Water-saving irrigation practices in rice paddies reverse the impact of root aerenchyma on methane emissions

Rice root aerenchyma (RA) and irrigation practices influence key physiological processes in rice paddies, affecting both yield and methane (CH₄) emissions. However, the interaction between RA and irrigation practices, and its implications for CH₄ mitigation, remains unclear, making it difficult to identify rice cultivars for CH₄ mitigation purposes. Here, we conducted a series of field and pot experiments to evaluate how RA affects grain yield and CH₄ emissions under two common irrigation regimes: continuous flooding (CF) and alternate wetting and drying (AWD). Our results show that the interaction between RA and irrigation regime significantly influenced both rice yield and CH₄ emissions. Under CF, increased RA formation was associated with higher rice yield and lower CH₄ emissions across a wide range of cultivars. These results could be explained by cultivars with well-developed RA increasing root oxygen loss, thereby stimulating CH₄ oxidation and promoting N availability to support plant growth. In AWD systems, no significant differences in rice yield, methanogenesis or methanotrophy were observed between cultivars with varying RA development. However, cultivars with well-developed RA increased CH₄ emissions by 28 %−32 % compared to those with less-developed RA, likely due to enhanced CH₄ transport from anaerobic deep soil layers to the atmosphere. Consistent with these findings, CH₄ emissions under AWD decreased when we inhibited RA development through root irrigation with brassinosteroids. In conclusion, we demonstrate that AWD in paddies can reverse the impact of RA on CH₄ emissions, highlighting the need for CH₄ mitigation strategies involving cultivar selection to account for variations in irrigation practices.