Rhizosphere microbiome dynamics enhance Polygonatum cyrtonema growth and quality in Carya cathayensis in-forest planting

Abstract Economic tree–medicinal plant intercropping delivers ecological and economic benefits for sustainable agroforestry, yet stage-dependent belowground interaction mechanisms remain poorly understood for in-forest medicinal planting. This study integrated field and pot experiments with multi-omics analysis to explore how in-forest planting with Carya cathayensis shapes rhizosphere metabolite-microbe dynamics and modulates P. cyrtonema growth and rhizome polysaccharide accumulation across different growth stages. Field and multi-omics data revealed that C. cathayensis interaction enhanced the growth and rhizome polysaccharide content of P. cyrtonema, modified soil properties (particularly pH), and altered rhizosphere metabolites and microbial communities, with stage-specific variations. Most metabolites were significantly upregulated during the vigorous growth stage (T1) and downregulated during the lodging stage (T2). The interaction increased microbial diversity and richness and single-kingdom network complexity at T1, alongside more cross-kingdom network complexity at both stages. Specific genera including uncultured_f_uncultured_o_Vicinamibacterales, norank_f_Vicinamibacteraceae, unclassified_p_Basidiomycota, unclassified_p_Rozellomycota were positively correlated with plant growth, while some taxa (e.g., Pseudomonas, Mortiella, Acidothermus, Saitozyma) negatively impacted growth, consistent with their correlation with rhizosphere metabolites. Pot experiments further verified that specific rhizosphere metabolites such as flavonoids and saponins mediate microbial community assembly. This study provides a theoretical framework for exploring belowground interactions in economic tree-medicinal plant intercropping systems and offers insights into optimizing P. cyrtonema management through targeted nutrient regulation and functional microbial applications.