unknown, hypothetical, tRNA genes, GTA and others) and genome modules (structure, lysis and DNA replication) are color-coded according to the legend below the figure.

Figure 3. Genome wide comparison between roseophage DSS3Φ8 and Caulobacter phage phiCbK.

White arrows represent ORFs for which no putative function can be attributed. Yellow, green, red and purple arrows represent structure, lysis, replication and packaging ORFs, respectively. Pink arrows stand for GTA structure, while orange arrows represent prophage-related ORFs. Grey color stands for hypothetical proteins. Related genes of these two phages are connected by blue shading. The color box corresponds to different amino acid identities.

Figure 4

(A) The maximum likelihood phylogenetic tree of DNA polymerase I of bacteriophages. Orange, blue and green colors represent Podoviridae, Myoviridae and Siphoviridae, respectively. Red color represents the CbK-like phages. Bootstrap = 500. (B) Zoom in of region B in Fig. 4A.

Figure 5. The maximum likelihood phylogenetic tree of concatenated protein sequences of RcGTA-like genes 12–15 from bacteriophages and bacteria.

The circle represents the phage-derived four GTA genes, while the diamond indicates the GTA gene cluster came from the bacteria. Bootstrap = 500. The width of the branch corresponds to the bootstrap value.

Figure 6. Rates of occurrences of DSS3Φ8 genes in various metagenomic databases.

The colors of the bars indicate the categories of genes. The absolute counts of retrieved reads were normalized against the data sizes of metagenomes and the average gene size.