Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria

The ecological importance of virus-host interactions is unclear due to the limited ability of metagenomics to resolve virus-host pairs and the infection state of individual cells. We addressed these problems using single-cell genomics combined with published metagenomic data on lake bacterioplankton. We obtained 862 medium- to high-quality single-cell amplified genomes (SAGs) from two water layers and two seasons in Lake Biwa, Japan. We assembled 176 viral (dsDNA phage) contigs in the SAGs, and identified novel virus-host pairs including the discovery of viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. A virus was detected in 133 (15.4%) SAGs through read mapping analysis. The viral detection rate showed little variation among samples (12.1-18.1%) but significant variation in host taxonomy (4.2-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were achieved by collective infection by diverse viruses, suggesting weak density-dependent virus-host selections, presumably because of their non-persistent interactions with viruses due to their fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their co-dominance with viruses is achieved by genomic microdiversification that diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Overall, we demonstrated that virus-host interactions are highly diverse within and between host lineages, which was overlooked by metagenomics analysis, as exemplified by the CL500-11 virus, which showed extremely high read coverages in cellular and virion metagenomes, but infected < 1% of host cells. Significance statementVirus-host interactions are among the most significant driving forces of microbial biogeochemical cycles and genomic diversification. Unlike experimental conditions, bacterial cells in the natural environment are not uniformly infected by a single virus, but interact with diverse viruses under heterogeneous eco-physiological and genetic conditions. The specificity and heterogeneity of infection are the keys to understanding complex virus-host interactions and the mechanisms behind their co-existence. However, these interactions remain unclear due to the limitations of conventional metagenomic approaches. We addressed this issue by detecting viral signals from single-cell-amplified genomes of lake bacterial communities. The results revealed novel virus-host pairs and their infection rates, suggesting that viral defense strategies differ among host lineages, reflecting their ecological characteristics.