Effects of Organic Fertilizer Type and Application Rate on Soil–Microbe Interactions, Yield, and Quality of Greenhouse Tomato

Soil nutrient imbalance and the decline of microbial diversity threaten the long-term sustainability of crop production in intensive agriculture. Organic fertilizers provide a promising means to improve soil-microbe-plant interactions, yet the combined effects of fertilizer type and application rate on soil function and crop productivity remain insufficiently understood. In this study, we investigated the agronomic and ecological responses of greenhouse tomato (<i>Solanum lycopersicum</i> L.) to three organic fertilizers-bone calcium fertilizer (BCF), bone mud fertilizer (BMF), and bio-organic fertilizer (BOF)-each applied at four rates (7500, 15,000, 30,000, and 45,000 kg·ha^-1). The highest tested BOF rate (45,000 kg·ha^-1) significantly increased net photosynthesis by 29.5%, stomatal conductance by 50.0%, and fruit yield by 40.8% compared with the unfertilized control. It also enhanced soil organic matter by 42.6% and total nitrogen by 82.0%, while increasing the relative abundance of Proteobacteria, a phylum closely associated with nutrient cycling and plant growth promotion. Network and path modeling revealed that changes in microbial diversity were positively associated with improved soil properties, which were subsequently linked to higher photosynthetic efficiency and yield formation, suggesting a potential microbiome-mediated pathway from fertilization to productivity. These effects were statistically consistent across measured endpoints. Our findings highlight that optimizing both the type and rate of organic fertilizer-particularly bio-organic fertilizer under greenhouse conditions-can enhance soil fertility, microbial function, and crop yield simultaneously. This study provides an evidence-based framework for precision fertilization strategies aimed at improving agroecosystem resilience and advancing sustainable tomato production.