Multi-omics evidence reveals acetogenesis as the primary metabolic bottleneck under ammonia stress

Anaerobic digestion (AD) is widely applied for its ability to convert organic waste into bioenergy, which helps to optimize the energy structure. However, ammonia inhibition, which is frequently associated with process instability in biogas plants, has significantly limited AD applications. Existing reviews have explored ammonia inhibition from various perspectives but have primarily focused on the methanogenesis process. By contrast,​ the contribution of impaired acetogenesis function to ammonia-induced inhibition has been largely overlooked. This review integrates molecular biological evidence to demonstrate that acetogenesis serves as the key link affecting ammonia-inhibited reactor performance, with a particular focus on the effects of ammonia stress on the dynamic succession, energy harvest, and enzymatic activities involved in acetogenesis. The impaired energy harvest and downregulation of enzymatic activities have been identified as the primary causes of the irreversible ammonia inhibition of acetogens, which then leads to the failure of the acetogenesis process, volatile fatty acid accumulation, and ultimately the irreversible deterioration of reactor performance. Furthermore, building on this new mechanistic insight, this review re-evaluates the efficiency and limitations of ammonia inhibition mitigation strategies. Future efforts should focus on developing innovative multi-data integration analysis strategies-such as combining activated cell sorting with targeted metaproteomics, and stable isotope probing with metabolomics-to overcome current methodological challenges in analyzing​ ammonia inhibition mechanism. These insights provide a new perspective on the ammonia inhibition mechanism and important guidance for the stable operation of fermentation systems.