Methanotrophs and copper

Thermophilic methanotrophs: in hot pursuit

Methane is a potent greenhouse gas responsible for 20–30% of global climate change effects. The global methane budget is ∼500–600 Tg y−1, with the majority of methane produced via microbial processes, including anthropogenic-mediated sources such as ruminant animals, rice fields, sewage treatment facilities and landfills. It is estimated that microbially mediated methane oxidation (methanotrophy) consumes >50% of global methane flux each year. Methanotrophy research has primarily focused on mesophilic methanotrophic representatives and cooler environments such as freshwater, wetlands or marine habitats from which they are sourced. Nevertheless, geothermal emissions of geological methane, produced from magma and lithosphere degassing micro-seepages, mud volcanoes and other geological sources, contribute an estimated 33–75 Tg y−1 to the global methane budget. The aim of this review is to summarise current literature pertaining to the activity of thermophilic and thermotolerant methanotrophs, both proteobacterial (Methylocaldum, Methylococcus, Methylothermus) and verrucomicrobial (Methylacidiphilum). We assert, on the basis of recently reported molecular and geochemical data, that geothermal ecosystems host hitherto unidentified species capable of methane oxidation at higher temperatures.

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal

We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.

Upland soil cluster γ dominates the methanotroph communities in the karst Heshang Cave

Microorganisms are thought to play a critical role in methane (CH4) consumption in karst caves and yet the presence and diversity of methane-oxidizing bacteria (MOB) remain a mystery. In Heshang Cave, CH4 concentration decreases from 1.9 ppm at the entrance to 0.65 ppm inside the cave. To explore the presence and diversity of MOB in this cave, weathered rocks and sediment samples were collected from the cave and subjected to molecular analysis. The abundances of MOB were 107-108 copies g-1 dry sample via quantification of the pmoA gene, which are comparable to or even higher than those reported in other terrestrial environments, and account for up to 20% of the total microbial communities. Phylogenetically, MOB communities were dominated by the 'high-affinity' upland soil cluster γ (USCγ), although the predominance of Type Ia MOB was also detected in the permanently waterlogged stream sediment. The estimated CH4 oxidation potential varied dramatically among samples in the range of 0.6-80 CH4 m-3 d-1. Collectively, this study provides compelling evidence that the high-affinity MOB capable of oxidizing CH4 at the atmospheric level are present in Heshang Cave, which may play an important role in the CH4 consumption, and supports karst caves as important atmospheric CH4 sinks.

Effect of temperature on methane oxidation and community composition in landfill cover soil

Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH₄) emissions in the United States. The majority of CH₄ generated in landfills is converted to carbon dioxide (CO₂) by CH₄-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH₄ oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH₄ oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH₄ oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH₄ oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH₄ g^-1 day^-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH₄ oxidation in vitro and that changing rates of CH₄ oxidation are in part driven by changes in methylotroph community structure.

A Mutagenic Screen Identifies a TonB-Dependent Receptor Required for the Lanthanide Metal Switch in the Type I Methanotroph "Methylotuvimicrobium buryatense" 5GB1C

Several of the metabolic enzymes in methanotrophic bacteria rely on metals for both their expression and their catalysis. The MxaFI methanol dehydrogenase enzyme complex uses calcium as a cofactor to oxidize methanol, while the alternative methanol dehydrogenase XoxF uses lanthanide metals such as lanthanum and cerium for the same function. Lanthanide metals, abundant in the earth's crust, strongly repress the transcription of mxaF yet activate the transcription of xoxF This regulatory program, called the "lanthanide switch," is central to methylotrophic metabolism, but only some of its components are known. To uncover additional components of the lanthanide switch, we developed a chemical mutagenesis system in the type I gammaproteobacterial methanotroph "Methylotuvimicrobium buryatense" 5GB1C and designed a selection system for mutants unable to repress the mxaF promoter in the presence of lanthanum. Whole-genome resequencing for multiple lanthanide switch mutants identified several unique point mutations in a single gene encoding a TonB-dependent receptor, which we have named LanA. The LanA TonB-dependent receptor is absolutely required for the lanthanide switch and controls the expression of a small set of genes. While mutation of the lanA gene does not affect the amount of cell-associated lanthanum, it is essential for growth in the absence of the MxaF methanol dehydrogenase, suggesting that LanA is involved in lanthanum uptake to supply the XoxF methanol dehydrogenase with its critical metal ion cofactor. The discovery of this novel component of the lanthanide regulatory system highlights the complexity of this circuit and suggests that further components are likely involved.IMPORTANCE Lanthanide metals, or rare earth elements, are abundant in nature and used heavily in technological devices. Biological interactions with lanthanides are just beginning to be unraveled. Until very recently, microbial mechanisms of lanthanide metal interaction and uptake were unknown. The TonB-dependent receptor LanA is the first lanthanum receptor identified in a methanotroph. Sequence homology searches with known metal transporters and regulators could not be used to identify LanA or other lanthanide metal switch components, and this method for mutagenesis and selection was required to identify the receptor. This work advances the knowledge of microbe-metal interactions in environmental niches that impact atmospheric methane levels and are thus relevant to climate change.

