Mechanistic Insights into the Differential Effects of Biochar and Organic Fertilizer on Nitrogen Loss Pathways in Vegetable Soils: Linking Soil Carbon, Aggregate Stability, and Denitrifying Microbes

Biochar and organic fertilizer applications are widely recognized as effective strategies for mitigating greenhouse gas emissions and controlling agricultural non-point source pollution in agroecosystems. However, the combined effects of these two approaches on greenhouse gas emissions and agricultural non-point source pollution remain insufficiently understood. Through consecutive field-based positioning plot trials, this study systematically examined the individual and combined effects of biochar and organic fertilizer amendments on N runoff loss (WTN) and gaseous emissions (N2O and NH3), N-cycling functional microbial communities, and soil physicochemical properties. Results demonstrated that conventional chemical fertilization resulted in 20.70% total N loss (4.48% gaseous emissions, 15.22% runoff losses). Biochar and organic fertilizer applications significantly reduced WTN losses by 8.06% and 7.43%, respectively, and decreased gaseous losses by 2.01% and 1.88%, while concurrently enhancing plant N uptake and soil residual N. Random forest analysis combined with partial least squares structural equation modeling revealed that soil organic carbon directly modulated nitrogen runoff losses and indirectly influenced aggregate stability and macroaggregate formation. Dissolved organic carbon (DOC) and recalcitrant organic carbon (ROC) exhibited dual regulatory effects on NH3 volatilization through both direct pathways and indirect mediation via aggregate stability. Notably, biochar and organic fertilizer amendments induced significant compositional shifts in nirS- and nirK-type denitrifying microbial communities. pH, cation exchange capacity (CEC), and iron oxide–carbon complexes (IOCS) were identified as key factors suppressing N2O emissions through inhibitory effects on Azoarcus and Bosea genera. Our findings demonstrate that biochar and organic fertilizers differentially modulate soil physicochemical properties and denitrifier community structure, with emission reduction disparities attributable to distinct mechanisms’ enhanced aggregate stability and modified denitrification potential through genus-level microbial community restructuring, particularly affecting Azoarcus and Bosea populations. This study offers valuable insights into the regulation of carbon sources for nitrogen management strategies within sustainable acidic soil vegetable production systems.