Diversity of Methanotrophic Bacteria in Tropical Upland Soils under Different Land Uses

Three upland soils from Thailand, a natural forest, a 16-year-old reforested site, and an agricultural field, were studied with regard to methane uptake and the community composition of methanotrophic bacteria (MB). The methane uptake rates were similar to rates described previously for forest and farmland soils of the temperate zone. The rates were lower at the agricultural site than at the native forest and reforested sites. The sites also differed in the MB community composition, which was characterized by denaturing gradient gel electrophoresis (DGGE) of pmoA gene fragments (coding for a subunit of particulate methane monooxygenase) that were PCR amplified from total soil DNA extracts. Cluster analysis based on the DGGE banding patterns indicated that the MB communities at the forested and reforested sites were similar to each other but different from that at the farmland site. Sequence analysis of excised DGGE bands indicated that Methylobacter spp. and Methylocystis spp. were present. Sequences of the “forest soil cluster” or “upland soil cluster α,” which is postulated to represent organisms involved in atmospheric methane consumption in diverse soils, were detected only in samples from the native forest and reforested sites. Additional sequences that may represent uncultivated groups of MB in the Gammaproteobacteria were also detected.     

Diversity and activity of methanotrophic bacteria in different upland soils

Samples from diverse upland soils that oxidize atmospheric methane were characterized with regard to methane oxidation activity and the community composition of methanotrophic bacteria (MB). MB were identified on the basis of the detection and comparative sequence analysis of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. MB commonly detected in soils were closely related to Methylocaldum spp., Methylosinus spp., Methylocystis spp., or the "forest sequence cluster" (USC alpha), which has previously been detected in upland soils and is related to pmoA sequences of type II MB (Alphaproteobacteria). As well, a novel group of sequences distantly related (<75% derived amino acid identity) to those of known type I MB (Gammaproteobacteria) was often detected. This novel "upland soil cluster gamma" (USC gamma) was significantly more likely to be detected in soils with pH values of greater than 6.0 than in more acidic soils. To identify active MB, four selected soils were incubated with (13)CH(4) at low mixing ratios (<50 ppm of volume), and extracted methylated phospholipid fatty acids (PLFAs) were analyzed by gas chromatography-online combustion isotope ratio mass spectrometry. Incorporation of (13)C into PLFAs characteristic for methanotrophic Gammaproteobacteria was observed in all soils in which USC gamma sequences were detected, suggesting that the bacteria possessing these sequences were active methanotrophs. A pattern of labeled PLFAs typical for methanotrophic Alphaproteobacteria was obtained for a sample in which only USC alpha sequences were detected. The data indicate that different MB are present and active in different soils that oxidize atmospheric methane.     

Diversity and Activity of Methanotrophic Bacteria in Different Upland Soils

Samples from diverse upland soils that oxidize atmospheric methane were characterized with regard to methane oxidation activity and the community composition of methanotrophic bacteria (MB). MB were identified on the basis of the detection and comparative sequence analysis of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. MB commonly detected in soils were closely related to Methylocaldum spp., Methylosinus spp., Methylocystis spp., or the “forest sequence cluster” (USC α), which has previously been detected in upland soils and is related to pmoA sequences of type II MB (Alphaproteobacteria). As well, a novel group of sequences distantly related (<75% derived amino acid identity) to those of known type I MB (Gammaproteobacteria) was often detected. This novel “upland soil cluster γ” (USC γ) was significantly more likely to be detected in soils with pH values of greater than 6.0 than in more acidic soils. To identify active MB, four selected soils were incubated with ¹³CH₄ at low mixing ratios (<50 ppm of volume), and extracted methylated phospholipid fatty acids (PLFAs) were analyzed by gas chromatography-online combustion isotope ratio mass spectrometry. Incorporation of ¹³C into PLFAs characteristic for methanotrophic Gammaproteobacteria was observed in all soils in which USC γ sequences were detected, suggesting that the bacteria possessing these sequences were active methanotrophs. A pattern of labeled PLFAs typical for methanotrophic Alphaproteobacteria was obtained for a sample in which only USC α sequences were detected. The data indicate that different MB are present and active in different soils that oxidize atmospheric methane.     

