Methane-oxidizing Bacteria Research Articles

Distribution and characteristic of nitrite-dependent anaerobic methane oxidation bacteria by comparative analysis of wastewater treatment plants and agriculture fields in northern China.

Nitrite-dependent anaerobic methane oxidation (n-damo) is a recently discovered biological process which has been arousing global attention because of its potential in minimizing greenhouse gases emissions. In this study, molecular biological techniques and potential n-damo activity batch experiments were conducted to investigate the presence and diversity of M. oxyfera bacteria in paddy field, corn field, and wastewater treatment plant (WWTP) sites in northern China, as well as lab-scale n-damo enrichment culture. N-damo enrichment culture showed the highest abundance of M. oxyfera bacteria, and positive correlation was observed between potential n-damo rate and abundance of M. oxyfera bacteria. Both paddy field and corn field sites were believed to be better inoculum than WWTP for the enrichment of M. oxyfera bacteria due to their higher abundance and the diversity of M. oxyfera bacteria. Comparative analysis revealed that long biomass retention time, low NHn}{}{}_{4}^{+} and high NOn}{}{}_{2}^{-} content were suitable for the growth of M. oxyfera bacteria.

Methanotrophy under Versatile Conditions in the Water Column of the Ferruginous Meromictic Lake La Cruz (Spain).

Lakes represent a considerable natural source of methane to the atmosphere compared to their small global surface area. Methanotrophs in sediments and in the water column largely control methane fluxes from these systems, yet the diversity, electron accepting capacity, and nutrient requirements of these microorganisms have only been partially identified. Here, we investigated the role of electron acceptors alternative to oxygen and sulfate in microbial methane oxidation at the oxycline and in anoxic waters of the ferruginous meromictic Lake La Cruz, Spain. Active methane turnover in a zone extending well below the oxycline was evidenced by stable carbon isotope-based rate measurements. We observed a strong methane oxidation potential throughout the anoxic water column, which did not vary substantially from that at the oxic/anoxic interface. Both in the redox-transition and anoxic zones, only aerobic methane-oxidizing bacteria (MOB) were detected by fluorescence in situ hybridization and sequencing techniques, suggesting a close coupling of cryptic photosynthetic oxygen production and aerobic methane turnover. Additions of nitrate, nitrite and to a lesser degree iron and manganese oxides also stimulated bacterial methane consumption. We could not confirm a direct link between the reduction of these compounds and methane oxidation and we cannot exclude the contribution of unknown anaerobic methanotrophs. Nevertheless, our findings from Lake La Cruz support recent laboratory evidence that aerobic methanotrophs may be able to utilize alternative terminal electron acceptors under oxygen limitation.

Spatio-temporal dynamics of soil CH4 uptake after application of N fertilizer with and without the nitrification inhibitor 3,4- dimethylpyrazole phosphate (DMPP)

Soil ecosystems actively regulate climate by controlling methane and nitrous oxide fluxes into the atmosphere. Soils have been, however, drastically altered by agricultural practices, such as nitrogen amendment which increases nitrous oxide emission while it reduces methane uptakes in well-aerated soils by affecting methane-oxidizing bacteria. New nitrification inhibitors, such as 3,4-dimethylpyrazole phosphate (DMPP), are often applied in combination with nitrogen-based fertilizer to increase plant productivity by increasing available ammonium and inhibiting denitrification processes reducing in turn nitrous oxide emissions. However, the increase in ammonium due to nitrification inhibition might also affect methane oxidizing bacteria. We therefore investigated the effects of nitrogen-based fertilizer and DMPP on methane and nitrous oxide fluxes in an extensively managed grassland. We also determined the spatial distribution of active methane oxidizing bacteria by radiolabeling. Short-term reduction in methane uptake and methanotrophic activity occurred after application of 600 kg N ha−1 while DMPP did not alter methane uptake but reduced nitrous oxide emission. The combination of both radio-labeling and field measurement revealed that methane uptake collapsed in the field when methanotrophic activity was inhibited not only in the surface but also in deeper soil. Finally, both methane uptake and methanotrophic activity recovered with time.

