Comparative Analysis of the Effects of Crude Metabolic Extracts of Three Biocontrol Bacteria on Microbial Community Structure Provides a New Strategy for the Biological Control of Apple Replant Disease

The crude metabolic extract from plant biocontrol bacteria plays a very important role in sustainable agricultural production. These extracts help maintain healthy plants and have very important application prospects in biotechnology related to alleviating apple replant disease (ARD). In this study, Bacillus velezensis XC1 (T1), Bacillus amyloliquefaciens QSB-6 (T2), and Lactobacillus reuteri LBR (T3) were examined to characterize the ability of their crude metabolic extracts to alleviate ARD. The high-throughput sequencing data of the soil microbial community structure were analyzed in relation to LBR crude metabolic extracts, and an extensive untargeted metabolomic analysis of UHPLC-Qex active components was performed. Active LC-MS/MS revealed that the main secondary metabolites involved in the biological control exerted by L. reuteri included 3-hydroxypropionaldehyde, extracellular polysaccharides (EPS), p-hydroxybenzoic acid, and azelaic acid. These crude metabolic extracts significantly inhibited the growth of soil pathogenic fungi, reduced the abundance of Fusarium, promoted the abundance of beneficial bacteria such as Pseudomonas, and optimized the soil microbial community structure. Improved modern extraction and purification technologies will be able to offer additional insights into the mechanism of action of these secondary metabolites and enable them to be used in biological preparations to prevent and control ARD in the future, as well as to allow harmful chemical fumigants to be discontinued.