A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Abstract

Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland soil following “wet-up”, when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicate that dry soil holds a diverse but low biomass reservoir of virions, of which only a subset thrives following wet-up. Viral richness decreases by 50% within 24 h post wet-up, while viral biomass increases four-fold within one week. Though recent hypotheses suggest lysogeny predominates in soil, our evidence indicates that viruses in lytic cycles dominate the response to wet-up. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO₂ efflux following wet-up of seasonally dry soils.

Rewetting of seasonally dry soils induces dramatic shifts in viral biomass and diversity. Combining stable isotope probing, metagenomics, and viromics Nicolas et al. provide evidence that viral lysis contributes to microbial turnover and the associated CO₂ efflux.