Linked sediment and water‐column methanotrophy at a man‐made gas blowout in the North Sea: Implications for methane budgeting in seasonally stratified shallow seas

AbstractLarge quantities of the greenhouse gas methane (CH4) are stored in the seafloor. The flux of CH4 from the sediments into the water column and finally to the atmosphere is mitigated by a series of microbial methanotrophic filter systems of unknown efficiency at highly active CH4‐release sites in shallow marine settings. Here, we studied CH4‐oxidation and the methanotrophic community at a high‐CH4‐flux site in the northern North Sea (well 22/4b), where CH4 is continuously released since a blowout in 1990. Vigorous bubble emanation from the seafloor and strongly elevated CH4 concentrations in the water column (up to 42 µM) indicated that a substantial fraction of CH4 bypassed the highly active (up to ∼2920 nmol cm−3 d−1) zone of anaerobic CH4‐oxidation in sediments. In the water column, we measured rates of aerobic CH4‐oxidation (up to 498 nM d−1) that were among the highest ever measured in a marine environment and, under stratified conditions, have the potential to remove a significant part of the uprising CH4 prior to evasion to the atmosphere. An unusual dominance of the water‐column methanotrophs by Type II methane‐oxidizing bacteria (MOB) is partially supported by recruitment of sedimentary MOB, which are entrained together with sediment particles in the CH4 bubble plume. Our study thus provides evidence that bubble emission can be an important vector for the transport of sediment‐borne microbial inocula, aiding in the rapid colonization of the water column by methanotrophic communities and promoting their persistence close to highly active CH4 point sources.

Improved enrichment culture technique for methane-oxidizing bacteria from marine ecosystems: the effect of adhesion material and gas composition.

Cultivation of microbial representatives of specific functional guilds from environmental samples depends largely on the suitability of the applied growth conditions. Especially the cultivation of marine methanotrophs has received little attention, resulting in only a limited number of ex situ cultures available. In this study we investigated the effect of adhesion material and headspace composition on the methane oxidation activity in methanotrophic enrichments obtained from marine sediment. Addition of sterilized natural sediment or alternatively the addition of acid-washed silicon dioxide significantly increased methane oxidation. This positive effect was attributed to bacterial adhesion on the particles via extracellular compounds, with a minimum amount of particles required for effect. As a result, the particles were immobilized, thus creating a stratified environment in which a limited diffusive gas gradients could build up and various microniches were formed. Such diffusive gas gradient might necessitate high headspace concentrations of CH4 and CO2 for sufficient concentrations to reach the methane-oxidizing bacteria in the enrichment culture technique. Therefore, high concentrations of methane and carbon dioxide, in addition to the addition of adhesion material, were tested and indeed further stimulated methane oxidation. Use of adhesion material in combination with high concentrations of methane and carbon dioxide might thus facilitate the cultivation and subsequent enrichment of environmentally important members of this functional guild. The exact mechanism of the observed positive effects on methane oxidation and the differential effect on methanotrophic diversity still needs to be explored.

Isolation of a methane-oxydizing bacterium for the study on single cell protein production from methane

Single cell protein (SCP) can be produced from biomass of different types of microorganisms that have high protein content such as yeast, filamentous fungi, algae and bacteria. In comparison to animal and plant protein sources, this kind of protein has several advantages, namely high protein and nutrient contents, being produced in fermenters with the use of variety of organic wastes, independence in agriculture land or climate conditions. Methane oxidizing bacteria (MOB) are considered as good candidates for SCP production and have been intensively studied recently. In the present study, a MOB strain BG3 was isolated from wastewater of an anaerobic digester via enrichment and isolation procedures using methane as the only carbon and energy sources. Strain BG3 comprised of oval-shaped cells of 0,8-1´16 -1,8 μm in size, almost nonmotile. Based on comparative analyses of the 16S rDNA partial sequences, strain BG3 was identified as a member of the Methylomonas genus, the most closely related species was Methylomonas koyamae (97% homology). This was also confirmed by analyses of sequence of the pmoA gene, encoding for a-subunit in the methane-monooxygenase in the strain. Besides methane, strain BG3 also utilized methanol for the growth. It has been shown that methane-fed culture of strain BG3 could produce 68.69 g crude protein per 100 g CDW and the according methane to biomass conversion efficiency was 2,8 m3 methane×kg-1 dry biomassas. Owing the capability of utilization of methane, the second important greenhouse gas, for the production of protein source for animal feed, strain BG3 would have a great application potential in Vietnam. Strain BG3 was designated as Methylomonas sp. BG3 and its 16S rDNA and pmoA gene sequences were deposited at the GenBank with accession numbers of KJ081955 and KJ081956, respectively.

