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Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Here we report on biogeochemical and molecular evidence (DNA-stable isotope probing of 16S rRNA and pmoA genes combined with pyrosequencing) showing that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities by N-assimilating methane-oxidizing bacteria in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization 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. Deep-sequencing of actively methane assimilating MOB revealed that methane amendment resulted in clear growth of Methylosarcina (type Ia MOB) related MOB while methane plus urea led to equal increase in Methylosarcina and Methylobacter-related MOB, indicating the differential growth requirements of representatives of these genera. Strikingly, type Ib MOB did not respond to methane nor to urea. Increase in 13C-assimilating by bacteria related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. The ammonia oxidation activity of nitrifying communities was inhibited by methane, and the growth of Nitrosospira and Nitrosomonas were suppressed by the combination urea with methane. In addition, the growth and activity of nitrite-oxidzing bacteria also was repressed by CH4. Results obtained by pyrosequencing analysis of 16S rRNA gene and functional genes were congruent. The results of this study for the first time provide comprehensive insights in the interactions between actively growing methanotrophs and ammonia oxidizers in a complex ecosystems like soil. |