Biomass Seedling Trays Drive Rhizosphere Microbiome Restructuring and PGPR Enrichment in Tomato

Tomato (Solanum lycopersicum) is a globally important high-value cash crop. However, long-term continuous cropping causes frequent soil-borne diseases and soil microecological imbalance, while overreliance on chemical pesticides leads to pesticide residues and water eutrophication. Plant growth-promoting rhizobacteria (PGPR) are key resources for addressing tomato cultivation challenges, with their functions partly depending on the rhizosphere microenvironment inherently shaped by seedling tray materials. Using rhizosphere soil and substrates of tomato at different growth stages under biomass (BM) and plastic (PM) seedling tray treatments, this study combined culture-independent and culture-dependent techniques to analyze microbial community characteristics and screen high-efficiency PGPR. Results showed that pH and available nitrogen drove microbial community assembly. BM significantly enriched beneficial taxa (e.g., Trichoderma and Bacillus) and enhanced culturable microbial abundance and genetic diversity, while PM enriched potential pathogens (e.g., Fusarium and Pyrenochaeta). The multifunctional strain S25095 from BM, with phosphate-solubilizing, potassium-solubilizing, and indole-3-acetic acid (IAA)-producing abilities, significantly promoted tomato shoot and root growth, outperforming single-functional strains and synthetic consortia. This study reveals the effects of growth stages and seedling tray treatments on tomato rhizosphere microorganisms, providing valuable PGPR resources for tomato cultivation.