Amplicon Sequencing Reveals Rhizosphere Fungal Dysbiosis Facilitates Goji Berry Root Rot Onset

Root rot in Lycium barbarum, an economically vital crop, is a critical barrier to its sustainable development in China. To elucidate the underlying micro-ecological mechanisms, this study aimed to characterize and compare the rhizosphere microbial communities of healthy and diseased plants from the Qaidam Basin. We employed PacBio full-length amplicon sequencing to analyze bacterial and fungal populations, complemented by network analysis and in vitro antagonistic assays. The results indicated that while microbial species richness was similar, the community structures of healthy and diseased soils were fundamentally different, suggesting that the disease is primarily driven by microbial dysbiosis rather than species loss. Healthy soil was enriched with beneficial Trichoderma, whereas diseased soil was dominated by the pathogen Fusarium, with an abundance 6.7 times higher than that in healthy soil. Network analysis revealed the healthy fungal community was significantly more stable (modularity index: 0.818) than the diseased network (0.4131), where Fusarium occupied a core hub position. Crucially, Trichoderma strains isolated from healthy soil exhibited strong antagonistic activity against Fusarium, with an average inhibition rate exceeding 75%. This study identifies Fusarium as the key pathogen of Goji root rot and native Trichoderma as a potent biocontrol agent, providing a scientific basis for a sustainable, micro-ecological control strategy.