Molecular Analyses of Novel Methanotrophic Communities in Forest Soil That Oxidize Atmospheric Methane

Abstract

Forest and other upland soils are important sinks for atmospheric CH 4 , consuming 20 to 60 Tg of CH 4 per year. Consumption of atmospheric CH 4 by soil is a microbiological process. However, little is known about the methanotrophic bacterial community in forest soils. We measured vertical profiles of atmospheric CH 4 oxidation rates in a German forest soil and characterized the methanotrophic populations by PCR and denaturing gradient gel electrophoresis (DGGE) with primer sets targeting the pmoA gene, coding for the ␣ subunit of the particulate methane monooxygenase, and the small-subunit rRNA gene (SSU rDNA) of all life. The forest soil was a sink for atmospheric CH 4 in situ and in vitro at all times. In winter, atmospheric CH 4 was oxidized in a well-defined subsurface soil layer (6 to 14 cm deep), whereas in summer, the complete soil core was active (0 cm to 26 cm deep). The content of total extractable DNA was about 10-fold higher in summer than in winter. It decreased with soil depth (0 to 28 cm deep) from about 40 to 1 g DNA per g (dry weight) of soil. The PCR product concentration of SSU rDNA of all life was constant both in winter and in summer. However, the PCR product concentration of pmoA changed with depth and season. pmoA was detected only in soil layers with active CH 4 oxidation, i.e., 6 to 16 cm deep in winter and throughout the soil core in summer. The same methanotrophic populations were present in winter and summer. Layers with high CH 4 consumption rates also exhibited more bands of pmoA in DGGE, indicating that high CH 4 oxidation activity was positively correlated with the number of methanotrophic populations present. The pmoA sequences derived from excised DGGE bands were only distantly related to those of known methanotrophs, indicating the existence of unknown methanotrophs involved in atmospheric CH 4 consumption.The atmospheric concentration of CH 4 , one of the most important greenhouse gases, has increased dramatically over the past 200 years. About 80 to 90% of atmospheric CH 4 is of biogenic origin (20). The major sink is the chemical destruction by OH˙and Cl˙radicals in the troposphere and stratosphere, respectively (9, 10). However, the capacity of these atmospheric sinks may decline, since the rising concentrations of other trace gases emitted by anthropogenic activity result in a reduction of OH˙radicals in the troposphere (27).The only biological sink for CH 4 is oxidation in soil. Atmospheric CH 4 is consumed in forest, agricultural, and other upland soils. CH 4 consumption in these soils is caused by methane-oxidizing bacteria. However, the identity of these methanotrophs is still unknown. The apparent half-saturation constant (K m ) for oxidation of atmospheric CH 4 (approximately 1.8 parts per million by volume [ppmv]) in upland soils ranges from 0.8 to 280 nM (6, 7, 13, 16). However, the K m of the common type I or II methanotrophs (0.8 to 66 M), which are available in culture collections, is 1 to 3 orders of magnitude higher, and these common methanotrophs are not abl...

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.…”

Plant species, temperature, and bedrock affect net methane flux out of grassland and forest soils

“…However, the response of soil methane oxidation to temperature is not only controlled by enzyme-based activity but also by the transport of methane in the gas phase and the exchange with soil water (King and Adamsen 1992). Sensitivity of soil methane consumption to temperature reflects a combination of microbial activities, population densities of methanotrophs, gas-phase methane concentrations, and soil water content (Henckel et al 2000;King and Adamsen 1992). Previous studies showed that temperature effects on methane oxidation may be more pronounced at lower temperatures <15°C (Steinkamp et al 2001).…”

Cell evolution and Earth history: stasis and revolution

“…However, the closest relative of proteobacterial methane monooxygenase is ammonium monooxygenase of b-proteobacteria, somewhat more divergent from methane oxygenases of a-and g-proteobacteria than they are from each other, suggesting that divergence in function of the two paralogues occurred in the ancestral rhodobacterium and methanooxygenase and methanotrophy also originated ca 2.7 Gyr ago, as suggested for methylotrophy. Some aerobic methanotrophs can scavenge methane even from the atmosphere (Henckel et al 2000). Aerobic methanotrophy needs more than 20 p.p.m.…”