A genomic view of methane oxidation by aerobic bacteria and anaerobic archaea

Methane is a powerful greenhouse gas, and its atmospheric concentration has been steadily increasing over the past 300 years. There are two major ways in which methane is removed from the environment: aerobic oxidation by a specialized group of bacteria and anaerobic oxidation by a specialized group of archaea. The former is important for keeping methane concentrations balanced in freshwater sediments and soils, whereas the latter is the major process in anoxic marine environments. The biochemistry of aerobic methane oxidation is relatively well understood, following intensive research efforts with a number of model organisms, but the biochemistry of anaerobic methane oxidation is not yet fundamentally understood and no anaerobic methane-oxidizer has been isolated in pure culture so far. Three recent studies using global approaches [1-3] have shed new light on both aerobic and anaerobic systems. Here, we first review background information on the two metabolic systems involving methane and then discuss the insights revealed through the three recent studies [1-3], as well as a fourth [4] that is useful for interpreting the new results on anaerobic methane oxidation [3].Three types of aerobic methanotrophs are recognized. Type I methanotrophs are γ-proteobacteria that have stacked membranes harboring methane monooxygenase (pMMO), the enzyme for primary methane oxidation, and that use the ribulose monophosphate (RuMP) cycle, which converts formaldehyde into multicarbon compounds, for building cell biomass [5]. Type II methanotrophs belong to the α-proteobacteria, have rings of pMMO-harboring membranes at the periphery of the cells, and use the serine cycle, an alternative pathway for converting formaldehyde into biomass; these bacteria also often contain a soluble (s) MMO in addition to pMMO [5]. The third type, type X methanotrophs, belong to the genus Methylococcus (γ-proteobacteria) and combine features characteristic of the other two types: they have stacked membra