Long-term compost fertilization enhanced soil disease suppressiveness by fostering interactions between root exudates...

A comprehensive understanding of the interplay between agricultural practices and the rhizosphere microbiome particularly the role of root exudates is essential for harnessing microbial potential in sustainable agriculture. In this study, we investigated how disease-suppressive soil alters root exudate profiles in pepper plants and how these elevated exudates influence rhizosphere microbiome assembly and modulate the antagonistic activity of Bacillus methylotrophicus 400 (BM400) against Phytophthora capsici. GC-MS analysis identified distinct compositional profiles of root exudates in the disease-suppressive soil, with marked enrichment of seven compounds. Mini-rhizobox experiments revealed that a mixture of seven enriched compounds (MSEC) altered rhizosphere microbiome assembly, explaining 11 % of bacterial community variation, and selected for in vitro antagonists of P. capsici, particularly within 20 mm proximity to chemical injection sites. Chemotactic assays indicated that most enriched compounds attract and are metabolized by BM400, enhancing its motility. RNA-seq analysis further demonstrated that MSEC suppressed transcription of BM400 genes linked to protein synthesis and sporulation, while upregulating urease-encoding genes. Notably, MSEC-driven microbiome modulation exhibited regional specificity across soils from Shanghai, Guangdong, and Yancheng. In summary, disease-suppressive soil alters root exudate composition, promoting recruitment of beneficial microbial taxa potentially via chemotaxis, and sustains the activity of BM400 by suppressing genes associated with excessive metabolic activity and sporulation.