Physicochemical characteristics of stored cattle manure affect methane emissions by inducing divergence of methanogens that have different interactions with bacteria

Greenhouse gas (GHG) emissions from manure management are an environmental concern that hinders the livestock industry. Methane (CH4) is the primary non-CO2 GHG emitted from outdoor manure storage facilities. Understanding the relationship between the microbial community and manure physicochemical characteristics, together with their contributions to CH4 emission during storage are of importance for mitigation and ecological significance. In this study, the archaeal and bacterial communities in manure were investigated using high-throughput sequencing, revealing that manure physicochemical characteristics have a major influence on the distribution and enrichment of methanogenic taxa as well as CH4 emission. Moisture and total phosphorus (TP) were positively correlated with Methanocorpusculum abundance in cow manure with high CH4 emission, while they were negatively correlated with Methanobacterium abundance in heifer manure with low CH4 emission at the species level. Quantitative PCR analysis of transcript abundance of alpha subunit of Methyl coenzyme-M reductase (mcrA) gene in cow manure disclosed relatively strong activity of Methanocorpusculum. sPLS regression and network analyses of microbial taxa revealed that different bacteria-methanogen patterns are associated with CH4 emission. Our data indicates that the manure physicochemical characteristics influence CH4 emissions by altering the divergence of methanogens that differ in transcriptional efficiency of mcrA gene and are correlated with some bacterial taxa, providing insights into the mechanisms of CH4 emission during manure storage.