High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph

Physiological basis for atmospheric methane oxidation and methanotrophic growth on air

Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.

Resource availability governs polyhydroxyalkanoate (PHA) accumulation and diversity of methanotrophic enrichments from wetlands

Aquatic environments account for half of global CH4 emissions, with freshwater wetlands being the most significant contributors. These CH4 fluxes can be partially offset by aerobic CH4 oxidation driven by methanotrophs. Additionally, some methanotrophs can convert CH4 into polyhydroxyalkanoate (PHA), an energy storage molecule as well as a promising bioplastic polymer. In this study, we investigate how PHA-accumulating methanotrophic communities enriched from wetlands were shaped by varying resource availability (i.e., C and N concentrations) at a fixed C/N ratio. Cell yields, PHA accumulation, and community composition were evaluated in high (20% CH4 and 10 mM NH4 +) and low resource (0.2% CH4 and 0.1 mM NH4 +) conditions simulating engineered and environmental settings, respectively. High resource availability decreased C-based cell yields, while N-based cell yields remained stable, suggesting nutrient exchange patterns differed between methanotrophic communities at different resource concentrations. PHA accumulation was only observed in high resource enrichments, producing approximately 12.6% ± 2.4% (m/m) PHA, while PHA in low resource enrichments remained below detection. High resource enrichments were dominated by Methylocystis methanotrophs, while low resource enrichments remained significantly more diverse and contained only a minor population of methanotrophs. This study demonstrates that resource concentration shapes PHA-accumulating methanotrophic communities. Together, this provides useful information to leverage such communities in engineering settings as well as to begin understanding their role in the environment.

Restoration effects of submerged macrophytes on methane production and oxidation potential of lake sediments

The restoration of submerged macrophytes is an important step in lake ecosystem restoration, during which artificially assisted measures have been widely used for macrophyte recolonization. Compared with natural restoration, the impact of artificially assisted methods on methane (CH₄) production and oxidation of lake sediments remains unclear. Therefore, after the restoration of submerged macrophytes in some parts of West Lake (Hangzhou, China), sediment samples from West Lake were collected according to restoration methods and plant coverage. The CH₄ production potential, oxidation potential, and microbial community structure in the sediment were discussed through whole-lake sample analysis and resampling verification from typical lake areas. From the analysis of the whole lake, the average daily CH₄ production potential (ADP) of artificially restored lake areas (0.12 μg g^-1 d^-1) was significantly lower than that of the naturally restored lake areas (0.52 μg g^-1 d^-1). From the resampling analysis of typical lake areas, the ADP of naturally restored lake areas was 1.8 times that of artificially restored lake areas (P < 0.01). Although there was no significant difference in the CH₄ oxidation potential between the two restoration methods, the presence of submerged macrophytes significantly increased the abundance of the dominant methanotroph Methylocaldum in the sediment, and the rate of increase in the abundance of the dominant methanotroph Methylosinus was significantly higher in artificially assisted restoration than in natural restoration. This study revealed that the artificially assisted restoration of submerged macrophytes reduced the potential for CH₄ production and increased the abundance of dominant methanotrophs in the lake sediment, which would be beneficial for the reduction of CH₄ emissions during lake ecological restoration and environmental management.

Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes

Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales, Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O2 and CH4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors.

Carbon-dependent growth, community structure and methane oxidation performance of a soil-derived methanotrophic mixed culture

Soil-borne methane-oxidizing microorganisms act as a terrestrial methane (CH4) sink and are potentially useful in decreasing global CH4 emissions. Understanding the ecophysiology of methanotrophs is crucial for a thorough description of global carbon cycling. Here, we report the in situ balance of soils from abandoned landfills, meadows and wetlands, their capacities to produce and oxidize CH4 at laboratory-scale and the isolation of a soil-borne methanotrophic-heterotrophic mixed culture that was used for carbon (C1 and C2) feeding experiments. We showed that even with similar soil properties, the in situ CH4 balance depends on land-use. Different soils had different potentials to adapt to increased CH4 availability, leading to the highest CH4 oxidation capacities for landfill and wetland soils. The most efficient mixed culture isolated from the landfill was dominated by the methanotrophs Methylobacter sp. and Methylosinus sp., which were accompanied by Variovorax sp. and Pseudomonas sp. and remained active in oxidizing CH4 when supplied with additional C-sources. The ratios between type I and type II methanotrophs and between methanotrophic and heterotrophic bacteria changed when C-sources were altered. A significant effect of the application of the mixed culture on the CH4 oxidation of soils was established but the extent varied depending on soil type.

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland

Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments.

