Methane emission and soil microbial communities in early rice paddy as influenced by urea-N fertilization

Background and aims Urea is widely used in rice farming systems to improve the nitrogen (N) availability and crop yield, yet its influence on CH4 emissions remains unclear. The present study aimed to identify the potential microbial mechanisms resulting in the N fertilizer-induced effects on CH4 emissions from paddies. Method A field experiment was conducted with (N1, 100 kg N ha(-1)) and without (N0) N fertilization. CH4 emission rate was measured every 3-7 day using the static chamber-gas chromatography method. Quantitative PCR (qPCR) and Illumina MiSeq sequencing approaches were employed to investigate the community composition and structure of methanogenic archaea and methanotrophic bacteria in rice rhizosphere soil at three time points (tillering stage 17d, heading stage 47d and mature stage 67 d). Results Urea application significantly stimulated the CH4 emissions from paddies, partially due to the decrease of redox potential (E-h) around the root region and the reduction of dissolved oxygen (DO) concentration at the soil-water interface. qPCR indicated a sharp increase in methanogenic archaeal 16S rRNA and methanotrophic bacterial pmoA gene copies with urea fertilization. Next-generation sequencing of these amplicons revealed that the diversity of both methanogenic and methanotrophic communities was decreased by urea input. Additionally, urea fertilization stimulated the genera Methanoregula (methanogen) and Methylococcus (type I methanotrophs) and inhibited the genus Methylocystis (type II methanotrophs). Conclusions Urea fertilization changed oxygen state of the paddy soil and water and thus changed the community structure of methanogens and methanotrophs, which resulted in increased CH4 emissions.