This is the first-time work to integrate transcriptome and metabolome sequencing data, providing a comprehensive knowledge of how the pathogen Armillaria solidipes affects the spore development, biofilm creation, and antifungal activity of Bacillus velezensis BY6. The dynamic growth of BY6 indicated that A. solidipes had a significant growth-inhibiting effect on BY6. Using scanning electron microscopy (SEM), it was discovered that the cell wall and cell membrane was compromised, resulting in the leakage of intracellular components. On the basis of gene and metabolite network analysis, several genes and metabolites are predominantly involved in the " Phosphotransferase system (PTS)", "Two-component system", and "Ubiquinone and other terpenoid-quinone biosynthesis" pathway. The mechanism by which A. solidipes inhibits the biological control ability of BY6 is influenced by numerous factors, including cell membrane damage (Folding, disintegration, disappearance), nutrient limitation (Pyruvic acid, Menadione concentration down-regulated), and spore and biofilm formation inhibition (Spo0 A, Spo0 B and Kin B ∼ D genes down-regulated). We conclude that interference of A. solidipes with the growth and development of BY6 results in a decrease in BY6 biocontrol levels. This result contributes to a complete and thorough understanding of the mechanism by which A. solidipes inhibits BY6′s biocontrol ability and identifies additional potential molecular targets. To further genetically modify the BY6 strains for tackle the problem of drug resistance.
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