Bacterial Methane Oxidation Research Articles

Лечебные грязи на побережье Тауйской губы Охотского моря

The article describes the results of studying the conditions of occurrence and composition of sulphide muds on the coast of the Tauysk Bay in the Sea of Okhotsk. Bacterial oxidation of methane, that migrated from the depths of aquatic sedimentary basins (catagenetic methane), plays a leading role in the formation of sulfide silty pelites. A genetic relationship was noted between the accumulations of therapeutic mud on the Tauysk Bay coast and possibly oil-and-gas- and coal-bearing depressions in the Yama-Tauy sedimentary basin. An environmentally safe method of extracting muds from the ice of reservoirs in the cold season is recommended.

Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer.

Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo-electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.

Large freshwater phages with the potential to augment aerobic methane oxidation

There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host–phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.

Resource partitioning among brachiopods and bivalves at ancient hydrocarbon seeps: A hypothesis.

Brachiopods were thought to have dominated deep-sea hydrothermal vents and hydrocarbon seeps for most of the Paleozoic and Mesozoic, and were believed to have been outcompeted and replaced by chemosymbiotic bivalves during the Late Cretaceous. But recent findings of bivalve-rich seep deposits of Paleozoic and Mesozoic age have questioned this paradigm. By tabulating the generic diversity of the dominant brachiopod and bivalve clades-dimerelloid brachiopods and chemosymbiotic bivalves-from hydrocarbon seeps through the Phanerozoic, we show that their evolutionary trajectories are largely unrelated to one another, indicating that they have not been competing for the same resources. We hypothesize that the dimerelloid brachiopods generally preferred seeps with abundant hydrocarbons in the bottom waters above the seep, such as oil seeps or methane seeps with diffusive seepage, whereas seeps with strong, advective fluid flow and hence abundant hydrogen sulfide were less favorable for them. At methane seeps typified by diffusive seepage and oil seeps, oxidation of hydrocarbons in the bottom water by chemotrophic bacteria enhances the growth of bacterioplankton, on which the brachiopods could have filter fed. Whereas chemosymbiotic bivalves mostly relied on sulfide-oxidizing symbionts for nutrition, for the brachiopods aerobic bacterial oxidation of methane and other hydrocarbons played a more prominent role. The availability of geofuels (i.e. the reduced chemical compounds used in chemosynthesis such as hydrogen sulfide, methane, and other hydrocarbons) at seeps is mostly governed by fluid flow rates, geological setting, and marine sulfate concentrations. Thus rather than competition, we suggest that geofuel type and availability controlled the distribution of brachiopods and bivalves at hydrocarbon seeps through the Phanerozoic.

Interactions of sulfur and methane-oxidizing bacteria in tropical estuarine sediments

The bacterial oxidation of sulfur and methane is central to the biogeochemical processes in sediments such as the tropical mangrove sediments. However, there is a lacuna of information on the seasonal interactions including the influence of monsoons which is a major driver of seasonal change, on sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), their activity and the environmental variables. To understand these interactions, the analysis was carried out on sediment samples that were sampled monthly for a year from Chorao mangrove, Goa, southwest coast of India. SOB (3.8×105CFU g-1) and MOB (0.90×105CFU g-1) had maximum average abundance in the surface sediments in the post-monsoon and monsoon season, respectively. The mean sulfur-oxidation activity (SOA) of 2.63mMday-1 and methane-oxidation activity (MOA) of 110.94mMday-1 were highest in surface sediments during the post-monsoon season. Generally, the activity of SOB and MOB in surface sediments of post-monsoon was 2.2 times(×) and 2.8× respectively higher than that in the monsoon season. Among the environmental parameters analyzed, protein and sulfide concentrations significantly (p < 0.001) influenced SOA and MOA, respectively. There was a significant difference in SOA (p < 0.003) and MOA (p < 0.036) in surface sediments between the monsoon and the post-monsoon season. During the monsoon season, when the system is a sink of terrestrial/anthropogenic material, the interrelationship of SOB with MOA (r = 0.617, p < 0.001) and SOB with SOA (r = 0.489, p < 0.05) aids in maintaining the homeostasis of the system.

