Bacillus-mediated transcriptional and metabolic reprogramming elicits defense priming in Coptis chinensis roots

The medicinal plant Coptis chinensis is highly susceptible to root rot caused predominantly by Fusarium spp., threatening yield and medicinal quality. Biological control agents (BCAs) from the genus Bacillus are promising, yet their host mechanisms remain incompletely defined. We evaluated a four-strain Bacillus consortium as BCAs in field-grown C. chinensis and profiled host roots using transcriptomics and metabolomics. Pre-inoculation with the BCA mixture resulted in a modest, albeit statistically non-significant, reduction in disease index following Fusarium solani challenge. Multi-omics analyses showed that BCA treatment reprogrammed genes and metabolites associated with amino acid metabolism, accompanied by increased glutamine (Gln) accumulation. Supplementing culture medium with exogenous Gln inhibited F. solani growth in a concentration-dependent manner in vitro. Notably, F. solani or BCAs alone elicited modest regulation of canonical defense genes, whereas BCA pre-inoculation followed by F. solani robustly up-regulated defense modules across MAPK signaling, plant–pathogen interaction, and hormone signaling (JA, ET, SA), consistent with molecular immune priming. These results suggest that the BCA consortium induces resistance- and priming-related molecular markers in C. chinensis by modulating amino acid metabolism and host immunity. These findings provide a mechanistic basis for the potential application of BCAs in the sustainable management of C. chinensis root rot.