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

<i>Pinellia ternata</i> (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. <b>Objectives:</b> This study explores the potential of microbial inoculants to mitigate these challenges through integrated metabolomic and transcriptomic analyses. <b>Methods</b>: 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 <i>P. ternata</i>. <b>Results and Discussion:</b> 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. <b>Implications:</b> These findings provide valuable insights into the mechanisms of microbial-plant interactions and establish a sustainable approach for cultivating <i>P. ternata</i>, addressing the challenges of continuous cropping while improving crop productivity and quality.