Colletotrichum fructicola-induced anthracnose in Epimedium sagittatum: pathogenesis, metabolic reprogramming, microbiome dysbiosis, and biofungicide control with carvacrol

Anthracnose is an emerging threat to Epimedium sagittatum, a cornerstone species in traditional Chinese medicine; however, its etiology in biodiversity hotspots remains unresolved. In this study, we comprehensively identified the anthracnose pathogens affecting E. sagittatum in China's Shennongjia Forest District. Through a combination of multi-locus phylogenetic analyses (based on ITS2, GAPDH, TUB2, and ACT sequences) and pathogenicity assays, we identified Colletotrichum fructicola as the primary causal agent. Beyond pathogen identification, we found that infection triggers a sharp decline in key flavonoids (epimedin A, B, and C; icariin; and icaritin). Concurrent rhizosphere microbiome profiling revealed a shift toward dysbiosis, characterized by the depletion of beneficial taxa (e.g., Annulohypoxylon, Rhizophagus, Bradyrhizobium, and Pseudomonas) and an enrichment of opportunistic ones (e.g., Rhizoclosmatium, Fusarium, and Coccidioides). Strikingly, in detached leaf assays, the plant-derived phenolic compound carvacrol inhibited the growth of C. fructicola by 86.7%. Together, our findings not only identify a pathogen of concern but also delineate a disease progression pathway primarily driven by metabolic reprogramming of the host (flavonoid depletion) and concomitant rhizosphere dysbiosis. We also propose carvacrol as a potent biocontrol agent. This work addresses critical knowledge gaps in medicinal plant pathology and proposes an eco-sustainable strategy for managing anthracnose.