Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions

Many soil protists are bacterivores, yet how protist predation reshapes bacterial metabolic interactions and functions remains poorly understood. Here, we combine global soil samples with microbial metabolic simulations, along with soil microcosm-pot validations, to investigate the influence of protists on bacterial metabolic interactions. Across 3,785 metabolic simulations spanning 757 soils, increased protists predicted higher bacterial metabolic interaction potential and cross-feeding but lower metabolic resource overlap and competition. These patterns were confirmed using an independent rhizosphere dataset and metagenomic analysis. Protist predation selected bacterial communities containing GC-rich genomes, acid-carbon-preferring taxa, and enhanced metabolite exchange. Additionally, exposing a synthetic community (SynCom) to protist predation elevated the expression of bacterial genes associated with plant growth-promoting functions. Consistently, microcosm- and pot-based experiments showed that protist addition increased bacterial cross-feeding over time and improved plant performance. Together, we establish a scalable framework to evaluate protist-driven bacterial cooperation and function to guide rational rhizosphere microbiome engineering.