Shotgun metagenomic analysis of methanogenic communities and physicochemical profiling of cattle manure fractions

Dairy farms are integral to food security and economic sustainability; however, they can also represent a significant source of greenhouse gas (GHG) emissions and nutrient losses, particularly in the form of methane (CH₄). In Mexico, manure management practices vary widely. Solid-liquid separation is increasingly adopted due to its recognition as one of the most effective upstream operations for GHG emissions mitigation from manure management, producing a nutrient-rich solid fraction and a liquid fraction suitable for fertilization. However, storing the liquid fraction for extended periods, particularly in large lagoons, can lead to anaerobic conditions conducive to CH4 production. A comprehensive physicochemical and microbiological assessment was performed on manure (BM) and its solid (SF) and liquid (LF) fractions. Metagenomic analysis was conducted to elucidate the dynamics of microbial communities related to methanogenesis. Total organic carbon (TOC) was identified as the only significant (PERMANOVA, p < 0.001) physicochemical parameter. SF and BM were primarily associated with hydrogenotrophic methanogenesis, whereas both hydrogenotrophic and acetoclastic methanogenesis were observed in LF. The acetoclastic pathway in LF was primarily attributed to the predominance of Methanothrix in the lagoons, which develops over a longer period than hydrogenotrophic methanogens and is characterized by maintaining low acetate concentrations. This study provides a baseline characterization of manure fractions from the Agricultural Experimental Center of Tecnológico de Monterrey (CAETEC), Mexico, as a first step towards identifying physicochemical parameters and microbial populations essential for evaluating potential manure management alternatives to mitigate CH₄ emissions.