Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics
4 affiliations
- 1Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
- 2DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- 3Department of Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
- 4Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, 94720, USA
Abstract
Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H 2 18 O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant 18 O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76–5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10 10 to 6.59 × 10 10 virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota—bacterial groups known to rapidly resuscitate following rewetting—suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance. IMPORTANCE Soil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H 2 18 O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ . Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.
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BibTeX
@article{trubl2026disentangling,
title = {{Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics}},
author = {Gareth Trubl and Simon Roux and Matthew Kellom and Dariia Vyshenska and Andy Tomatsu and Kanwar Singh and Jeffrey A. Kimbrel and Emiley A. Eloe‐Fadrosh and Rex R. Malmstrom and Jennifer Pett‐Ridge and Steven J. Blazewicz},
journal = {mSystems},
year = {2026},
month = jun,
doi = {10.1128/msystems.01136-25},
url = {https://doi.org/10.1128/msystems.01136-25},
note = {CC BY},
}
RIS
TY - JOUR
TI - Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics
AU - Gareth Trubl
AU - Simon Roux
AU - Matthew Kellom
AU - Dariia Vyshenska
AU - Andy Tomatsu
AU - Kanwar Singh
AU - Jeffrey A. Kimbrel
AU - Emiley A. Eloe‐Fadrosh
AU - Rex R. Malmstrom
AU - Jennifer Pett‐Ridge
AU - Steven J. Blazewicz
PY - 2026
DA - 2026/06/29
JO - mSystems
DO - 10.1128/msystems.01136-25
UR - https://doi.org/10.1128/msystems.01136-25
AB - Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H 2 18 O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant 18 O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76–5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10 10 to 6.59 × 10 10 virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota—bacterial groups known to rapidly resuscitate following rewetting—suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance. IMPORTANCE Soil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H 2 18 O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ . Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.
SN - 2379-5077
ER -