Recent findings in methanotrophs: genetics, molecular ecology, and biopotential

The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.

Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss

Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d-1 and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d-1, respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.

Enhancement of electron transfer via magnetite in nitrite-dependent anaerobic methane oxidation system

Nitrite-dependent anaerobic methane oxidation (n-DAMO) is a novel denitrification process that simultaneously further removes and utilizes methane from anaerobic effluent from wastewater treatment plants. However, the metabolic activity of n-DAMO bacteria is relative low for practical application. In this study, conductive magnetite was added into lab-scale sequencing batch reactor inoculated with n-DAMO bacteria to study the influence on n-DAMO process. With magnetite amendment, the nitrogen removal rate could reach 34.9 mg N·L-1d-1, nearly 2.5 times more than that of control group. Magnetite significantly facilitated the interspecies electron transfer and built electrically connected community with high capacitance. Enzymatic activities of electron transport chain were significantly elevated. Functional gene expression and enzyme activities associated with nitrogen and methane metabolism had been highly up-regulated. These results not only propose a useful strategy in n-DAMO application but also provide insights into the stimulating mechanism of magnetite in n-DAMO process.

Tuning Pd species via electronic metal-support interaction for methane combustion

Utilizing catalytic combustion to convert methane (CH4) into CO2 and H2O stands as one of the most effective approaches for mitigating unburnt CH4 emissions from natural gas engines. Supported Pd catalysts have been extensively researched for their role in low-temperature CH4 combustion, with their catalytic activity greatly influenced by metal-support interactions. Surface interaction Pd phases, as a special type of Pd species originating from metal-support interactions on supported Pd catalysts, show controversial catalytic performance in CH4 combustion. Moreover, the impact of electronic metal-support interactions (EMSI, which refers to metal-support interactions associated with electron transfer) remains unclear. Hence, we opted for Ce-Zr solid solutions with different Ce:Zr molar ratios as supports and synthesized a range of supported Pd catalysts with varying EMSI intensities. Characterization revealed that as the oxygen vacancy concentration on the support increased, electron transfer weakened, leading to a higher Pd-O-Ce content, resulting in a lower CH4 activation barrier and better catalytic performance. This study offers a promising approach for regulating EMSI and active Pd species on supported catalysts in practical applications.

Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands

Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.

Effects of fir-wood biochar on CH4 oxidation rates and methanotrophs in landfill cover soils packed at three different proctor compaction levels

Application of biochar to landfill cover soils can purportedly improve methane (CH4) oxidation rates, but understanding the combined effects of soil texture, compaction, and biochar on the activity and composition of the methanotrophs is limited. The amendment of wood biochar on two differently textured landfill cover soils at three compaction levels of the Proctor density was explored by analyzing changes in soil physical properties relevant to methane oxidation, the effects on CH4 oxidation rates, and the composition of the methanotrophic community. Loose soils with and without biochar were pre-incubated to equally elevate the CH4 oxidation rates. Hereafter, soils were compacted and re-incubated. Methane oxidation rates, gas diffusivity, water retention characteristics, and pore size distribution were analyzed on the compacted soils. The relative abundance of methanotrophic bacteria (MOB) was determined at the end of both the pre-incubation and incubation tests of the packed samples. Biochar significantly increased porosity at all compaction levels, enhancing diffusion coefficients. Also, a re-distribution in pore sizes was observed. Increased gas diffusivity from low compaction and amendment of biochar, though, did not reflect higher methane oxidation rates due to high diffusive oxygen fluxes over the limited height of the compacted soil specimens. All soils, with and without biochar, were strongly dominated by Type II methanotrophs. In the sandy soil, biochar amendment strongly increased MOB abundance, which could be attributed to a corresponding increase in the relative abundance of Methylocystis species, while no such response was observed in the clayey soil. Compaction did not change the community composition in either soil. Fir-wood biochar addition to landfill cover soils may not always enhance methanotrophic activity and hence reduce fugitive methane emissions, with the effect being soil-specific. However, especially in finer and more compacted soils, biochar amendment can maintain soil diffusivity above a critical level, preventing the collapse of methanotrophy.

Distribution, reactivity and vertical fluxes of methane in the Guadalquivir Estuary (SW Spain)

The influence of temperature, salinity, sediment-water-atmosphere exchanges and oxidation rate on the variability of methane (CH4) in the Guadalquivir Estuary has been studied. The database corresponds to 3 intensive samplings carried out in summer (2021 and 2022) and winter (2022). An increase in CH4 concentration towards the interior of the estuary has been observed, more intense during summer (19-371 nmol L-1). The influence of temperature and salinity on the variability of CH4 concentration is negligible, with contributions below 1 nmol L-1. Water-atmosphere fluxes increase inland in summer (28-574 μmol m-2 d-1), being generally higher than in winter (18-80 μmol m-2 d-1). Similarly, benthic fluxes remain relatively constant in winter (10 ± 6 μmol m-2 d-1) and increase inland in summer (7-212 μmol m-2 d-1). In the innermost station of the estuary, with salinities lower than 1, there is a significant increase in benthic fluxes, with values above 9000 μmol m-2 d-1. CH4 oxidation rates increase towards low salinities, being especially high in summer (489 nmol L-1 d-1). Based on the information obtained, CH4 variability in the Guadalquivir Estuary is mainly controlled by water-atmosphere fluxes, benthic fluxes and oxidation in the water column. The uncertainty associated with the quantification of these processes does not allow an adequate assessment of the influence of lateral inputs, although there is experimental evidence of their importance in the Guadalquivir.

Cadmium reduced methane emissions by stimulating methane oxidation in paddy soils

Flooded rice paddy fields are a significant source of anthropogenic methane (CH4) emissions. Cadmium (Cd) is one of the most common and toxic contaminants in paddy soils. However, little is known about how the soil microbial communities associated with CH4 emissions respond to the increasing Cd-stress in paddies. In this study, we employed isotopically 13C-labelled CH4, high-throughput sequencing analysis, and gene quantification analysis to reveal the effect and mechanism of Cd on CH4 emissions in paddy soils. Results showed that 4.0 mg kg-1 Cd addition reduced CH4 emissions by 16-99% in the four tested paddy soils, and significantly promoted the transformation of 13CH4 to 13CO2. Quantitative polymerase chain reaction (qPCR) demonstrated that Cd addition increased the abundances of pmoA gene, the ratios of methanogens to methanotrophs (mcrA/pmoA) showed a positive correlation with CH4 emissions (R2 = 0.798, p < 0.01). Furthermore, the composition of the microbial community containing the pmoA gene was barely affected by Cd addition (p > 0.05). This observation was consistent with the findings of a pure incubation experiment where methanotrophs exhibited high tolerance to Cd. We argue that microbial feedback to Cd stress amplifies the contribution of methanotrophs to CH4 oxidation in rice fields through the complex interactions occurring among soil microbes. Our study highlights the overlooked association between Cd and CH4 dynamics, offering a better understanding of the role of rice paddies in global CH4 cycling.