Upland Soil Cluster Gamma dominates methanotrophic communities in upland grassland soils

Aerobic methanotrophs in upland soils consume atmospheric methane, serving as a critical counterbalance to global warming; however, the biogeographic distribution patterns of their abundance and community composition are poorly understood, especial at a large scale. In this study, soils were sampled from 30 grasslands across >2000 km on the Qinghai-Tibetan Plateau to determine the distribution patterns of methanotrophs and their driving factors at a regional scale. Methanotroph abundance and community composition were analyzed using quantitative PCR and Illumina Miseq sequencing of pmoA genes, respectively. The pmoA gene copies ranged from 8.2 × 10⁵ to 1.1 × 10⁸ per gram dry soil. Among the 30 grassland soil samples, Upland Soil Cluster Gamma (USCγ) dominated the methanotroph communities in 26 samples. Jasper Ridge Cluster (JR3) was the most dominant methanotrophic cluster in two samples; while Methylocystis, cluster FWs, and Methylobacter were abundant in other two wet soil samples. Interestingly, reanalyzing the pmoA genes sequencing data from existing publications suggested that USCγ was also the main methanotrophic cluster in grassland soils in other regions, especially when their mean annual precipitation was <500 mm. Canonical Analysis of Principal Coordinates including all soil samples indicated that the methanotrophic community composition was significantly correlated with local environmental factors, among which mean annual precipitation and pH showed the strongest correlations. Variance partitioning analysis showed that environmental factors and spatial distance were significant factors affecting the community structure of methanotrophs, and environmental properties were more important factors. Collectively, these findings indicate that atmospheric methane may be mainly oxidized by USCγ in upland soils. They also highlight the key role of water availability and pH in determining the abundance and community profiles of grassland soil methanotrophs.

Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments

Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "Methylotetracoccus oryzae" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.

Biological conversion of propane to 2-propanol using group I and II methanotrophs as biocatalysts

Propane is the main component of liquefied petroleum gas and is derived from crude oil processing. Methanotrophic bacteria can convert various alkanes using methane monooxygenase enzyme to primary alcohols. These are further oxidized to various aldehydes by alcohol dehydrogenases or methanol dehydrogenases. In this study, 2-propanol was produced from propane using the whole cells of Methylosinus trichosporium OB3b, Methylomicrobium alcaliphilum 20Z, and Methylomonas sp. DH-1 as the biocatalysts. The biocatalytic process of converting propane to 2-propanol was optimized by the use of several inhibitors and additives, such as EDTA, sodium phosphate, and sodium formate to prevent oxidation of 2-propanol to acetone and to enhance conversion of propane to propanol. The maximum titer of 2-propanol was 0.424 g/L, 0.311 g/L, and 0.610 g/L for Methylomonas sp. DH-1, M. alcaliphilum 20Z, and M. trichosporium OB3b whole cells, respectively. These results showed that type I and type II methanotrophs could be used as the potent biocatalyst for conversion of propane to propanol.

Activity and Identification of Methanotrophic Bacteria in Arable and No-Tillage Soils from Lublin Region (Poland)

Methanotrophic bacteria are able to use methane (CH₄) as a sole carbon and energy source. Photochemical oxidation of methane takes place in the stratosphere, whereas in the troposphere, this process is carried out by methanotrophic bacteria. On the one hand, it is known that the efficiency of biological CH₄ oxidation is dependent on the mode of land use but, on the other hand, the knowledge of this impact on methanotrophic activity (MTA) is still limited. Thus, the aim of the study was to determine the CH₄ oxidation ability of methanotrophic bacteria inhabiting selected arable and no-tillage soils from the Lublin region (Albic Luvisol, Brunic Arenosol, Haplic Chernozem, Calcaric Cambisol) and to identify bacteria involved in this process. MTA was determined based on incubation of soils in air with addition of methane at the concentrations of 0.002, 0.5, 1, 5, and 10%. The experiment was conducted in a temperature range of 10-30 °C. Methanotrophs in soils were identified by next-generation sequencing (NGS). MTA was confirmed in all investigated soils (in the entire range of the tested methane concentrations and temperatures, except for the arable Albic Luvisol). Importantly, the MTA values in the no-tillage soil were nearly two-fold higher than in the cultivated soils. Statistical analysis indicated a significant influence of land use, type of soil, temperature, and especially methane concentration (p < 0.05) on MTA. Metagenomic analysis confirmed the presence of methanotrophs from the genus Methylocystis (Alphaproteobacteria) in the studied soils (except for the arable Albic Luvisol). Our results also proved the ability of methanotrophic bacteria to oxidize methane although they constituted only up to 0.1% of the total bacterial community.

Oxidation and reduction of redox-sensitive elements in the presence of humic substances in subsurface environments: A review

The oxidation and reduction (redox) processes of redox-sensitive elements (RSE) in the presence of humic substances (HS) have become a significantly important issue in the terms of biogeochemical cycles. Redox processes are crucial for determining the speciation, mobility, toxicity, and bioavailability of RSE in natural environments. It is known that HS act as an effective redox mediator for accepting and donating electrons, and thereby transfers them to RSE. We review the recent progress in the field of the redox processes of RSE including As, Cr, Cu, Fe, Hg, and Se in the presence of HS. The extent and rate of the redox processes of these RSE are significantly affected by the concentration of functional groups and the chemical composition of HS. In subsurface environments, pH, ionic strength, and the presence of competitive components, microorganisms, and oxygen need to be considered to elucidate the redox processes of RSE in the presence of HS. In addition, improved analytical techniques for the characterization of HS has the potential to advance the study on the redox processes of RSE in the presence of HS. It may contribute to understanding the mechanism for the redox processes between RSE and HS in the biogeochemical cycles.