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System.

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.

Summer profundal hypoxia determines the coupling of methanotrophic production and the pelagic food web in a subtropical reservoir

Summary We investigated how profundal redox conditions determine the inter‐annual variation in methane oxidising bacteria (MOB) contribution to zooplankton production in a deep subtropical reservoir. Two hydrological regimes which affect MOB activity are considered: (i) reduced MOB activity resulting from high profundal oxygen saturation promoted by water column disturbance during the period of summer stratification; and (ii) increased MOB activity due to high profundal oxygen saturation during winter mixing. Four years of field stable‐isotope analyses revealed that oxygen saturation of profundal waters during summer stratification was negatively correlated with winter MOB contribution. This relationship is consistent with our theoretical ecosystem modelling. Although the ecosystem model simulation predicted positive effects of profundal oxygen supply during winter mixing on MOB contribution, the stable isotope mixing model indicated that the effects were secondary. Winter oxygen supply did not enhance MOB activity when methane accumulation during the preceding summer was low. Our findings suggest that summer profundal hypoxia plays the primary role in determining methanotrophic food‐web activity and methane‐derived carbon cycling in deep lakes.

Land Use Affects Carbon Sources to the Pelagic Food Web in a Small Boreal Lake.

Small humic forest lakes often have high contributions of methane-derived carbon in their food webs but little is known about the temporal stability of this carbon pathway and how it responds to environmental changes on longer time scales. We reconstructed past variations in the contribution of methanogenic carbon in the pelagic food web of a small boreal lake in Finland by analyzing the stable carbon isotopic composition (δ13C values) of chitinous fossils of planktivorous invertebrates in sediments from the lake. The δ13C values of zooplankton remains show several marked shifts (approx. 10 ‰), consistent with changes in the proportional contribution of carbon from methane-oxidizing bacteria in zooplankton diets. The results indicate that the lake only recently (1950s) obtained its present state with a high contribution of methanogenic carbon to the pelagic food web. A comparison with historical and palaeobotanical evidence indicates that this most recent shift coincided with agricultural land-use changes and forestation of the lake catchment and implies that earlier shifts may also have been related to changes in forest and land use. Our study demonstrates the sensitivity of the carbon cycle in small forest lakes to external forcing and that the effects of past changes in local land use on lacustrine carbon cycling have to be taken into account when defining environmental and ecological reference conditions in boreal headwater lakes.

Enrichment and characteristics of mixed methane-oxidizing bacteria from a Chinese coal mine.

In methane-rich environments, methane-oxidizing bacteria usually occur predominantly among consortia including other types of microorganisms. In this study, artificial coal bed gas and methane gas were used to enrich mixed methanotrophic cultures from the soil of a coal mine in China, respectively. The changes in microbial community structure and function during the enrichment were examined. The microbial diversity was reduced as the enrichment proceeded, while the capacity for methane oxidation was significantly enhanced by the increased abundance of methanotrophs. The proportion of type II methanotrophs increased greatly from 7.84% in the sampled soil to about 50% in the enrichment cultures, due to the increase of methane concentration. After the microbial community of the cultures got stable, Methylomonas and Methylocystis became the dominant type I and type II methanotrophs, while Methylophilus was the prevailing methylotroph. The sequences affiliated with pigment-producing strains, Methylomonas rubra, Hydrogenophaga sp. AH-24, and Flavobacterium cucumis, could explain the orange appearance of the cultures. Comparing the two cultures, the multi-carbon sources in the artificial coal bed gas caused more variety of non-methanotrophic bacteria, but did not help to maintain the diversity or to increase the quantity and activity of methanotrophs. The results could help to understand the succession and interaction of microbial community in a methane-driven ecosystem.