Methane oxidation and methylotroph population dynamics in groundwater mesocosms

Extraction of natural gas from unconventional hydrocarbon reservoirs by hydraulic fracturing raises concerns about methane migration into groundwater. Microbial methane oxidation can be a significant methane sink. Here, we inoculated replicated, sand‐packed, continuous mesocosms with groundwater from a field methane release experiment. The mesocosms experienced thirty‐five weeks of dynamic methane, oxygen and nitrate concentrations. We determined concentrations and stable isotope signatures of methane, carbon dioxide and nitrate and monitored microbial community composition of suspended and attached biomass. Methane oxidation was strictly dependent on oxygen availability and led to enrichment of ¹³C in residual methane. Nitrate did not enhance methane oxidation under oxygen limitation. Methylotrophs persisted for weeks in the absence of methane, making them a powerful marker for active as well as past methane leaks. Thirty‐nine distinct populations of methylotrophic bacteria were observed. Methylotrophs mainly occurred attached to sediment particles. Abundances of methanotrophs and other methylotrophs were roughly similar across all samples, pointing at transfer of metabolites from the former to the latter. Two populations of Gracilibacteria (Candidate Phyla Radiation) displayed successive blooms, potentially triggered by a period of methane famine. This study will guide interpretation of future field studies and provides increased understanding of methylotroph ecophysiology.

Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates

Lake methane (CH₄ ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH₄ oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH₄ oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH₄ oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH₄ oxidation rates in lakes and that information on the MOB community can help predict CH₄ oxidation rates and thus emissions from lakes.

Niche partitioning of methane-oxidizing bacteria along the oxygen-methane counter gradient of stratified lakes

Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen-methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen-methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and pmoA genes, and 16S rRNA and pmoA transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen-methane interface. The interface sometimes harbored additional taxa. Within the dominant Methylococcales, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions. Candidatus Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen-methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.

SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter

Marine bacterioplankton face stiff competition for limited nutrient resources. SAR11, a ubiquitous clade of very small and highly abundant Alphaproteobacteria, are known to devote much of their energy to synthesizing ATP-binding cassette periplasmic proteins that bind substrates. We hypothesized that their small size and relatively large periplasmic space might enable them to outcompete other bacterioplankton for nutrients. Using uptake experiments with ¹⁴ C-glycine betaine, we discovered that two strains of SAR11, Candidatus Pelagibacter sp. HTCC7211 and Cand. P. ubique HTCC1062, have extraordinarily high affinity for glycine betaine (GBT), with half-saturation (K _s ) values around 1 nM and specific affinity values between 8 and 14 L mg cell^-1  h^-1 . Competitive inhibition studies indicated that the GBT transporters in these strains are multifunctional, transporting multiple substrates in addition to GBT. Both strains could use most of the transported compounds for metabolism and ATP production. Our findings indicate that Pelagibacter cells are primarily responsible for the high affinity and multifunctional GBT uptake systems observed in seawater. Maximization of whole-cell affinities may enable these organisms to compete effectively for nutrients during periods when the gross transport capacity of the heterotrophic plankton community exceeds the supply, depressing ambient concentrations.

Differentiated Mechanisms of Biochar Mitigating Straw-Induced Greenhouse Gas Emissions in Two Contrasting Paddy Soils

Straw returns to the soil is an effective way to improve soil organic carbon and reduce air pollution by straw burning, but this may increase CH₄ and N₂O emissions risks in paddy soils. Biochar has been used as a soil amendment to improve soil fertility and mitigate CH₄ and N₂O emissions. However, little is known about their interactive effect on CH₄ and N₂O emissions and the underlying microbial mechanisms. In this study, a 2-year pot experiment was conducted on two paddy soil types (an acidic Utisol, TY, and an alkaline Inceptisol, BH) to evaluate the influence of straw and biochar applications on CH₄ and N₂O emissions, and on related microbial functional genes. Results showed that straw addition markedly increased the cumulative CH₄ emissions in both soils by 4.7- to 9.1-fold and 23.8- to 72.4-fold at low (S1) and high (S2) straw input rate, respectively, and significantly increased mcrA gene abundance. Biochar amendment under the high straw input (BS2) significantly decreased CH₄ emissions by more than 50% in both soils, and increased both mcrA gene and pmoA gene abundances, with greatly enhanced pmoA gene and a decreased mcrA/pmoA gene ratio. Moreover, methanotrophs community changed distinctly in response to straw and biochar amendment in the alkaline BH soil, but showed slight change in the acidic TY soil. Straw had little effect on N₂O emissions at low input rate (S1) but significantly increased N₂O emissions at the high input rate (S2). Biochar amendment showed inconsistent effect on N₂O emissions, with a decreasing trend in the BH soil but an increasing trend in the TY soil in which high ammonia existed. Correspondingly, increased nirS and nosZ gene abundances and obvious community changes in nosZ gene containing denitrifiers in response to biochar amendment were observed in the BH soil but not in the TY soil. Overall, our results suggested that biochar amendment could markedly mitigate the CH₄ and N₂O emissions risks under a straw return practice via regulating functional microbes and soil physicochemical properties, while the performance of this practice will vary depending on soil parent material characteristics.

Development of a novel methanotrophic process with the helper micro-organism Hyphomicrobium sp. NM3

AIMS

Microbial consortia can be more efficient at biological processes than single isolates. The purposes of this study were to design and evaluate a synthetic microbial consortium containing the methanotroph Methylocystis sp. M6 and the helper Hyphomicrobium sp. NM3, and develop a novel methanotrophic process for this consortium utilizing a dialysis membrane.

