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

Abstract

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-labelled 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 labelling (i.e., lytic activity) of more than 5,000 virus populations. The active viruses lysed hosts from 197 microbial families across 28 prokaryote 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 labelling 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 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.