Enhanced methane oxidation efficiency by digestate biochar in landfill cover soil: Microbial shifts and carbon metabolites insights

The ability of biochar to enhance the oxidation of methane (CH4) in landfill cover soil by promoting the growth and activity of methane-oxidizing bacteria (MOB) has attracted significant attention. However, the optimal characteristics of digestate-derived biochar (DBC) for promoting the MOB community and CH4 removal performance remain unclear. This study examined how the CH4 oxidation capacity and respiratory metabolism of MOB life process are affected by the application of DBC compared with the most commonly used woody-derived biochar (WBC). The addition of both WBC and DBC enhanced CH4 oxidation, with DBC exhibiting a nearly twofold increase in cumulative CH4 oxidation mass (7.14 mg CH4 g-1) compared to WBC. The high ion-exchange capacity of DBC was found to be more favorable for the growth of Type I MOB, which have more efficient metabolic pathways for CH4 oxidation. Type I MOB which are abundant in DBC may prefer monovalent positive ions, while the charge-rich nature of DBC may also have hindered extracellular protein aggregation. The superiority of DBC in terms of CH4 oxidation thus highlights the underlying mechanisms of biochar-MOB interactions, offering potential biochar options for landfill cover soil.

Effects of Hydrophobic Biochar-Modified Landfill Soil Cover on Methane Oxidation

Landfill cover soils play an important role in mitigating landfill methane (CH4) emissions. Incorporating biochar into the soil has proven effective in reducing CH4 emissions. However, the role of hydrophobic biochar in this context remains underexplored. This study investigated the CH4 removal efficiency of a biochar-modified landfill soil cover column (RB) and hydrophobic biochar-modified landfill soil cover column (RH) under varying CH4 influx gas concentrations (25 and 35%), simulated CH4 inflow rates (10, 15, and 20 ml/min), and temperatures (20, 25, 30, 35, and 40 °C). RH consistently outperformed RB in terms of CH4 removal efficiency under these experimental conditions. The optimal conditions for CH4 degradation by both RB and RH were observed at a CH4 influx gas concentration of 35%, a simulated CH4 inflow rate of 10 ml/min, and a temperature of ~30 °C. RH achieved a CH4 removal rate of up to 99.96%. In summary, the addition of hydrophobic biochar enhanced the air permeability and hydrophobicity of landfill cover soils, providing a promising alternative to conventional cover soils for reducing CH4 emissions from landfills.

Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean

Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.

Impact of temperature on the performance of compost-based landfill biocovers

Methane (CH4) emissions from landfills are a major contributor to global greenhouse gas emissions. Compost-based biocovers offer a viable approach to reduce CH4 emissions from landfills; however, the effectiveness in climates with varying temperatures is not well understood. The methane removal performances of two compost-based biocover materials (food and yard waste compost) were examined under different temperature conditions using laboratory column experiments. A reactive transport model was used to simulate the experimental results to develop a better quantitative understanding of the effect of temperature on overall methane removal efficiency. As expected, experimental results indicated that the oxidation rate was influenced by temperature, as it was reduced when the temperature decreased from 22 °C to 8 °C. However, some oxidation was observed at a lower temperature, which was confirmed by CO2 concentrations above the initial level and the observed temperatures above the exposure temperature along the height of biocover column. Furthermore, results showed that when the compost-based materials were subjected to 8 °C and then increased to 22 °C, methane oxidation within the material recovered quickly and returned to similar oxidation rates as observed before the temperature was reduced, suggesting that compost-based biocovers may not be affected by cyclic temperature variations when used in colder climates. Methane oxidation capacity was limited by the maximum oxidation rate, the biocover porosity, and the gas saturation profile that affects residence time and overall methane oxidation in the columns. The model results show that the CH4 oxidation rate was reduced by one order of magnitude when the temperature decreased from 22 °C to 8 °C. Therefore, the calculated Q10 values were 4.19 and 5.18 for the food and yard waste compost, respectively. Overall, compost-based landfill biocovers, such as food and yard waste compost, are capable of mitigate CH4 emissions from old and small landfills under different temperature conditions.

Bioinspired microenvironment modulation of metal-organic framework-based catalysts for selective methane oxidation

Inspiration from natural enzymes enabling creationary catalyst design is appealing yet remains extremely challenging for selective methane (CH4) oxidation. This study presents the construction of a biomimetic catalyst platform for CH4 oxidation, which is constructed by incorporating Fe-porphyrin into a robust metal-organic framework, UiO-66, furnished with saturated monocarboxylic fatty acid bearing different long alkyl chains. The catalysts demonstrate the high efficiency in the CH4 to methanol (CH3OH) conversion at 50 °C. Moreover, the selectivity to CH3OH can be effectively regulated and promoted through a fine-tuned microenvironment by hydrophobic modification around the Fe-porphyrin. The long-chain fatty acids anchored on the Zr-oxo cluster of UiO-66 can not only tune the electronic state of the Fe sites to improve CH4 adsorption, but also restrict the amount of H2O2 around the Fe sites to reduce the overoxidation. This behavior resembles the microenvironment regulation in methane monooxygenase, resulting in high CH3OH selectivity.

Beyond Reduction Cocatalysts: Critical Role of Metal Cocatalysts in Photocatalytic Oxidation of Methane with Water

Environmentally sustainable and selective conversion of methane to valuable chemicals under ambient conditions is pivotal for the development of next-generation photocatalytic technology. However, due to the lack of microscopic knowledge about non-thermal methane conversion, controlling and modulating photocatalytic oxidation processes driven by photogenerated holes remain a challenge. Here, we report novel function of metal cocatalysts to accept photogenerated holes and dominate selectivity of methane oxidation, which is clearly beyond the conventional concept in photocatalysis that the metal cocatalysts loaded on the surfaces of semiconductor photocatalysts mostly capture photogenerated electrons and dominate reduction reactions exclusively. The novel photocatalytic role of metal cocatalysts was verified by operando molecular spectroscopy combined with real-time mass spectrometry for metal-loaded Ga2O3 model photocatalysts under methane and water vapor at ambient temperature and pressure. Our concept of metal cocatalysts that work as active sites for both photocatalytic oxidation and reduction provides a new understanding of photocatalysis and a solid basis for controlling non-thermal redox reactions by metal-cocatalyst engineering.