METHODS AND RESULTS

Hyphomicrobium increased the methane-oxidation rate (MOR), biomass and stability at a dilution rate of 0·067 day^-1 in fed-batch co-culture. qRT-PCR showed that Methylocystis population increased gradually with time, whereas Hyphomicrobium population remained stable despite cell washing, confirming synergistic population interaction. At 0·1 day^-1 , spiking of Hyphomicrobium effectively increased the methanotrophic activity, after which Hyphomicrobium population decreased with time, indicating that the consortium is optimal at <0·1 day^-1 . When Hyphomicrobium was grown in dialysis membrane within the bioreactor, MOR increased linearly up to 155·1 ± 1·0 mmol l^-1  day^-1 at 0·067, 0·1, 0·2 and 0·4 day^-1 , which is the highest observed value for a methanotrophic reactor.

CONCLUSIONS

Hyphomicrobium sp. NM3 is a promising helper micro-organism for methanotrophs. Hyphomicrobium-methanotroph consortia used concurrently with existing methods can produce an efficient and stable methane oxidation system.

SIGNIFICANCE AND IMPACT OF THE STUDY

This novel methanotrophic process is superior to those previously reported in the literature, and can provide efficient and stable methane oxidation.

Novel approaches and reasons to isolate methanotrophic bacteria with biotechnological potentials: recent achievements and perspectives

The recent drop in the price of natural gas has rekindled the interests in methanotrophs, the organisms capable of utilizing methane as the sole electron donor and carbon source, as biocatalysts for various industrial applications. As heterologous expression of the methane monooxygenases in more amenable hosts has been proven to be nearly impossible, future success in methanotroph biotechnology largely depends on securing phylogenetically and phenotypically diverse methanotrophs with relatively high growth rates. For long, isolation of methanotrophs have relied on repeated single colony picking after initial batch enrichment with methane, which is a very rigorous and time-consuming process. In this review, three unconventional isolation methods devised for facilitation of the isolation process, diversification of targeted methanotrophs, and/or screening of rapid growers are summarized. The soil substrate membrane method allowed for isolation of previously elusive methanotrophs and application of high-throughput extinction plating technique facilitated the isolation procedure. Use of a chemostat with gradually increased dilution rates proved effective in screening for the fastest-growing methanotrophs from environmental samples. Development of new isolation technologies incorporating microfluidics and single-cell techniques may lead to discovery of previously unculturable methanotrophs with unexpected metabolic potentials and thus, certainly warrant future investigation.

The hunt for the most-wanted chemolithoautotrophic spookmicrobes

Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.

Co-cultivation of the strictly anaerobic methanogen Methanosarcina barkeri with aerobic methanotrophs in an oxygen-limited membrane bioreactor

Wetlands contribute to 30% of global methane emissions due to an imbalance between microbial methane production and consumption. Methanogenesis and methanotrophy have mainly been studied separately, and little is known about their potential interactions in aquatic environments. To mimic the interaction between methane producers and oxidizers in the environment, we co-cultivated the methanogenic archaeon Methanosarcina barkeri with aerobic Methylocystaceae methanotrophs in an oxygen-limited bioreactor using acetate as methanogenic substrate. Methane, acetate, dissolved oxygen, available nitrogen, pH, temperature, and cell density were monitored to follow system stability and activity. Stable reactor operation was achieved for two consecutive periods of 2 months. Fluorescence in situ hybridization micrographs indicated close association between both groups of microorganisms. This association suggests that the methanotrophs profit from direct access to the methane that is produced from acetate, while methanogens are protected by the concomitant oxygen consumption of the methanotrophs. This proof of principle study can be used to set up systems to study their responses to environmental changes.

Positive diversity-functioning relationships in model communities of methanotrophic bacteria

Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH₄ at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH₄ consumption and community size were positively correlated. The temporal CH₄ consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.

Microbial and Isotopic Evidence for Methane Cycling in Hydrocarbon-Containing Groundwater from the Pennsylvania Region

The Pennsylvania region hosts numerous oil and gas reservoirs and the presence of hydrocarbons in groundwater has been locally observed. However, these methane-containing freshwater ecosystems remain poorly explored despite their potential importance in the carbon cycle. Methane isotope analysis and analysis of low molecular weight hydrocarbon gases from 18 water wells indicated that active methane cycling may be occurring in methane-containing groundwater from the Pennsylvania region. Consistent with this observation, multigenic qPCR and gene sequencing (16S rRNA genes, mcrA, and pmoA genes) indicated abundant populations of methanogens, ANME-2d (average of 1.54 × 10⁴mcrA gene per milliliter of water) and bacteria associated with methane oxidation (NC10, aerobic methanotrophs, methylotrophs; average of 2.52 × 10³pmoA gene per milliliter of water). Methane cycling therefore likely represents an important process in these hydrocarbon-containing aquifers. The microbial taxa and functional genes identified and geochemical data suggested that (i) methane present is at least in part due to methanogens identified in situ; (ii) Potential for aerobic and anaerobic methane oxidation is important in groundwater with the presence of lineages associated with both anaerobic an aerobic methanotrophy; (iii) the dominant methane oxidation process (aerobic or anaerobic) can vary according to prevailing conditions (oxic or anoxic) in the aquifers; (iv) the methane cycle is closely associated with the nitrogen cycle in groundwater methane seeps with methane and/or methanol oxidation coupled to denitrification or nitrate and nitrite reduction.

Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants

Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland). Methanotrophic bacteria were isolated from plants by adding sterile fragments of different parts of plants (roots and stems) to agar mineral medium (nitrate mineral salts (NMS)) and incubated at different methane values (1–20% CH4). Single colonies were streaked on new NMS agar media and, after incubation, transferred to liquid NMS medium. Bacterial growth dynamics in the culture solution was studied by optical density—OD600 and methane consumption. Changes in the methane concentration during incubation were controlled by the gas chromatography technique. Characterization of methanotrophs was made by fluorescence in situ hybridization (FISH) with Mg705 and Mg84 for type I methanotrophs and Ma450 for type II methanotrophs. Identification of endophytes was performed after 16S ribosomal RNA (rRNA) and mmoX gene amplification. Our study confirmed the presence of both types of methanotrophic bacteria (types I and II) with the predominance of type I methanotrophs. Among cultivable methanotrophs, there were different strains of the genus Methylomonas and Methylosinus. Furthermore, we determined the potential of the examined bacteria for methane oxidation, which ranged from 0.463 ± 0.067 to 5.928 ± 0.169 μmol/L CH4/mL/day.

Atmospheric CH4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature

The response of methanotrophic bacteria capable of oxidizing atmospheric CH₄ to climate warming is poorly understood, especially for those present in Arctic mineral cryosols. The atmospheric CH₄ oxidation rates were measured in microcosms incubated at 4 °C and 10 °C along a 1-m depth profile and over a range of water saturation conditions for mineral cryosols containing type I and type II methanotrophs from Axel Heiberg Island (AHI), Nunavut, Canada. The cryosols exhibited net consumption of ~2 ppmv CH₄ under all conditions, including during anaerobic incubations. Methane oxidation rates increased with temperature and decreased with increasing water saturation and depth, exhibiting the highest rates at 10 °C and 33% saturation at 5 cm depth (260 ± 60 pmol CH₄ gdw^-1 d^-1 ). Extrapolation of the CH₄ oxidation rates to the field yields net CH₄ uptake fluxes ranging from 11 to 73 μmol CH₄  m^-2 d^-1 , which are comparable to field measurements. Stable isotope mass balance indicates ~50% of the oxidized CH₄ is incorporated into the biomass regardless of temperature or saturation. Future atmospheric CH₄ uptake rates at AHI with increasing temperatures will be determined by the interplay of increasing CH₄ oxidation rates vs. water saturation and the depth to the water table during summer thaw.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

Effect of CH4/O2 ratio on fatty acid profile and polyhydroxybutyrate content in a heterotrophic-methanotrophic consortium

Understanding the role of heterotrophic-methanotrophic (H-Meth) communities is important for improvement of methane (CH4) oxidation capacities (MOC) particularly in conjunction with bio-product development in industrial bio-filters. Initially, a H-Meth consortium was established and enriched from marine sediments and characterized by next generation sequencing of the 16s rDNA gene. The enriched consortium was subjected to 10-50% CH4 (i.e., 0.20-1.6 CH4/O2 ratios) to study the effects on MOCs, biomass growth, fatty acid profiles and biopolymer (e.g. polyhydroxybutyrate; PHB) content. Methylocystis, Methylophaga and Pseudoxanthomonas dominated the H-Meth consortium. Culture enrichment of the H-Meth consortium resulted in 15-20-folds higher MOC compared to seed sediments. Increasing CH4 concentration (and decreased O2 levels) yielded higher MOCs, but did not improve total fatty acid contents. PHB contents varied between 2.5% and 8.5% independently of CH4/O2 ratios. The results suggest that H-Meth consortia could potentially be used in industrial bio-filters for production of biopolymer/biofuel precursors from CH4.

Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows

The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.

Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging

The majority of microbial cells in global soils exist in a spectrum of dormant states. However, the metabolic processes that enable them to survive environmental challenges, such as nutrient-limitation, remain to be elucidated. In this work, we demonstrate that energy-starved cultures of Pyrinomonas methylaliphatogenes, an aerobic heterotrophic acidobacterium isolated from New Zealand volcanic soils, persist by scavenging the picomolar concentrations of H2 distributed throughout the atmosphere. Following the transition from exponential to stationary phase due to glucose limitation, the bacterium up-regulates by fourfold the expression of an eight-gene operon encoding an actinobacteria-type H2-uptake [NiFe]-hydrogenase. Whole-cells of the organism consume atmospheric H2 in a first-order kinetic process. Hydrogen oxidation occurred most rapidly under oxic conditions and was weakly associated with the cell membrane. We propose that atmospheric H2 scavenging serves as a mechanism to sustain the respiratory chain of P. methylaliphatogenes when organic electron donors are scarce. As the first observation of H2 oxidation to our knowledge in the Acidobacteria, the second most dominant soil phylum, this work identifies new sinks in the biogeochemical H2 cycle and suggests that trace gas oxidation may be a general mechanism for microbial persistence.

