Utilizing Microbial Inoculants to Alleviate Continuous Cropping Obstacles: Insights into the Metabolites and Transcriptomic Responses of .

(Thunb.) Breit is a widely used medicinal herb in Traditional Chinese Medicine (TCM). Still, its sustainable cultivation is threatened by continuous cropping obstacles, which disrupt soil ecosystems, reduce yield, and degrade quality. This study explores the potential of microbial inoculants to mitigate these challenges through integrated metabolomic and transcriptomic analyses. : Soil samples from fields with and without continuous cropping issues were used to compare the effects of microbial inoculants on the secondary metabolism and gene expression of . Metabolomic profiling identified 20,969 metabolites, with significant changes in lipid-like molecules (22.2%), organic acids (9.1%), and phenylpropanoids (7.0%) under microbial treatment. Notable increases in phenylalanine and caffeic acid levels were observed in microbial-inoculated plants. Correspondingly, transcriptomic analysis revealed the upregulation of phenylalanine ammonia-lyase (PAL) and other stress-related genes, confirming the metabolic shifts. Clustering and machine learning analyses highlighted the critical roles of metabolites and genes in enhancing plant resilience. Microbial inoculants improved secondary metabolite production. These findings provide valuable insights into the mechanisms of microbial-plant interactions and establish a sustainable approach for cultivating , addressing the challenges of continuous cropping while improving crop productivity and quality.