Sustained nitrogen release and nitrogen-cycling functional genes jointly shape NH3-N2O loss trade-offs under long-term controlled-release fertilization.

Simultaneously mitigating ammonia (NH3) volatilization and nitrous oxide (N2O) emissions without compromising crop productivity remains a critical challenge in sustainable nitrogen management. Drawing on a long-term field experiment established in 2013, this study integrated multi-year gaseous nitrogen loss measurements with metagenomic sequencing to assess the performance of polymer-coated fertilizer (PCF) and sulfur-coated fertilizer (SCF) relative to conventional urea (CU) in intensive maize production. Both coated urea treatments substantially suppressed NH3 losses relative to CU, with PCF achieving consistent reductions of 72.3%-92.8% and SCF showing more variable reductions of 28.8%-89.7%. However, sustained nitrogen release from coated urea concurrently stimulated N2O production, with increases of 8.3%-114.3% under PCF and 15.5%-88.9% under SCF. Critically, NH3 mitigation substantially outweighed the N2O penalty, enabling PCF to reduce the combined NH3 and N2O losses by 39.8%-69.5% and yield-scaled losses by 45.9%-70.9%, respectively, while enhancing crop yield by 4.7%-11.2%. Soil enzyme assays and metagenomic analyses suggested that NH3 suppression was associated with reduced urease activity and enrichment of archaeal ammonia oxidation and downstream nitrification genes under PCF, whereas elevated N2O emissions were correlated with sustained soil inorganic nitrogen replenishment that appeared to override concurrent declines in denitrification genes. These findings suggest that PCF reduces the combined NH3 and N2O losses while sustaining crop productivity, although the N2O penalty outweighed the climate benefit of NH3 mitigation in three of four years. The net environmental performance of controlled-release fertilizers therefore depends on the indicators evaluated and was associated with nitrogen release dynamics and the corresponding functional gene networks.