Effects of Long-Term CO2 Enrichment on Soil-Atmosphere CH4 Fluxes and the Spatial Micro-Distribution of Methanotrophic Bacteria

Background

Effects of elevated atmospheric CO₂ concentrations on plant growth and associated C cycling have intensively been studied, but less is known about effects on the fluxes of radiatively active trace gases other than CO₂. Net soil-atmosphere CH₄ fluxes are determined by the balance of soil microbially-driven methane (CH₄) oxidation and methanogenesis, and both might change under elevated CO₂.

Methods and Results

Here, we studied CH₄ dynamics in a permanent grassland exposed to elevated CO₂ for 14 years. Soil-atmosphere fluxes of CH₄ were measured using large static chambers, over a period of four years. The ecosystem was a net sink for atmospheric CH₄ for most of the time except summer to fall when net CH₄ emissions occurred. We did not detect any elevated CO₂ effects on CH₄ fluxes, but emissions were difficult to quantify due to their discontinuous nature, most likely because of ebullition from the saturated zone. Potential methanotrophic activity, determined by incubation of fresh sieved soil under standardized conditions, also did not reveal any effect of the CO₂ treatment. Finally, we determined the spatial micro-distribution of methanotrophic activity at less than 5× atmospheric (10 ppm) and elevated (10000 ppm) CH₄ concentrations, using a novel auto-radiographic technique. These analyses indicated that domains of net CH₄ assimilation were distributed throughout the analyzed top 15 cm of soils, with no dependence on CH₄ concentration or CO₂ treatment.

Conclusions

Our investigations suggest that elevated CO₂ exerts no or only minor effects on CH₄ fluxes in the type of ecosystem we studied, at least as long as soil moisture differences are small or absent as was the case here. The autoradiographic analyses further indicate that the spatial niche of CH₄ oxidation does not shift in response to CO₂ enrichment or CH₄ concentration, and that the same type of methanotrophs may oxidize CH₄ from atmospheric and soil-internal sources.

Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation

We have previously observed that methane supplied to lake sediment microbial communities as a substrate not only causes a response by bona fide methanotrophic bacteria, but also by non-methane-oxidizing bacteria, especially by members of the family Methylophilaceae. This result suggested that methane oxidation in this environment likely involves communities composed of different functional guilds, rather than a single type of microbe. To obtain further support for this concept and to obtain further insights into the factors that may define such partnerships, we carried out microcosm incubations with sediment samples from Lake Washington at five different oxygen tensions, while methane was supplied at the same concentration in each. Community composition was determined through 16S rRNA gene amplicon sequencing after 10 and 16 weeks of incubation. We demonstrate that, in support of our prior observations, the methane-consuming communities were represented by two major types: the methanotrophs of the family Methylococcaceae and by non-methanotrophic methylotrophs of the family Methylophilaceae. However, different species persisted under different oxygen tensions. At high initial oxygen tensions (150 to 225 µM) the major players were, respectively, species of the genera Methylosarcina and Methylophilus, while at low initial oxygen tensions (15 to 75 µM) the major players were Methylobacter and Methylotenera. These data suggest that oxygen availability is at least one major factor determining specific partnerships in methane oxidation. The data also suggest that speciation within Methylococcaceae and Methylophilaceae may be driven by niche adaptation tailored toward specific placements within the oxygen gradient.

Characterization of Methylocystis strain JTA1 isolated from aged refuse and its tolerance to chloroform

To accelerate the efficiency of methane biodegradation in landfills, a Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, JTA1, which can utilize methane as well as acetate, was isolated from the Laogang MSW landfills, Shanghai, China. Strain JTA1 was a member of genus Methylocystis on the basis of 16S rRNA and pmoA gene sequence similarity. The maximum specific cell growth rates (micro(max) = 0.042 hr(-1), R2 = 0.995) was derived through Boltzmann simulation, and the apparent half-saturation constants (K(m(app)) = 7.08 mmol/L, R2 = 0.982) was calculated according to Michaelis-Menton hyperbolic model, indicating that Methylocystis strain JTA1 had higher-affinity potential for methane oxidation than other reported methanotrophs. By way of adding the strain JTA1 culture, the methane consumption of aged refuse reached 115 mL, almost two times of control experiment. In addition, high tolerance of Methylocystis strain JTA1 to chloroform could facilitate the methane oxidation of aged refuse bio-covers. At the chloroform concentration of 50 mg/L, the methane-oxidation rate of bio-cover reached 0.114 mL/(day x g), much higher than the highest rate, 0.0135 mL/(day x g), of reported bio-covers. In conclusion, strain JTA1 opens up a new possibility for environmental biotechnology, such as soil or landfills bioremediation and wastewater decontamination.