Aerobic methane oxidation under copper scarcity in a stratified lake

Aerobic methane-oxidizing bacteria (MOB) substantially reduce methane fluxes from freshwater sediments to the atmosphere. Their metalloenzyme methane monooxygenase (MMO) catalyses the first oxidation step converting methane to methanol. Its most prevalent form is the copper-dependent particulate pMMO, however, some MOB are also able to express the iron-containing, soluble sMMO under conditions of copper scarcity. So far, the link between copper availability in different forms and biological methane consumption in freshwater systems is poorly understood. Here, we present high-resolution profiles of MOB abundance and pMMO and sMMO functional genes in relation to copper, methane and oxygen profiles across the oxic-anoxic boundary of a stratified lake. We show that even at low nanomolar copper concentrations, MOB species containing the gene for pMMO expression are present at high abundance. The findings highlight the importance of copper as a micronutrient for MOB species and the potential usage of copper acquisition strategies, even under conditions of abundant iron, and shed light on the spatial distribution of these microorganisms.

The influence of biochar and compost mixtures, water content, and gas flow rate, on the continuous adsorption of methane in a fixed bed column

Biofiltration is an excellent alternative for the treatment of diffuse emissions of methane (CH₄) that cannot be treated by physical/chemical means or recovered for energy. Despite the advances on CH₄ biological treatment technologies, they are limited by the low aqueous solubility of CH₄ into the biofilm where CH₄ mineralization occurs. In this study, the CH₄ adsorption kinetics, adsorption capacity and transport behavior of CH₄ was studied in batch experiments and in a fixed-bed column by varying the biochar and compost mixtures under 5-levels, 3 different water contents (dry, 15% and 30% water holding capacity), and 2 inlet flow rates. Experimental results were formally tested using analysis of variance (ANOVA) in order to draw objective conclusions based on statistical inference. As CH₄ biofiltration requires water addition to maintain microbial activity, these results indicate adsorption capacity is not lost with water addition if biochar content is the dominant packing material. The Langmuir isotherm described the data best (R² = 0.99). Maximum adsorption capacity by monolayer adsorption, or q_max, is relatively similar with or without the addition of water as long as the biochar component is the dominant material at 3.5 mg CH₄/g medium for a 7:1 biochar: compost, v/v mixture. Empirical regression models for q_o, k_Th, (Thomas model) and τ and K_YN (Yoon-Nelson model) were developed for the break through curves of CH₄. The current work demonstrates the applicability of utilizing biochar, a relatively inexpensive adsorbent, can compensate for the low solubility of CH₄ and overcome the rate-limiting step of mass transfer from the gas phase and into the methanotrophic biofilm. Further, biochar may be a reliable back-up system for CH₄ storage especially for fluctuating inlet loads that may be encountered in industrial applications adsorbing up to 13 mg CH₄/g biochar under dry conditions.

Microbial Mercury Methylation in Aquatic Environments: A Critical Review of Published Field and Laboratory Studies

Methylmercury (MeHg) is an environmental contaminant of concern because it biomagnifies in aquatic food webs and poses a health hazard to aquatic biota, piscivorous wildlife and humans. The dominant source of MeHg to freshwater systems is the methylation of inorganic Hg (IHg) by anaerobic microorganisms; and it is widely agreed that in situ rates of Hg methylation depend on two general factors: the activity of Hg methylators and their uptake of IHg. A large body of research has focused on the biogeochemical processes that regulate these two factors in nature; and studies conducted within the past ten years have made substantial progress in identifying the genetic basis for intracellular methylation and defining the processes that govern the cellular uptake of IHg. Current evidence indicates that all Hg methylating anaerobes possess the gene pair hgcAB that encodes proteins essential for Hg methylation. These genes are found in a large variety of anaerobes, including iron reducers and methanogens; but sulfate reduction is the metabolic process most often reported to show strong links to MeHg production. The uptake of Hg substrate prior to methylation may occur by passive or active transport, or by a combination of both. Competitive inhibition of Hg uptake by Zn speaks in favor of active transport and suggests that essential metal transporters are involved. Shortly after its formation, MeHg is typically released from cells, but the efflux mechanisms are unknown. Although methylation facilitates Hg depuration from the cell, evidence suggests that the hgcAB genes are not induced or favored by Hg contamination. Instead, high MeHg production can be linked to high Hg bioavailability as a result of the formation of Hg(SH)₂, HgS nanoparticles, and Hg-thiol complexes. It is also possible that sulfidic conditions require strong essential metal uptake systems that inadvertently bring Hg into the cytoplasm of Hg methylating microbes. In comparison with freshwaters, Hg methylation in open ocean waters appears less restricted to anoxic environments. It does seem to occur mainly in oxygen deficient zones (ODZs), and possibly within anaerobic microzones of settling organic matter, but MeHg (CH₃Hg⁺) and Me₂Hg ((CH₃)₂Hg) have been shown to form also in surface water samples from the euphotic zone. Future studies may disclose whether several different pathways lead to Hg methylation in marine waters and explain why Me₂Hg is a significant Hg species in oceans but seemingly not in most freshwaters.

