Ammonia inhibition often occurs during anaerobic digestion (AD) of N-rich organic waste. To decipher how ammonia affects microbial electron transfer activity and energy generation pathways, this study implemented mesophilic reactors subjected to incremental increase in ammonia concentrations from 600 to 5000 mg NH4+-N/L through urea regulation. The first comprehensive analyses of AD performance, mass and energy flow, thermodynamics, microbial communities, and metabolic activities were conducted in the digesters. The results showed that accumulation of volatile fatty acids, a reduction in methane production, and a mere 18.5% of the energy flow being directed towards biogas generation occurred under 4000 mg NH4+-N/L. Furthermore, we demonstrated that the changes in the Gibbs free energy were effective in evaluating the feasibility of propionic and butyric acid degradation under ammonia stress, but not for acetate. The alteration in microbial community composition indicated that the growth of acetogens surpassed that of methanogens under ammonia stress. Metagenomic analysis revealed a significant decrease in the abundance of genes associated with electron transfer and ATP generation, resulting in reduced efficiency in methanogenesis. Based on these findings, the supplementation of electrons via electro-fermentation into the AD system emerged as a potential approach to mitigate ammonia inhibition and enhance overall process efficiency.
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