Inhibition of methane oxidation in a slurry surface crust by inorganic nitrogen: an incubation study

Livestock slurry is an important source of methane (CH). However, depending on the dry matter content of the slurry, a floating crust may form where methane-oxidizing bacteria (MOB) and CH oxidation activity have been found, suggesting that surface crusts may reduce CH emissions from slurry. However, it is not known how MOB in this environment interact with inorganic nitrogen (N). We studied inhibitory effects of ammonium (NH), nitrate (NO), and nitrite (NO) on potential CH oxidation in a cattle slurry surface crust. At headspace concentrations of 100 and 10,000 ppmv, CH oxidation was assayed at salt concentrations up to 500 mM. First-order rate constants were used to evaluate the strength of inhibition. Nitrite was the most potent inhibitor, reducing methanotrophic activity by up to 70% at only 1 mM NO. Methane-oxidizing bacteria were least sensitive to NO, tolerating up to 30 mM NO at 100 ppmv CH and 50 mM NO at 10,000 ppmv CH without any decline in activity. The inhibition by NH increased progressively, and no range of tolerance was observed. Methane concentrations of 10,000 ppmv resulted in 50- to 100-fold higher specific CH uptake rates than 100 ppmv CH but did not change the inhibition patterns of N salts. In slurry surface crusts, MOB maintained activity at higher concentrations of NH and NO than reported for MOB in soils and sediments, possibly showing adaptation to high N concentrations in the slurry environment. Yet it appears that the effectiveness of surface crusts as CH sinks will depend on inorganic N concentrations.

Microbial CH(4) and N(2)O Consumption in Acidic Wetlands

Acidic wetlands are global sources of the atmospheric greenhouse gases methane (CH(4)), and nitrous oxide (N(2)O). Consumption of both atmospheric gases has been observed in various acidic wetlands, but information on the microbial mechanisms underlying these phenomena is scarce. A substantial amount of CH(4) is consumed in sub soil by aerobic methanotrophs at anoxic-oxic interfaces (e.g., tissues of Sphagnum mosses, rhizosphere of vascular plant roots). Methylocystis-related species are likely candidates that are involved in the consumption of atmospheric CH(4) in acidic wetlands. Oxygen availability regulates the activity of methanotrophs of acidic wetlands. Other parameters impacting on the methanotroph-mediated CH(4) consumption have not been systematically evaluated. N(2)O is produced and consumed by microbial denitrification, thus rendering acidic wetlands as temporary sources or sinks for N(2)O. Denitrifier communities in such ecosystems are diverse, and largely uncultured and/or new, and environmental factors that control their consumption activity are unresolved. Analyses of the composition of N(2)O reductase genes in acidic wetlands suggest that acid-tolerant Proteobacteria have the potential to mediate N(2)O consumption in such soils. Thus, the fragmented current state of knowledge raises open questions concerning methanotrophs and denitrifiers that consume atmospheric CH(4) and N(2)O in acidic wetlands.

Acetate utilization as a survival strategy of peat-inhabiting Methylocystis spp

Representatives of the genus Methylocystis are traditionally considered to be obligately methanotrophic bacteria, which are incapable of growth on multicarbon substrates. Here, we describe a novel member of this genus, strain H2s, which represents a numerically abundant and ecologically important methanotroph population in northern Sphagnum-dominated wetlands. This isolate demonstrates a clear preference for growth on methane but is able to grow slowly on acetate in the absence of methane. Strain H2s possesses both forms of methane monooxygenase (particulate and soluble MMO) and a well-developed system of intracytoplasmic membranes (ICM). In cells grown for several transfers on acetate, these ICM are maintained, although in a reduced form, and mRNA transcripts of particulate MMO are detectable. These cells resume their growth on methane faster than those kept for the same period of time without any substrate. Growth on acetate leads to a major shift in the phospholipid fatty acid composition. The re-examination of all type strains of the validly described Methylocystis species showed that Methylocystis heyeri H2(T) and Methylocystis echinoides IMET10491(T) are also capable of slow growth on acetate. This capability might represent an important part of the survival strategy of Methylocystis spp. in environments where methane availability is variable or limited.

Effect of substrate interaction on oxidation of methane and benzene in enriched microbial consortia from landfill cover soil

The interaction of methane and benzene during oxidation in enriched methane-oxidizing consortium (MOC) and in benzene-oxidizing consortium (BOC) from landfill cover soil was characterized. Oxidation of both methane and benzene occurred in the MOC due to the coexistence of bacteria responsible for benzene oxidation, as well as methanotrophs, whereas in the BOC, only benzene was oxidized, not methane. Methane oxidation rates in the MOC were decreased with increasing benzene/methane ratio (mol/mol), indicating its methane oxidation was inhibited by the benzene coexistence. Benzene oxidation rates in the MOC, however, were increased with increasing benzene/methane ratio. The benzene oxidation in the BOC was not affected by the coexistence of methane or by the ratio of methane/benzene ratio (mol/mol). No effect of methane or benzene was found on the dynamics of functional genes, such as particulate methane monooxygenase and toluene monooxygenase, in association with oxidation of methane and benzene in the MOC and BOC.

