Organic Nitrogen Substitution Enhances Carbon Sequestration but Increases Greenhouse Gas Emissions in Maize Cropping Systems

Excessive chemical fertilizers degrade soil and increase greenhouse gas (GHG) emissions. Organic substitution of nitrogen fertilizers is recognized as a sustainable agricultural-management practice, yet its dual role in carbon sequestration and emissions renders the net GHG balance (NGHGB) uncertain. To assess the GHG mitigation potential of organic substitution strategies, this study analyzed GHG fluxes, soil organic carbon (SOC) dynamics, indirect GHG emissions, and Net Primary Productivity (NPP) based on a long-term field positioning experiment initiated in 2016. Six fertilizer regimes were systematically compared: no fertilizer control (CK); only phosphorus and potassium fertilizer (PK); total chemical fertilizer (NPK); 1/3 chemical N substituted with sheep manure (OF1); dual substitution protocol with 1/6 chemical N substituted by sheep manure and 1/6 substituted by straw-derived N (OF2); complete chemical N substitution with sheep manure (OF3). The results showed that OF1 and OF2 maintained crop yields similar to those under NPK, whereas OF3 reduced yield by over 10%; relative to NPK, OF1, OF2, and OF3 significantly increased SOC sequestration rates by 50.70–149.20%, reduced CH₄ uptake by 7.9–70.63%, increased CO₂ emissions by 1.4–23.9%, decreased N₂O fluxes by 3.6–56.2%, and mitigated indirect GHG emissions from farm inputs by 24.02–63.95%. The NGHGB was highest under OF1, 9.44–23.99% greater than under NPK. These findings demonstrate that partial organic substitution increased carbon sequestration, maintained crop yields, whereas high substitution rates increase the risk of carbon emissions. The study results indicate that substituting 1/3 of chemical nitrogen with sheep manure in maize cropping systems represents an effective fertilizer management approach to simultaneously balance productivity and ecological sustainability.