Virome DNA stable isotope probing reveals diverse active soil virus communities across ecosystem contexts

Viruses are increasingly recognized as important players in soil ecosystems, but the active lytic virus populations that influence microbe-mediated terrestrial ecosystem processes remain mostly uncharacterized. Here, we trace ¹³C-labeled glucose from host microorganisms into virus genomic DNA to identify virus populations actively involved in soil carbon (C) cycling, i.e., viruses that lysed ¹³C-incorporating microbes. We present experimental evidence of isotope labeling (i.e., lytic activity) of more than 5,000 virus populations. The active viruses lysed hosts from 197 microbial families across 28 prokaryotic phyla. Viral lysis was greater in C-limited agricultural soils compared with C-rich forest soils, highlighting C availability/inputs as key factors that mediate virus life cycles. Active viruses disproportionately lysed microorganisms in the Bacillota, Bacteroidota, and Pseudomonadota phyla, likely reflecting glucose-induced growth responses of microbial copiotrophs within those groups. Supporting this, we observed that the degree of virus genome isotope labeling was positively correlated with the growth potential of the microbial hosts. Furthermore, the active viruses exhibited unique genomic characteristics compared to the inactive viruses, including a greater prevalence of lysogeny-associated genes and distinct profiles of putative auxiliary metabolism genes in the active virus genomes. Overall, our results demonstrate a link between microbial growth traits and virus activity and suggest that substrate-induced viral lysis significantly influences microbial population turnover in soil. Our results also show that virus activity in response to C inputs is highly variable among soil contexts, with implications for the varying ecosystem-scale influences of viruses among terrestrial environments.IMPORTANCEIn this study, we used a new method of detecting active viruses that lyse (kill) their microorganism hosts in soil. We accomplished this by tracing "heavy" versions of carbon from soil microorganisms into the DNA of their virus parasites. This showed that there are thousands of different potentially active virus populations in soil and that the microorganisms that get lysed the most are those that grow the fastest. However, the activity of viruses was very high in some ecosystems (agricultural soils) and much lower in others (forest soils). Our results show that viruses can play an important role in influencing soil microbial communities, but that the size of their effects is very different in different types of ecosystems. Our study also describes a new method that can be extended to further explore the roles and importance of viruses across different environmental conditions and different ecosystem types.