Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

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.

A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments

“…Notably, this PmoA lineage included a number of sequences obtained in cultivation-independent studies from various freshwater environments, that is, peatlands, lake sediments, boreal forest and alpine fen soils (Pester et al, 2004;Jaatinen et al, 2005;Bussmann et al, 2006;Danilova and Dedysh, 2014;Cheema et al, 2015;Danilova et al, 2015). This PmoA lineage is also addressed as OSC (Organic Soil Cluster) cluster of uncultivated methanotrophs, which occur predominantly in peatlands and in some upland soils (Knief, 2015). Given that the presence of RubisCO is one of the characteristic features of type X (Methylococcus-like) methanotrophs (Whittenbury and Dalton, 1981;Whittenbury, 1981;Baxter et al, 2002), we made an attempt to detect genes coding for this enzyme in spiral-shaped methanotrophs using the primer set developed by Alfreider et al (2003).…”

“…Therefore, the pmoA gene encoding β-subunit of particulate MMO is widely used as a functional gene marker for methanotrophs (McDonald et al, 2008;Dumont, 2014). The vast majority of pmoA gene sequences that are currently deposited in the GenBank database were obtained in cultivationindependent studies; only 3% of these sequences were retrieved from cultured methanotrophic bacteria (Knief, 2015). Many currently recognized pmoA lineages, therefore, are not represented by characterized organisms, and this limits interpretation of results obtained in pmoA-based studies.…”

Metagenomic Binning Recovers a Transcriptionally Active Gammaproteobacterium Linking Methanotrophy to Partial Denitrification in an Anoxic Oxygen Minimum Zone

“…The OPU3 clade has been detected in a wide range of marine habitats, including the deep sea (Jensen et al, 2008;Lesniewski et al, 2012), methane seeps and oil spills (Wasmund et al, 2009;Tavormina et al, 2010;Kessler et al, 2011;Rivers et al, 2013), and OMZs (Hayashi et al, 2007;Tavormina et al, 2013). These studies suggest a low-to-no oxygen niche for OPU3, with members of this group being particularly prevalent in Eastern Pacific OMZs (Tavormina et al, 2008(Tavormina et al, , 2010(Tavormina et al, , 2013Knief, 2015). These OPU clades cluster apart from other denitrifying methanotrophs (Figure 1; Tavormina et al, 2008Tavormina et al, , 2010.…”

Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions

“…Aerobic and anaerobic methane oxidation are the only two processes known for biotic methane consumption (12,14). Aerobic methane-oxidizing bacteria (methanotrophs), in particular, play a vital role in the global climate because they can mitigate up to 90% of the biogenically produced methane in soils and sediments (15, 16).…”

“…Microbial methane utilization plays a significant role in global climate and is an important part of the carbon cycle (12,13). Aerobic and anaerobic methane oxidation are the only two processes known for biotic methane consumption (12,14).…”