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 DSS3 Phi 8, which infects marine roseobacter Ruegeria pomeroyi DSS-3. DSS3 Phi 8 is a lytic siphovirus. Genomic analysis showed that DSS3 Phi 8 is most closely related to a group of siphoviruses, CbK-like phages, which infect freshwater bacterium Caulobacter crescentus. DSS3 Phi 8 contains a smaller capsid and has a reduced genome size (146 kb) compared to the CbK-like phages (205-279 kb). DSS3 Phi 8 contains the DNA polymerase gene which is closely related to T7-like podoviruses. DSS3 Phi 8 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 DSS3 Phi 8 genome. Genomic analysis suggests that DSS3 Phi 8 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.