Environmental controls on the abundance of methanotrophs and methanogens in peat bog lakes

The aim of the present study was to identify the factors that influence the composition of methanogens and methanotrophs in the background prokaryotic community in peat bog lakes. We hypothesized that the microbial composition is a function of the physicochemical conditions of the water and a function of depth-dependent oxygen (DO) concentrations. To address this aim, we collected water samples from subsurface and near-bottom layers, representing oxic and anoxic conditions in 4 peat bog lakes in NE Poland. The structure of methanogenic Archaea and methane-oxidizing bacteria (MOB) was determined with double labeled-fluorescence in situ hybridization (DOPE-FISH). The results showed significant differences in Procaryota communities between the oxic (subsurface) and suboxic/anoxic (near-bottom) layers in peat bog lakes (t-test, p < 0.05). The methanogens from the Archaea domain were observed in anoxic periods, while methanotrophs were present regardless of water depth and season. The abundance of methanogens was inversely correlated with DO and CO₂. Methanotrophs adapted better to the changing habitat conditions. The nonmetrical multidimensional scaling (NMS) and partial least square regression (PLS-R) models showed that the methanotrophs in subsurface layers are positively associated with temperature, DOC, and TON while negatively associated with pH. The DO availability is not a prerequisite condition for the presence of methanothrophs. The most important factors for MOB at the bottom were CO₂ and TON. Due to a significant role of methanotrophs in the control of the methane emission flux rates, there is a need for further research on factors responsible for methanotroph development in peat bog lakes.

Methanotrophic contribution to biodegradation of phenoxy acids in cultures enriched from a groundwater-fed rapid sand filter

Drinking water supply is in many parts of the world based on groundwater. Groundwater often contains methane, which can be oxidized by methanotrophs upon aeration. Sand from rapid sand filters fed with methane-rich groundwater can remove some pesticides (Hedegaard and Albrechtsen in Water Res 48:71-81, 2014). We enriched methanotrophs from filter sand and investigated whether they could drive the degradation of various pesticides. To enrich for methanotrophs, we designed and operated four laboratory-scale, continuously methane-fed column reactors, inoculated with filter sand and one control column fed with tap water. When enrichments were obtained, methane was continuously supplied to three reactors, while the fourth was starved for methane for 1 week, and the reactors were spiked with ten pesticides at groundwater-relevant concentrations (2.1-6.6 μg/L). Removal for most pesticides was not detected at the investigated contact time (1.37 min). However, the degradation of phenoxy acids was observed in the methanotrophic column reactor starved for methane, while it was not detected in the control column indicating the importance of methanotrophs. Phenoxy acid removal, using dichlorprop as a model compound, was further investigated in batch experiments with methanotrophic biomass collected from the enrichment reactors. Phenoxy acid removal (expressed per gram of matrix sand) was substantially improved in the methanotrophic enrichment compared to parent filter sand. The presence of methane did not clearly impact dichlorprop removal but did impact mineralization. We suggest that other heterotrophs are responsible for the first step in dichlorprop degradation, while the subsequent steps including ring-hydroxylation are driven by methanotrophs.

Biocatalytic Oxidations of Substrates through Soluble Methane Monooxygenase from Methylosinus sporium 5

Methane, an important greenhouse gas, has a 20-fold higher heat capacity than carbon dioxide. Earlier, through advanced spectroscopy and structural studies, the mechanisms underlying the extremely stable C–H activation of soluble methane monooxygenase (sMMO) have been elucidated in Methylosinus trichosporium OB3b and Methylococcus capsulatus Bath. Here, sMMO components—including hydroxylase (MMOH), regulatory (MMOB), and reductase (MMOR)—were expressed and purified from a type II methanotroph, Methylosinus sporium strain 5 (M. sporium 5), to characterize its hydroxylation mechanism. Two molar equivalents of MMOB are necessary to achieve catalytic activities and oxidized a broad range of substrates including alkanes, alkenes, halogens, and aromatics. Optimal activities were observed at pH 7.5 for most substrates possibly because of the electron transfer environment in MMOR. Substitution of MMOB or MMOR from another type II methanotroph, Methylocystis species M, retained specific enzyme activities, demonstrating the successful cross-reactivity of M. sporium 5. These results will provide fundamental information for further enzymatic studies to elucidate sMMO mechanisms.

Methane and nitrous oxide cycling microbial communities in soils above septic leach fields: Abundances with depth and correlations with net surface emissions

Onsite septic systems use soil microbial communities to treat wastewater, in the process creating potent greenhouse gases (GHGs): methane (CH₄) and nitrous oxide (N₂O). Subsurface soil dispersal systems of septic tank overflow, known as leach fields, are an important part of wastewater treatment and have the potential to contribute significantly to GHG cycling. This study aimed to characterize soil microbial communities associated with leach field systems and quantify the abundance and distribution of microbial populations involved in CH₄ and N₂O cycling. Functional genes were used to target populations producing and consuming GHGs, specifically methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) for CH₄ and nitric oxide reductase (cnorB) and nitrous oxide reductase (nosZ) for N₂O. All biomarker genes were found in all soil samples regardless of treatment (leach field, sand filter, or control) or depth (surface or subsurface). In general, biomarker genes were more abundant in surface soils than subsurface soils suggesting the majority of GHG cycling is occurring in near-surface soils. Ratios of production to consumption gene abundances showed a positive relationship with CH₄ emissions (mcrA:pmoA, p < 0.001) but not with N₂O emission (cnorB:nosZ, p > 0.05). Of the three measured soil parameters (volumetric water content (VWC), temperature, and conductivity), only VWC was significantly correlated to a biomarker gene, mcrA (p = 0.0398) but not pmoA or either of the N₂O cycling genes (p > 0.05 for cnorB and nosZ). 16S rRNA amplicon library sequencing results revealed soil VWC, CH₄ flux and N₂O flux together explained 64% of the microbial community diversity between samples. Sequencing of mcrA and pmoA amplicon libraries revealed treatment had little effect on diversity of CH₄ cycling organisms. Overall, these results suggest GHG cycling occurs in all soils regardless of whether or not they are associated with a leach field system.

