High endophytic fungal diversity and the antagonistic Aspergillus niger Bzrh13 are associated with Atractylodes macrocephala root rot resistance

Root rot severely impairs the growth of Atractylodes macrocephala , a valuable medicinal plant. Despite the recognized importance of endophytic fungi in plant health, the endophytic fungal community associated with A. macrocephala root rot remains poorly characterized. Combining internal transcribed spacer amplicon sequencing and cultivation-based approaches, we characterized the fungal microbiomes of healthy and diseased rhizomes from three production regions. Healthy rhizomes consistently showed higher richness and diversity, along with a microbiome composition distinct from that of diseased ones. Fusarium was identified as the dominant pathogenic genus in diseased rhizomes. Among 28 isolates, F. graminearum Qssd1 and F. oxysporum Qsrd11 exhibited the strongest root rot virulence. Aspergillus , Cladosporium , and Sterigmatomyces were the core endophytes of healthy rhizomes. Notably, Aspergillus niger Bzrh13 inhibited Fusarium mycelial growth, conidial germination, and root rot progression in both detached rhizomes and potted plants. Co-occurrence network analysis revealed significant negative correlations between the relative abundance of Fusarium and Aspergillus / Cladosporium , indicating potential antagonistic interactions. Transcriptomic analysis further revealed that antagonistic A. niger Bzrh13 significantly downregulated key biosynthetic genes involved in the production of three Fusarium mycotoxins (aurofusarin, zearalenone, and fusarielin H), which was validated by quantitative real-time PCR (qRT-PCR). Collectively, our study suggests that higher endophytic fungal diversity and the antagonistic activity of A. niger Bzrh13 are associated with root rot resistance in A. macrocephala . These findings provide a preliminary experimental basis for the development of microbiological management strategies against A. macrocephala root rot.