Whole-genome and Comparative Genomic Analysis Reveal the Biocontrol and Plant Growth-Promoting Potential of Bacillus velezensis JN.Y2 Against Oat Anthracnose

Oat anthracnose, primarily caused by Colletotrichum cereale , represents a significant threat to oat production, necessitating the development of sustainable biocontrol alternatives. In this study, we characterized an oat endophytic bacterium, Bacillus velezensis JN.Y2, isolated from healthy oat leaves in Inner Mongolia. In vitro assays demonstrated that B. velezensis JN.Y2 possesses an inhibitory activity against C. cereale (74.49%) and exhibits a broad antifungal spectrum. Greenhouse and three-year multi-location field trials confirmed its beneficial biocontrol efficacy, which remained stable even under fluctuating climatic conditions and high disease pressure, consistently outperforming conventional chemical treatments. Beyond disease suppression, B. velezensis JN.Y2 significantly enhanced oat growth and grain yield, supported by its ability to produce IAA, solubilize nutrients, and secrete diverse hydrolytic enzymes. Complete genome sequencing revealed a 3.87 Mb circular chromosome containing 13 secondary metabolite BGCs and 4 AOIs for RiPPs, including Amylocyclicin and LCI. Comparative genomic analysis highlighted an "open" pangenome and identified 411 unique genes associated with specialized metabolism and environmental sensing. While B. velezensis JN.Y2 shares high sequence synteny with B. velezensis CBMB205, distinct variations in the sporulation kinase kinA and secondary metabolite pathways suggest a fine-tuned adaptation to the oat endosphere. Furthermore, biosafety evaluations confirmed a relatively high level of genetic stability and a lack of active antibiotic resistance. Collectively, these findings provide a beneficial molecular foundation for the application of B. velezensis JN.Y2 as a reliable and secure biocontrol agent in sustainable agriculture.