Methanotrophic Communities in Brazilian Ferralsols from Naturally Forested,Afforested, and Agricultural Sites

Conversion of forests to farmland permanently lowers atmospheric methane consumption due to unresolved reasons. Alphaproteobacterial methanotrophs were predominant in forested soils and gammaproteobacterial species were predominant in farmland soils of subtropical ferralsols in Brazil. The capability of atmospheric methane consumption was obliterated in farmland soils, suggesting a shift from oligotrophic to copiotrophic species.Aerobic methanotrophic communities in aerated soils are the largest biological sink for atmospheric methane (CH₄) (3, 4, 10, 17). Forest soil communities exhibit the highest consumption rates on a global scale (4, 26). The conversion to farmland lowers the sink capacity (26, 28, 29), but it can be restored by afforestation (27). Sink reconstitution is faster in tropical regions than in temperate regions (12, 15). The impact of this land use change on atmospheric CH₄-consuming communities has scarcely been addressed (21, 25). The objective of the present study was to gain insight into CH₄ oxidation kinetics and the composition of methanotrophic communities in soils from a naturally forested site, an afforested site, and two farmland sites from a subtropical region in South America (Mata Atlântica, Brazil).Soils from an area in Brazil to the west of São Paulo and close to Caucaia do Alto (46°55′W to 47°06′W, 23°39′S to 23°47′S) were sampled in April 2005. The soil type at any site was a ferralsol (8a). The natural forest site was not managed for over 100 years (pH 3.6), whereas the reforested site was restored 20 years ago (pH 3.8). The humus layer was removed before sampling the forest soils. A nearby located conventionally farmed acre (pH 6.1) and an organically farmed acre (pH 6.2) were also sampled. Both sites were forests 50 to 100 years ago, and the forest sites were part of a formerly continuously forested region. Soils were sampled in three spatial replicates from the top 10 cm. Samples were pooled, transported within 2 weeks to Germany, and manually homogenized, and aliquots were stored at −20°C for molecular analyses and at 2°C for activity analyses.     

Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USCα clade

Forest soils are a major biological sink for atmospheric methane, yet the identity and physiology of the microorganisms responsible for this process remain unclear. Although members of the upland soil cluster α (USCα) are assumed to represent methanotrophic bacteria adapted to the oxidation of the trace level of methane in the atmosphere and to be an important sink of this greenhouse gas, so far they have resisted isolation. In particular, the question of whether the atmospheric methane oxidizers are able to obtain all their energy and carbon solely from atmospheric methane still waits to be answered. In this study, we performed stable-isotope probing (SIP) of RNA and DNA to investigate the assimilation of (13) C-methane and (13) C-acetate by USCα in an acidic forest soil. RNA-SIP showed that pmoA mRNA of USCα was not labelled by (13) C of supplemented (13) C methane, although catalysed reporter deposition - fluorescence in situ hybridization (CARD-FISH) targeting pmoA mRNA of USCα detected its expression in the incubated soil. In contrast, incorporation of (13) C-acetate into USCαpmoA mRNA was observed. USCαpmoA genes were not labelled, indicating that they had not grown during the incubation. Our results indicate that the contribution of alternative carbon sources, such as acetate, to the metabolism of the putative atmospheric methane oxidizers in upland forest soils might be substantial.     

Conversion of hardwood forests to spruce and pine plantations strongly reduced soil methane sink in Germany

Well‐drained forest soils are thought to be a significant sink for atmospheric methane. Recent research suggests that land use change reduces the soil methane sink by diminishing populations of methane oxidizing bacteria. Here we report soil CH₄ uptake from ‘natural’ mature beech forests and from mature pine and spruce plantations in two study areas of Germany with distinct climate and soils. The CH₄ uptake rates of both beech forests at Solling and Unterlüß were about two–three times the CH₄ uptake rates of the adjacent pine and spruce plantations, indicating a strong impact of forest type on the soil CH₄ sink. The CH₄ uptake rates of sieved mineral soils from our study sites confirmed the tree species effect and indicate that methanotrophs were mainly reduced in the 0–5 cm mineral soil depth. The reasons for the reduction are still unknown. We found no site effect between Solling and Unterlüß, however, CH₄ uptake rates from Solling were significantly higher at the same effective CH₄ diffusivity. This potential site effect was masked by higher soil water contents at Solling. Soil pH (H₂O) explained 71% of the variation in CH₄ uptake rates of sieved mineral soils from the 0–5 cm depth, while cation exchange capacity, soil organic carbon, soil nitrogen and total phosphorous content were not correlated with CH₄ uptake rates. Comparing 1998–99, annual CH₄ uptake rates increased by 69–111% in the beech and spruce stands and by 5–25% in the pine stands, due primarily to differences in growing season soil moisture. Cumulative CH₄ uptake rates from November throughout April were rather constant in both years. The CH₄ uptake rates of each stand were separately predicted using daily average soil matric potential and a previously developed empirical model. The model results revealed that soil matric potential explains 53–87% of the temporal variation in CH₄ uptake. The differences between measured and predicted annual CH₄ uptake rates were less than 10%, except for the spruce stand at Solling in 1998 (17%). Based on data from this study and from the literature, we calculated a total reduction in the soil CH₄ sink of 31% for German forests due in part to conversion of deciduous to coniferous forests.     

