Microbial community shifts and biogas conversion computation during steady, inhibited and recovered stages of thermophilic methane fermentation on chicken manure with a wide variation of ammonia

•Microbial community shifts with inhibition was investigated in CH4 fermentation (55°C).•TAN cased VFA accumulation and then synergistically inhibited process over 6g/L.•The unrecoverable Archaeal dynamic affected by ammonia makes the resilience weak.•Methanothermobacter has higher tolerance than Methanosarcina on ammonia inhibition.•Hydrolytic and acidogenic bacteria dynamic were significantly after inhibition. The thermophilic methane fermentation of chicken manure (10% TS) was investigated within a wide range of ammonia. Microbiological analysis showed significant shifts in Archaeal and Bacterial proportions with VFA accmulation and CH4 formation before and after inhibition. VFA accumulated sharply with lower methane production, 0.29 L/g VS, than during the steady stage, 0.32L/g VS. Biogas production almost ceased with the synergy inhibition of TAN (8000mg/L) and VFA (25,000mg/L). Hydrogenotrophic Methanothermobacter thermautotrophicus str. was the dominate archaea with 95% in the inhibition stage and 100% after 40days recovery compared to 9.3% in the steady stage. Aceticlastic Methanosarcina was not encountered with coincided phenomenal of high VFA in the inhibition stage as well as recovery stage. Evaluation of the microbial diversity and functional bacteria indicated the dominate phylum of Firmicutes were 94.74% and 84.4% with and without inhibition. The microbial community shifted significantly with elevated ammonia concentration affecting the performance.