The development of low-carbon, water-efficient rice cultivation systems is crucial for sustainable agriculture. Nevertheless, although alternate wet-dry irrigation (IAWD) can save water and promote the mineralization of soil organic nitrogen (N), it may reduce soil organic carbon (SOC) sequestration and increase ammonia (NH3) volatilization. To address this trade-off, a magnesium–modified biochar–based fertilizer (MBF) was applied to optimize biochar’s inherently high C:N ratio while enable controlled nitrogen release. A two-year field split-plot experiment was conducted to evaluate the effects of two irrigation regimes (main plots) and five fertilization practices (subplots) on SOC, soil inorganic N, water–N use efficiency, yield, and NH3 emissions. Results showed that IAWD combined with N fertilizer reduction and MBF enhanced stem/leaf-to-grain N translocation through the modulation of crop growth rates, increasing yield and grain N use efficiency (NUEg). Correlation analysis demonstrated that higher soil NH4+ –N suppressed SOC priming, while reduced NH4+–N during basal fertilization and increased SOC limited NH3 emissions and improved water use efficiency (WUE). Structural equation modeling indicated NH3 emissions directly reduced NUE and indirectly affected WUE. Compared with conventional fertilization, the treatment of 25 % N reduction combined with 10 t ha⁻1 MBF (N3/4B2) increased SOC by 14.40 %, optimized NH4+–N distribution (reduction during basal fertilization but enhancement during topdressing periods), reduced NH₃ emissions by 10.78 %, and increased yield by 4.82 % and WUE by 10.86 % (two–year averages). Thus, TOPSIS modeling confirmed IAWDN3/4B2 as a sustainable strategy integrating water-saving, yield stability, carbon sequestration, and NH3 mitigation.
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