Constraints on methane oxidation in ice‐covered boreal lakes

AbstractBoreal lakes can be ice covered for a substantial portion of the year at which time methane (CH4) can accumulate below ice. The amount of CH4 emitted at ice melt is partially determined by the interplay between CH4 production and CH4 oxidation, performed by methane‐oxidizing bacteria (MOB). Yet the balance between oxidation and emission and the potential for CH4 oxidation in various lakes during winter is largely unknown. To address this, we performed incubations at 2°C to screen for wintertime CH4 oxidation potential in seven lakes. Results showed that CH4 oxidation was restricted to three lakes, where the phosphate concentrations were highest. Molecular analyses revealed that MOB were initially detected in all lakes, although an increase in type I MOB only occurred in the three lake water incubations where oxidation could be observed. Accordingly, the increase in CO2 was on average 5 times higher in these three lake water incubations. For one lake where no oxidation was measured, we tested if temperature and CH4 availability could trigger CH4 oxidation. However, regardless of incubation temperatures and CH4 concentrations, ranging from 2 to 20°C and 1–500 μM, respectively, no oxidation was observed. Our study indicates that some lakes with active wintertime CH4 oxidation may have low emissions during ice melt, while other and particularly nutrient poor lakes may accumulate large amounts of CH4 below ice that, in the absence of CH4 oxidation, will be emitted following ice melt. This variability in CH4 oxidation rates between lakes needs to be accounted for in large‐scale CH4 emission estimates.

Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance.

Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4l(-1)d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters.

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.

Diploptene <i>δ</i><sup>13</sup>C values from contemporary thermokarst lake sediments show complex spatial variation

Abstract. Cryospheric changes in northern high latitudes are linked to significant greenhouse gas flux to the atmosphere, for example, methane that originates from organic matter decomposition in thermokarst lakes. The set of pathways that link methane production in sediments, via oxidation in the lake system, to the flux of residual methane to the atmosphere is complex and exhibits temporal and spatial variation. The isotopic signal of bacterial biomarkers (hopanoids, e.g. diploptene) in sediments has been used to identify contemporary ocean-floor methane seeps and, in the geological record, periods of enhanced methane production (e.g. the PETM). The biomarker approach could potentially be used to assess temporal changes in lake emissions through the Holocene via the sedimentary biomarker record. However, there are no data on the consistency of the signal of isotopic depletion in relation to source or on the amount of noise (unexplained variation) in biomarker values from modern lake sediments. We assessed methane oxidation as represented by the isotopic signal of biomarkers from methane oxidising bacteria (MOB) in multiple surface sediment samples in three distinct areas known to emit varying levels of methane in two shallow Alaskan thermokarst lakes. Diploptene was present and had δ13C values lower than −38 ‰ in all sediments analysed, suggesting methane oxidation was widespread. However, there was considerable variation in δ13C values within each area. The most 13C-depleted diploptene was found in an area of high methane ebullition in Ace Lake (diploptene δ13C values between −68.2 and −50.1 ‰). In contrast, significantly higher diploptene δ13C values (between −42.9 and −38.8 ‰) were found in an area of methane ebullition in Smith Lake. δ13C values of diploptene between −56.8 and −46.9 ‰ were found in the centre of Smith Lake, where ebullition rates are low but diffusive methane efflux occurs. The small-scale heterogeneity of the samples may reflect patchy distribution of substrate and/or MOB within the sediments. The two ebullition areas differ in age and type of organic carbon substrate, which may affect methane production, transport, and subsequent oxidation. Given the high amount of variation in surface samples, a more extensive calibration of modern sediment properties, within and among lakes, is required before down-core records of hopanoid isotopic signatures are developed.

