Pelagiphages in the Podoviridiae family integrate into host genomes

Abstract

The Pelagibacterales order (SAR11) in Alphaproteobacteria dominates marine surface bacterioplankton communities, where it plays a key role in carbon and nutrient cycling. SAR11 phages, known as pelagiphages, are among the most abundant phages in the ocean. Four pelagiphages that infect Pelagibacter HTCC1062 have been reported. Here we report 11 new pelagiphages in the Podoviridae family. Comparative genomic analysis revealed that they are all closely related to previously reported pelagiphages HTVC011P and HTVC019P, in the HTVC019Pvirus genus. HTVC019Pvirus pelagiphages share a core genome of 15 genes, with a pan-genome of 234 genes. Phylogenomic analysis clustered these pelagiphages into three subgroups. Integrases were identified in all but one pelagiphage genomes. Evidence of site-specific integration was obtained by high-throughput sequencing and sequencing PCR amplicons containing predicted integration sites, demonstrating the capacity of these pelagiphages to propagate by both lytic and lysogenic infection. HTVC019P, HTVC021P, HTVC022P, HTVC201P and HTVC121P integrate into tRNA-Cys genes. HTVC011P, HTVC025P, HTVC105P, HTVC109P, HTVC119P and HTVC200P target tRNA-Leu genes, while HTVC120P integrates into the tRNA-Arg. Evidence of pelagiphage integration was also retrieved from Global Ocean Survey (GOS) database, suggesting the occurrence of pelagiphage integration in situ. The capacity of HTVC019Pvirus pelagiphages to integrate into host genomes suggests they could impact SAR11 populations by a variety of mechanisms, including mortality, genetic transduction, and prophage-induced viral immunity. HTVC019Pvirus pelagiphages are a rare example of a lysogenic phage that can be implicated in ecological processes on broad scales, and thus have potential to become a useful model for investigating strategies of host infection and phage-dependent horizontal gene transfer.\n\nIMPORTANCEPelagiphages are ecologically important because of their extraordinarily high census numbers, which makes them potentially significant agents in the viral shunt, a concept that links viral predation to the recycling of dissolved organic matter released from lysing plankton cells. Lysogenic Pelagiphages, such as the HTVC019Pvirus pelagiphages we investigate here, are also important because of their potential to contribute to the hypothesized processes such as the \"Piggy-Back-the-Winner\" and \"King-of-the-Mountain\". The former explains nonlinearities in virus to host ratios by postulating increased lysogenization of successful host cells, while the latter postulates host-density dependent propagation of defensive alleles. Here we report multiple Pelagiphage isolates, and provided detailed evidence of their integration into SAR11 genomes. The development of this ecologically significant experimental system for studying phage-dependent processes is progress towards the validation of broad hypotheses about phage ecology with specific examples based on knowledge of mechanisms.