Long-term use of organic and inorganic fertilizers can have a negative impact on greenhouse gas (GHG) emissions and nutrient stoichiometry in paddy soil. However, production of sufficient crops to meet food and feed demands globally requires the use of fertilizer in crop production. In the present study, we assessed the environmental impacts of five fertilizer treatments in a rice–rice–fallow cropping system: no fertilizer (CK); inorganic nitrogen, phosphorus, and potassium fertilizers (NPK); manure (M); inorganic phosphorus and potassium fertilizers with manure (PKM); and inorganic nitrogen, phosphorus, and potassium fertilizers with manure (NPKM). Soil parameters were analyzed to examine the relationships between GHG emissions, net ecosystem carbon budgets (NECBs), and soil nutrient stoichiometric ratios. Both the PKM and NPKM treatments increased grain yield and the soil carbon–nitrogen (C:N), carbon–phosphorus (C:P), and nitrogen–phosphorus (N:P) ratios compared to the CK treatment; they also decreased the nitrogen–potassium (N:K) ratio. In the combined fertilization treatments, the fallow season accounted for 9–13% of annual methane (CH4) emissions, whereas early rice accounted for 55–62 % and late rice contributed 38–45 %. Compared to the CK, PKM and NPKM fertilization increased the annual nitrous oxide (N2O) emissions by 52–73 % and 103–115 %, respectively, in both the rice and fallow seasons. In early rice, the C:P ratio and GHG intensity (GHGI) were negatively correlated with CH4 and N2O emissions, whereas both yield and CH4 emissions had strong positive associations with global warming potential (GWP). In the late rice season, GHGI was negatively correlated with carbon dioxide (CO2) and CH4 emissions, and N2O had strong positive associations with GWP. CO2 and N2O emission levels were greater from late rice than from early rice, although CH4 emissions from early rice contributed more to the annual GWP, resulting in higher carbon equivalent emissions but a lower carbon efficiency ratio in early rice output. A Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) optimization analysis suggested that PKM was the best fertilization method to improve yield while minimizing negative environmental impacts, followed in descending order by the NPKM, NPK, and M treatments.
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