Molecular ecology of methane-oxidising bacteria in drained and flooded peat
Evidence has shown that changes in land-use can affect the potential of the soil to act as a methane sink. The Lakenheath site consists of drained fenland peat, which is being re-converted to wetland. At the time of this study the site consisted of four land-use types, an intensively cultivated plot, unmanaged grassland, woodland, and wetland. Peat cores were taken from the four plots and compared for their ability to act as a methane sink. CH4 uptake was measured throughout the depth profiles using gas chromatography. Clear differences in methane oxidation rates were recorded with depth and land-use. The woodland soil showed the highest capacity for atmospheric methane oxidation, and the wetland soil was only profile that had a distinct peak of methane oxidation activity (just above the water table). Despite the change in land-use, all four soils had the capacity to oxidise both high and low concentrations of methane and so acted as a methane sink. The only exception to this was the wetland soil after persistent rainfall. The uppermost layers were water saturated and all soil sections failed to oxidise methane.
Methanotroph diversity in the four soils was compared using molecular biological and enrichment techniques. Total DNA was extracted from depth profiles of the four soils and PCR amplified with 16S rRNA methanotroph group-specific primers and primers specific to subunits of the pMMO and AMO (pmoA and amoA), sMMO (mmoX) and MDH (methanol dehydrogenase, mxaF). In addition, DNA was extracted from the top 5 cm of the cultivated (drained) and flooded soil and PCR amplified with primers specific to subunits of the pMMO and AMO. These PCR products were cloned and gene libraries constructed for each soil. No significant differences were observed in retrieved methanotroph sequences from these two soils, suggesting that the methanotroph population had not altered after flooding. The sequences obtained in the molecular study were predominantly amoA sequences from nitrifiers and pmoA sequences from type II methanotrophs. No type I pmoA sequences were retrieved. Type I methanotrophs, however, were isolated directly from the peat soil in the enrichment study.