A centrifuge tube reactor for the determination of bacterial methane oxidation enrichment factors without influence of diffusion related isotope fractionation

Biotransformation of methane at landfill sites can be estimated by applying compound specific stable isotope analysis of methane from the anaerobic and the cover layer surface zone. Next to these two input parameters, merely the knowledge of the carbon isotopic fractionation of the bacterial methane oxidation in terms of the enrichment factor (ε) is required. However, many factors and conditions have been described to affect ε. These include temperature, the applied landfill cover, the type of expressed methane monooxygenase (MMO), and cell density. In this work we investigated the microbial methane oxidation with respect to temperature and type of methanotrophic enrichment culture. A newly designed setup was used to overcome potential CH4-substrate limitations such as diffusion that could affect the determined values of ε by improper and inhomogeneous mixing. The isotopic fractionation was determined based on the stable carbon isotope analysis of methane and carbon dioxide. The obtained value for isotopic fractionation was ε22°C = −0.0136 ± 0.0036. Also for the first time, bulk stable isotope analysis of bacterial cell mass was performed by flow injection analysis isotope ratio mass spectrometry.

Emission and Sink of Greenhouse Gases in Soils of Moscow

The first inventory and zoning of the emission and sink of methane and carbon dioxide in the urban structure of greenhouse gases from soils and surface technogenic formations (STFs) (Technosols) on technogenic, recrementogenic, and natural sediments have been performed with consideration for the global warming potential under conditions of different formation rate of these gases, underflooding, and sealing. From gas geochemical criteria and anthropogenic pedogenesis features, the main sources of greenhouse gases, their intensity, and mass emission were revealed. The mass fractions of emissions from the sectors of waste and land use in the inventories of greenhouse gas emissions have been determined. New sources of gas emission have been revealed in the first sector, the emissions from which add tens of percent to the literature and state reports. In the second sector, emissions exceed the available data in 70 times. Estimation criteria based on the degree of manifestation and chemical composition of soil-geochemical anomalies and barrier capacities have been proposed. The sink of greenhouse gases from the atmosphere and the internal (latent) sink of methane in soils and STFs have been determined. Ecological functions of soils and STFs have been shown, and the share of latent methane sink has been calculated. The bacterial oxidation of methane in soils and STFs exceeds its emission to the atmosphere in almost hundred times.

Characterization of methane oxidation in a simulated landfill cover system by comparing molecular and stable isotope mass balances

Biological methane oxidation may be regarded as a method of aftercare treatment for landfills to reduce climate relevant methane emissions. It is of social and economic interest to estimate the behavior of bacterial methane oxidation in aged landfill covers due to an adequate long-term treatment of the gas emissions.Different approaches assessing methane oxidation in laboratory column studies have been investigated by other authors recently. However, this work represents the first study in which three independent approaches, ((i) mass balance, (ii) stable isotope analysis, and (iii) stoichiometric balance of product (CO2) and reactant (CH4) by CO2/CH4-ratio) have been compared for the estimation of the biodegradation by a robust statistical validation on a rectangular, wide soil column.Additionally, an evaluation by thermal imaging as a potential technique for the localization of the active zone of bacterial methane oxidation has been addressed in connection with stable isotope analysis and CO2/CH4-ratios. Although landfills can be considered as open systems the results for stable isotope analysis based on a closed system correlated better with the mass balance than calculations based on an open system. CO2/CH4-ratios were also in good agreement with mass balance. In general, highest values for biodegradation were determined from mass balance, followed by CO2/CH4-ratio, and stable isotope analysis. The investigated topsoil proved to be very suitable as a potential cover layer by removing up to 99% of methane for CH4 loads of 35–65gm–2d–1 that are typical in the aftercare phase of landfills. Finally, data from stable isotope analysis and the CO2/CH4-ratios were used to trace microbial activity within the reactor system. It was shown that methane consumption and temperature increase, as a cause of high microbial activity, correlated very well.