Origin and preservation of bacteriohopanepolyol signatures in Sphagnum peat from Bissendorfer Moor (Germany)

Distributions of bacteriohopanepolyols (BHPs) in a peat core from the Bissendorfer Moor (Germany) were investigated in order to test the utility of BHPs as indicators of microbial processes in peats. Between 13 and 22 BHPs in each sample (23 structures in total) were identified, with total concentration ranging from 160–2800μg/gTOC. We have tentatively ascribed sources of most BHPs at the site via comparison of known BHP source organisms with recent microbiological studies of the peat microbiome. Members of the Alpha-, Beta- and Gammaproteobacteria and specifically the genera Burkholderia, Bradyrhizobium and Rhodoblastus, as well as other phyla including the cyanobacteria, Acidobacteria and Acetobacteria are among the most likely sources. Additionally, BHP signatures which could be assigned directly to methane oxidising bacteria (35-aminobacteriohopanepentol and 35-aminobacteriohopanetetrol) were present only at very low level, supporting previous studies which have shown that the majority of precursor organisms biosynthesising hopanoids in peat environments are heterotrophs. The surface layers also contained a highly unusual signature comprising high concentrations of unsaturated compounds, including unsaturated bacteriohopanetetrol pseudopentose, which has only been reported in Gloeocapsa cyanobacteria. This genus is known to occur in symbiotic association with host Sphagnum species and has the ability to fix atmospheric N2, which is a well known trait among members of the peat microbiome and among hopanoid producing microorganisms. The apparent capacity for hopanoids to protect organisms from external stresses such as low pH is therefore likely to be a significant factor accounting for the high BHP contributions from heterotrophs, methanotrophs and phototrophic organisms in Sphagnum peats.

Evaluation and update of cutoff values for methanotrophic pmoA gene sequences.

The functional pmoA gene is frequently used to probe the diversity and phylogeny of methane-oxidizing bacteria (MOB) in various environments. Here, we compared the similarities between the pmoA gene and the corresponding 16S rRNA gene sequences of 77 described species covering gamma- and alphaproteobacterial methanotrophs (type I and type II MOB, respectively) as well as methanotrophs from the phylum Verrucomicrobia. We updated and established the weighted mean pmoA gene cutoff values on the nucleotide level at 86, 82, and 71% corresponding to the 97, 95, and 90% similarity of the 16S rRNA gene. Based on these cutoffs, the functional gene fragments can be entirely processed at the nucleotide level throughout software platforms such as Mothur or QIIME which provide a user-friendly and command-based alternative to amino acid-based pipelines. Type II methanotrophs are less divergent than type I both with regard to ribosomal and functional gene sequence similarity and GC content. We suggest that this agrees with the theory of different life strategies proposed for type I and type II MOB.

Model-Based Feasibility Assessment of Membrane Biofilm Reactor to Achieve Simultaneous Ammonium, Dissolved Methane, and Sulfide Removal from Anaerobic Digestion Liquor.

In this study, the membrane biofilm reactor (MBfR) is proposed to achieve simultaneous removal of ammonium, dissolved methane, and sulfide from main-stream and side-stream anaerobic digestion liquors. To avoid dissolved methane stripping, oxygen is introduced through gas-permeable membranes, which also from the substratum for the growth of a biofilm likely comprising ammonium oxidizing bacteria (AOB), anaerobic ammonium oxidation (Anammox) bacteria, denitrifying anaerobic methane oxidation (DAMO) microorganisms, aerobic methane oxidizing bacteria (MOB), and sulfur oxidizing bacteria (SOB). A mathematical model is developed and applied to assess the feasibility of such a system and the associated microbial community structure under different operational conditions. The simulation studies demonstrate the feasibility of achieving high-level (>97.0%), simultaneous removal of ammonium, dissolved methane, and sulfide in the MBfRs from both main-stream and side-stream anaerobic digestion liquors through adjusting the influent surface loading (or hydraulic retention time (HRT)) and the oxygen surface loading. The optimal HRT was found to be inversely proportional to the corresponding oxygen surface loading. Under the optimal operational conditions, AOB, DAMO bacteria, MOB, and SOB dominate the biofilm of the main-stream MBfR, while AOB, Anammox bacteria, DAMO bacteria, and SOB coexist in the side-stream MBfR to remove ammonium, dissolved methane, and sulfide simultaneously.

