The climate-driven acceleration of forest disease outbreaks has intensified the demand for sustainable biocontrol strategies. In this study, we evaluated the effects of the endophytic bacterium Bacillus amyloliquefaciens csuftcsp75 on soil properties, microbial communities, and functional metabolism in soils affected by Pinus massoniana shoot blight. Soil physicochemical analysis, carbon substrate utilization profiling (AWCD), and diversity indices (the Shannon, Simpson, and McIntosh indices) were integrated to assess the microbial responses under different inoculation treatments. The csuftcsp75 treatment significantly improved soil nutrient availability—especially available phosphorus and potassium—and was associated with enhanced microbial metabolic activity and sustained functional diversity. Principal component analysis and correlation mapping revealed strong associations between labile nutrients and microbial responses. Comparative analysis showed that csuftcsp75 promoted a balanced and metabolically rich microbial community, while less compatible strains exhibited transient or unstable effects. These findings support a dual-pathway model wherein nutrient-driven metabolic activation and ecological integration jointly determine biocontrol efficacy. This study highlights the importance of matching microbial inoculants with local soil environments to optimize functional outcomes. This work provides a theoretical basis for applying endophytic Bacillus in forest disease management and contributes to the development of ecologically coherent biocontrol strategies.

Background/Objectives: Plant growth-promoting rhizobacteria (PGPR), particularly Bacillus spp., are pivotal in enhancing plant defense mechanisms against pathogens. This study aims to investigate the metabolic reprogramming of pine needles induced by Bacillus csuftcsp75 in response to the pathogen Diplodia pinea P9, evaluating its potential as a sustainable biocontrol agent. Methods: Using liquid chromatography–mass spectrometry (LC-MS/MS), we performed a principal component analysis and a cluster analysis to assess the metabolic alterations in treated versus control groups. This study focused on specific metabolites associated with plant defense. Results: Our findings indicate that treatment with Bacillus csuftcsp75 significantly modifies the metabolic profiles of pine needles, leading to notable increases in metabolites associated with flavonoid biosynthesis, particularly phenylpropanoid metabolism, as well as amino acid metabolism pathways. These metabolic changes indicate enhanced systemic acquired resistance (SAR) and induced systemic resistance (ISR), with treated plants exhibiting elevated levels of defense-related compounds such as 5-hydroxytryptophol and oleanolic acid. Conclusions: This study reveals that Bacillus csuftcsp75 enhances defense against pathogen P9 by modulating pine needle metabolism and activating key immune pathways, inducing systemic acquired resistance and induced systemic resistance, offering a natural alternative to chemical pesticides in sustainable agriculture.