Effects of agronomic treatments on structure and function of ammonia-oxidizing communities

The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the beta subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 microg of NH(4)(+)-N ml(-1), to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function.     

PCR profiling of ammonia-oxidizer communities in acidic soils subjected to nitrogen and sulphur deposition

Communities of ammonia-oxidizing bacteria (AOB) were characterized in two acidic soil sites experimentally subjected to varying levels of nitrogen and sulphur deposition. The sites were an acidic spruce forest soil in Deepsyke, Southern Scotland, with low background deposition, and a nitrogen-saturated upland grass heath in Pwllpeiran, North Wales. Betaproteobacterial ammonia-oxidizer 16S rRNA and ammonia monooxygenase (amoA) genes were analysed by cloning, sequencing and denaturing gradient gel electrophoresis (DGGE). DGGE profiles of amoA and 16S rRNA gene fragments from Deepsyke soil in 2002 indicated no effect of nitrogen deposition on AOB communities, which contained both Nitrosomonas europaea and Nitrosospira. In 2003, only Nitrosospira could be detected, and no amoA sequences could be retrieved. These results indicate a decrease in the relative abundance of AOB from the year 2002 to 2003 in Deepsyke soil, which may be the result of the exceptionally low rainfall in spring 2003. Nitrosospira-related sequences from Deepsyke soil grouped in all clusters, including cluster 1, which typically contains only sequences from marine environments. In Pwllpeiran soil, 16S rRNA gene libraries were dominated by nonammonia oxidizers and no amoA sequences were detectable. This indicates that autotrophic AOB play only a minor role in these soils even at high nitrogen deposition.     

土壤湿度对中国南部热带森林土壤甲烷吸收的影响

森林土壤是一个重要的大气甲烷的汇。然而,相较于寒带和温带,在热带尤其是东南亚地区,森林土壤甲烷通量的观测较少,这限制了目前对热带森林土壤甲烷通量与环境因子之间关系的认识,也给热带森林土壤甲烷汇的估算带来了一定的不确定性。在中国海南省吊罗山国家森林公园的热带森林土壤,采用激光光谱法测量了2016年9月至2018年9月逐月的土壤甲烷通量,并分析了其与周围环境因子的关系。结果表明：研究区土壤是甲烷的汇,山顶样地的年平均吸收量为0.95 kg CH₄-C hm^-2 a^-1,山脚样地的年平均吸收量为1.93 kg CH₄-C hm^-2 a^-1。干季(11月—次年4月)的甲烷吸收通量明显高于湿季(5—10月),占到全年甲烷吸收的68%。山顶样地年平均土壤湿度为19.2%,年内的波动较小(2.8%)。而山脚样地的年平均湿度相对较低,为12.7%,且年内波动大(5.4%)。土壤湿度是控制甲烷吸收最主要的环境因子,可以解释月际甲烷吸收变化的76%,甲烷吸收通量与土壤温度的相...     

Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane

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 alpha 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 microg 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.     

Methane consumption in two temperate forest soils

Forest soils are thought to be an important sink for atmospheric methane. To evaluate methane consumption,¹⁴C-labeled methane was added to the headspace of intact soil cores collected from a mixed mesophytic forest and from a red spruce forest located in the central Appalachian Mountains. Both soils consumed the added methane at initially high rates that decreased as the methane mixing ratio of the air decreased. The mixed mesophytic forest soil consumed an average of 2 mg CH₄ m^–2 d^–1 versus 1 mg CH, m^–2 d^–1 for the spruce forest soil. The addition of acetylene to the headspace completely suppressed methane consumption by the soils, suggesting that an aerobic methane-consuming microorganism mediated the process. At both forest sites, methane mixing ratios in soil air spaces were greater than that in the air overlying the soil surface, indicating that these soils had the ability to produce methane. Models of methane emission from forest soils to the atmosphere must represent methane flux as the balance between production and consumption of methane, which are controlled by very different factors     

Effects of Agronomic Treatments on Structure and Function of Ammonia-Oxidizing Communities

The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the β subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 μg of NH₄⁺-N ml⁻¹, to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function.     

