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BACKGROUND Ammonia nitrogen affects the methane fermentation of chicken manure, both the process resilience and the functional microbial community dynamics. In this study, a mesophilic continuous stirred‐tank reactor (CSTR) was investigated with total ammonia nitrogen (TAN) varied from 2000 mg L−1 to 16000 mg L−1. RESULTS 16S‐rDNA cloning and TRFLP results revealed that the microbial community shifts significantly responding to TAN. Aceticlastic Methanosarcina acetivorans increased gradually from 17% in the steady stage to 72% in the recovered stage with high resistance compared with aceticlastic Methanosaeta, which almost disappeared at high TAN. In contrast, hydrogenotrophic Methanoculleus increased from 2% in the steady stage to 30% in the inhibited stage and decreased to 13% in the recovered stage. The abundances of the dominant Firmicutes were 74% and 92%, with and without inhibition, and 58% in the recovered stage. Bacteroidetes decreased from 17% in the steady stage to 4% in the inhibited stage and thrived to 31% in the recovered stage. CONCLUSION Process resilience was proven even after serious inhibition. Recoverable shifted archaeal and chaotic shifted bacterial communities with functional stability were observed. This result reveals that TAN has an obvious effect on microbial community shifts and the functional resilience of the process. © 2014 Society of Chemical Industry

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