Microbial oxidation as a methane sink beneath the West Antarctic Ice Sheet

Aquatic habitats beneath ice masses contain active microbial ecosystems capable of cycling important greenhouse gases, such as methane (CH4). A large methane reservoir is thought to exist beneath the West Antarctic Ice Sheet, but its quantity, source and ultimate fate are poorly understood. For instance, O2 supplied by basal melting should result in conditions favourable for aerobic methane oxidation. Here we use measurements of methane concentrations and stable isotope compositions along with genomic analyses to assess the sources and cycling of methane in Subglacial Lake Whillans (SLW) in West Antarctica. We show that sub-ice-sheet methane is produced through the biological reduction of CO2 using H2. This methane pool is subsequently consumed by aerobic, bacterial methane oxidation at the SLW sediment–water interface. Bacterial oxidation consumes >99% of the methane and represents a significant methane sink, and source of biomass carbon and metabolic energy to the surficial SLW sediments. We conclude that aerobic methanotrophy may mitigate the release of methane to the atmosphere upon subglacial water drainage to ice sheet margins and during periods of deglaciation. Subglacial lakes contain active microbial ecosystems capable of cycling methane. In a subglacial lake in West Antarctica, methane that is produced is subsequently consumed, limiting the potential for methane emissions during lake drainage.

Methane turnover and methanotrophic communities in arctic aquatic ecosystems of the Lena Delta, Northeast Siberia.

Large amounts of organic carbon are stored in Arctic permafrost environments, and microbial activity can potentially mineralize this carbon into methane, a potent greenhouse gas. In this study, we assessed the methane budget, the bacterial methane oxidation (MOX) and the underlying environmental controls of arctic lake systems, which represent substantial sources of methane. Five lake systems located on Samoylov Island (Lena Delta, Siberia) and the connected river sites were analyzed using radiotracers to estimate the MOX rates, and molecular biology methods to characterize the abundance and the community composition of methane-oxidizing bacteria (MOB). In contrast to the river, the lake systems had high variation in the methane concentrations, the abundance and composition of the MOB communities, and consequently, the MOX rates. The highest methane concentrations and the highest MOX rates were detected in the lake outlets and in a lake complex in a flood plain area. Though, in all aquatic systems, we detected both, Type I and II MOB, in lake systems, we observed a higher diversity including MOB, typical of the soil environments. The inoculation of soil MOB into the aquatic systems, resulting from permafrost thawing, might be an additional factor controlling the MOB community composition and potentially methanotrophic capacity.

Methanobactin and the Link between Copper and Bacterial Methane Oxidation.

Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu(2+) to Cu(1+). In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs.

A Review on Biogas Interception Processes in Municipal Landfill

Biogas in landfill is being captured by natural and engineered processes. The natural processes are represented by biological activities such as bacterial methane oxidation and plant uptake for carbon dioxide at topsoil layer. Landfill gas is transported through soil layers in landfill top or in nearby areas before being released to the atmosphere. Whilst transported in the soil layers the biogas is mixed with atmospheric air and the methane may hence be oxidized by the methanotrophic bacteria in the soil using oxygen from atmosphere. Methane oxidation is affected by different environmental factors such as; temperature, water content, nutrients, substrate and oxygen concentrations. One of the ways to decrease greenhouse emissions in the future is to plant fast growing woody crops thereby sequestering carbon and displacing fossil fuels by harvesting woody biomass for bio-energy, or by storing carbon in long-lived woody products. Plant uptake for carbon dioxide is affected by some parameters such as; CO2 concentration, nitrogen concentration, water content and temperature. The engineered processes are represented by various physical biogas extractions; gas is collected using network of collection pipes and wells. The gas collection efficiency in landfills is between 40-90%. Landfill gas can be collected by either a passive or an active collection system. Passive gas collection systems use existing variations in landfill pressure and gas concentrations to vent landfill gas into the atmosphere or a control system. Active gas collection is considered a good means of landfill gas collection. An active collection system composed of extraction wells connected to header pipe to a pump that delivers gas for energy recovery.

Environmental factors affecting methane distribution and bacterial methane oxidation in the German Bight (North Sea)

River estuaries are responsible for high rates of methane emissions to the atmosphere. The complexity and diversity of estuaries require detailed investigation of methane sources and sinks, as well as of their spatial and seasonal variations. The Elbe river estuary and the adjacent North Sea were chosen as the study site for this survey, which was conducted from October 2010 to June 2012. Using gas chromatography and radiotracer techniques, we measured methane concentrations and methane oxidation (MOX) rates along a 60 km long transect from Cuxhaven to Helgoland. Methane distribution was influenced by input from the methane-rich mouth of the Elbe and gradual dilution by methane-depleted sea water. Methane concentrations near the coast were on average 30 ± 13 nmol L−1, while in the open sea, they were 14 ± 6 nmol L−1. Interestingly, the highest methane concentrations were repeatedly detected near Cuxhaven, not in the Elbe River freshwater end-member as previously reported. Though, we did not find clear seasonality we observed temporal methane variations, which depended on temperature and presumably on water discharge from the Elbe River. The highest MOX rates generally coincided with the highest methane concentrations, and varied from 2.6 ± 2.7 near the coast to 0.417 ± 0.529 nmol L−1 d−1 in the open sea. Turnover times varied from 3 to >1000 days. MOX rates were strongly affected by methane concentration, temperature and salinity. We ruled out the supposition that MOX is not an important methane sink in most of the Elbe estuary and adjacent German Bight.

