Abstract
<title>Abstract</title> <p>Background Clubroot disease, caused by Plasmodiophora brassicae, is a devastating threat to Chinese cabbage production worldwide. Biocontrol strategies, particularly using Bacillus subtilis, offer a sustainable management alternative, yet the integrated mechanisms involving rhizosphere microbiome and metabolome remodeling remain unclear. Here, we investigated the biocontrol efficacy and underlying mechanisms of B. subtilis PZ-1 against clubroot in a susceptible Chinese cabbage variety through a pot experiment with four treatments: control (S), P. brassicae inoculated alone (SP), B. subtilis inoculated alone (SB), and co-inoculation of B. subtilis and P. brassicae (SBP). Results B. subtilis PZ-1 inoculation significantly suppressed disease, achieving a control efficacy of 73.81%, while also promoting plant growth. Microbial community analysis revealed that B. subtilis inoculation counteracted the pathogen-induced dysbiosis. It significantly enriched beneficial bacterial taxa Bacillus, Streptomyces, Microbacterium, Luteimonas, and fungal taxa Penicillium, Humicola, Chaetomium, while drastically reducing the abundance of the pathogen-associated Olpidiaceae. Co-occurrence network analysis indicated that B. subtilis enhanced the complexity and stability of the microbial inter-kingdom network, fostering a more cooperative community. Non-targeted metabolomics identified distinct metabolic profiles among treatments. Co-inoculation uniquely regulated metabolites chetoseminudin C and cis-Zeatin-O-glucoside compared to the other treatments, involving key defense-related pathways such as phenylpropanoid biosynthesis. Integrated analysis showed strong correlations between these differential metabolites and the restructured beneficial microbial communities. Conclusion Our findings demonstrate that B. subtilis PZ-1 effectively controls clubroot by concurrently remodeling the soil microbiome into a disease-suppressive state and reprogramming the rhizosphere metabolome, highlighting its potential as a powerful biocontrol agent and providing insights for rhizosphere microbiome engineering in sustainable disease management.</p>