Intercropping with Peucedanum praeruptorum reshapes rhizosphere microbiome and metabolite to enhance Pseudostellaria heterophylla disease resistance

Intercropping is a sustainable cultivation strategy for managing the challenges of continuous monoculture and disease. Nevertheless, the interaction mechanism of intercropping between Pseudostellaria heterophylla and Peucedanum praeruptorum remains unknown. Herein, we investigated the differences in microbial communities of P. heterophylla , secretion metabolites of the co-cultured solution, and gene expression transcription of P. praeruptorum in a field/hydroponic intercropping experiment between P. heterophylla and P. praeruptorum . Compared to monoculture, intercropping significantly suppressed leaf spot (up to 30.8%) and damping-off (up to 90.2%) of P. heterophylla . Microbial community analysis of P. heterophylla showed that bacterial α-diversity was significantly increased, and bacteria (i.e., Pseudomonas and Paenibacillus ) were enriched. The metabolite profile of the co-cultured solution between P. heterophylla and P. praeruptorum showed that intercropping significantly enriched phenylpropanoid/flavonoid pathway metabolites, such as scopoletin and marmesin. In addition, the transcriptomic profile of P. praeruptorum roots revealed that intercropping significantly upregulated expression of phenylpropanoid/flavonoid biosynthesis genes, such as 4CL , F6H , and CYP81G1 , which may drive the secretion of these metabolites. Finally, an in vitro assay confirmed that these metabolites can inhibit pathogens ( Fusarium oxysporum , Alternaria alternata ) and promote bacteria ( P. mandelii , Bacillus tequilensis ). We revealed that intercropping-linked transcriptional reprogramming of P. praeruptorum is associated with elevated levels of phenylpropanoid metabolites in co-culture solution, which correlates with reshaped rhizosphere microbiota and alleviated disease symptoms. This study provides mechanistic insights into intercropping-mediated disease suppression and support the development of sustainable cultivation strategies for disease management in medicinal plants.