Osburn, E. | bioRxiv Science

bioRxiv2026

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

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.

microbiology↗

bioRxiv2025

Functional diversity of soil microbial communities increases with ecosystem development

Land abandonment is the single largest process of land-use change in the Global North driving succession and afforestation at continental scales, but assessing its impacts on soil microbial communities remains a challenge. Here, we established a nationwide successional gradient of paired grassland and forest sites to track developments in microbial structure and functioning following land abandonment and gradually changing plant communities. We show that microbes generally respond through threshold dynamics, leading to increasing functional but decreasing taxonomic diversity. Succession also increased the specialization of microbial nutrient (C-N-P) cycling genes while decreasing genetic redundancy, highlighting a putative trade-off between two desirable ecosystem properties: functional diversity and functional redundancy. Increasing fungal functional diversity underpinned higher microbial C-cycling capacity, underscoring the causal link between functional traits and ecosystem processes. Changing litter quality similarly provided a mechanistic link between plant and microbial communities despite otherwise largely decoupled successional developments. Land abandonment is frequently touted as an opportunity to increase biodiversity and carbon storage. Our results show that deeper knowledge about the multifaceted development of soil microbial communities and its links to plant communities during succession may be needed to fully grasp the impacts of global land abandonment processes.

ecology↗