Biofiltration of methane

The on-going annual increase in global methane (CH₄) emissions can be largely attributed to anthropogenic activities. However, as more than half of these emissions are diffuse and possess a concentration less than 3% (v/v), physical-chemical treatments are inefficient as an abatement technology. In this regard, biotechnologies, such as biofiltration using methane-oxidizing bacteria, or methanotrophs, are a cost-effective and efficient means of combating diffuse CH₄ emissions. In this review, a number of abiotic factors including temperature, pH, water content, packing material, empty-bed residence time, inlet gas flow rate, CH₄ concentration, as well biotic factors, such as biomass development, are reviewed based on empirical findings on CH₄ biofiltration studies that have been performed in the last decades.

Active pathways of anaerobic methane oxidation across contrasting riverbeds

Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems but we know little about AOM in rivers, whose role in the global carbon cycle is increasingly recognized. We measured AOM potentials driven by different electron acceptors, including nitrite, nitrate, sulfate, and ferric iron, and identified microorganisms involved across contrasting riverbeds. AOM activity was confined to the more reduced, sandy riverbeds, whereas no activity was measured in the less reduced, gravel riverbeds where there were few anaerobic methanotrophs. Nitrite-dependent and nitrate-dependent AOM occurred in all sandy riverbeds, with the maximum rates of 61.0 and 20.0 nmol CO₂ g⁻¹ (dry sediment) d⁻¹, respectively, while sulfate-dependent and ferric iron-dependent AOM occurred only where methane concentration was highest and the diversity of AOM pathways greatest. Diverse Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea were detected in the sandy riverbeds (16S rRNA gene abundance of 9.3 × 10⁵ to 1.5 × 10⁷ and 2.1 × 10⁴ to 2.5 × 10⁵ copies g⁻¹ dry sediment, respectively) but no other known anaerobic methanotrophs. Further, we found M. oxyfera-like bacteria and M. nitroreducens-like archaea to be actively involved in nitrite- and nitrate/ferric iron-dependent AOM, respectively. Hence, we demonstrate multiple pathways of AOM in relation to methane, though the activities of M. oxyfera-like bacteria and M. nitroreducens-like archaea are dominant.

Evolutionary History of Copper Membrane Monooxygenases

Copper membrane monooxygenases (CuMMOs) oxidize ammonia, methane and some short-chain alkanes and alkenes. They are encoded by three genes, usually in an operon of xmoCAB. We aligned xmo operons from 66 microbial genomes, including members of the Alpha-, Beta-, and Gamma-proteobacteria, Verrucomicrobia, Actinobacteria, Thaumarchaeota and the candidate phylum NC10. Phylogenetic and compositional analyses were used to reconstruct the evolutionary history of the enzyme and detect potential lateral gene transfer (LGT) events. The phylogenetic analyses showed at least 10 clusters corresponding to a combination of substrate specificity and bacterial taxonomy, but with no overriding structure based on either function or taxonomy alone. Adaptation of the enzyme to preferentially oxidize either ammonia or methane has occurred more than once. Individual phylogenies of all three genes, xmoA, xmoB and xmoC, closely matched, indicating that this operon evolved or was consistently transferred as a unit, with the possible exception of the methane monooxygenase operons in Verrucomicrobia, where the pmoB gene has a distinct phylogeny from pmoA and pmoC. Compositional analyses indicated that some clusters of xmoCAB operons (for example, the pmoCAB in gammaproteobacterial methanotrophs and the amoCAB in betaproteobacterial nitrifiers) were compositionally very different from their genomes, possibly indicating recent lateral transfer of these operons. The combined phylogenetic and compositional analyses support the hypothesis that an ancestor of the nitrifying bacterium Nitrosococcus was the donor of methane monooxygenase (pMMO) to both the alphaproteobacterial and gammaproteobacterial methanotrophs, but that before this event the gammaproteobacterial methanotrophs originally possessed another CuMMO (Pxm), which has since been lost in many species.

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.

Bio-Methanol Production Using Treated Domestic Wastewater with Mixed Methanotroph Species and Anaerobic Digester Biogas

The development of cost-effective methods, which generate minimal chemical wastewater, for methanol production is an important research goal. In this study, treated wastewater (TWW) was utilized as a culture solution for methanol production by mixed methanotroph species as an alternative to media prepared from commercial or chemical agents, e.g., nitrate mineral salts medium. Furthermore, a realistic alternative for producing methanol in wastewater treatment plants using biogas from anaerobic digestion was proposed. By culturing mixed methanotroph species with nitrate and phosphate-supplemented TWW in municipal wastewater treatment plants, this study demonstrates, for the first time, the application of biogas generated from the sludge digester of municipal wastewater treatment plants. NaCl alone inhibited methanol dehydrogenase and the addition of 40 mM formate as an electron donor increased methanol production to 6.35 mM. These results confirmed that this practical energy production method could enable cost-effective methanol production. As such, methanol produced in wastewater treatment plants can be used as an eco-friendly energy and carbon source for biological denitrification, which can be an alternative to reducing the expenses required for the waste water treatment process.