Computational Study of Single Metal Atom Anchored on Black Phosphorus for Methane Oxidation to Methanol by Nitrous Oxide

Direct conversion of methane to the high-value-added transportable chemicals is of great challenge, which requires high energy input to break the strong C-H bond. Developing efficient catalysts for methane oxidation to methanol under mild conditions is of vital importance. In this work, the single transition metal atoms (TM = Fe, Co, Ni, Cu) anchored on black phosphorus (TM@BP) were studied as catalysts to assist the methane oxidation to methanol by means of first-principles calculations. The results indicate that Cu@BP exhibits an outstanding catalytic activity through the radical reaction pathways and the formation of the Cu-O active site is the rate-determining with an energy barrier of 0.48 eV. Meanwhile, electronic structure calculations and dynamic simulations show that Cu@BP offer excellent thermal stability. Our calculations provide a new approach for the rational design of single atom catalysts for methane oxidation to methanol.

Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments

Conventional aerobic CH₄-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O₂ gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH₄ with the help of riboflavin when O₂ was unavailable. Within the MOB consortium, MOB transformed CH₄ to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH₄ oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH₄ emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH₄ sink in iron-rich sediments.

Environmental assessment of landfill gas mitigation using biocover and gas collection with energy utilisation at aging landfills

A life cycle-based environmental assessment was conducted on the mitigation of landfill gas emissions, by implementing biocover and gas collection along with energy utilisation at aging landfills. Based on recent studies about gas generation at Danish landfills, the efficiency of the mitigation technologies involved and the composition of substituted energy production, 15 scenarios were modelled using the EASETECH life cycle assessment model, through which potential environmental impacts in the category "Climate change" were calculated. In all scenarios, biocover and gas collection systems with energy utilisation led to significant environmental improvements compared to the baseline scenario with no emission mitigation action. Scenarios representing biocovers with methane oxidation efficiencies between 70 and 90 % were environmentally superior in terms of climate change impact - in comparison to scenarios with 20-30 years of gas collection and energy utilisation (collection efficiencies between 40 and 80 %). Combining gas collection with energy utilisation and the subsequent installation of a biocover saw major improvements in comparison to where only gas collection and energy utilisation were in effect. Overall, it can be concluded that a biocover under the given assumptions is environmentally more appropriate than gas collection and utilisation at aging landfills, mainly due to methane emissions escaping through the landfill cover during and after the gas collection period playing a crucial role in the latter situation. Maintaining high methane oxidation efficiency for a biocover throughout the lifetime of a landfill is vital for reducing environmental impacts.

Characterization of methanotrophic community and activity in landfill cover soils under dimethyl sulfide stress

Landfill cover soil is the environmental interface between landfills and the atmosphere and plays an important role in mitigating CH₄ emission from landfills. Here, stable isotope probing microcosms with CH₄ or CH₄ and dimethyl sulfide (DMS) were carried out to characterize activity and community structure of methanotrophs in landfill cover soils under DMS stress. The CH₄ oxidation activity in the landfill cover soils was not obviously influenced at the DMS concentration of 0.05%, while it was inhibited at the DMS concentrations of 0.1% and 0.2%. DMS-S was mainly oxidized to sulfate (SO₄^2-) in the landfill cover soils. In the landfill cover soils, DMS could inhibit the expression of bacteria and decrease the abundances of pmoA and mmoX genes, while it could prompt the expression of pmoA and mmoX genes. γ-Proteobacteria methanotrophs including Methylocaldum, Methylobacter, Crenothrix and unclassified Methylococcaceae and α-Proteobacteria methanotrophs Methylocystis dominated in assimilating CH₄ in the landfill cover soils. Of them, Methylobacter and Crenothrix had strong tolerance to DMS or DMS could promote the growth and activity of Methylobacter and Crenothrix, while Methylocaldum had weak tolerance to DMS and showed an inhibitory effect. Metagenomic analyses showed that methanotrophs had the genes of methanethiol oxidation and could metabolize CH₄ and methanethiol simultaneously in the landfill cover soils. These findings suggested that methanotrophs might metabolize sulfur compounds in the landfill cover soils, which may provide the potential application in engineering for co-removal of CH₄ and sulfur compounds.

Study on the effect of landfill gas on aerobic municipal solid waste degradation: Lab-scale model and tests

Aeration is of great importance in landfill remediation. However, most existing studies on aerobic waste degradation ignore the presence of landfill gases. In this study, gas characteristics during aerobic waste degradation in the presence of landfill gas in lab-scale lysimeters were investigated. Oxygen (O₂) was intermittently injected into municipal solid waste. Changes in the gas concentration and reaction rate of methane (CH₄), carbon dioxide (CO₂), and O₂ during the reaction process were monitored and calculated. The results showed that all reactions, including aerobic degradation, CH₄ oxidation, and anaerobic waste degradation, occurred simultaneously during landfill aeration. The maximum O₂ consumption rate was 0.013 mol day^-1 kg^-1 dry waste. CH₄ production was stimulated after the O₂ content was insufficient to sustain the aerobic environment. Higher CH₄ production was likely attributed to the remaining substrate and biomass from dead aerobic microorganisms decomposed by growing anaerobic microorganisms. Based on the biochemical reaction and principle of mass conservation, a gas balance model during waste aeration was established to analyze the proportions of aerobic waste degradation, CH₄ oxidation, and anaerobic waste degradation. The CH₄ oxidation reaction was more advantageous than the aerobic waste degradation reaction during aeration. With an increase in gas injection times, the anaerobic reaction gradually weakened. The maximum proportion of CH₄ oxidation reaction could achieve at 21.4 % during aeration, which is of great significance for the waste degradation reaction. The maximum proportion of aerobic waste degradation and the minimum proportion of anaerobic waste degradation were approximately 16.0 % and 74.2 %, respectively. The results show that landfill gas should be considered in the progress of landfill aeration. This study provides a novel approach for calculating the proportion of reactions during landfill aeration, which deepens the understanding of the reaction process and contributes to the design of aerobic landfill projects.

