Comparative transcriptome analysis reveals defense mechanisms of Bacillus velezensis ZY1 against bacterial fruit blotch in watermelon

Watermelon ( Citrullus lanatus ) is a globally important horticultural crop, yet its production is severely constrained by bacterial fruit blotch (BFB), a destructive disease caused by Acidovorax citrulli . This study investigates the biocontrol potential of Bacillus velezensis ZY1 in promoting watermelon growth and suppressing BFB. The results demonstrate that B. velezensis ZY1 effectively inhibits A. citrulli proliferation while enhancing plant immunity by upregulating defense-related genes and increasing the activities of key defense enzymes, including superoxide dismutase, polyphenol oxidase, catalase, peroxidase, β-1,3-glucanase, chitinase, and lipoxygenase. To elucidate the molecular mechanisms underlying B. velezensis ZY1-mediated biocontrol, it was conducted a comparative transcriptome analysis of watermelon true leaves treated with B. velezensis ZY1 versus a sterile water control. Transcriptome sequencing identified 1688 up-regulated and 479 down-regulated genes in plants exposed to B. velezensis ZY1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses revealed significant activation of transcription factors and disease resistance genes, which were further validated by quantitative retrotranscripted PCR. Differential expression analysis indicated that B. velezensis ZY1 modulates the mitogen-activated protein kinase (MAPK) and plant hormone signaling pathways, enhancing plant resistance to pathogens. This study expands transcriptomic resources and provides a molecular framework for understanding B. velezensis ZY1-induced systemic resistance against BFB, offering an effective strategy for controlling A. citrulli . • Bacillus velezensis ZY1 inhibited the plant pathogens and controlled bacterial fruit blotch. • Bacillus velezensis ZY1 can enhance the activity of defense enzymes in watermelon and watermelon resistance to pathogens. • Bacillus velezensis ZY1 induces the expression of hormone-related genes in watermelon and upregulates the genes in the MAPK signaling pathway.