Microbial electrolysis cell (MEC) is a new way to enhance degradation of food waste anaerobic digestate and recover methane. Through long-term operation, the start-up method, organic load, and methane production mechanism of the digestate have been optimized. At an organic load of 4000 mg/L, MEC increased methane production by 3–4 times and COD removal by 20.3% compare with anaerobic digestion (AD). The abundance of bacteria Fastidiosipila and Geobacter, which participated in the acid degradation and direct electron transfer in the MEC, increased dramatically than that in the AD. The dominant methanogenic archaea in the MEC and AD was Methanobacterium (44.4–56.3%) and Methanocalculus (70.05%), respectively. Geobacter and Methanobacterium dominated the MEC by direct electron transfer of organic matter into synthetic methane intermediates. MEC showed a perfect COD removal efficiency of the digestate, meanwhile CH4 as a clean energy was obtained. Thus, MEC was a promising technology for deep energy from digestate.
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