Fertilization enhances rice productivity by promoting phosphorus uptake and altering soil microbiota

Fertilization can enhance crop yield and improve soil health. However, its effects on nutrient uptake, soil microbiota, and rice yield remain unclear. Herein, we designed a double-cropping system with different fertilization treatments to determine their contributions to paddy soil agroecosystem and rice yield. Soil samples were collected before planting the early rice, after harvesting early rice, and after harvesting the late rice. Soil physicochemical properties, and rice yield, and rice nutrient (total nitrogen, phosphorus, and potassium contents) were determined. Variation of soil microbiota were also determined by high-throughput sequencing. We found that soil potassium content significantly improved during the planting process (P < 0.05), while rice phosphorus displayed significant variation under fertilization (P < 0.05). Notably, late rice yield was significantly higher than early rice yield (P < 0.001) after fertilization treatment. Furthermore, rice yield was positively correlated with available soil phosphorus (P < 0.05), indicating that fertilization promoted phosphorus uptake. Organic fertilizer altered the soil microbiota and increased Chloroflexi phyla abundance, while organic fertilizer combined with a compound microbial agent increased the diversity of soil microbial communities. A partial least squares path model revealed that fertilizer treatment directly positively affected rice yield by influencing phosphorus uptake and Shannon index (P < 0.01). Collectively, this study demonstrates that organic fertilization with compound microbial agents can stabilize soil nutrients, increase soil microbial diversity, and improve rice yield, thereby offering a guide for enhancing fertilizer utilization and improving agroecosystems.