Intercropping with Peucedanum praeruptorum enhances Pseudostellaria heterophylla disease resistance via cross-kingdom metabolite-microbiota crosstalk

Pseudostellaria heterophylla , a valuable shade-tolerant Chinese medicinal herb, suffers yield loss from soil-borne diseases under monoculture, with limited sustainable solutions. Intercropping with Peucedanum praeruptorum (a coumarin-producing herb) offers eco-friendly disease control, but its mechanism remains unclear. Here, we integrated field/hydroponic experiments (three intercropping densities: 4:1, 3:1, 2:1 rows of P. heterophylla : P. praeruptorum ), multi-omics analyses, and in vitro validation to address this gap. Intercropping significantly suppressed leaf spot (up to 30.8%), mosaic disease (up to 50.8%), and damping-off (up to 90.2%) compared to monoculture. Rhizosphere microbial communities were reshaped: α-diversity increased, beneficial bacteria ( Pseudomonas , Paenibacillus ) were enriched, and fungal assembly shifted to deterministic processes. Metabolomics identified 520–718 differential metabolites, with phenylpropanoid/flavonoid pathways enriched (key metabolites: scopoletin, marmesin). Transcriptomics of P. praeruptorum roots revealed upregulated biosynthetic genes ( 4CL , F6H , CYP81G1 ) driving metabolite secretion. Functional assays confirmed these metabolites directly inhibited pathogens ( Fusarium oxysporum , Alternaria alternata ) and promoted beneficial bacteria ( Pseudomonas mandelii , Bacillus tequilensis ). We uncovered a ”companion plant-transcriptome-metabolome-microbiome-host” axis: intercropping induces P. praeruptorum transcriptional reprogramming to secrete metabolites that reshape the rhizosphere microbiota, synergistically enhancing P. heterophylla resistance. This study reveals a novel cross-species regulatory mechanism, providing actionable insights for sustainable medicinal herb cultivation by leveraging plant-microbe-metabolite crosstalk to reduce chemical fungicide inputs.