Integrating transcriptome, metabolome and microbiome to explore the interaction mechanism between secondary metabolites and root-associated bacteria of Codonopsis pilosula

This study aims to explore the mechanisms underlying the interactions between the secondary metabolism and root-associated bacteria of Codonopsis pilosula . This study collected root and rhizosphere soil samples from various C. pilosula cultivars and employed metabolome, transcriptome, and microbiome analysis to assess the variations in volatile organic compounds (VOCs), root-associated bacterial communities, terpenoid biosynthetic genes, and terpenoid metabolites across these cultivars. Significant differences were observed in VOC secretion from roots, terpenoid metabolite accumulation, and the composition and structure of root-associated bacterial communities among the cultivars. A total of 57 differentially expressed genes within the terpenoid synthesis pathway were identified, and terpenoid biosynthetic pathways in C. pilosula were constructed by integrating terpenoid differential metabolites. Furthermore, correlation analysis between VOCs and root-associated bacteria suggested that certain VOCs, such as acetoin, may play a role in shaping the composition of the root microbiome, particularly with respect to bacteria like Nitrospira and RB41 . Acetoin had been experimentally proven to promote the germination of C. pilosula seeds. Additionally, correlations between root-associated bacteria and both terpenoid synthesis genes and metabolites suggested that bacteria such as Nitrospira may influence the synthesis of terpenoid compounds like abscisic acid by modulating the expression of related biosynthetic genes. Collectively, this study provides preliminary insights into the mechanisms of secondary metabolite-root-associated bacterial interactions in C. pilosula , offering valuable guidance for the scientific cultivation and enhancement of the medicinal value of C. pilosula in future. • Cultivars differences in C. pilosula were revealed by multi-omics. • Terpenoid synthesis pathway was predicted based on model plants. • Correlation analysis of secondary metabolites and root bacteria was carried out. • Seed germination was promoted by volatile compounds acetoin.