Soil organic nitrogen rather than fertilizer drives dinitrogen losses in flooded rice systems

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. ... mehrNeglecting 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.