Variation in Soil Methane Release or Uptake Responses to Biochar Amendment: A Separate Meta-analysis

Agricultural soils play an important role in the atmospheric methane (CH₄) budget, where paddy soils can contribute significant CH₄ to atmosphere whereas upland soils may act as a source or sink of atmospheric CH₄, dependent on soil water conditions. Biochar amendments have effects on soil CH₄ production or oxidation processes in individual experiments, but the causative mechanisms are yet to be fully elucidated. To synthesize the response of soil CH₄ release or uptake to biochar amendment, we performed a meta-analysis using data from 61 peer-reviewed papers with 222 updated paired measurements. When averaged across all studies, biochar amendment significantly decreased CH₄ release rates by 12% for paddy soils and 72% for upland soils, and CH₄ uptake rates by 84% for upland soils. Neither soil CH₄ release nor uptake responses to biochar amendment were significant in field soils. Nitrogen (N) fertilizer application would weaken the response of soil CH₄ release or uptake to biochar amendment. Biochar-incurred decreases in soil CH₄ release and uptake rates were the largest in medium-textured soils or neutral-pH soils. Soil CH₄ release or uptake responses to biochar were also significantly altered by biochar characteristics, such as feedstock source, C/N ratio, pH, and pyrolysis temperature. The results of this synthesis suggest that the role of biochar in soil CH₄ mitigation potential might have been exaggerated, particularly in fields when biochar is applied in combination with N fertilizer.     

Response of methanotrophic communities to afforestation and reforestation in New Zealand

Methanotrophs use methane (CH₄) as a carbon source. They are particularly active in temperate forest soils. However, the rate of change of CH₄ oxidation in soil with afforestation or reforestation is poorly understood. Here, soil CH₄ oxidation was examined in New Zealand volcanic soils under regenerating native forests following burning, and in a mature native forest. Results were compared with data for pasture to pine land-use change at nearby sites. We show that following soil disturbance, as little as 47 years may be needed for development of a stable methanotrophic community similar to that in the undisturbed native forest soil. Corresponding soil CH₄-oxidation rates in the regenerating forest soil have the potential to reach those of the mature forest, but climo-edaphic fators appear limiting. The observed changes in CH₄-oxidation rate were directly linked to a prior shift in methanotrophic communities, which suggests microbial control of the terrestrial CH₄ flux and identifies the need to account for this response to afforestation and reforestation in global prediction of CH₄ emission.     

Fluxes of N2O,CH4 and CO2 on afforested boreal agricultural soils

After drainage of natural boreal peatlands, the decomposition of organic matter increases and peat soil may turn into a net source of CO₂ and N₂O, whereas CH₄ emission is known to decrease. Afforestation is a potential mitigation strategy to reduce greenhouse gas emission from organic agricultural soils. A static chamber technique was used to evaluate the fluxes of CH₄, N₂O and CO₂ from three boreal organic agricultural soils in western Finland, afforested 1, 6 or 23 years before this study. The mean emissions of CH₄ and N₂O during the growing seasons did not correlate with the age of the tree stand. All sites were sources of N₂O. The highest daily N₂O emission during the growing season, measured in the oldest site, was as high as 29 mg N₂O m^–2d^–1. In general, organic agricultural soils are sinks for methane. Here, the oldest site acted as a small sink for methane, whereas the two youngest afforested organic soils were sources for methane with maximum emission rates (up to 154 mg m^–2d^–1) similar to those reported for minerogenous natural peatlands. Soil respiration rates decreased with the age of the forest. The high soil respiration in the younger sites, probably resulted from the high biomass production of herbs, could create soil anaerobiosis and increase methane production. Our results show that afforestation of agricultural peat soils does not abruptly terminate the N₂O emissions during the first two decades, and afforestation can even enhance methane emission for a few years. The carbon accumulation in the developing tree stand can partly compensate the carbon loss from soil.     

