Antagonistic microbiota drive soil suppressiveness against Sclerotinia sclerotiorum, a widespread soil-borne fungal plant pathogen

Disease-suppressive soils, where suppression is conferred by the soil microbiome, have been studied for various soil-borne fungal pathogens. However, little is known about soils suppressive to Sclerotinia sclerotiorum , the causal agent of Sclerotinia stem rot (SSR), a major disease in broadacre crops, and their underlying microbial mechanisms. This study aimed to uncover the microbiome-mediated basis of SSR suppression by identifying a SSR-suppressive soil compared to a SSR-conducive soil, profiling microbial communities, and validating microbial drivers of suppressiveness to inform biocontrol strategies. We identified a suppressive soil that inhibited fungal basal infection and carpogenic germination of sclerotia. Suppressiveness was microbiome-mediated and transferable to soils conducive to the disease. Microbiome profiling revealed distinct community structures between the suppressive and conducive soils, with the suppressive soil enriched in known biocontrol taxa. In contrast, a remnant vegetation soil was highly susceptible to SSR and lacked these key biocontrol microbes. Microbial network analysis identified Bacillus as a keystone taxon and potential driver of suppressiveness. The suppressive soil also exhibited denser microbial co-occurrence networks. Cultivation and antagonism assays confirmed higher numbers of biocontrol bacteria, with Bacillus and Streptomyces species, including species not previously reported against S. sclerotiorum , suppressing fungal growth and reducing SSR in plant assays. Higher soil pH and a lower carbon-to‑nitrogen ratio were correlated with suppressiveness. These findings confirm the existence of SSR-suppressive soils and demonstrate that abundant antagonistic microbiota can inhibit sclerotia germination and myceliogenic growth, providing new mechanistic insights and a foundation for SSR management through microbiome enhancement and improved soil health. • Microbiome-mediated S. sclerotiorum suppression shown in a suppressive soil • Physico-chemical properties and microbiota of a SSR-suppressive soil revealed • Known bacterial and fungal biocontrol genera enriched in a SSR-suppressive soil • Soil suppressiveness linked to Bacillus and Streptomyces as dominant antagonists • Suppressive soils may serve as sources of native bacterial biocontrol candidates