Batch culture studies have demonstrated that methanotrophs and ammonia oxidizers can carry out oxidation of the growth substrate of each other, but in complex environment their functional interplays are poorly understood.Here we report the biogeochemical and molecular evidences that facilitative interaction of ammonia on methane oxidation was accompanied by competitive inhibition of nitrifying communities in a paddy soil using DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing techniques.Pairwise comparison between microcosms amended with CH4, CH-4+urea, and urea indicated that urea amendment stimulated methane oxidation activity by 6-fold during a 19-days incubation period, while ammonia oxidation activity was significantly inhibited in the presence of CH4.Pyrosequencing of the 16S rRNA genes at the whole microbial community levels revealed that urea fertilization resulted in rapid growth of methanotrophs, especially Methylobacter, and both nitrifying communities appeared to be suppressed