Soil organic nitrogen rather than fertilizer drives dinitrogen losses in flooded rice systems
- Yuanyuan Lei
- Zhijun Wei
- Kaiye Ye
- Kees Jan van Groenigen
- Yu Liu
- Hongna Cui
- Klaus Butterbach-Bahl
- Pete Smith
- Deli Chen
- Shu Kee Lam
- William R. Horwath
- Wulf Amelung
- Chaopu Ti
- Wei Zhou
- Jingrui Yang
- Hongbo He
- Xudong Zhang
- Sheng Zhou
- Xiaoyuan Yan
- Longlong Xia
2026-04-22
Rice production underpins food security but relies heavily on nitrogen (N) fertilization, much of which is lost as gaseous emissions. Dinitrogen (N 2 ) represents the largest N loss, yet its sources remain poorly constrained because biological dinitrogen (N 2 ) fluxes are difficult to quantify against the atmospheric background. Here, we apply an in situ 15 N tracing–membrane inlet mass spectrometry ( 15 N–MIMS) technique to simultaneously measure N 2 , ammonia (NH 3 ), and nitrous oxide (N 2 O) emissions and partition their soil- versus fertilizer-derived origins across the growing season in conventional japonica rice and hybrid rice. We find that soil organic N (SON) accounts for most N 2 emissions (72 to 75%), overturning the prevailing assumption that fertilizer dominates this loss pathway, which is independently confirmed by a 14-y fertilization experiment. In contrast, NH 3 originates mainly from fertilizer (71 to 77%) and N 2 O derives from both sources in near-equal proportions. We identify a previously unrecognized “microbial N pump”, in which rapid microbial assimilation of fertilizer-derived ammonium (NH 4 + ) induces stoichiometric imbalance and stimulates SON mineralization, mobilizing soil-derived NH 4 + that ultimately fuels N 2 emissions, with depleted SON partially replenished through microbial N turnover. Neglecting SON contributions causes systematic overestimation of fertilizer-derived N 2 and NH 3 losses by ~35%. Hybrid rice increases yield by 59% and reduces yield-scaled gaseous N losses by 43% through enhanced fertilizer uptake and microbial N use efficiency. Together, these findings reveal an underappreciated pathway of fertilization-driven soil N losses, revise N budgets for flooded rice systems, and demonstrate that cultivar-informed management can simultaneously enhance rice productivity and environmental sustainability.