Protist Predation Rapidly Reshapes Soil Microbial Gene Expression Linked to Nutrient Processing, Resistance, Virulence, and Gene Mobility Traits

Protists are ubiquitous soil predators that regulate bacterial communities and biogeochemical cycling, yet how their predation alters expression of nutrient-cycling genes and traits linked to antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in natural soils remains poorly understood. Here, we used a short-term soil microcosm experiment to distinguish the effects of moisture-stimulated resident protists from enhanced predation by an introduced exogenous predatory protist community. Using quantitative stable isotope probing (qSIP) and metagenomic and metatranscriptomic analyses, we tracked protist activity and microbial responses over 3 days. Enhanced predation rapidly reshaped transcriptionally active microbial communities, increasing expression of nitrogen and phosphorus cycling genes while concurrently elevating diversity and transcription of ARGs, VFs, and MGEs, including multidrug-efflux systems, motility-, biofilm-related traits, and phage-associated elements. Metagenome-assembled genome─resolved analyses showed that some resident soil populations were activated by wet-up and remained transcriptionally active under predation pressure, encoding nutrient-cycling, resistance, virulence, and mobility traits that contributed to the functional background of wetted soils. These results suggest that, even over short time periods, protist predation links soil nutrient processing with environmentally relevant resistance and genetic mobility pathways, acting as a crucial ecological driver of gene expression related to nutrient processing and microbial interaction traits during environmental change.