Virome DNA stable isotope probing reveals diverse active soil phage communities across ecosystem types

Viruses are increasingly recognized as major players in soil ecosystems, but the active lytic phage populations that directly influence microbe-mediated terrestrial ecosystem processes remain mostly uncharacterized. Here, we identify active phage populations in soil by tracing 13C-labelled substrates from host microorganisms into virus genomic DNA. We present experimental evidence of isotope labelling (i.e., lytic activity) of more than 5,000 phage populations, all represented by high-quality (>90% complete) genomes. The active phages infected hosts from 197 microbial families across 28 prokaryote phyla. Phage lysis was much greater overall in carbon-limited agricultural soils compared with carbon-rich forest soils, highlighting C availability as a key factor that mediates virus life cycles in soil. In both agricultural and forest soils, the active phages disproportionately lysed microbial lineages in the Actinomycetota, Bacteroidota, and Pseudomonadota phyla. Furthermore, the degree of virus genome isotope labelling was positively correlated with the maximum growth rates of the microbial hosts. This provides evidence for the "cull-the-winner" model of viral lysis, whereby viruses selectively lyse successful, fast-growing microbial populations in soil. Interestingly, the active phage populations were more likely to be potentially lysogenic than inactive virus populations, suggesting key effects of lysogenic populations on soil microorganisms and functions. Overall, our results demonstrate direct links among microbial life strategies, lytic virus activity, and soil biogeochemistry. Our results also show that virus activity is highly variable among soil contexts, with implications for the varying ecosystem-scale influences of viruses among terrestrial environments.