Long-Term Green Manure Incorporation with Reduced Chemical Fertilizer Enhances Soil Quality and Rice Yield by Altering Soil Microbial Communities’ Structure and Functions in Paddy Soils

Excessive use of chemical fertilizers degrades soil health and threatens sustainable crop production, which can be mitigated by partially substituting chemical fertilizers with Chinese milk vetch (Astragalus sinicus L., MV, as green manure). However, the mechanisms through which MV incorporation alters soil microbial community structure and function, enhances soil quality and crop productivity, as well as its long-term effects in paddy soils, are still not fully understood. In this study, we investigated the responses of soil physical, chemical, and biological properties (to comprehensively evaluate soil quality); microbial community structure and function; rice productivity; and the sustainable yield index (SYI) to five fertilizer treatments based on a 13-year field experiment in a paddy’s soil in Henan, China. The treatments included: CK (no chemical fertilizer and no MV), F100 (100% chemical fertilizer), MVF80, MVF60 and MVF40 (80%, 60%, and 40% of the chemical fertilizer rate combined with MV, respectively). Compared with the F100 treatment, MVF60 slightly increased rice yield by 1.71% and significantly improved SYI by 5.10%. All MV treatments significantly increased soil organic carbon (SOC, by 14.4–16.3%) and microbial biomass carbon (MBC, by 16.7–20.1%). MVF60 and MVF40 significantly reduced bulk density, and increased macroaggregate content and mean weight diameter (MWD). MVF80 significantly enriched soil total phosphorus (TP), total potassium (TK), mineral nitrogen (Nmin), and urease (UE). The improvement in these soil properties resulted in a marked increase (by 11.6–20.1%) in the soil quality index (SQI) under all MV treatments. Random forest analysis identified MBC and Nmin as the most important predictors of SQI. Moreover, MV incorporation increased the relative abundance of beneficial taxa (Firmicutes, Clostridium_sensu_stricto_1, Bradyrhizobium, and Nigrospora), which were positively correlated with SQI (p < 0.05), while reducing the relative abundance of pathogenic fungal genera such as Fusarium. Furthermore, regression analysis revealed strong positive correlations between SQI and both rice yield and SYI. In summary, long-term MV incorporation with a 40% reduction in chemical fertilizer (MVF60) constitutes an effective and sustainable nutrient management approach for rice production in southern China. This practice enhances soil quality through improved physical structure, nutrient cycling, and microbial community structure and function, ultimately resulting in higher and more stable yields.