Fungal-mediated enhancement of yield and quality in Chrysanthemum morifolium under integrated rotation and organic management.

Continuous cropping obstacles (CCOs), driven by microbial dysbiosis, hinder sustainable Chrysanthemum morifolium production. While rotation and organic amendments are known to alleviate CCOs, their impact on microbial interactomes remains unclear. This study evaluated 10 agronomic treatments during a full cultivation cycle, ranging from monoculture (CK) to integrated rotation systems combined with bio-organic fertilizer or vermicompost (Rot_Org and Rot_Org_Ver), in a field with five-year continuous cropping history of Chrysanthemum morifolium. We integrated soil physicochemical analysis, enzyme profiling, and high-throughput sequencing (16S/ITS) with phytochemical assessments. Results showed integrated management improved soil nutrients and enzyme activities (e.g., sucrase, protease), reduced bacterial α-diversity, but enriched beneficial fungal taxa (Ascomycota, Mortierellomycota), which responded more strongly to AN/AP shifts than bacteria. Pathogen abundance declined under vermicompost-amended rotation (Rot_Org_Ver). XGBoost modeling with SHAP interpretation identified fungal positive cohesion as the paramount biological predictor of yield, which also correlated with flavonoid and phenolic acid accumulation. We conclude that assembling a stable, cohesive fungal interactome-rather than increasing species richness-is the primary mechanism coupling soil health restoration with crop productivity, providing a theoretical framework for ecological intensification in medicinal plant cultivation.