Synergy effects of Methylomonas koyamae and Hyphomicrobium methylovorum under methanethiol stress

Methanotrophs are able to metabolize volatile organic sulfur compounds (VOSCs), excrete organic carbon during CH₄ oxidation, and influence microbial community structure and function of the ecosystem. In return, microbial community structure and environmental factors can affect the growth metabolism of methanotrophs. In this study, Methylomonas koyamae and Hyphomicrobium methylovorum were used for model organisms, and methanethiol (MT) was chosen for a typical VOSC to investigate the synergy effects under VOSC stress. The results showed that when Hyphomicrobium methylovorum was co-cultured with Methylomonas koyamae in the medium with CH₄ used as the carbon source, the co-culture had better MT tolerance relative to Methylomonas koyamae and oxidized all CH₄ within 120 h, even at the initial MT concentration of 2000 mg m^-3. The optimal co-culture ratios of Methylomonas koyamae to Hyphomicrobium methylovorum were 4:1-12:1. Although MT could be converted spontaneously to dimethyl disulfide (DMDS), H₂S, and CS₂ in air, faster losses of MT, DMDS, H₂S, and CS₂ were observed in each strain mono-culture and the co-culture. Compared with Hyphomicrobium methylovorum, MT was degraded more quickly in the Methylomonas koyamae culture. During the co-culture, the CH₄ oxidation process of Methylomonas koyamae could provide carbon and energy sources for the growth of Hyphomicrobium methylovorum, while Hyphomicrobium methylovorum oxidized MT to help Methylomonas koyamae detoxify. These findings are helpful to understand the synergy effects of Methylomonas koyamae and Hyphomicrobium methylovorum under MT stress and enrich the role of methanotrophs in the sulfur biogeochemical cycle. KEY POINTS: • The co-culture of Methylomonas and Hyphomicrobium has better tolerance to CH₃SH. • Methylomonas can provide carbon sources for the growth of Hyphomicrobium. • The co-culture of Methylomonas and Hyphomicrobium enhances the removal of CH₄ and CH₃SH.

pH dependence of arsenic speciation in paddy soils: The role of distinct methanotrophs

Arsenic (As) is a priority environmental pollutant in paddy field. The coupling of arsenate (As(V)) reduction with anaerobic methane (CH₄) oxidation was recently demonstrated in paddy soils and has been suggested to serve as a critical driver for As transformation and mobilization. However, whether As(V)-dependent CH₄ oxidation is driven by distinct methanotrophs under different pH conditions remains unclear. Here, we investigated the response of As(V)-dependent CH₄ oxidation to pH shifts (pH 5.5-8.0) by employing isotopically labelled CH₄. Furthermore, the underlying mechanisms were also investigated in well-controlled anoxic soil suspension incubations. Our results showed that As(V)-dependent CH₄ oxidation is highly sensitive to pH changes (1.6-6.8 times variation of arsenite formation). A short-term (0-10 d) pH shift from near-neutral pH to acidic conditions (i.e., pH 5.5, -85% arsenite formation) had an inhibitory effect on As(V)-dependent CH₄ oxidation. However, prolonged acidic conditions (i.e., >15 d) had no significant influence on As(V)-dependent CH₄ oxidation. The microbial analyses indicated that As reduction in paddies can be driven by anaerobic CH₄ oxidation archaea (ANME) and methanotrophs. And, methanotrophs may serve as a critical driver for As(V)-dependent CH₄ oxidation. Moreover, type I methanotrophs Methylobacter were more active in oxidizing CH₄ than type II methanotrophs Methylocystis when the pH ≥ 6.5. However, Methylocystis had a higher tolerance to soil acidification than Methylobacter. This study illustrates that As(V)-dependent CH₄ oxidation could be dominated by distinct methanotrophs along with pH shifts, which eventually enhances As release in paddy soils.

Coupling methanotrophic denitrification to anammox in a moving bed biofilm reactor for nitrogen removal under hypoxic conditions

Simultaneous removal of ammonium and nitrate was achieved in a methane-fed moving bed biofilm reactor (MBBR). In the reactor, methanotrophic microorganisms oxidized methane under hypoxic conditions likely to methanol, hence providing an electron donor to denitrifiers to reduce nitrate to nitrite that then allowed anaerobic ammonium oxidizing bacteria (Anammox) to remove excess ammonium as N₂. The ammonium and nitrate removal rates reached 72.09 ± 5.81 mgNH₄⁺-N/L/d and 62.61 ± 4.17 mgNO₃^--N/L/d when the MBBR was operated in continuous mode. Nitrate removal by the methane-fed mixed consortia was confirmed in a batch test revealing a CH₄/NO₃^- molar removal ratio of 1.15. The functional populations were unveiled by FISH analysis and 16S rRNA gene sequencing, which showed that the biofilm was dominated by Anammox bacteria (Candidatus Kuenenia) and diverse taxa associated with the capacity for denitrification: aerobic methanotrophs (Methylobacter, Methylomonas, and unclassified Methylococcaceae), methylotrophic denitrifiers (Opitutaceae and Methylophilaceae), and other heterotrophic denitrifiers (Ignavibacteriaceae, Anaerolineaceae, Comamonadaceae, Rhodocyclaceae and Thauera). Neither DAMO archaea nor DAMO bacteria were found in the sequencing analysis, indicating that more unknown community members possess the metabolic capacity of methanotrophic denitrification.

Anaerobic methane oxidation coupled to arsenate reduction in paddy soils: Insights from laboratory and field studies

Anaerobic methane oxidation (AOM) coupled to nitrate, sulfate and iron has been most extensively studied. Recently, AOM coupled with arsenate reduction (AOM-AsR) was demonstrated in laboratory microcosm incubation, however whether AOM-AsR is active in the field conditions remains elusive. Here, we used 13C-labeled methane (13CH4) to investigate the AOM-AsR process in both anaerobic microcosms and field conditions with identical soils. Our results revealed the occurrence of AOM-AsR in the field, but AOM-AsR in the field was not as active as that which occurred in the laboratory (AOM-AsR contributed approximately 33.87% and 80.76% of total As release in the field and laboratory studies, respectively). This occurred because the laboratory setting provided a more suitable condition for the AOM-AsR process. Moreover, the results suggested that the relative abundance of mcrA from the ANME-2d was the most abundant. Our results clearly demonstrate that the AOM-AsR is active in both the laboratory and field conditions. Moreover, the results highlight the potential risk the AOM-AsR for pose for As contamination in rice paddies.

