Multifaceted antifungal mechanisms of volatile organic compounds emitted from <i>Pseudomonas chlororaphis</i> ZL3 against <i>Botrytis cinerea</i>

To develop an effective approach to inhibit <i>Botrytis cinerea</i>, a new biocontrol strain, <i>Pseudomonas chlororaphis</i> ZL3, was screened and exhibited excellent biocontrol potential. Nevertheless, the antifungal mechanism of <i>P. chlororaphis</i> volatile organic compounds (VOCs) against <i>B. cinerea</i> is still unclear. In this study, VOCs emitted from <i>P. chlororaphis</i> ZL3 were found to have potent inhibitory effects on mycelium growth, conidia germination, and sclerotium formation. Subsequently, the antifungal mechanism was revealed via the biophysical, transcriptomic, and metabolomic analysis. Compared to the control groups, the relative conductivities increased dramatically, while the ergosterol content decreased sharply, determining that VOCs could enhance cell membrane permeability and destroy cell membrane integrity. Additionally, VOCs could also inhibit ATPase activity and reduce reactive oxygen species (ROS) accumulation, thereby adversely interfering with energy metabolism. The superoxide dismutase (SOD) and catalase (CAT) activities were significantly reduced in <i>B. cinerea</i> mycelia, presenting the impairment of the antioxidant defense mechanism. Furthermore, most of the differential expression genes (DEGs) were involved in lipid metabolism, membrane transport, energy production, and conversion, indicating that the VOCs might affect the structure and function of cell membranes and energy metabolism. The differential metabolites were mainly involved in the alteration of amino acid metabolism and lipid metabolism. Together, these findings provide valuable insights into the molecular responses of <i>B. cinerea</i> to <i>P. chlororaphis</i> ZL3 VOCs and support the potential development of novel biological fumigants.IMPORTANCEBiological control is a sustainable alternative way for the control of gray mold. The volatile organic compounds emitted from <i>Pseudomonas chlororaphis</i> ZL3 had high inhibitory activity against <i>Botrytis cinerea</i>, but the antifungal mechanism is largely unknown. This study attempted to interpret the comprehensive antifungal mechanism, providing a theoretical foundation for the application of volatile organic compound (VOC)-mediated biological fumigants in the future.