Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil

•CH4 emissions were positively related to mcrA/pmoA.•Soil potassium, oxalate, acetate and succinate significantly affect dominant methanogens.•Organic fertilizer increased the relative abundance of acetoclastic Methanosaeta.•Organic fertilizer decreased the relative abundance of hydrogenotrophic Methanocella. [Display omitted] Paddy soil accounts for 10% of global atmospheric methane (CH4) emissions. Many types of fertilizers may enhance CH4 emissions, especially organic fertilizer. The aim of this study was to explore the effects of different fertilizers on CH4 and methanogen patterns in paddy soil. This experiment involved four treatments: chemical fertilizer (CT), organic fertilizer (OT), mixed with chemical and organic fertilizer (MT), and no fertilizer (ctrl). The three fertilization treatments were applied with total nitrogen at the same rate of 300 kg N ha−1. Paddy CH4, soil physicochemical variables and methanogen communities were quantitatively analyzed. Rhizosphere soil mcrA and pmoA gene copy numbers were determined by qPCR. Methanogenic 16S rRNA genes were identified by MiSeq sequencing. The results indicated CH4 emissions were significantly higher in OT (145.31 kg ha−1) than MT (84.62 kg ha−1), CT (77.88 kg ha−1) or ctrl (32.19 kg ha−1). Soil organic acids were also increased by organic fertilization. CH4 effluxes were significantly and negatively related to mcrA and pmoA gene copy numbers, and positively related to mcrA/pmoA. Above all, hydrogenotrophic Methanocella and acetoclastic Methanosaeta were the predominant methanogenic communities; these communities were strictly associated with soil potassium, oxalate, acetate, and succinate. Application of organic fertilizer promoted the dominant acetoclastic methanogens, but suppressed the dominant hydrogenotrophic methanogens. The transformation in methanogenic community structure and enhanced availability of C substrates may explain the increased CH4 production in OT compared to other treatments. Compared to OT, MT may partially mitigate CH4 emissions while guaranteeing a high rice yield. On this basis, we recommend the local fertilization pattern should change from 300 N kg ha−1 of organic manure to the same level of mixed fertilization. Moreover, we suggest multiple combinations of mixed fertilization merit more investigation in the future.