Organics composition and microbial analysis reveal the different roles of biochar and hydrochar in affecting methane oxidation from paddy soil

Biochar and hydrochar, as valuable and eco-friendly soil remediation materials from greenwaste, have potential to enhance methane oxidation in paddy soil. But the mechanism of biomass carbon on the improvement of methane-oxidizing bacteria communities in paddy soil has not been adequately elucidated. In the present study, the effect of different-temperature rice straw-based biomass carbon (RB400, RB600, RH250 and RH300) on methane oxidation were investigated by analyzing the soil dissolved organic matter (DOM), physicochemical properties and changes in microbial community structure. The results of the 17-day incubation experiment showed that the methane oxidation rate increased under all types of biomass carbon in the first 6 days. The enhancement of methane oxidation rate was more pronounced for biochar compared to hydrochar, with RB600 being the most effective treatment. The result of excitation-emission matrix (EEM) fluorescence spectroscopy showed that less DOM were released from the soil in the biochar treatments compared to the hydrochar treatments and protein-like were detected only in the hydrochar group. Microbial analysis further showed that hydrochar inhibited the growth of Bacillus, Methylobacter, and Methylocystis, while RB600 significantly increased the relative abundance of methanotrophs (responsible for methane oxidation), such as Methylocystis and Methylobacter, which was consistent with their different effects on the methane oxidation rate. Moreover, from the analysis of principal component analysis (PCA) and canonical correspondence analysis (CCA), Methylobacter and Methylocystis were negatively respond to H/C of biomass carbon. The present study provides a deeper understanding of the effect of biomass carbon obtained by different processes on methane oxidation when applied to soil from the perspective of organic matter and microbial communities.

Prospecting the significance of methane-utilizing bacteria in agriculture

Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.

Optimization of nitrogen feeding strategies for improving polyhydroxybutyrate production from biogas by Methylocystis parvus str. OBBP in a stirred tank reactor

The design of efficient cultivation strategies to produce bioplastics from biogas is crucial for the implementation of this biorefinery process. In this work, biogas-based polyhydroxybutyrate (PHB) production and CH₄ biodegradation performance was investigated for the first time in a stirred tank bioreactor inoculated with Methylocystis parvus str. OBBP. Decreasing nitrogen loading rates in continuous mode and alternating feast:famine regimes of 24 h-cycles, and alternating feast:famine regimes of 24 h:24 h and 24 h:48 h were tested. Continuous N feeding did not support an effective PHB production despite the occurrence of nitrogen limiting conditions. Feast-famine cycles of 24 h:24 h (with 50% stoichiometric nitrogen supply) supported the maximum PHB production (20 g-PHB m^-3 d^-1) without compromising the CH₄-elimination capacity (25 g m^-3 h^-1) of the system. Feast:famine ratios ≤1:2 entailed the deterioration of process performance at stoichiometric nitrogen inputs ≤60%.

Use of methanotrophically activated biochar in novel biogeochemical cover system for carbon sequestration: Microbial characterization

Biochar-amended soils have been explored to enhance microbial methane (CH₄) oxidation in landfill cover systems. Recently, research priorities have expanded to include the mitigation of other components of landfill gas such as carbon dioxide (CO₂) and hydrogen sulfide (H₂S) along with CH₄. In this study, column tests were performed to simulate the newly proposed biogeochemical cover systems, which incorporate biochar-amended soil for CH₄ oxidation and basic oxygen furnace (BOF) slag for CO₂ and H₂S mitigation, to evaluate the effect of cover configuration on microbial CH₄ oxidation and community composition. Biogeochemical covers included a biochar-amended soil (10% w/w), and methanotroph-enriched activated biochar amended soil (5% or 10% w/w) as a biocover layer or CH₄ oxidation layer. The primary outcome measures of interest were CH₄ oxidation rates and the structure and abundance of methane-oxidation bacteria in the covers. All column reactors were active in CH₄ oxidation, but columns containing activated biochar-amended soils had higher CH₄ oxidation rates (133 to 143 μg CH₄ g^-1 day^-1) than those containing non-activated biochar-amended soil (50 μg CH₄ g^-1 day^-1) and no-biochar soil or control soil (43 μg CH₄ g^-1 day^-1). All treatments showed significant increases in the relative abundance of methanotrophs from an average relative abundance of 5.6% before incubation to a maximum of 45% following incubation. In activated biochar, the abundance of Type II methanotrophs, primarily Methylocystis and Methylosinus, was greater than that of Type I methanotrophs (Methylobacter) due to which activated biochar-amended soils also showed higher abundance of Type II methanotrophs. Overall, biogeochemical cover profiles showed promising potential for CH₄ oxidation without any adverse effect on microbial community composition and methane oxidation. Biochar activation led to an alteration of the dominant methanotrophic communities and increased CH₄ oxidation.

CS2 increasing CH4-derived carbon emissions and active microbial diversity in lake sediments

Lakes are important methane (CH₄) sources to the atmosphere, especially eutrophic lakes with cyanobacterial blooms accompanied by volatile sulfur compound (VSC) emissions. CH₄ oxidation is a key strategy to mitigate CH₄ emission from lakes. In this study, we characterized the fate of CH₄-derived carbon and active microbial communities in lake sediments with CS₂ used as a typical VSC, based on the investigation of CH₄ and VSC fluxes from Meiliang Bay in Lake Taihu. Stable isotope probing microcosm incubation showed that the efficiency of CH₄-derived carbon incorporated into organic matter was 21.1% in the sediment with CS₂ existence, which was lower than that without CS₂ (27.3%). SO₄^2--S was the main product of CS₂ oxidation under aerobic condition, accounting for 59.3-62.7% of the input CS₂-S. CS₂ and CH₄ coexistence led to a decrease of methanotroph and methylotroph abundances and stimulated the production of extracellular polymeric substances. CS₂ and its metabolites including total sulfur, SO₄^2- and acid volatile sulfur acted as the main drivers influencing the active microbial community structure in the sediments. Compared with α-proteobacteria methanotrophs, γ-proteobacteria methanotrophs Methylomicrobium, Methylomonas, Crenothrix and Methylosarcina were more dominant in the sediments. CH₄-derived carbon mainly flowed into methylotrophs in the first stage. With CH₄ consumption, more CH₄-derived carbon flowed into non-methylotrophs. CS₂ could prompt more CH₄-derived carbon flowing into non-methanotrophs and non-methylotrophs, such as sulfur-metabolizing bacteria. These findings can help elucidate the influence of VSCs on microorganisms and provide insights to carbon fluxes from eutrophic lake systems.

