Paddy fields are important anthropogenic emission sources of methane (CH4). However, it is not clear how rice root development and rhizosphere soil properties affect CH4 emissions. Therefore, we selected rice varieties with similar growth periods but different root traits in the local area. We measured CH4 emission fluxes, cumulative CH4 emissions, root dry weight, root length, and the dissolved organic carbon (DOC), microbial biomass carbon (MBC), redox potential (Eh), ammonium nitrogen (NH4+–N), and nitrate nitrogen (NO3−–N) contents in rhizosphere soil. Methanogens and methanotrophs are crucial factors influencing CH4 emissions; thus, their abundance and community composition were also assessed. The result showed that CH4 fluxes of each rice variety reached the peak at tillering stage and jointing-booting stage. The CH4 emissions in tillering stage were the largest in each growth period. CH4 emissions had negative correlations with root length, root dry weight, Eh NO3−–N, methanotroph abundance, and the pmoA/mcrA ratio, and positive correlations with NH4+–N, MBC, DOC, and methanogen abundance. Path analysis confirmed methanogens and methanotrophs as direct influences on CH4 emissions. Root development and rhizosphere soil properties affect CH4 emissions indirectly through these microbes. This study suggests that choosing rice varieties with good root systems and managing the rhizosphere soil can effectively reduce CH4 emissions.
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