Transcriptomic and metabolomic analyses provide evidence on the biocontrol mechanism responsible for the inhibition of Botrytis cinerea and Alternaria alternata by Bacillus velezensis in kiwifruit

Botrytis cinerea and Alternaria alternata are major pre- and postharvest plant pathogens of kiwifruit and responsible for significant economic losses. Although synthetic fungicides are the main source of controlling these pathogens, their use can lead to pathogen resistance, pollution of the environment, and their residues on agricultural produce can represent a health risk to humans. Bacillus velezensis is an ecofriendly bacterium with biocontrol potential. The objectives of the present study were to determine the efficacy of B. velezensis against B. cinerea and A. alternata, both of which are pre- and postharvest pathogens of kiwifruit, and investigate the mechanisms responsible for its biocontrol activity using transcriptomic and metabolomic methodology. Dual cultures of B. velezensis and either B. cinerea or A. alternata versus single cultures were used to conduct a transcriptomic and metabolomic analyses to provide insight into the mechanism by which B. velezensis inhibits B. cinerea and A. alternata. A total of 2499 and 3248 differentially expressed genes (DEGs) were identified in the B. velezensis/B. cinerea and B. velezensis/A. alternata comparisons, respectively. Genes related to sporulation, virulence, and hydrolase activity were downregulated in B. cinerea and A. alternata. Genes associated with MAPK signaling and the TCA cycle were also downregulated. Our study provides new insights into mechanism underlying the inhibition of B. cinerea and A. alternata by B. velezensis. Our results also demonstrate the potential of B. velezensis as a biocontrol agent against these two major pathogens of kiwifruit.