Multi-omics integration to elucidate the antibacterial mechanism of Streptomyces sp. strain PBSH9

Potato common scab, incited by pathogenic Streptomyces species, poses a significant threat to agriculture. The biocontrol agent Streptomyces sp. strain PBSH9 has shown remarkable field efficacy, yet its underlying antibacterial mechanisms remain unclear. To bridge this knowledge gap, we employed an integrated transcriptomic, proteomic, and metabolomic approach to compare PBSH9 under high (8-day) and low (2-day) antibacterial activity conditions. Transcriptomics identified 2,653 differentially expressed genes (DEGs), primarily enriched in oxidative phosphorylation and β-lactam resistance pathways. Proteomics quantified 32 differentially abundant proteins (DAPs), which were also predominantly involved in energy metabolism. Critically, metabolomic profiling of 1,299 differential metabolites (DAMs) revealed the core of the antibacterial activity: a massive > 28-fold accumulation of the antibiotics L-anticapsin and bacilysin, coupled with a significant 1.08- to 2.85-fold increase in several aminoglycoside antibiotics, including neomycin B and kanamycin. This enhanced antibiotic production was supported by the systematic upregulation of energy metabolism pathways, such as oxidative phosphorylation and the TCA cycle. Multi-dimensional correlation networks linked antibiotic accumulation to DEGs (st, phzF) and DAPs. Our findings demonstrate that the potent biocontrol activity of PBSH9 stems from a metabolic reprogramming that fuels the synergistic accumulation of a diverse antibiotic arsenal. This study provides a comprehensive molecular blueprint for optimizing and engineering this promising biocontrol strain.