Combined Effects of Carbon and Nitrogen Source to Optimize Growth of Proteobacterial Methanotrophs

Methane, a potent greenhouse gas, and methanol, commonly called wood alcohol, are common by-products of modern industrial processes. They can, however, be consumed as a feedstock by bacteria known as methanotrophs, which can serve as useful vectors for biotransformation and bioproduction. Successful implementation in industrial settings relies upon efficient growth and bioconversion, and the optimization of culturing conditions for these bacteria remains an ongoing effort, complicated by the wide variety of characteristics present in the methanotroph culture collection. Here, we demonstrate the variable growth outcomes of five diverse methanotrophic strains – Methylocystis sp. Rockwell, Methylocystis sp. WRRC1, Methylosinus trichosporium OB3b, Methylomicrobium album BG8, and Methylomonas denitrificans FJG1 – grown on either methane or methanol, at three different concentrations, with either ammonium or nitrate provided as nitrogen source. Maximum optical density (OD), growth rate, and biomass yield were assessed for each condition. Further metabolite and fatty acid methyl ester (FAME) analyses were completed for Methylocystis sp. Rockwell and M. album BG8. The results indicate differential response to these growth conditions, with a general preference for ammonium-based growth over nitrate, except for M. denitrificans FJG1. Methane is also preferred by most strains, with methanol resulting in unreliable or inhibited growth in all but M. album BG8. Metabolite analysis points to monitoring of excreted formic acid as a potential indicator of adverse growth conditions, while the magnitude of FAME variation between conditions may point to strains with broader substrate tolerance. These findings suggest that methanotroph strains must be carefully evaluated before use in industry, both to identify optimal conditions and to ensure the strain selected is appropriate for the process of interest. Much work remains in addressing the optimization of growth strategies for these promising microorganisms since disregarding these important steps in process development could ultimately lead to inefficient or failed bioprocesses.

Eutrophication exacerbates the impact of climate warming on lake methane emission

Net methane (CH₄) emission from lakes depends on two antagonistic processes: CH₄ production (methanogenesis) and CH₄ oxidation (methanotrophy). It is unclear how climate warming will affect the balance between these processes, particularly among lakes of different trophic status. Here we show that methanogenesis is more sensitive to temperature than methanotrophy, and that eutrophication magnifies this temperature sensitivity. Using laboratory incubations of water and sediment from ten tropical, temperate and subarctic lakes with contrasting trophic states, ranging from oligotrophic to hypereutrophic, we explored the temperature sensitivity of methanogenesis and methanotrophy. We found that both processes presented a higher temperature sensitivity in tropical lakes, followed by temperate, and subarctic lakes; but more importantly, we found that eutrophication triggered a higher temperature sensitivity. A model fed by our empirical data revealed that increasing lake water temperature by 2 °C leads to a net increase in CH₄ emissions by 101-183% in hypereutrophic lakes and 47-56% in oligotrophic lakes. We conclude that climate warming will tilt the CH₄ balance towards higher lake emission and that this impact will be exacerbated by the eutrophication of the lakes.

Increases in temperature and nutrient availability positively affect methane-cycling microorganisms in Arctic thermokarst lake sediments

Arctic permafrost soils store large amounts of organic matter that is sensitive to temperature increases and subsequent microbial degradation to methane (CH₄) and carbon dioxide (CO₂). Here, we studied methanogenic and methanotrophic activity and community composition in thermokarst lake sediments from Utqiag˙vik (formerly Barrow), Alaska. This experiment was carried out under in situ temperature conditions (4°C) and the IPCC 2013 Arctic climate change scenario (10°C) after addition of methanogenic and methanotrophic substrates for nearly a year. Trimethylamine (TMA) amendment with warming showed highest maximum CH₄production rates, being 30% higher at 10°C than at 4°C. Maximum methanotrophic rates increased by up to 57% at 10°C compared to 4°C. 16S rRNA gene sequencing indicated high relative abundance of Methanosarcinaceae in TMA amended incubations, and for methanotrophic incubations Methylococcaeae were highly enriched. Anaerobic methanotrophic activity with nitrite or nitrate as electron acceptor was not detected. This study indicates that the methane cycling microbial community can adapt to temperature increases and that their activity is highly dependent on substrate availability.

Horizontal gene transfer of three co-inherited methane monooxygenase systems gave rise to methanotrophy in the Proteobacteria

The critical role that bacterial methanotrophs have in regulating the environmental concentrations of the potent greenhouse gas, methane, under aerobic conditions is dependent on monooxygenase enzymes which oxidise the substrate as both a carbon and energy source. Despite the importance of these organisms, the evolutionary origins of aerobic methane oxidation capability and its relationship to proteobacterial evolution is not well understood. Here we investigated the phylogenetic relationship of proteobacterial methanotrophs with related, non-methanotrophic bacteria using 16S rRNA and the evolution of two forms of methane monooxygenase: membrane bound (pMMO and pXMO) and cytoplasmic (sMMO). Through analysis we have concluded that extant proteobacterial methanotrophs evolved from up to five ancestral species, and that all three methane monooxygenase systems, pMMO, pXMO and sMMO, were likely present in the ancestral species (although pXMO and sMMO are not present in most of the present day methanotrophs). Here we propose that the three monooxygenase systems entered the ancestral species by horizontal gene transfer, with these likely to have pre-existing physiological and metabolic attributes that supported conversion to methanotrophy. Further, we suggest that prior to these enzyme systems developing methane oxidation capabilities, the membrane-bound and cytoplasmic monooxygenases were already both functionally and phylogenetically associated. These results not only suggest that sMMO and pXMO have a far greater role in methanotrophic evolution than previously understood but also implies that the co-inheritance of membrane bound and cytoplasmic monooxygenases have roles additional to that of supporting methanotrophy.

