Unraveling the growth-promoting mechanisms of PGPR combined with organic fertilizer in bamboo shoots: Insights from rhizosphere microbial restructuring and metabolomic profiling

Excessive application of chemical fertilizers adversely affects soil health, while plant growth-promoting rhizobacteria (PGPR) have garnered increasing interest owing to their unique advantages. However, the mechanisms by which PGPR influence bamboo shoots growth remain poorly understood. In this study, fertilization treatments ( Bacillus amyloliquefaciens , Azotobacter chroococcum combined with organic fertilizer) were conducted in Chimonobambusa neopurpurea bamboo fields in southwestern China. By integrating yield measurements, rhizosphere multi-omics (16S/ITS sequencing and untargeted metabolomics), and microbe-metabolite association analysis, we investigated the underlying mechanisms. The results indicated that combining PGPR and organic fertilizer significantly increased bamboo shoot number, weight, and nutritional quality (amino acids and trace element content). Fertilization enhanced soil enzyme activities and the predicted cellulolysis functions, accelerating organic matter decomposition and nutrient release. Sequencing data showed decreased fungal diversity alongside bacterial α-diversity that did not change significantly, leading to a restructured rhizosphere community towards a robust, bacteria-dominated network driven by stochastic processes. Metabolomic profiling identified phytosphingosine (PS) as a core metabolite that increased following fertilization. PS exhibited negative correlations with several putative pathogenic taxa and positive correlations with key soil physicochemical attributes and nutrients. Partial Least Squares Path Modeling (PLSPM) suggested that PGPR enhance bamboo shoot growth through dual mechanisms: pathogen suppression and nutrient supply enhancement. This study represents the systematic investigation of the multi-scale growth-promoting pathways mediated by PGPR combined with organic fertilizer in bamboo, revealing a synergistic mechanism between plant growth and defense. These findings provide theoretical and technical foundations for the sustainable bamboo and crop production.