In recent years, anthropogenic activities have increased nitrogen (N) input into terrestrial ecosystems, profoundly impacting soil organic carbon (SOC) sequestration. However, the potential mechanisms through which N affects mineral-associated organic carbon (MAOC) and particulate organic carbon (POC) remain unclear. To address this gap, we conducted a 12-year field trial applying continuous N application (0, 90, 180, 270, and 360 kg N·ha−1) in a maize agro-ecosystem. We assessed plant biomass (yield, straw, and root biomass), microbial properties (enzyme activity, biomass, and diversity), soil chemistry (pH, N availability, and base ions), mineralogy (oxides and silicates), and SOC fractions to elucidate the primary control mechanisms influencing MAOC and POC. Our findings showed that N application increased SOC and POC by 6.56%–10.4% and 43.1%–54.0%, respectively, but decreased MAOC by 7.31%–17.1%. And N application increased plant biomass, but decreased soil pH (pH from 6.7 to 5.6), base ion concentrations (K⁺, Na⁺, Ca2⁺, Mg2⁺), amorphous oxides, and illite content. Partial least squares path model (PLS-PM) and correlation analyses indicated that N application enhances root biomass while increasing microbial decomposition, and ultimately their combined effect increased POC. The decline in MAOC is primarily attributed to soil acidification decreasing the C input from microbial residues, altering mineral composition and diminishing the minerals' capacity to protect SOC. Thus, our study demonstrates that N addition predominantly increases POC through enhanced root biomass, while reducing MAOC by decreasing microbial biomass and weakening mineral protection. These insights provide a deeper understanding of the mechanisms governing SOC fraction dynamics in answer to N inputs in agroecosystems.
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