Methane oxidation and diversity of aerobic methanotrophs in forest and agricultural soddy-podzolic soils

- Soddy-podzolic soils exhibit high-affinity methane oxidation.
- Managed soils showed decreased methane oxidation rates.
- Uncultured methanotrophs of novel phylogenetic cluster predominate in forest soil.
- Pronounced shift to cultured methanotrophs was observed after agricultural loading.
- Linkage between CH4 flux and methanotrophs communities structure is proposed.

Soddy-podzolic soils are widely distributed in European Russia, but their role as a sink for atmospheric methane is poorly documented and there is no information on the methanotroph diversity. We analysed the potential CH4-oxidation rates in soil samples and showed that the rate was significantly higher in forest soil than in arable soil, 1.21 and 0.40 ng CH4 g soil −1day−1, respectively. PCR-DGGE and clone library analysis indicated the distinct methanotrophic communities in these soils. The pmoA sequences associated with uncultured soil methanotrophs, referred to as NUSC, dominated forest soil, while in agricultural soil, type I (Methylobacter, Methylocaldum) and type II (Methylocystis, Methylosinus) methanotrophs were dominant. A newly developed primer set was applied in qPCR analysis and revealed that the copy number of pmoA genes of NUSC methanotrophs in forest soil was (9.2 ± 0.87) × 104 g soil−1, whereas the transcript number was (1.33 ± 0.31) × 106 g soil −1. We concluded that differences between the CH4 oxidation rates between forest and agriculture soils were driven by the structure of the methane-oxidizing community and that a novel group of methanotrophs may be an active participant in this process.