Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake

The use of metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and the ecological relationships between viruses and hosts remain poorly understood. In this study, we conducted a large-scale metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion ( Ca. Nitrosoarchaeum). Comparison with published metagenomes revealed phylogeographic connectivity of viral communities in geographically isolated habitats, probably following the phylogeographic connectivity of their hosts. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous, and abundant viral groups in freshwater systems, with high lytic replication rates in surface waters. This result suggested that freshwater Actinobacteria are under high viral lytic pressure, which likely facilitated their genomic micro-diversification to elude viral recognition.