Bacillus subtilis KC Improves Pepper Productivity and Modulates the Rhizosphere Microbiome Under Integrated Fertilization

Pepper (Capsicum annuum L.) is a lucrative crop, but problems arise when it is cultivated intensively, such as soil-borne disease outbreaks, excessive chemical fertilization, and soil degradation, reducing pepper’s yield and quality. Here, we experimentally investigated how the biocontrol agent Bacillus subtilis affects pepper growth, disease incidence, fruit quality, soil physicochemical properties, and its rhizosphere microbial community. In plate confrontation assays, this strain has a strong antagonistic effect against Phytophthora capsici, a major plant pathogenic oomycete causing pepper blight, inhibiting its mycelial growth by 56%. Field experiments show that, compared with the fertilizer control group (CF+OF), adding a biocontrol agent (CF+OF+KC) significantly reduces disease incidence, to 3% (a 85.7% reduction). Notably, the activity of systematic host defense enzymes (PAL, PPO) was negatively associated with disease incidence. In response, pepper yield increased by 17%, while its vitamin C content—a key fruit quality indicator—was greatly enhanced, by 55.1%. In terms of microbial community composition, the biocontrol agent-treated group had increased relative abundances of specific bacterial taxa, such as Lactobacillus, Sphingomonas, and Kosakonia, with less-abundant fungal genera, namely Pseudeurotium, Wardomyces, and Fusarium. The abundance of specific bacterial taxa, such as Lactobacillus, was positively associated with pepper fruit’s vitamin C content and soil available nitrogen. Inferred functional profiling suggested that biocontrol agent treatment was associated with an enrichment of microbial growth- and metabolism-related pathways while reducing the predicted abundance of pathogen-associated virulence pathways. Collectively, these findings provide a theoretical framework and technical basis for leveraging beneficial microbial inoculants in eco-friendly pepper cultivation, contributing to its future sustainability.