A coupled multi‐component approach for bacterial methane oxidation in landfill cover layers

AbstractMethane (CH4), which has a 25 times higher global warming potential than carbon dioxide (CO2), can be oxidated by methanotrophic bacteria into carbon dioxide and water. The biological oxidation of methane can be considered in the passive aftercare phase of landfills in order to reduce climate‐damaging methane emissions. Methanotrophic bacteria are situated within the landfill cover layer and convert the harmful methane emissions arising from the degradation of organic waste to the less harmful carbon dioxide. Hence, the passive aftercare of landfills in terms of methane oxidation layers is an efficient method to reduce contributions to the greenhouse effect.To model the coupled processes during phase transition from methane to carbon dioxide, the well‐known Theory of Porous Media (TPM) combined with the Mixture Theory has been used in order to develop a multi‐component Finite Element calculation concept, see [1, 3]. The thermodynamic consistent model analyzes the relevant gas productions of methane, carbon dioxide and oxygen. The model also accounts for the driving phenomena of production, diffusion and advection. (© 2014 Wiley‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Micro‐aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south‐Alpine Lake Lugano (Switzerland)

We measured seasonal variations in the vertical distribution of methane concentration, methane oxidation rates, and lipid biomarkers in the northern basin of Lake Lugano. Methane consumption below the oxic—anoxic interface co‐occurred with concentration maxima of 13C‐depleted C16 fatty acid biomarkers (with δ13C values as low as −70‰) in the anoxic water column, as well as characteristic δ13CCH4 profiles. We argue that the conspicuous methane concentration gradients are primarily driven by (micro‐)aerobic methane oxidation (MOx) below the chemocline. We measured a strong MOx potential throughout the anoxic water column, while MOx rates at in situ O2 concentration &gt; 10 nmol L−1 were undetectable. Similarly, we found MOx‐related biomarkers and gene sequences encoding the particulate methane monooxygenase in the anoxic, but not the oxic, water. The mechanism of (episodic) oxygen supply sustaining the MOx community in anoxic waters is still uncertain. Our results indicate that a bacterial methanotrophic community is responsible for the methane consumption in Lake Lugano, without detectable contribution from archaeal methanotrophs. Bacterial populations that accumulated both at the suboxic—anoxic interface and in the deeper anoxic hypolimnion, where maximum potential MOx rates were observed throughout the year (1.5–2.5 µmol L−1 d−1) were mainly related to Methylobacter sp. Close relatives are found in lacustrine environments throughout the world, and their potential to thrive under micro‐ and anoxic conditions in Lake Lugano may imply that micro‐aerobic methane oxidation is important in methane cycling and competition for methane and oxygen in stratified lakes worldwide.

Bacterial methane oxidation in landfill cover layers ‐ a coupled FE multiphase description

AbstractLandfill gas is composed of methane (CH4) and (CO2) at a ratio of about (60% – 40%), whereby the impact of methane on the greenhouse effect is about 25 times higher than that of carbon dioxide. Bacterial methane oxidation, taking place in the landfill cover layer, helps to reduce the climate active emissions from landfill sites. This contribution presents a theoretical and numerical approach to model the coupled processes of bacterial methane oxidation. An isothermal biphasic model based on the Theory of Porous Media (TPM) and Mixture Theory is introduced as well as the coupled finite element (FE) calculation concept. (© 2013 Wiley‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Put a ring on it

The structure of a bacterial methane oxidation complex reveals how protein-protein interactions can mediate coupling of proton, electron and substrate delivery to a metal active site.

