Bacillus velezensis enhances tomato seedling productivity by coordinating functional traits and substrate properties systematically

• Inoculation with Bacillus velezensis boosted substrate metabolism and nutrition. • Bacillus velezensis enhanced tomato seedling metabolism. • Simple PCA framework coordinated substrate and plant metabolic intensities. • Framework validated by tomato seedling reproductive rate. • Optimal tomato seedling productivity with both inoculation and nutrients, then inoculation alone. Developing greenhouse horticulture can contribute to ensuring food security. Seedlings and substrates are two critical factors, and producing high-quality seedlings by using renewable substrates rich in organic matter is appealing. While it is hard to mineralize nutrients from organic matter, adding plant growth-promoting rhizobacteria may be a good method. Therefore, in our study, with 5 × 10 10 CFU Bacillus methylotrophicus ( Ba ) inoculated, germinated tomato seeds were sown in 50-hole trays with substrates containing 30% organic carbon and low available nutrients. Nutrient solutions were supplied on the 15th, 20th, and 30th days after sowing. Four treatments were set up: control (CK), inoculation only (B), nutrients supplement only (NS), and both inoculation and nutrients supplement (B+NS). On the 30th day after sowing, the enhanced effects of Ba on improving nutrient availability in substrate and coordinating substrate properties and plant functional traits were verified by reproductive rate (leaf number), principal component analysis (PCA) was used to simply illustrate the coordination of them in a framework systematically. B or B+NS treatment significantly improved various aspects of tomato seedling growth compared to NS treatment. Specifically, B or B+NS raised organic carbon mineralization rate by 166.52% or 44.27%, activities of urease, sucrase and catalase by 355.56% or 305.56%, 215.29% or 287.56%, 10.90% or 15.55%, and root vigor by 104.53% or 15.10%, mass and total K accumulation by 36.63% or 56.10% and 49.99% or 66.56%, mass fraction allocated to the above-ground by 3.33% or 5.01%, and finally leaf number by 38.34% or 60.65%. Metabolic intensities of all organs (substrate) were the highest (second - highest) at B+NS treatment, and the second - highest (highest) at B treatment. Based on the plant carbon economics theory and correlations with reproductive rate, we provided a simple and effective method by two applications of PCA, established a framework coordinating substrate properties and functional traits of root, stem and leaf, with each component considered as a whole separately to calculate its metabolic intensity. This study contributes to the sustainable greenhouse horticulture and the understanding between environment and plant functional traits systematically.