Influence of biomass density and food to microorganisms ratio on the mixed culture type I methanotrophs enriched from activated sludge

Methanotrophic based process can be the remedy to offset the wastewater treatment facilities increasing energy requirements due to methanotroph's unique ability to integrate methane assimilation with multiple biotechnological applications like biological nitrogen removal and methanol production. Regardless of the methanotrophic process end product, the challenge to maintain stable microbial growth in the methanotrophs cultivation bioreactor at higher cell densities is one of the major obstacles facing the process upscaling. Therefore, a series of consecutive batch tests were performed to attentively investigate the biomass density influence on type I methanotrophs bacterial growth. In addition, food to microorganisms (F/M), carbon to nitrogen (C/N) and nitrogen to microorganisms (N/M) ratio effect on the microbial activity was studied for the first time. It was clarified that the F/M ratio is the most influencing factor on the microbial growth at higher biomass densities rather than the biomass density increase, whereas C/N and N/M ratio change, while using nitrate as the nitrogen source, does not influence methanotrophs microbial growth. These study results would facilitate the scaling up of methanotrophic based biotechnology by identifying that F/M ratio as the key parameter that influences methanotrophs cultivation at high biomass densities.

A systematic comparison of two empirical gas-liquid mass transfer determination methodologies to characterize methane biodegradation in stirred tank bioreactors

This study aimed at systematically comparing the potential of two empirical methods for the estimation of the volumetric CH₄ mass transfer coefficient (k_la_CH4), namely gassing-out and oxygen transfer rate (OTR), to describe CH₄ biodegradation in a fermenter operated with a methanotrophic consortium at 400, 600 and 800 rpm. The k_la_CH4 estimated from the OTR methodology accurately predicted the CH₄ elimination capacity (EC) under CH₄ mass transfer limiting conditions regardless of the stirring rate (∼9% of average error between empirical and estimated ECs). Thus, empirical CH₄-ECs of 37.8 ± 5.8, 42.5 ± 5.4 and 62.3 ± 5.2 g CH₄ m^-3 h^-1vs predicted CH₄-ECs of 35.6 ± 2.2, 50.1 ± 2.3 and 59.6 ± 3.4 g CH₄ m^-3 h^-1 were recorded at 400, 600 and 800 rpm, respectively. The rapid Co²⁺-catalyzed reaction of O₂ with SO₃^-2 in the vicinity of the gas-liquid interphase during OTR determinations, mimicking microbial CH₄ uptake in the biotic experiments, was central to accurately describe the k_la_CH4.

Chalkophores

Copper-binding metallophores, or chalkophores, play a role in microbial copper homeostasis that is analogous to that of siderophores in iron homeostasis. The best-studied chalkophores are members of the methanobactin (Mbn) family-ribosomally produced, posttranslationally modified natural products first identified as copper chelators responsible for copper uptake in methane-oxidizing bacteria. To date, Mbns have been characterized exclusively in those species, but there is genomic evidence for their production in a much wider range of bacteria. This review addresses the current state of knowledge regarding the function, biosynthesis, transport, and regulation of Mbns. While the roles of several proteins in these processes are supported by substantial genetic and biochemical evidence, key aspects of Mbn manufacture, handling, and regulation remain unclear. In addition, other natural products that have been proposed to mediate copper uptake as well as metallophores that have biologically relevant roles involving copper binding, but not copper uptake, are discussed.

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.

Characterization of toluene metabolism by methanotroph and its effect on methane oxidation

Methanotrophs not only oxidize CH₄, but also can oxidize a relatively broad range of other substrates, including trichloroethylene, alkanes, alkenes, and aromatic compounds. In this study, Methylosinus sporium was used as a model organism to characterize toluene metabolism by methanotrophs. Reverse transcription quantitative PCR analysis showed that toluene enhanced the mmoX expression of M. sporium. When the toluene concentration was below 2000 mg m^-3, the kinetics of toluene metabolism by M. sporium conformed to the Michaelis-Menten equation (V_max = 0.238 g g_{dry weight}^-1 h^-1, K _m  = 545.2 mg m^-3). The use of a solid-phase extraction technique followed by a gas chromatography-mass spectrometry analysis and molecular docking calculation showed that toluene was likely to primarily bind the di-iron center structural region of soluble methane monooxygenase (sMMO) hydroxylase and then be oxidized to o-cresol. Although M. sporium oxidized toluene, it did not incorporate toluene into its biomass. The coexistence of toluene and CH₄ could influence CH₄ oxidation, the growth of methanotrophs, and the distribution of CH₄-derived carbon, which were related to the ratio of the toluene concentration to biomass. These results would be helpful to understand the metabolism of CH₄ and non-methane volatile organic compounds in the environment.

Rapid isolation of fast-growing methanotrophs from environmental samples using continuous cultivation with gradually increased dilution rates

Methanotrophs have recently gained interest as biocatalysts for mitigation of greenhouse gas emission and conversion of methane to value-added products; however, their slow growth has, at least partially, hindered their industrial application. A rapid isolation technique that specifically screens for the fastest-growing methanotrophs was developed using continuous cultivation with gradually increased dilution rates. Environmental samples collected from methane-rich environments were enriched in continuously stirred tank reactors with unrestricted supply of methane and air. The reactor was started at the dilution rate of 0.1 h^-1, and the dilution rates were increased with an increment of 0.05 h^-1 until the reactor was completely washed out. The shifts in the overall microbial population and methanotrophic community at each step of the isolation procedure were monitored with 16S rRNA amplicon sequencing. The predominant methanotrophic groups recovered after reactor operations were affiliated to the gammaproteobacterial genera Methylomonas and Methylosarcina. The methanotrophic strains isolated from the reactor samples collected at their respective highest dilution rates exhibited specific growth rates up to 0.40 h^-1; the highest value reported for methanotrophs. The novel isolation method developed in this study significantly shortened the time and efforts needed for isolation of methanotrophs from environmental samples and was capable of screening for the methanotrophs with the fastest growth rates.

