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Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses

Chen, Yin, Dumont, Marc G., McNamara, Niall P., Chamberlain, Paul M., Bodrossy, Levente, Stralis-Pavese, Nancy, Murrell, J. Colin
Environmental microbiology 2008 v.10 no.2 pp. 446-459
Calluna vulgaris, Methylocella, Methylocystis, community structure, fatty acids, gamma-Proteobacteria, genes, habitats, heathlands, messenger RNA, methane, methanotrophs, microarray technology, oxidation, peatlands, soil, soil sampling, United Kingdom
The active methanotroph community was investigated for the first time in heather (Calluna)-covered moorlands and Sphagnum/Eriophorum-covered UK peatlands. Direct extraction of mRNA from these soils facilitated detection of expression of methane monooxygenase genes, which revealed that particulate methane monooxygenase and not soluble methane monooxygenase was probably responsible for CH₄ oxidation in situ, because only pmoA transcripts (encoding a subunit of particulate methane monooxygenase) were readily detectable. Differences in methanotroph community structures were observed between the Calluna-covered moorland and Sphagnum/Eriophorum-covered gully habitats. As with many other Sphagnum-covered peatlands, the Sphagnum/Eriophorum-covered gullies were dominated by Methylocystis. Methylocella and Methylocapsa-related species were also present. Methylobacter-related species were found as demonstrated by the use of a pmoA-based diagnostic microarray. In Calluna-covered moorlands, in addition to Methylocella and Methylocystis, a unique group of peat-associated type I methanotrophs (Gammaproteobacteria) and a group of uncultivated type II methanotrophs (Alphaproteobacteria) were also found. The pmoA sequences of the latter were only distantly related to Methylocapsa and also to the RA-14 group of methanotrophs, which are believed to be involved in oxidation of atmospheric concentrations of CH₄. Soil samples were also labelled with ¹³CH₄, and subsequent analysis of the ¹³C-labelled phospholipid fatty acids (PLFAs) showed that 16:1ω7, 18:1ω7 and 18:1ω9 were the major labelled PLFAs. The presence of ¹³C-labelled 18:1ω9, which was not a major PLFA of any extant methanotrophs, indicated the presence of novel methanotrophs in this peatland.