<i>Bacillus amyloliquefaciens</i> JK2 suppresses <i>Phytophthora capsici</i> via genetic information disruption and ROS modulation in pepper plants

<italic>Phytophthora capsici</italic>, a devastating soil-borne oomycete pathogen, poses a significant threat to global pepper production. Biocontrol using antagonistic bacteria offers a sustainable alternative to chemical fungicides. In this study, <italic>Bacillus amyloliquefaciens</italic> JK2, isolated from peach, exhibited 90.48% <italic>in vitro</italic> inhibition against <italic>P. capsici</italic>. Transcriptomic analysis identified 2,464 differentially expressed genes (DEGs) in <italic>P. capsici</italic> under JK2 co-culture, with downregulation in ribosome biogenesis and RNA polymerase pathways, and upregulation in fatty acid degradation and amino acid biosynthesis. These findings suggest that JK2 disrupts RNA synthesis and protein translation, thereby inhibiting the growth of pathogens. Pot experiments demonstrated that JK2 reduced disease incidence by 27.67%, and delayed hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) accumulation, while enhancing superoxide dismutase (SOD, 159.39%), peroxidase (POD, 93.37%), and catalase (CAT, 479.19%) activities in pepper plants. Our results highlight JK2's dual role in directly suppressing <italic>P. capsici</italic> and priming host antioxidant defenses, positioning it as a promising biocontrol agent for sustainable agriculture.