Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria

Many major marine bacterial lineages such as SAR11, , SAR116, and several lineages have members that are abundant, relatively slow-growing, and genome-streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the RCA lineage, another abundant group of bacteria in the ocean. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2 and CRP-3) show a similar genomic content and architecture with SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology between CRP-1, CRP-2, CRP-3 and HMO-2011 resulted in contribution of the RCA phages to the dominance of HMO-2011-type phage in the ocean. CRP-4 and CRP-5 are similar to the roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and appear to form two new phage genera. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean compared to most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages. Metagenomic fragment recruitment analyses suggest the critical need for isolating phages from the abundant but “unculturable” bacteria in the marine ecosystem.