Abstract
Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.
Highlights
In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.”
The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of particulate methane monooxygenase (pmoA) paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care
The pmoA gene encoding the βsubunit of the particulate methane monooxygenase is the most frequently used marker, as it is present in most aerobic methanotrophic bacteria with exceptions among the Beijerinckiaceae (Table 1)
Summary
Known sources are freshwater and permafrost ecosystems, some animal species and termites, and the release of methane from geological processes, wildfires and hydrates Another 50–65% of the total emissions are due to anthropogenic activities including ruminant husbandry, fossil fuel extraction and use, rice paddy agriculture and emissions from landfills and waste, resulting in a current elevation of the atmospheric methane concentration by a factor of 2.5 compared to preindustrial times (IPCC, 2013). All these ecosystems with source function for atmospheric methane are typical habitats of methane-oxidizing bacteria These include freshwater and marine sediments and water columns, aquifers, floodplains, peat bogs, high-arctic, and tundra wetlands, upland soils, rice paddies, landfill covers, and sewage sludge (Hanson and Hanson, 1996; Conrad, 2007; Bowman, 2014).
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