Healthy wheat roots are enriched in Bacillus sp. XN303, conferring resistance to Fusarium crown rot, promoting seedling growth, and detoxifying deoxynivalenol.
BACKGROUND Fusarium crown rot (FCR), caused predominantly by Fusarium pseudograminearum, is a devastating soil-borne disease threatening global wheat production. Systematic discovery of keystone microbial taxa with biocontrol potential from the wheat microbiome remains poorly explored. This study aimed to identify core microbiome biomarkers associated with FCR resistance and functionally validate candidate biocontrol agents. RESULTS Bacterial and fungal communities across five wheat compartments (rhizosphere, root, stem, leaf, grain) were profiled under FCR challenge. Host compartment niche was the primary driver of wheat microbial community assembly. FCR infection reduced root and stem microbial α-diversity, strengthened homogeneous selection-dominated deterministic fungal assembly in stems, coincided with declined dispersal limitation in root bacterial assembly, and disrupted microbial network stability. Integrated analysis identified Bacillus ASV_2195, enriched in healthy wheat roots, as a core FCR resistance biomarker. The corresponding strain, Bacillus sp. XN303, was isolated. Whole-genome sequencing of XN303 uncovered gene clusters encoding antimicrobial compounds and plant-beneficial traits. Functionally, XN303 directly inhibited F. pseudograminearum growth by 71.64%, reduced the FCR disease index by 79.21%, and lowered pathogen density in rhizosphere soil and stems by 22.89% and 20.28%, respectively, in pot assays. In addition, XN303 demonstrated the capacity to detoxify deoxynivalenol (DON) and activate jasmonic acid-mediated defense priming in wheat. CONCLUSION Bacillus sp. XN303, identified through microbiome-guided screening, confers robust FCR protection via pathogen antagonism, DON detoxification, growth promotion, and defense priming, representing a potential candidate biocontrol agent for sustainable FCR management. © 2026 Society of Chemical Industry.