Methane production and oxidation–-A review on the pmoA and mcrA gene abundances for understanding the functional potentials of agricultural soils

Global efforts to avert climate change cannot succeed without tackling the emission of methane from soil and other ecosystems. Methane is a greenhouse gas that retains heat in the atmosphere and causes global warming. Its production is the last step of organic matter decomposition, and it is produced by methanogenic archaea bearing the functional gene mcrA (encoding methyl-coenzyme M reductase). Methane production involves the reduction of acetate or carbon dioxide in a microaerophilic or anaerobic environment under the catalytic actions of methyl-coenzyme M to generate methane. On the other hand, methane-oxidizing bacteria, also known as methanotrophs, through the catalytic action of particulate methane monooxygenase (pMMO), oxidize methane and reduce its emission to the atmosphere. In essence, both production and consumption of methane happen within the soil. Methanotrophs and methanogens inhabit the same soil environment. In fact, a shift in the balance between methanogen and methanotroph activities and abundances could influence soil methane emission and global warming. In this review, we highlight recent advances in drivers of methane flux, pmoA (encoding pMMO) and mcrA gene abundances, methane emission and control, relationships between microbial functional gene abundances and soil functions, and methods for studying the pmoA and mcrA gene abundances in soil. We also highlight gaps that need to be filled and the impact of the mcrA/pmoA gene abundance ratio in driving the methane emission rate in soil. We also discuss the various abiotic factors that control pmoA and mcrA gene abundances.