Revisiting the passive biocover system at Klintholm landfill, six years after construction

A biocover system was established at Klintholm landfill in Denmark in 2009 to mitigate methane emissions, and the system exhibited high mitigation efficiency during the first year after implementation. The biocover system was revisited in 2016/2017, and a series of field and laboratory tests were carried out to evaluate functionality about six years after establishment. Three field campaigns were executed in three different barometric pressure conditions, namely increasing, stable and decreasing. Local surface flux measurements and gas concentration profiles in the methane oxidation layer showed that barometric pressure changes had a significant effect on gas emission and methane oxidation. Elevated concentrations of oxygen were observed in the gas distribution layer, and field data showed that significant methane oxidation took place in this location. This finding was verified in laboratory-based methane oxidation incubation tests. Temperatures higher than ambient temperature were observed throughout the methane oxidation layer, with average temperatures ranging between 13 and 27 °C, even in the coldest month of the year. Field measurements showed that total methane emissions from the whole landfill cell were at the same level or lower than measurements performed in 2009/2010 after implementation of the biocover system, and laboratory tests showed methane oxidation potential approximately equal to former tests. In spite of an inhomogeneous distribution of landfill gas load to the methane oxidation layer, the performance of the biocover system had not declined over the 6-7 years since its establishment, even though no maintenance had been carried out in the intervening years.

Copper stimulation on methane-supported perchlorate reduction in a membrane biofilm reactor

The present study demonstrated that the perchlorate reduction rate in a methane-based membrane biofilm reactor was significantly enhanced from 14.4 to 25.6 mg-Cl/L/d by increasing copper concentration in the feeding medium from 1 to 10 μM, indicating a stimulatory effect of copper on the methane-supported perchlorate reduction process. Batch tests further confirmed that the increased copper concentration enhanced both methane oxidation and perchlorate reduction rates, which was supported by an increasing trend of functional genes (pmoA for methanotrophs and pcrA for specific perchlorate reducers) abundances through quantitative polymerase chain reaction (qPCR). Both 16S rRNA gene sequencing and functional genes (pmoA and pcrA) sequencing jointly revealed that the biofilm supplied with a higher copper concentration exhibited a more diverse microbial community. The methane-supported perchlorate reduction was accomplished through a synergistic association of methanotrophs (Methylocystis, Methylomonas, and Methylocystaceae) and perchlorate reducers (Dechloromonas, Azospira, Magnetospirillum, and Denitratisoma). Acetate may function as the key syntrophic linkage between methanotrophs and perchlorate reducers. It was proposed that the increased copper concentration improved the activity of particulate methane monooxygenase (pMMO) for methane oxidation or promoted the biosynthesis of intracellular carbon storage compounds polyhydroxybutyrate (PHB) in methanotrophs for generating more acetate available for perchlorate reduction.

Methane emissions from Icelandic landfills - A comparison between measured and modelled emissions

This study compares methane (CH₄) emissions from five Icelandic landfills, quantified using tracer gas dispersion to modelled emission rates using the IPCC FOD model. The average CH₄ emission rates measured from the investigated landfills were 475.4 kg CH₄ h^-1 (Álfsnes landfill), 32.5 kg CH₄ h^-1 (Fíflholt), 40.8 kg CH₄ h^-1 (Gufunes), 9.8 kg CH₄ h^-1 (Kirkjuferjuhjáleiga) and 78.4 kg CH₄ h^-1 (Stekkjarvík). At three of the landfills (Álfsnes, Fíflholt and Kirkjuferjuhjáleiga), the modelled emission was higher than the measured emission by factors ranging from 1.1 to 4.8, neglecting any CH₄ oxidation in the cover soils. Even though CH₄ oxidation might play a role at some of the investigated landfills, and thus reduce the gap between modelled and measured emissions, it is likely that the model overestimated CH₄ generation due to uncertainties in input model parameters. Assuming that the measured emissions at the five landfills are representative of all the waste disposed in Iceland from 2007 to 2016, the measured emission should be extrapolated to 817 kg CH₄ h^-1, which is relatively close to the modelled national emission of 936 kg CH₄ h^-1 in 2017. This study showed that the application of the IPCC FOD model at national level is appropriate for estimating landfill CH₄ emissions in Iceland. CH₄ emissions from landfills in Iceland can be reduced by expanding or implementing gas collection or biocover systems for optimised microbial oxidation.

Elucidation of dominant energy metabolic pathways of methane, sulphur and nitrogen in respect to mangrove-degradation for climate change mitigation

Mangroves play a key role in ecosystem balancing and climate change mitigation. It acts as a source and sink of methane (CH₄), a major greenhouse gas responsible for climate change. Energy metabolic pathways of methane production (methanogenesis) and oxidation (methanotrophy) are directly driven by sulphur (S) and nitrogen (N) metabolism and salinity in coastal wetlands. To investigate, how mangrove-degradations, affect the source-sink behaviour of CH₄; the pathways of CH₄, S and N were studied through whole-genome metagenomic approach. Soil samples were collected from degraded and undisturbed mangrove systems in Sundarban, India. Structural and functional microbial diversities (KEGG pathways) of CH₄, S and N metabolism were analysed and correlated with labile carbon pools and physico-chemical properties of soil. Overall, the acetoclastic pathway of methanogenesis was dominant. However, the relative proportion of conversion of CO₂ to CH₄ was more in degraded mangroves. Methane oxidation was higher in undisturbed mangroves and the serine pathway was dominant. After serine, the ribulose monophosphate pathway of CH₄ oxidation was dominant in degraded mangrove, while the xylulose monophosphate pathway was dominant in undisturbed site as it is more tolerant to salinity and higher pH. The assimilatory pathway (AMP) of S-metabolism was dominant in both systems. But in AMP pathway, adenosine triphosphate sulfurylase enzyme reads were higher in degraded mangrove, while NADPH-sulfite reductase abundance was higher in undisturbed mangrove due to higher salinity, and pH. In N-metabolism, the denitrification pathway was predominant in degraded sites, whereas the dissimilatory nitrate reduction pathway was dominant in undisturbed mangroves. The relative ratios of sulphur reducing bacteria (SRB): methanogens were higher in degraded mangrove; however, methanotrophs:methanogens was higher in undisturbed mangrove indicated lower source and greater sink capacity of CH₄ in the system. Microbial manipulation in mangrove-rhizosphere for regulating major energy metabolic pathways of methane could open-up a new window of climate change mitigation in coastal wetlands.