Effect of plant succession, ploughing, and fertilization on the microbiological oxidation of atmospheric methane in a heathland soil

Abstract: The effect of plant succession on methane uptake was measured on intact soil cores collected from seven heathland sites. Six of the sites had undergone either secondary succession with grass or oak, ammonium fertilization or ploughing, while the seventh site was located in the native heathland. There was a positive relationship between methane uptake rate and time elapsed since the plant invasion had taken place in the native heathland. The native heathland site showed an insignificant atmospheric methane uptake of 0.01 mg CH₄ m⁻² d⁻¹, whereas the established oak brushwood (70 years old) and the grass invaded heathland (13 years old) showed rates of 1.36 mg CH₄ m⁻² d⁻¹ and 0.73 mg CH₄ m⁻² d⁻¹, respectively. In the fertilized heathland plot (112 kg N ha⁻¹ six years prior to this study) grass had become the dominating species and showed a methane oxidation rate of 0.28 mg CH₄ m⁻² d⁻¹. Ploughing of the heathland resulted in methane oxidation rates seven times the rates measured in the native heathland. The results suggested that an increased future atmospheric nitrogen deposition in heathlands and other nutrient poor ecosystems may have a stimulating effect on the soil sink for atmospheric methane.     

Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils.

Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes for Nitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospira cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.     

Microbial and Environmental Controls of Methane Fluxes Along a Soil Moisture Gradient in a Pacific Coastal Temperate Rainforest

Most studies of greenhouse gas fluxes from forest soils in the coastal rainforest have considered carbon dioxide (CO₂), whereas methane (CH₄) has not received the same attention. Soil hydrology is a key driver of CH₄ dynamics in ecosystems, but the impact on the function and distribution of the underlying microbial communities involved in CH₄ cycling and the resultant net CH₄ exchange is not well understood at this scale. We studied the growing season variations of in situ CH₄ fluxes, microbial gene abundances of methanotrophs (CH₄ oxidizers) and methanogens (CH₄ producers), soil hydrology, and nutrient availability in three typical forest types across a soil moisture gradient. CH₄ displayed a spatial variability changing from a net uptake in the upland soils (3.9–46 µmol CH₄ m^?2 h^?1) to a net emission in the wetter soils (0–90 μmol CH₄ m^?2 h^?1). Seasonal variations of CH₄ fluxes were related to soil hydrology in both upland and wet soils. Thus, in the upland soils, uptake rates increased with the decreasing soil moisture, whereas CH₄ emission was inversely related to the water table depth in the wet soils. Spatial variability of CH₄ exchange was related to the abundance of genes involved in CH₄ oxidation and production, but there was no indication of a temporal link between microbial groups and CH₄ exchange. Our data show that the abundances of genes involved in CH₄ oxidation and production are strongly influenced by soil moisture and each other and grouped by the upland–wetland classification but not forest type.     

The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration

Methanotrophic communities were studied in several periodically water-saturated gleyic soils. When sampled, each soil had an oxic upper layer and consumed methane from the atmosphere (at 1.75 ppmv). In most gleyic soils the K(m(app)) values for methane were between 70 and 800 ppmv. These are higher than most values observed in dry upland soils, but lower than those measured in wetlands. Based on cultivation-independent retrieval of the pmoA-gene and quantification of partial pmoA gene sequences, type II (Alphaproteobacteria) methanotrophs of the genus Methylocystis spp. were abundant (> 10(7) pmoA target molecules per gram of dry soil). Type I (Gammaproteobacteria) methanotrophs related to the genera Methylobacter and Methylocaldum/Methylococcus were detected in some soils. Six pmoA sequence types not closely related to sequences from cultivated methanotrophs were detected as well, indicating that diverse uncultivated methanotrophs were present. Three Gleysols were incubated under different mixing ratios of (13)C-labelled methane to examine (13)C incorporation into phospholipid fatty acids (PLFAs). Phospholipid fatty acids typical of type II methanotrophs, 16:0 and 18:1omega7c, were labelled with (13)C in all soils after incubation under an atmosphere containing 30 ppmv of methane. Incubation under 500 ppmv of methane resulted in labelling of additional PLFAs besides 16:0 and 18:1omega7c, suggesting that the composition of the active methanotrophic community changed in response to increased methane supply. In two soils, 16:1 PLFAs typical of type I methanotrophs were strongly labelled after incubation under the high methane mixing ratio only. Type II methanotrophs are most likely responsible for atmospheric methane uptake in these soils, while type I methanotrophs become active when methane is produced in the soil.