Wei Quan, Chengzhong Zheng, Ayaz Muhammad, Hui Chen, Chunyang Wang, Chenlu Liu, Zhigang Liu, Bao-Zhu Dong, Hong-You Zhou
BACKGROUND: Endophytic bacteria serve as important resources for the development of novel biocontrol agents for sustainable agriculture. This 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 explore 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 potentially associated with chemotaxis (flagellar rod protein FlgC) and nitrogen metabolism and assimilation (regulatory protein YutI). CONCLUSIONS: This integrated study provides genomic insights into the dual function of Ba. YN.J3 and its unique genetic determinants. The flgC and yutI gene families, in particular, offer potential genomics insights into 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.