Compartmentation of microbial communities in structure and function for methane oxidation coupled to nitrification-denitrification

A hollow-fiber membrane biofilm reactor was designed and constructed to achieve simultaneous nitrification-denitrification coupled to methane oxidation in low O₂/CH₄ ratio and high nitrogen removal rate. Three O₂/CH₄ ratio stages were operated. Ammonia removal rates reached 77.5 and 95 mg/(L·d) at the O₂/CH₄ ratio of 1.47 and 2.1, respectively. Microbial community analysis revealed that aeration through physical partition and O₂/CH₄ ratio stages achieved compartmentation of microbial community in structure and function. Combined functional genes analysis using qPCR, the aeration through gas distributer was proved to promote the enrichment of autotrophic ammonia oxidizers in the suspended liquid/mixed filler samples, and the aeration through hollow-fiber membrane favored the growth of methanotrophs and heterotrophic nitrification-aerobic denitrification bacteria. This study helps to develop effective regulatory strategies for high nitrogen removal based on the understanding of the community assembly process and the key driving factors.

Validation and optimization of key biochar properties through iron modification for improving the methane oxidation capacity of landfill cover soil

Knowledge of various BC properties in stimulating the methane (CH₄) oxidation capacity of landfill cover soil (LCS) is still limited, restricting the optimization of BC performance. To validate key BC properties and seek a feasible way for enhancing BC performance, this study prepared BCs with distinctly varying characteristics through iron (Fe) modification. Then, batch incubation experiments under different CH₄ and oxygen concentrations were conducted. Pore volume, cation exchange capacity (CEC), and surface area of BC collectively accounted for 78.5% of the variances in the microbial community structures, with pore volume being the most important factor. These correlated well with the differences in the CH₄ oxidation capacities among the different BC-amended LCS. At a low ratio of 15% (v/v) in LCS, BCs' pH not affected their performance but homogeneity could be a limiting factor. Fe modification proved a promising approach to more efficiently improve the three key BC properties (especially pore volume) and thus optimize BC performance than increasing pyrolysis temperature did. Fe-modified BCs encouraged a bacterial consortium (methanotroph, methylotrophs, and nitrogen-fixing bacteria) in the soil with significantly improved CH₄ oxidation capacities by up to 26%-74% compared to that of pristine BC.

Methylomonas albis sp. nov. and Methylomonas fluvii sp. nov.: Two cold-adapted methanotrophs from the river Elbe and emended description of the species Methylovulum psychrotolerans

Three strains of methanotrophic bacteria (EbA^T, EbB^T and Eb1) were isolated from the River Elbe, Germany. These Gram-negative, rod-shaped or coccoid cells contain intracytoplasmic membranes perpendicular to the cell surface. Colonies and liquid cultures appeared bright-pink. The major cellular fatty acids were 12:0 and 14:0, in addition in Eb1 the FA 16:1ω5t was also dominant. Methane and methanol were utilized as sole carbon sources by EbB^T and Eb1, while EbA^T could not use methanol. All strains oxidize methane using the particulate methane monooxygenase. Both strains contain an additional soluble methane monooxygenase. The strains grew optimally at 15-25 °C and at pH 6 and 8. Based on 16S rRNA gene analysis recovered from the full genome, the phylogenetic position of EbA^T is robustly outside any species clade with its closest relatives being Methylomonas sp. MK1 (98.24%) and Methylomonas sp. 11b (98.11%). Its closest type strain is Methylomonas methanica NCIMB11130 (97.91%). The 16S rRNA genes of EbB^T are highly similar to Methylomonas methanica strains with Methylomonas methanica R-45371 as the closest relative (99.87% sequence identity). However, average nucleotide identity (ANI) and digital DNA-DNA-hybridization (dDDH) values reveal it as distinct species. The DNA G + C contents were 51.07 mol% and 51.5 mol% for EbA^T and EbB^T, and 50.7 mol% for Eb1, respectively. Strains EbA^T and EbB^T are representing two novel species within the genus Methylomonas. For strain EbA^T we propose the name Methylomonas albis sp. nov (LMG 29958, JCM 32282) and for EbB^T, we propose the name Methylomonas fluvii sp. nov (LMG 29959, JCM 32283). Eco-physiological descriptions for both strains are provided. Strain Eb1 (LMG 30323, JCM 32281) is a member of the species Methylovulum psychrotolerans. This genus is so far only represented by two isolates but Eb1 is the first isolate from a temperate environment; so, an emended description of the species is given.

Draft genome sequence data of methanotrophic Methylovulum psychrotolerans strain S1L and Methylomonas paludis strain S2AM isolated from hypoxic water column layers of boreal lakes

Methanotrophic bacteria inhabit a wide range of natural (e.g. wetlands, lakes and soils) and anthropogenic (e.g. wastewater treatment plants and landfills) environments. They play a crucial role in mitigating atmospheric emissions of the greenhouse gas methane. There is also a growing interest in applying methanotrophs in the bioconversion of biogas - and natural gas - methane into value-added products (e.g. chemicals and single-cell protein). Hence, isolation and genome sequencing of methanotrophic bacteria is needed to provide important data on their functional capabilities. Here, we describe the de novo assembled draft genome sequences of Methylovulum psychrotolerans strain S1L isolated from hypoxic water column layer of boreal Lake Lovojärvi (Southern Finland), comprising total of 5090628 bp in 11 contigs with G+C - content of 50.9% and containing 4554 coding sequences. The draft genome of strain S1L represents the first published genome of M. psychrotolerans strain isolated from lake ecosystems. In addition, we present the genome sequence of Methylomonas paludis strain S2AM, isolated from water column of boreal Lake Alinen Mustajärvi (Southern Finland), comprising 3673651 bp in 1 contig with G+C - content of 48.2% and 3294 coding sequences. The draft genome of strain S2AM represents the first published genome of M. paludis. The preliminary genome annotation analysis of both S1L and S2AM identified genes encoding oxidation of methane, methanol, formaldehyde and formate, assimilation of carbon, ammonium and nitrate, N2 fixation, as well as various enzymes enabling the survival in hypoxic conditions, i.e. high-affinity oxidase, hemerythrins, fermentation enzymes (for production of acetate, succinate and H2) and respiratory nitrite reductases. The draft genomes have been deposited at GenBank under the accession JAGVVN000000000 for S1L and CP073754 for S2AM.

