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•Mesophilic AD performed better than thermophilic AD with increasing OLR.•Microbial communities displayed distinct structures and dynamics in MR and TR.•Mesophilic AD had greater richness and evenness of bacteria species.•Larger shifts of bacterial phylogeny were observed in MR.•Methanosaeta dominated in MR while Methanothermobacter was favored in TR.
Thermophilic and mesophilic anaerobic digestion reactors (TR and MR) using food waste as substrate were compared with emphasis on microbial responses to increasing organic loading rate (OLR). At OLR ranging from 1.0 to 2.5gVSL−1d−1, MR exhibited more stable performance compared to TR in terms of methane yield. Amplicons pyrosequencing results revealed the distinct microbial dynamics in the two reactors. Primarily, MR had greater richness and evenness of bacteria species. With OLR elevated, larger shifts of bacterial phylogeny were observed in MR; Methanosaeta dominated in archaeal community in MR while Methanothermobacter and Methanoculleus were favored in TR. The high functional redundancy in bacterial community integrated with acetoclastic methanogenesis in MR resulted in its better performance; whereas delicate interactions between hydrogen-producer and hydrogenotrophic methanogens in TR were much more prone to disruption. These results are conductive to understanding the microbial mechanisms of low methane yield during food waste anaerobic digestion.