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

Summary

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 microbial hosts that incorporated the 13C-glucose. We present experimental evidence of isotope labelling (i.e., lytic activity) of more than 5,000 virus populations, all represented by high-quality (>90% complete) genomes. The active viruses lysed hosts from 197 microbial families across 28 prokaryote phyla. Substrate-induced viral lysis was much 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 growth responses of copiotrophic microbial populations within those taxa to the glucose additions. Supporting this, we observed that the degree of virus genome isotope labelling was positively correlated with the growth potential (maximum growth rate) 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 (AMGs) in the active virus genomes. Overall, our results demonstrate a link between microbial growth traits and virus activity in the context of substrate inputs and suggest that induction of lysogenic viruses to lysis significantly influences the soil C cycle. Our results also show that virus activity in response to labile C inputs is highly variable among soil contexts, with implications for the varying ecosystem-scale influences of viruses among terrestrial environments.

Outcomes reported

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 microbial hosts that incorporated the 13C-glucose. We present experimental evidence of isotope labelling (i.e., lytic activity) of more than 5,000 virus populations, all represented by high-quality (>90% complete) genomes. The active viruses lysed hosts from 197 microbial families across 28 prokaryote phyla. Substrate-induced viral lysis was much 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 growth responses of copiotrophic microbial populations within those taxa to the glucose additions. Supporting this, we observed that the degree of virus genome isotope labelling was positively correlated with the growth potential (maximum growth rate) 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 (AMGs) in the active virus genomes. Overall, our results demonstrate a link between microbial growth traits and virus activity in the context of substrate inputs and suggest that induction of lysogenic viruses to lysis significantly influences the soil C cycle. Our results also show that virus activity in response to labile C inputs is highly variable among soil contexts, with implications for the varying ecosystem-scale influences of viruses among terrestrial environments.

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