Field Root-Associated Microbiome Characteristics of Astragalus membranaceus and Its Transcriptomic Response to Purpureocillium lilacinum BP2-7 Treatment

Astragalus membranaceus suffers severe yield and quality losses due to root rot caused by Fusarium solani. To address this, we analyzed the root-associated microbial communities of healthy and diseased plants in northwest China using high-throughput sequencing. Combining community analysis with pot experiments and transcriptomic profiling, we elucidated the molecular mechanisms by which the biocontrol fungus Purpureocilliu lilacinum BP2-7 suppresses root rot. Root rot reshaped root-associated microbial structure, affecting fungal diversity more than bacterial diversity. The antagonistic effect of P. lilacinum BP2-7 against F. solani reached 71.43% in plate assays and 63.7% control efficacy in pot experiments, representing the first report of P. lilacinum application for managing root rot in A. membranaceus. Transcriptomic analysis revealed that P. lilacinum BP2-7 promotes the transition of plants from a damaged to a recovering state by modulating translation and metabolic processes, and enhancing protein homeostasis, while moderately downregulating defense-related responses to alleviate pathogen-induced excessive defense mechanisms. Additionally, twenty candidate genes involved in the direct inhibition of F. solani were identified, suggesting a role in enhancing host resistance. This study supports eco-friendly biocontrol strategies and advances understanding of plant–microbe interactions for managing soil-borne diseases in other important crops.