Bacillus-Mediated Transcriptional and Metabolic Reprogramming Mitigates Root Rot in Coptis chinensis

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 Bacillus are promising, yet their host mechanisms remain incompletely defined. We evaluated four Bacillus strains as BCAs in field-grown C. chinensis and profiled host roots by transcriptomics and metabolomics. Pre-inoculation with the BCA mixture reduced disease severity following Fusarium solani (Fs) challenge. Multi-omics analyses showed that BCA treatment activated genes linked to nitrogen assimilation, accompanied by increased glutamine (Gln) accumulation. Supplementing potato dextrose agar with exogenous Gln inhibited F. solani growth in a concentration-dependent manner at 7 d. Notably, Fs or BCAs alone elicited modest regulation of canonical defense genes, whereas BCA pre-inoculation followed by Fs robustly up-regulated defense modules across MAPK signaling, plant–pathogen interaction, and hormone signaling (JA, ET, SA), consistent with immune priming. BCAs mitigate root rot in C. chinensis by reprogramming nitrogen and amino acid metabolism and by priming host immunity. These findings inform BCA-based strategies for sustainable management of C. chinensis root rot.