Whole-Genome Analysis Reveals the Growth-Promoting and Biocontrol Potential of Bacillus amyloliquefaciens Ba. YN. J3 isolated from Avena sativa

Background Endophytic bacteria serve as important resources for the development of novel biocontrol agents for sustainable agriculture. The present study provides a detailed characterization of a newly isolated oat endophyte, Bacillus amyloliquefaciens Ba. YN. J3, using an integrated analysis of phenotypic, genomic, and comparative genomic data to uncover its biocontrol and plant growth-promoting (PGP) potential. Results The current findings indicate that Ba. YN. J3 possessed efficient PGP and biocontrol potential both in vitro and in planta . Additionally, Ba. YN. J3 showed broad-spectrum antifungal activity against six major phytopathogens and was found to produce multiple cell wall-degrading enzymes (CWDEs) and siderophores, significantly increasing the growth of several crop species and regulating defense enzymes in oats. The complete 4.06 Mb genome of Ba. YN. J3 contains numerous gene clusters encoding vital secondary metabolites (e.g., surfactin, fengycin), CWDEs, and proteins associated with PGP functions and chemotaxis. The genome also harbors a robust set of genes related to abiotic stress tolerance, suggesting its potential to survive and function effectively in challenging field environments. Furthermore, comparative genomic analysis revealed 830 strain-specific genes, including two unique gene families critically linked to chemotaxis (flagellar rod protein FlgC) and nitrogen fixation (regulatory protein YutI). Conclusions This integrated study elucidates the potent dual function of Ba. YN. J3 and its unique genetic determinants. The flgC and yutI gene families, in particular, offer novel insights into the molecular basis of its targeted antagonism and nutritional self-sufficiency. Hence, the current findings highlight Ba. YN. J3 as a promising candidate for the development of effective biopesticides and biofertilizers.