High-Throughput Isolation of novel viruses infecting fastidious and ecologically important bacteria from the Western English Channel

Phages are ubiquitous in marine environments, act as major drivers of global biogeochemistry and catalyse evolution and population dynamics in marine microbial communities. Viral induced lysis is essential for recycling cell-bound organic material, and thereby influeces global carbon cycles. However, our capacity to translate recent advances in viral metagenomics methods into quantitative models of carbon flux is hampered by (1) poor recovery of genomes of viruses infecting important taxa such as SAR11 and OM43; (2) difficulty in predicting kinetics from in silico protein prediction; and (3) poor accuracy of in silico host prediction. Thus, culturing of viruses for experimental measurement of virally-mediated carbon flux is critically important for model parameterisation. Isolation and culturing of viruses, however, comes with its own challenges. Viruses for highly abundant, but fastidious microbial hosts are particulary challenging, as many taxa cannot be propagated on plates, prohibiting the use of traditional plaque assays. Here, we present a novel method of sequential enrichment and Dilution-to-Extinction viral isolation that has yielded over 100 phage isolates infecting ecologically relevant marine heterotrophs, including the first known viruses for the important methylotrophic OM43 clade. Genome sequencing of 24 new phages infecting SAR11 revealed nine different viral populations from the Western English Channel. Recruitment of viral metagenomic data from global oceans shows these populations are well represented in high latitude and temperate environments. Interestingly, not all isolated populations had representatives in viral metagenomes from the same location, suggesting either a rapid turnover of viral populations, or revealing biases of sequence recovery by metagenomics. Both possibilities highlight the importance of renewing viral cultivation methods to better understand marine host-virus dynamics and provide relevant model systems for experimental analyses. We hope our work will improve viral isolation efforts significantly and unlock previously uncultivable or unknown marine viruses for the wider research community – and undoubtedly allow for many fascinating insights into the world’s most abundant predators.