Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils

Abstract

Summary: The activity and abundance of methanotrophic bacteria were measured in an acidic and a neutral forest soil. The soils exhibited high uptake rates (>30 µg CH 4 m −2 h −1 ) of atmospheric CH 4 at all measurement times throughout the vegetation period. The abundances of various phylogenetic groups of methanotrophs, including some uncultured putative ones, were measured using real‐time polymerase chain reaction assays. Each assay specifically targeted the pmoA gene or mmoX gene of a particular group of methanotrophs, or the amoA gene of ammonia‐oxidizing bacteria. As yet uncultured methanotrophs of a group previously named ‘forest soil cluster’ or ‘USCα’ were numerically dominant in the acidic soil, while cultured but taxonomically uncharacterized methanotrophs of a group ‘Cluster I’ were dominant in the neutral soil. Each group was detected in numbers equivalent to about 10 6 pmoA gene copies per gram dry weight of soil and comprised >90% of the detectable methanotrophic bacteria in the respective soil. As the numbers of ammonia‐oxidizing bacteria were similar but not higher, they could not have accounted for the observed CH 4 uptake rates due to their low cell‐specific CH 4 oxidation activity. Based on CH 4 flux and bacterial abundance data, estimated cell‐specific CH 4 oxidation rates of the detected methanotrophic bacteria were 540–800 × 10 −18 mol cell −1 h −1 , which is high compared with literature values of cultured methanotrophic bacteria. These estimated cell‐specific CH 4 oxidation rates are sufficiently high to allow not only maintenance but even growth on atmospheric CH 4 alone. Transcripts of mRNA of the pmoA gene were detected in the acidic soil, demonstrating that USCα methanotrophs expressed pmoA under ambient methane mixing ratios. On the other hand, pmoA trancripts of Cluster I or of other methanotrophic groups were not detectable. Our study suggests that USCα and Cluster I methanotrophs are adapted to the low concentration of methane in forest soils by possessing high cell‐specific CH 4 oxidation activities.