A novel methanotrophic co-metabolic system with high soluble methane monooxygenase activity to biodegrade refractory organics in pulping wastewater

Pulping wastewater still contains massive refractory organics after biotreatment, with high colority, low biodegradability, and lasting biotoxicity. To eliminate refractory organics in pulping wastewater, a methanotrophic co-metabolic system in a gas cycle Sequencing Batch Biofilm Reactor (gcSBBR) seeded by soil at a ventilation opening of coal mine was quickly built on the 92nd day. The removal rate of COD, colority and TOC was 53.28%, 50.59% and 51.60%, respectively. Analysis of 3D-EEM indicated that glycolated protein-like, melanoidin-like or lignocellulose-like, and humic acid-like decreased by 7.85%, 5.02% and 1.74%, respectively. Moreover, this system exhibited high activity of soluble methane monooxygenase (sMMO) and mmoX encoding sMMO reached up to 7.89 × 10⁵ copies/μL. Methanotrophs, namely, Methylocaldum (8.28%), Methylococcus (6.06%) and Methylomonas (0.07%), were detected by 16S rRNA sequencing. And other bacteria were dominated by Denitratisoma, Anaerolineaceae_uncultured and Methylophilaceae_uncultured. Refractory organics was biodegraded through the synergy among microorganisms, and a postulated synergy pathway was put forward.

Recent Advances in the Genetic Manipulation of Methylosinus trichosporium OB3b

Methanotrophic bacteria utilize methane as their sole carbon and energy source. Studies of the model Type II methanotroph Methylosinus trichosporium OB3b have provided insight into multiple aspects of methanotrophy, including methane assimilation, copper accumulation, and metal-dependent gene expression. Development of genetic tools for chromosomal editing was crucial for advancing these studies. Recent interest in methanotroph metabolic engineering has led to new protocols for genetic manipulation of methanotrophs that are effective and simple to use. We have incorporated these newer molecular tools into existing protocols for Ms. trichosporium OB3b. The modifications include additional shuttle and replicative plasmids as well as improved gene delivery and genotyping. The methods described here render gene editing in Ms. trichosporium OB3b efficient and accessible.

Methanobactins: Maintaining copper homeostasis in methanotrophs and beyond

Methanobactins (Mbns) are ribosomally produced, post-translationally modified natural products that bind copper with high affinity and specificity. Originally identified in methanotrophic bacteria, which have a high need for copper, operons encoding these compounds have also been found in many non-methanotrophic bacteria. The proteins responsible for Mbn biosynthesis include several novel enzymes. Mbn transport involves export through a multidrug efflux pump and re-internalization via a TonB-dependent transporter. Release of copper from Mbn and the molecular basis for copper regulation of Mbn production remain to be elucidated. Future work is likely to result in the identification of new enzymatic chemistry, opportunities for bioengineering and drug targeting of copper metabolism, and an expanded understanding of microbial metal homeostasis.

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane-Oxidizing Upland Soil Cluster α

Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. The 16S rRNA gene sequence recovered was distinctive and suggests this crucial group as a new genus within the Beijerinckiaceae, close to Methylocapsa. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high-affinity activity of methane oxidation to USCα cells in situ. Analysis of the global biogeography of this group further revealed its presence in previously unrecognized habitats, such as subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane.

Enrichments of methanotrophic-heterotrophic cultures with high poly-β-hydroxybutyrate (PHB) accumulation capacities

Methanotrophic-heterotrophic communities were selectively enriched from sewage sludge to obtain a mixed culture with high levels of poly-β-hydroxybutyrate (PHB) accumulation capacity from methane. Methane was used as the carbon source, N₂ as sole nitrogen source, and oxygen and Cu content were varied. Copper proved essential for PHB synthesis. All cultures enriched with Cu could accumulate high content of PHB (43.2%-45.9%), while only small amounts of PHB were accumulated by cultures enriched without Cu (11.9%-17.5%). Batch assays revealed that communities grown with Cu and a higher O₂ content synthesized more PHB, which had a wider optimal CH₄:O₂ range and produced a high PHB content (48.7%) even though in the presence of N₂. In all methanotrophic-heterotrophic communities, both methanotrophic and heterotrophic populations showed the ability to accumulate PHB. Although methane was added as the sole carbon source, heterotrophs dominated with abundances between 77.2% and 85.6%. All methanotrophs detected belonged to type II genera, which formed stable communities with heterotrophs of different PHB production capacities.

Metagenomics profiling for assessing microbial diversity in both active and closed landfills

The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×10⁷ and 1.50×10⁷, respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.

Metals and Methanotrophy

Aerobic methanotrophs have long been known to play a critical role in the global carbon cycle, being capable of converting methane to biomass and carbon dioxide. Interestingly, these microbes exhibit great sensitivity to copper and rare-earth elements, with the expression of key genes involved in the central pathway of methane oxidation controlled by the availability of these metals. That is, these microbes have a "copper switch" that controls the expression of alternative methane monooxygenases and a "rare-earth element switch" that controls the expression of alternative methanol dehydrogenases. Further, it has been recently shown that some methanotrophs can detoxify inorganic mercury and demethylate methylmercury; this finding is remarkable, as the canonical organomercurial lyase does not exist in these methanotrophs, indicating that a novel mechanism is involved in methylmercury demethylation. Here, we review recent findings on methanotrophic interactions with metals, with a particular focus on these metal switches and the mechanisms used by methanotrophs to bind and sequester metals.