Biocontrol of citrus melanose Diaporthe citri by Bacillus subtilis M23

•M23 inhibits the growth of the citrus melanose pathogen Diaporthe citri.•M23 possesses lipopeptide biosynthesis genes.•Lipopeptide extracts of M23 impair fungal development in D. citri.•M23 has potential as a biocontrol agent against D. citri. Citrus melanose, caused by Diaporthe citri, is one of the most prevalent and important fungal diseases of citrus crops globally. However, the overuse of chemical fungicides for disease control has an adverse impact on citrus production. In contrast, biological control agents (BCAs) are environmentally friendly and have become essential tools for plant disease control. In the present study, Bacillus subtilis M23, a strain isolated from healthy citrus leaves, significantly suppressed the mycelial growth of D. citri, the causal agent of citrus melanose, in vitro. The fermentation broth of B. subtilis M23 also exhibited good antifungal activity against D. citri on citrus plants in greenhouse and field experiments. Lipopeptides (LPs) produced by M23 exhibited excellent antifungal activity against D. citri, with a 50 % effective concentration (EC50) of approximately 1.00 and 0.28 μg/mL for inhibition of mycelial growth and conidial germination, respectively. LP biosynthesis genes were identified in the M23 genome using a PCR assay. Notably, LP extracts significantly reduced the formation of pycnidia and ATP biosynthesis in D. citri. Comparative transcriptome analysis revealed significant differences in the expression of genes associated with fungal vacuole, oxidoreductase activity and endopeptidase activity in D. citri treated with B. subtilis M23. Both RNA-seq and RT-qPCR analysis provided similar results on the expression of selected genes. Collectively, our data provided convincing data supporting the biocontrol potential of B. subtilis M23 for the management of citrus melanose.