Indigenous Soil Microbiota Shapes Bacillus subtilis-Mediated Biocontrol Against Potato Bacterial Wilt Revealed by Integrated Rhizosphere Microbiome and Metabolome Profiles

The inconsistent field performance of microbial biocontrol agents is often linked to resident soil microbiota, yet how indigenous microbiota influence Bacillus-mediated suppression of potato bacterial wilt remains insufficiently understood. In this study, sterilized and non-sterilized soils were used to evaluate how indigenous soil microbiota affect the biocontrol efficacy of Bacillus subtilis against Ralstonia solanacearum. Disease development, pathogen abundance, B. subtilis abundance, full-length 16S rRNA amplicon sequencing, and untargeted metabolomics were integrated to characterize rhizosphere microbial and metabolic responses. Soil microbial background strongly influenced disease progression and Bacillus performance. Under sterilized-soil conditions, R. solanacearum abundance remained 3–5-fold higher and disease severity increased more rapidly, whereas in non-sterilized soil, B. subtilis significantly reduced disease index and pathogen abundance. Microbiome analyses showed that sterilized soil was associated with limited Bacillus-mediated pathogen buffering, whereas non-sterilized soil supported the enrichment of potentially beneficial taxa, including Burkholderia, Devosia, and Rhizobium, together with soil-context-dependent microbial association patterns and shifts in predicted functional potential. Metabolomic profiling further revealed that Bacillus-associated metabolic profiles were highly soil-context-dependent, with low overlap between sterilized and non-sterilized soils under Bacillus treatment, as indicated by a Jaccard similarity of 0.059. In non-sterilized soil, Bacillus treatment was associated with defense-related metabolic profiles involving aromatic defense-related compounds and metabolites associated with antimicrobial activity and systemic resistance, whereas sterilized soil showed stronger damage-compensation-associated metabolic patterns. These findings suggest that indigenous soil microbiota may shape the ecological expression of B. subtilis-mediated biocontrol and highlight the importance of considering resident microbial backgrounds for potato bacterial wilt biocontrol.