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

Abstract

The activity and abundance of methanotrophic bacteria were measured in an acidic and a neutral forest soil. The soils exhibited high uptake rates (>30 microg CH4 m(-2) h(-1)) of atmospheric CH4 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 'USC alpha' 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 CH4 uptake rates due to their low cell-specific CH4 oxidation activity. Based on CH4 flux and bacterial abundance data, estimated cell-specific CH4 oxidation rates of the detected methanotrophic bacteria were 540-800 x 10(-18) mol cell(-1) h(-1), which is high compared with literature values of cultured methanotrophic bacteria. These estimated cell-specific CH4 oxidation rates are sufficiently high to allow not only maintenance but even growth on atmospheric CH4 alone. Transcripts of mRNA of the pmoA gene were detected in the acidic soil, demonstrating that USC alpha methanotrophs expressed pmoA under ambient methane mixing ratios. On the other hand, pmoA transcripts of Cluster I or of other methanotrophic groups were not detectable. Our study suggests that USC alpha and Cluster I methanotrophs are adapted to the low concentration of methane in forest soils by possessing high cell-specific CH4 oxidation activities.

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

“…The MOB community capable of the consumption of atmospheric methane was studied in different forest and grassland soils and was found to exclude members of the type I group. It was suggested to consist primarily of type II MOB [35] and also of distinct, uncultivated clades distant from type I and type II MOB [23,29,33,46]. In all studies discussed, the MOB community is exposed to environmental extremes such as freeze-thaw cycles, low pH values, or low substrate concentrations and was found to be restricted to certain taxonomic groups of MOB.…”

“…Members of the Methylocystaceae and Beijerinckiaceae are termed type II MOB and belong to the α-subdivision of the Proteobacteria phylum [10][11][12][13][14][15][16][17][18][19][20][21]. The diversity and composition of MOB have been investigated in several environments such as freshwater sediments [8,42], landfill soils [59], rice field soils [22,24], habitats with only atmospheric methane concentrations [29,33,35], and peat bogs with very low pH values [39,40].…”

Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2

“…Their apparent K m values (0.1-1.1 M CH 4 ), however, are higher than those of dry upland soils but lower than those of wetlands. PLFA-labeling experiments with 13 Cmethane at a low mixing ratio (30 ppmv) have shown that USC␣ and Methylocystis spp., but not type I methanotrophs, are active at low methane concentrations in the hydromorphic soil tested (11), thereby corroborating the hypothesis that Methylocystis spp. oxidize atmospheric methane in situ.…”

“…In contrast to methanotrophs in the aerobic interfaces of methanogenic environments, the methanotrophs active in dry, well aerated upland soils, for example, forest soils, consume methane with high apparent affinity (K m(app) values of 0.01-0.28 M CH 4 ) (6). Molecular studies have indicated the presence of type II methanotrophs in most upland soils (10,11) and have provided increasing evidence that, in these soils, the most abundant methanotrophs belong to several uncultivated groups, including upland soil cluster ␣ (USC␣) and upland soil cluster ␥ (USC␥) (10,12,13). Members of USC␣ and USC␥ are presumed to be specialized oligotrophs adapted to living solely on atmospheric methane.…”

Ammonia oxidation coupled to CO 2 fixation by archaea and bacteria in an agricultural soil

“…The abundance of archaeal amoA genes and transcripts in the different SIP fractions was quantified by qPCR using primers amo196F and amo277R as previously described (5,16). The 25-μL reaction mixture contained 12.5 μL of SYBRGreen Jump-Start Taq ReadyMix, 0.5 μM of each primer, 200 ng BSA·mL −1 , 4.0 mM MgCl 2 , and 1.0 μL template DNA or cDNA (50). The abundance of bacterial amoA genes and transcripts in the different SIP fractions was quantified by qPCR using primers amoA-1F and amoA-2R as previously described (16,51).…”