Deciphering metabolic regulatory mechanisms in vital anaerobes for enhanced biogas production from protein-rich waste

Anaerobic digestion (AD) systems generate biogas from protein-rich waste, with certain anaerobes modulating gene regulatory networks (GRNs) to manage ammonia toxicity. This study reconstructs GRN models for five key anaerobes—a hyper-ammonia-producing anaerobe Acetoanaerobium sticklandii H1, an anaerobic sulfur-reducing bacterium Desulfovibrio vulgaris Hildenborough, a hydrogenotrophic methanogen Methanothermobacter thermautotrophicus ΔH, a heterotrophic methanogen Methanosarcina mazei Gö1, and a methylotrophic methanogen Methanoculleus bourgensis MS2T—using genome-wide data to understand their metabolic regulation in AD processes. These GRNs integrate gene regulatory elements, thereby revealing species-specific adaptations that facilitate ammonia tolerance, substrate metabolism, and methane production. Regulatory elements, such as ExsA, PtxR, and GadW, influence pathways for carbon, nitrogen, and energy metabolism. A. sticklandii and M. mazei were crucial for carbon source utilization, whereas M. bourgensis adapted to ammonium-rich conditions without a typical ammonium uptake system. The results of our study provide insights into the metabolic interactions and regulatory roles within biogas-producing communities. This work proposes a framework for designing synthetic microbial communities to enhance biomethane yield from protein-based substrates, supporting AD efficiency improvements.