Partial organic fertilizer substitution and water-saving irrigation can reduce greenhouse gas emissions in aromatic rice paddy by regulating soil microorganisms while increasing yield and aroma

As the global leader in rice production, China's paddy fields contribute substantially to greenhouse gas emissions through methane (CH₄) and nitrous oxide (N₂O) releases. Aromatic rice cultivation practices have been optimized to enhance the aroma, so the relationship between its cultivation and greenhouse gas emissions from paddy fields is unclear. To investigate how aroma-enhancing cultivation practices drive microbial community dynamics in aromatic rice paddies and their implications for greenhouse gas emissions, a two-year experiment in five ecological locations (Xingning, Nanxiong, Conghua, Luoding, and Zengcheng) compared two farming practices: partial organic substitution for inorganic fertilizers combined with water-saving irrigation (IOF+W) and traditional cultivation (CK). The CH₄ and N₂O emissions, soil microbial composition and function, global warming potential (GWP), nitrogen use efficiency, yield, and the content of 2-acetyl-1-pyrroline (2-AP) were measured and analyzed. The main purpose was to investigate the impact of IOF+W on CH₄ and N₂O emissions and their relationship with soil microorganisms. The results showed that IOF+W significantly reduced CH₄ emission fluxes and totals (36.95%) and GWP (31.29%), while significantly increasing N₂O emission fluxes and totals (14.82%). The soil microbial community structure was reshaped by the IOF+W treatment, which suppressed methanogens but enhanced the abundances of nitrifying and denitrifying bacteria. Key enzymatic activities involved in CH₄ production, such as methyl-coenzyme M reductase, formylmethanofuran dehydrogenase, and methyltransferase, decreased. In contrast, the activity of the key CH₄-oxidizing enzyme methanol dehydrogenase increased. This shift led to an overall attenuation of the CH₄ production metabolism while enhancing the CH₄ oxidation metabolism. In addition, the activities of pivotal enzymes involved in denitrification and nitrification were improved, thus enhancing nitrogen nitrification and denitrification metabolism. Moreover, the IOF+W treatment significantly increased nitrogen use efficiency (47.83%), yield (14.77%), and 2-AP content (13.78%). Therefore, the IOF+W treatment demonstrated good efficacy as a sustainable strategy for achieving productive, green, resource-efficient, and premium-quality aromatic rice cultivation in South China.