Eco-evolutionary dynamics of active virus-host interactions in a freshwater lake: revealed through metaHi-C

Detecting active phage-bacteria interactions in natural microbial communities remains a major limitation for understanding their ecological dynamics and associated co-evolutionary processes. Here, we applied metaHi-C, a chromosome conformation capture method, to resolve active virus-host associations in a freshwater microbial community. From >900 microbial and >33,000 viral Hi-C-assembled genomes, we identified 100 high-confidence phage-host linkages spanning major freshwater bacterial lineages, including Limnohabitans, Acidimicrobium, Synechococcus, Candidatus Nanopelagicus, Candidatus Planktophila, Candidatus Methylopumilus and Polynucleobacter. The inferred networks revealed diverse infection patterns, including broad-host-range phages, cellular-level co-infection, kill-the-winner dynamics and one-to-one interactions. These ecological patterns were associated with signatures of diversifying selection in host-interaction genes, consistent with host-range expansion, alongside conserved genomic regions in broad-host-range and co-infecting phages, indicating functional constraints on essential infection modules. Together, these results demonstrate that metaHi-C enables direct linking of community-level infection dynamics to underlying evolutionary processes, revealing how these forces shape bacterial population dynamics of freshwater bacteria.