Co-application of alternate wetting and drying irrigation and Bacillus subtilis increases yield and reduces N2O emissions in paddy ecosystem

Alternate wetting and drying irrigation (WD) is an effective water-saving practice for rice production but often increases nitrous oxide (N 2 O) emissions. Plant growth-promoting bacteria such as Bacillus subtilis (BS) can enhance crop growth; however, the combined effects of WD and BS on rice yield and N 2 O emissions remain unclear. A 3-year field experiment using two japonica rice cultivars was conducted to evaluate the effects of two irrigation regimes (continuous flooding (CF) and WD) and Bacillus subtilis (BS) application (without BS, -BS; and with BS, +BS) on rice yield and N 2 O emissions. Results showed that BS application significantly increased rice yield under both irrigation regimes. Compared with CF-BS, CF+BS and WD+BS increased yield by 3.4-6.0% and 5.8-12.7%, respectively, mainly due to a higher total spikelet number. CF+BS had no significant effect on N 2 O emissions, whereas WD-BS markedly increased cumulative N 2 O emissions, while WD+BS reduced emissions by 30.0-41.0% compared with WD-BS. The WD+BS treatment enhanced root oxidation activity and increased root surface area and volume density in the 20–40 cm soil layer. It also decreased soil NO 3 - -N content, raised the NH 4 + /NO 3 - ratio, and enhanced urease and sucrase activities, thereby promoting the accumulation of dissolved organic carbon (DOC) and microbial biomass nitrogen (MBN), along with a higher abundance of the nitrous oxide reductase gene ( nosZ ) associated with N 2 O reduction. Overall, integrating WD with BS increased rice yield while mitigating N 2 O emissions. Enhanced root function, and aboveground agronomic traits, improved soil enzyme activity, and optimized nitrogen transformation and microbial processes were the key mechanisms achieving high yield with reduced environmental impact.