Seasonal shifts in the diet of lake zooplankton revealed by phospholipid fatty acid analysis

Summary1. We analysed the phospholipid fatty acid (PLFA) profiles of seston and of the dominant zooplankter, Daphnia longispina, through the open water period in a small, dystrophic lake to investigate seasonal variation in the diet of Daphnia. Phytoplankton, heterotrophic bacteria, green sulphur bacteria and methane‐oxidizing bacteria (MOB) were all present in the water column of the lake, and previous studies have indicated that vertically migrating Daphnia can exploit all these potential food sources.2. For adult Daphnia, although there was some correspondence between the PLFA profile of Daphnia and the concurrent seston PLFA profile, strongest correlations were between the Daphnia PLFA profile and those of potential food sources determined 7 days earlier. This interval presumably reflects the time it takes for adult Daphnia to turn over their fatty acid pool.3. A correlation between the concentration of polyunsaturated fatty acids (PUFAs) in the epi‐ and metalimnion and measured primary production indicated that, within the total PLFA fraction, PUFAs can be useful biomarkers for phytoplankton in food‐web studies. Algal PUFAs contributed appreciably to total PLFAs in adult Daphnia during spring and summer, but less so in autumn.4. Daphnia in the lake actually reached their highest biomass in autumn, when methanotrophic activity was also highest, and the highest magnitude of MOB‐specific PLFAs was recorded in both adult and juvenile Daphnia. A strong relationship existed between δ13C values of Daphnia reported previously and the proportion of MOB‐specific PLFAs in Daphnia. Autumnal mixing evidently stimulates bacterial oxidation of methane from the hypolimnion, and exploitation of the methanotrophic bacteria sustains a high Daphnia population late in the season.5. Our results show that the PLFA composition of freshwater zooplankton like Daphnia corresponds rather well to that of their in situ diet of phytoplankton and bacteria, with a lag period of around 1 week in the case of adult animals. The PLFA profile of seston revealed the dominant available food sources, and relating these to the Daphnia PLFA profile provided insights into seasonal changes in Daphnia diet.

Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study

The stratified water column of the Black Sea is partitioned into oxic, suboxic, and euxinic zones, each characterized by different biogeochemical processes and by distinct microbial communities. In 2003, we collected particulate matter by large volume in situ filtration at the highest resolution to date for lipid biomarker analysis and bacterioplankton for enumeration of major prokaryotic groups. Abundances of several prokaryotic groups were estimated using CARD-FISH probes specific for Bacteria, Archaea ( Crenarchaeota and Euryarchaeota), epsilonproteobacteria (mainly sulfide oxidizers) and sulfate reducing bacteria. We also measured a wide range of bacterial and archaeal lipid biomarkers. Depth distributions of diagnostic biomarkers are matched with zonation of microbial processes, including aerobic bacterial oxidation of methane, oxidation of ammonium by bacteria and archaea, metal reduction, and sulfide oxidation at the chemocline, and bacterial sulfate reduction and anaerobic oxidation of methane by archaea in the anoxic zone. Cell densities for archaea and sulfate reducing bacteria are estimated based on water column biomarker concentrations and compared with CARD-FISH results.

Methanobactin‐promoted dissolution of Cu‐substituted borosilicate glass

ABSTRACTMineral weathering plays an important role in the global cycling of carbon and metals and there is an increasing realization that subsurface microbial activity may be a key factor controlling specific biogeochemical reactions and their rates. Methanobactin (mb) is an extracellular copper‐binding compound excreted by methanotrophs to acquire copper for the regulation of methane oxidation. Bioavailable Cu regulates the expression and activity of pMMO vs. sMMO (particulate vs. soluble methane monooxygenase, respectively), key enzymes responsible for bacterial methane oxidation. In this study, we investigate the effect of mb on the dissolution of Cu‐substituted borosilicate glass at low temperature and near neutral pH conditions, using batch dissolution experiments. Methanobactin promotes the dissolution of Cu‐substituted glasses at rates faster than control experiments. Glasses with lower concentrations of copper (80 p.p.m.) or no copper are dissolved more rapidly by mb than those with more abundant copper (800 p.p.m.). Within the first 2 h of reaction, mb sorption onto glass surfaces limits mass transfer of Cu into solution, and at higher concentrations (100 µmol) of the ligand, inhibits dissolution rates of all glass formulations. These results suggest that both the concentration of mb in solution and the solid phase Cu concentration impact silicate weathering rates and related cycling of carbon in near‐surface geological settings.