Temporal bacterial diversity and detection of putative methanotrophs in surface mats of Lonar crater lake

The phylogenetic diversity of bacterial communities in microbial mats of two different seasons from saline and hyperalkaline Lonar Lake was investigated using 16S rRNA gene library analysis. Arthrospira (Cyanobacteria) related clones (>80% of total clones) dominated libraries of both the seasons. Clear differences were found in both the seasons as the operational taxonomic units (OTUs) related to Fusibacter (LAI-1 and LAI-59) and Tindallia magadiensis (LAI-27) found in post-monsoon were not found in the pre-monsoon library. Likewise, OTUs related to Planococcus rifietensis (LAII-67), Bordetella hinzii (LAII-2) and Methylobacterium variabile (LAII-25) found in the pre-monsoon were not found in post-monsoon. The study was extended to identify methanotrophs in the surface mats. Libraries constructed with type I and type II methanotroph specific 16S rRNA gene primers showed the presence of clones (LAMI-99 and LAMII-2) closely related to Methylomicrobium buryaticum and Beijerinckiaceae family members. Denaturing gradient gel electrophoresis (DGGE) fingerprinting based on protein-coding genes (pmoA and mxaF) further confirmed the detection of Methylomicrobium sp. Hence, we report here for the first time the detection of putative methanotrophs in surface mats of Lonar Lake. The finding of clones related to organisms with interesting functional attributes such as assimilation of C(1) compounds (LAII-25, LAMI-39, LAMI-99 and LAMII-2), non-sulfur photosynthetic bacteria (LAMII-43) and clones distantly affiliated to organisms of heavily polluted environments (LAI-59 and LAMII-52), is of significant note. These preliminary results would direct future studies on the functional dynamics of microbial mat associated food web chain in the extreme environment.

Notes on the temperature dependence of carbon isotope fractionation by aerobic CH(4)-oxidising bacteria

While the importance of environmental analyses based on isotope discrimination has been growing, uncertainties remain about underlying phenomena. Published results on the temperature dependence of carbon isotope fractionation during methane oxidation in various media show different trends. A decrease in fractionation is generally expected with temperature, but some data for methane oxidation in aqueous media show an inverse relationship. This apparent contradiction was probed by representing the first methane oxidation step as three elementary processes: the adsorption of methane on the bacterial cell wall, the desorption of methane from the wall, and the conversion of methane into methanol mediated by methane monooxygenase (MMO) enzymes. Assuming that the proportion of vacant adsorption sites is stationary, a formula for the composite fractionation factor alpha was obtained. It was shown that alpha not only expresses the fractionation that may occur in each elementary process, but that it also depends on the ratio of the kinetic rates for conversion into methanol and desorption. This result and experimental data were used to estimate the activation energy for the desorption of methane from methanotroph cell wall in aqueous medium ( approximately 200 kJ/mol). Simple Rosso models of bacterial maximal-specific growth rate were then used to demonstrate that alpha and the isotope fractionation from the MMO-mediated conversion into methanol alone could vary in opposite ways as temperature changes, but that care must be exercised when using fitted relationships across wide temperature ranges.

Different atmospheric methane-oxidizing communities in European beech and Norway spruce soils

Norway spruce (Picea abies) forests exhibit lower annual atmospheric methane consumption rates than do European beech (Fagus sylvatica) forests. In the current study, pmoA (encoding a subunit of membrane-bound CH(4) monooxygenase) genes from three temperate forest ecosystems with both beech and spruce stands were analyzed to assess the potential effect of tree species on methanotrophic communities. A pmoA sequence difference of 7% at the derived protein level correlated with the species-level distance cutoff value of 3% based on the 16S rRNA gene. Applying this distance cutoff, higher numbers of species-level pmoA genotypes were detected in beech than in spruce soil samples, all affiliating with upland soil cluster alpha (USCalpha). Additionally, two deep-branching genotypes (named 6 and 7) were present in various soil samples not affiliating with pmoA or amoA. Abundance of USCalpha pmoA genes was higher in beech soils and reached up to (1.2 +/- 0.2) x 10(8) pmoA genes per g of dry weight. Calculated atmospheric methane oxidation rates per cell yielded the same trend. However, these values were below the theoretical threshold necessary for facilitating cell maintenance, suggesting that USCalpha species might require alternative carbon or energy sources to thrive in forest soils. These collective results indicate that the methanotrophic diversity and abundance in spruce soils are lower than those of beech soils, suggesting that tree species-related factors might influence the in situ activity of methanotrophs.

Methanotrophs and copper

Methanotrophs, cells that consume methane (CH(4)) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH(4), the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH(4) to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH(4) fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH(4) oxidation by the particulate CH(4) monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs.

