Microbial community disruption and Fusarium solani as the causal agent of root rot in a medicinal crop, Cyclocodon lancifolius

Abstract BACKGROUND Cyclocodon lancifolius , a traditional Chinese medicinal herb with considerable pharmacological and commercial value, is increasingly threatened by root rot disease during large‐scale cultivation. Despite its rising economic significance, the disease's etiology, associated microbial dynamics, and effective management strategies remain largely unclear. This study addresses these gaps by systematically characterizing the microbial communities of healthy and diseased plants, identifying the primary pathogenic agents, and assessing the in vitro antifungal efficacy of selected fungicides. RESULTS The findings revealed a marked reduction in microbial diversity within both diseased root tissues and their surrounding rhizosphere soils. This decline was accompanied by pronounced shifts in microbial community composition, characterized by an increased abundance of pathogenic fungi, with Fusarium solani being particularly dominant. Pathogenicity tests confirmed that F. solani is the principal pathogen, because isolates DHG1 and DHG2 successfully induced typical root rot symptoms. Optimal growth conditions for the pathogen included alkaline environments (pH 6–9) and moderate temperatures (25–28 °C), with lactose and proline identified as the preferred carbon and nitrogen sources, respectively. Among the tested fungicides, fludioxonil was the most potent in vitro , and hymexazol elicited the most uniform inhibitory response. CONCLUSION This research constitutes the first in‐depth investigation into root rot affecting C. lancifolius , by incorporating microbial community dynamics, pathogen characterization, and fungicide efficacy assessment. F. solani was identified as the primary pathogen. Its environmental preferences and chemical sensitivities were evaluated, offering valuable insights for early diagnosis, targeted intervention, and the development of sustainable cultivation practices for this underexplored medicinal plant. © 2025 Society of Chemical Industry.