A long-term field experiment was carried out (since 2008) for evaluating the effects of different substitution rates of inorganic nitrogen (N) fertilizer by green manure (GM) on yield stability and N balance under double rice cropping system. Treatments included, (1) N0 (no N fertilizer and no green manure); (2) N100 (recommended rate of N fertilizer and no green manure); (3) N100-M (recommended rate of N fertilizer and green manure); (4) N80-M (80% of recommended N fertilizer and green manure); (5) N60-M (60% of recommended N fertilizer and green manure); and (6) M (green manure without N fertilization). Results showed that, among all treatments, annual crop yield under N80-M treatment was highest. Crop yield did not show significant differences between N100-M and N80-M treatments. Substitution of different N fertilizer rates by GM reduced the yield variability index. Compared to the N0 treatment, yield variability index of early rice under N100-M, N80-M, and N60-M treatments was decreased by 11%, 26%, and 36%, respectively. Compared to the N0 treatment, yield variability index of late rice was decreased by 12%, 38%, 49%, 47%, and 24% under the N100, N100-M, N80-M, N60-M, and M treatments, respectively. During period of 2009–2013 and 2014–2018, nitrogen recovery efficiency (NRE) was highest under N80-M treatment and N balance was highest under N100 treatment. NRE of all treatments with GM was increased over the time from 2009–2013 to 2014–2018. All treatments with GM showed increasing trend of SOC over the years. Substitution of N fertilizer by GM also increased C inputs and soil C:N ratio compared to the N100 and N0 treatments. Boosted regression model indicated that C input, N uptake and AN were most influencing factors of crop yield. Thus, we concluded that N fertilization rates should be reduced by 20% under GM rotation to attain high yield stability of double rice cropping system through increasing NRE and C inputs.
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