Activity and community structure of methane-oxidising bacteria in a wet meadow soil

The structure and activity of the methane-oxidising microbial community in a wet meadow soil in Germany were investigated using biogeochemical, cultivation, and molecular fingerprinting techniques. Both methane from the atmosphere and methane produced in anaerobic subsurface soil were oxidised. The specific affinity (first-order rate constant) for methane consumption was highest in the top 20 cm of soil and the apparent half-saturation constant was 137-300 nM CH(4), a value intermediate to measured values in wetland soils versus well-aerated upland soils. Most-probable-number (MPN) counting of methane-oxidising bacteria followed by isolation and characterisation of strains from the highest positive dilution steps suggested that the most abundant member of the methane-oxidising community was a Methylocystis strain (10(5)-10(7) cells g(-1) d.w. soil). Calculations based on kinetic data suggested that this cell density was sufficient to account for the observed methane oxidation activity in the soil. DNA extraction directly from the same soil samples, followed by PCR amplification and comparative sequence analyses of the pmoA gene, also detected Methylocystis. However, molecular community fingerprinting analyses revealed a more diverse and dynamic picture of the methane-oxidising community. Retrieved pmoA sequences included, besides those closely related to Methylocystis spp., others related to the genera Methylomicrobium and Methylocapsa, and there were differences across samples which were not evident in MPN analyses.

The global methane cycle: recent advances in understanding the microbial processes involved

The global budget of atmospheric CH4 , which is on the order of 500-600 Tg CH4 per year, is mainly the result of environmental microbial processes, such as archaeal methanogenesis in wetlands, rice fields, ruminant and termite digestive systems and of microbial methane oxidation under anoxic and oxic conditions. This review highlights recent progress in the research of anaerobic CH4 oxidation, of CH4 production in the plant rhizosphere, of CH4 serving as substrate for the aquatic trophic food chain and the discovery of novel aerobic methanotrophs. It also emphasizes progress and deficiencies in our knowledge of microbial utilization of low atmospheric CH4 concentrations in soil, CH4 production in the plant canopy, intestinal methanogenesis and CH4 production in pelagic water.

The quest for atmospheric methane oxidizers in forest soils

Aerobic methanotrophs in forest soils are the largest biological sink for atmospheric methane (CH4 ). Community structures in 53 soils from Europe, Russia, North and South America, Asia and New Zealand located in boreal, temperate and tropical forests were analysed and maximal abundances of 2.1 × 10(7) methanotrophs g(-1)   DW were measured. In acidic soils, the most frequently detected pmoA genotypes were Upland Soil Cluster α (USCα) and Methylocystis spp. Phospholipid fatty acids that were labelled by consumption of (14/13) CH4 suggested the activity of type II methanotrophs. Cluster 1 (Methylocystaceae), USCγ and Methylocystis spp. were frequently detected genotypes in pH-neutral soils. Genotypes with ambiguous functional affiliation were co-detected (Clusters MR1, RA21, 2) and may represent aerobic methanotrophs, ammonia oxidizers or enzymes with an unknown function. The physiological traits of atmospheric CH4 oxidizers are largely unknown because organisms possessing the key forest soil pmoA genotypes (USCα, USCγ, Cluster 1) have not been cultivated. Some methanotrophic strains belonging to the family Methylocystaceae have been shown to oxidize CH4 at atmospheric mixing ratios. Methylocystis strain SC2 was found to have an alternative particulate CH4 monooxygenase responsible for CH4 oxidation at atmospheric mixing ratios. pH, forest type and temperature might be environmental factors that shape methanotrophic communities in forest soils. However, specific effects on individual species are largely unknown, and only a limited number of studies have addressed environmental controls of methanotrophic diversity, pointing to the need for future research in this area.

Activity and structure of methanotrophic communities in landfill cover soils

The composition of the methanotrophic community in soil covers on five landfills in Northern and Eastern Germany was investigated by means of diagnostic microarray and terminal restriction fragment length polymorphism (T-RFLP), both targeting the pmoA gene of methanotrophs. Physical and chemical properties of the 15 sampled soil profiles varied greatly, thus providing for very different environmental conditions. The potential methane oxidation activity, assessed using undisturbed soil cores, varied between 0.2 and 28 µg CH4 gdw (-1)  h(-1) , the latter amounting to 426 g CH4 m(-2)  h(-1) . Total nitrogen was found to be the soil variable correlating most strongly with methanotrophic activity. Explaining close to 50% of the observed variability, this indicates that on the investigated sites activity and thus abundance of methanotrophs may have been nitrogen-limited. Variables that enhance organic matter and thus nitrogen accumulation, such as field capacity, also positively impacted methanotrophic activity. In spite of the great variability of soil properties and different geographic landfill location, both microarray and T-RFLP analysis suggested that the composition of the methanotrophic community on all five sites, in all profiles and across all depths was similar. Methylocystis, Methylobacter and Methylococcus species, including Methylococcus-related uncultivated methanotrophs, were predominantly detected among type II, Ia and Ib methanotrophs, respectively. This indicates that the high methane fluxes typical for landfill environments may be the most influential driver governing the community composition, or other variables not analysed in this study. Principal component analysis suggested that community diversity is most influenced by the site from which the samples were taken and second, from the location on the individual sites, i.e. the soil profile. Landfill and individual profiles reflect the combined impact of all effective variables, including those that were not measured in this study.