The Diversity of Methanotrophs

Aerobic methane oxidation has been documented in a variety of pelagic environments. Although it is known that there is significant spatial variation in the distribution of the process, little is known about the organisms which carry it out and together, these factors indicate potential differences in the community composition of methanotrophs - both spatially and temporally.

Three clades (OPU1, OPU3 and Group X) are proposed to contribute to oceanic methane oxidation and are distinct from the phylotypes described for methanotrophs found in marine sediments, suggesting that they are adapted to a planktonic lifestyle. This study aims to elucidate the distribution of aerobic methanotrophs and the abundances of the different lineages in relation to location.

Water column samples were taken from various depths at 3 distinct marine environments: an active methane seep, a near-shore submarine canyon and within an oligotrophic gyre. Benthic water samples were also taken from along the California continental margin, above a methane seeping canyon and at sites adjacent to a white smoker hydrothermal vent. A recent PCR-based method, monooxygenase intergenic spacer analysis (MISA) was carried out, using newly developed primers, to determine the differences in the composition of monooxygenase genes (used to identify methanotrophs) spatially and temporally. This can be used to infer the distribution of planktonic aerobic methanotrophs. Clone library and q-PCR analysis were also used to assess the abundance and distribution of the methanotroph lineages, OPU1, OPU3 and Group X.

Of the active seep sites, the methane seeping canyon was the most interesting. All three expected clades were present according to the MISA analysis, and two other clades were also found. One corresponded to the clone library as a divergent monooxygenase termed ‘Group W’, but the other was not discernable. This shows that with new primers more groups can be discovered and therefore further our knowledge of these important microbes. The abundance of each clade varied horizontally and vertically as the most numerous and diverse assemblages were found close to the seep, with less activity and abundance being found further away and towards the epipelagic.

The communities at the non-seep sites were more closely tied to the local methane maximum (200-300m) and they varied according to depth. The surveys of the bottom waters revealed the presence of all clades, albeit in varying abundances; and this, with the presence of OPU’s 1 and 3 along the California continental margin, suggests that they comprise a broadly distributed methane sink in the deep ocean. The oligotrophic gyre showed no detectable abundance of any of the clades, although a single peak represented a member of a super family termed ‘Group O’ whose role in methane oxidation remains to be discovered. However, this suggests that perhaps the monooxygenase community in oligotrophic open ocean systems is distinct from those found in deep waters and continental margins. Again, further work into producing new primers may reveal novel OTU’s which could play a vital role in the oxidation process.

Further evidence for community differences according to environment comes from the findings from the hydrothermal vent. Here, only a member of OPU3 was found suggesting that there may be site-specific OTU’s; resulting in habitat-related variation in the distribution of what is usually a broadly distributed clade.

The findings of this study imply a broad spectrum of monooxygenase diversity throughout different marine systems, including novel groups. As groups are still being found and characterised, it would be prudent to continue developing primers and techniques to further investigate the methane oxidation process as the recent MISA assay, described in this study, goes to show that a lot more can be found. Further understanding of the way methane is cycled may become incredibly useful in the future in the fight to reduce global warming and climate change, not to mention the fact that it is vitally important for life in the oceans.

A review of: Patricia L Tavormina, William Ussler III, Samantha B Joye, Benjamin K Harrison and Victoria J Orphan (2010) Distributions of putative aerobic methanotrophs in diverse pelagic marine environments. The ISME Journal 4, 700–710.