Distinct Response of Bacterial and Fungal Communities to Nitrogen Decrement and Green Manure Incorporation Under Slow-Release Nitrogen Fertilizer Application

Excessive nitrogen (N) fertilization in rice production causes severe environmental consequences, and slow-release N fertilizer and green manure incorporation have been proposed as a sustainable alternative. However, how such integrated practices impact the rhizosphere microbiome and its linkages to plant performance remains poorly understood. In a field experiment with slow-release N fertilizer application, we explored the effects of 20% N reduction (RND) and RND combined with green manure (RNDG) on rhizosphere soil properties, rice growth, and bacterial and fungal communities. Compared with normal N application (RN), RND treatment had negative effects on rice growth, while it can be mitigated by the RNDG treatment. Fungal communities were more sensitive to RND and RNDG treatments than bacterial communities. Specific functional groups, including bacteria involved in N transformation and plant pathogenic fungi, decreased under RND and RNDG treatments. Deterministic processes dominated community assembly for both bacterial and fungal communities; however, the deterministic contribution was strengthened for bacteria under RND and RNDG, whereas it was relaxed for fungi under RND treatment. Correlation analysis revealed that the bacterial community was primarily associated with soil ammonium and nitrate, whereas the fungal community was linked to available phosphorus and plant phosphorus. Overall, integrating green manure with a 20% N reduction effectively compensates for yield loss, enhances bacterial diversity, and reshapes the microbiome toward a more disease-suppressive state. These findings provide a microbial ecological basis for developing green and efficient fertilization strategies in paddy rice systems.