Methane oxidation at the water‐ice interface of an ice‐covered lake

AbstractLakes are important components of the global methane (CH4) cycle. In seasonally ice‐covered lakes, CH4 transported by ebullition (bubbling) from anoxic sediments gets trapped at the water‐ice interface. If not oxidized by methane‐oxidizing bacteria (MOB), this can potentially lead to high episodic CH4 emissions at ice‐melt. To understand the fate of CH4 trapped below ice, we measured depth‐distributions of CH4 concentrations in the water column near bubbles trapped below ice in Lake Erken. We also performed a 21 d incubation experiment at low temperature (2.3 ± 0.2°C) to investigate the potential for CH4 oxidation. During most sampling occasions, we found steep CH4 concentration gradients just below the ice with a 13‐fold decrease from the surface to a depth of 20 cm. In vitro incubations revealed that CH4 oxidation can occur at low temperatures typical for the water‐ice interface. CH4 oxidation was observed as a significant decrease in CH4 concentration, a significant increase in stable isotope 13C signature, and an increase in MOB during the incubation. Thus, CH4 accumulating in the top 20 cm of the water column, fed by diffusion from CH4 in trapped bubbles, may fuel significant CH4 oxidation. Since northern latitude lakes can be ice‐covered for many months of the year and significant amounts of CH4 accumulate below the ice, the extent of CH4 oxidation under these low temperature‐conditions is important for understanding the potential CH4 emissions to the atmosphere during ice‐melt.

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.

Does acidification of a soil biofilter compromise its methane-oxidising capacity?

A biofilter made using volcanic pumice soil from a landfill in Taupo, New Zealand has been found to mitigate CH4 emissions from New Zealand dairy effluent ponds. However, the biofilter after drying out following almost 5 years of use removed little or no CH4. Furthermore, H2S present in the biogas (from the dairy effluent ponds) had increased the acidity (pH) in the soil biofilter from 5.2 to 3.72 during this 5-year period. In this study, we adjusted the soil moisture to 60 % water-holding capacity (WHC) and investigated the CH4-oxidising capacity of a reconstituted acidic soil biofilter operating at low pH (3.72) and characterised the abundance and diversity of methane-oxidising bacteria (MOB) using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The acidic soil biofilter achieved a maximum CH4 removal rate of 30.3 g m–3 h–1. Both types I and II MOB communities, along with some uncultured novel MOB strains or species in the biofilter column, were present. Among these, Methylocapsa-like type II methanotrophs were significantly more prominent than the other MOB. Other MOB, Methylococcus (type I), Methylobacter/Methylomonas/Methylosarcina (type I) genera, Methylosinus and Methylocystis (type II), were least abundant. During the 90-day study, the population of Methylocapsa-like MOB increased 4-fold, demonstrating the ability of these soil microorganisms to grow under acidic pH conditions in the biofilter, whereas the populations of type I MOB remained stable, and the populations of type II MOB (except Methylocapsa) decreased. Our results indicated that (i) a soil biofilter can effectively regain efficiency if sufficient moisture levels are maintained, regardless of the soil acidity; (ii) changes in the MOB population did not compromise the capacity of the volcanic pumice soil to oxidise CH4; (iii) the more acidic environment (pH 3.72) tends to favour the growth and activity of acid loving Methylocapsa-like MOB while being detrimental to the growth of Methylobacter/Methylocystis/Methylococcus group of MOB; and (iv) novel species or strains of uncultured Methylomicrobium/Methylosarcina/Methylobacter (type I MOB) could be present in the soil biofilter. This study has revealed the MOB population changes in the biofilter with acidification did not compromise its capacity to oxidise CH4 demonstrating that soil biofilter can operate effectively under acidic conditions.