Catalytic machinery of methane oxidation in particulate methane monooxygenase (pMMO)

In this focused review, we portray the recently reported 2.5 Å cyro-EM structure of the particulate methane monooxygenase (pMMO) from M. capsulatus (Bath). The structure of the functional holo-pMMO near atomic resolution has uncovered the sites of the copper cofactors including the location of the active site in the enzyme. The three coppers seen in the original X-ray crystal structures of the enzyme are now augmented by additional coppers in the transmembrane domain as well as in the water-exposed C-terminal subdomain of the PmoB subunit. The cryo-EM structure offers the first glimpse of the catalytic machinery capable of methane oxidation with high selectivity and efficiency. The findings are entirely consistent with the biochemical and biophysical findings previously reported in the literature, including the chemistry of hydrocarbon hydroxylation, regeneration of the catalyst for multiple turnovers, and the mechanism of aborting non-productive cycles to ensure kinetic competence.

Geochemical evidence for fugitive gas contamination and associated water quality changes in drinking-water wells from Parker County, Texas

Extensive development of horizontal drilling and hydraulic fracturing enhanced energy production but raised concerns about drinking-water quality in areas of shale-gas development. One particularly controversial case that has received significant public and scientific attention involves possible contamination of groundwater in the Trinity Aquifer in Parker County, Texas. Despite extensive work, the origin of natural gas in the Trinity Aquifer within this study area is an ongoing debate. Here, we present a comprehensive geochemical dataset collected across three sampling campaigns along with integration of previously published data. Data include major and trace ions, molecular gas compositions, compound-specific stable isotopes of hydrocarbons (δ¹³C-CH₄, δ¹³C-C₂H₆, δ²H-CH₄), dissolved inorganic carbon (δ¹³C-DIC), nitrogen (δ¹⁵N-N₂), water (δ¹⁸O, δ²H, ³H), and noble gases (He, Ne, Ar), boron (δ¹¹B) and strontium (⁸⁷Sr/⁸⁶Sr) isotopic compositions of water samples from 20 drinking-water wells from the Trinity Aquifer. The compendium of data confirms mixing between a deep, naturally occurring salt- (Cl >250 mg/L) and hydrocarbon-rich groundwater with a low-salinity, shallower, and younger groundwater. Hydrocarbon gases display strong evidence for sulfate reduction-paired oxidation, in some cases followed by secondary methanogenesis. A subset of drinking-water wells contains elevated levels of hydrocarbons and depleted atmospherically-derived gas tracers, which is consistent with the introduction of fugitive thermogenic gas. We suggest that gas originating from the intermediate-depth Strawn Group ("Strawn") is flowing along the annulus of a Barnett Shale gas well, and is subsequently entering the shallow aquifer system. This interpretation is supported by the expansion in the number of affected drinking-water wells during our study period and the persistence of hydrocarbon levels over time. Our data suggest post-genetic secondary water quality changes occur following fugitive gas contamination, including sulfate reduction paired with hydrocarbon oxidation and secondary methanogenesis. Importantly, no evidence for upward migration of brine or natural gas associated with the Barnett Shale was identified.

Fermentation, methanotrophy and methanogenesis influence sedimentary Fe and As dynamics in As-affected aquifers in Vietnam

High arsenic (As) concentrations in groundwater are a worldwide problem threatening the health of millions of people. Microbial processes are central in the (trans)formation of the As-bearing ferric and ferrous minerals, and thus regulate dissolved As levels in many aquifers. Mineralogy, microbiology and dissolved As levels can vary sharply within aquifers, making high-resolution measurements particularly valuable in understanding the linkages between them. We conducted a high spatial resolution geomicrobiological study in combination with analysis of sediment chemistry and mineralogy in an alluvial aquifer system affected by geogenic As in the Red River delta in Vietnam. Microbial community analysis revealed a dominance of fermenters, methanogens and methanotrophs whereas sediment mineralogy along a 46 m deep core showed a diversity of Fe minerals including poorly crystalline Fe (II/III) and Fe(III) (oxyhydr)oxides such as goethite, hematite, and magnetite, but also the presence of Fe(II)-bearing carbonates and sulfides which likely formed as a result of microbially driven organic carbon (OC) degradation. A potential important role of methane (CH₄) as electron donor for reductive Fe mineral (trans)formation was supported by the high abundance of Candidatus Methanoperedens, a known Fe(III)-reducing methanotroph. Overall, these results imply that OC turnover including fermentation, methanogenesis and CH₄ oxidation are important mechanisms leading to Fe mineral (trans)formation, dissolution and precipitation, and thus indirectly affecting As mobility by changing the Fe-mineral inventory.

Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors

The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1-P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME-1 and ANME-2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.

Change in microbial profile and environmental conditions in a constructed wetland system treating greywater

The objective of this work was to verify the relationships between environmental conditions and microbial processes along a raw-light greywater flow in an improved constructed wetland (CW) system. Physicochemical analysis and high-throughput DNA sequencing were performed in the different zones to investigate the environmental conditions and microbial communities. The results showed that the system operated predominantly under anaerobic conditions, with redox potential (Eh) increasing from the inlet (-342.9 mV) to the outlet (-316.4 mV). Conversely, the chemical oxygen demand (COD) decreased along the greywater flow, suggesting negative correlation between these characteristics. The zones of the evapotranspiration and treatment tank (CEvaT) were characterized by lower community diversity and richness and by the presence of specific groups: Proteobacteria and Synergistetes related to the first steps of the conversion of organic carbon, in the bottom layer inside the anaerobic chamber (AnC); methanogens (Methanosaeta and Methanobacterium) and sulphate-reducing bacteria (Desulfovibrio, Desulforhabdus and Desulfomonile) in the middle layer; and microorganisms associated with the nitrogen cycle and oxygen release (Acinetobacter, Novosphingobium, Candidatus Nitrososphaera) in the top layer. On the other hand, the increase of the ORP and decrease of organic matter concentrations were associated with higher community diversity and richness in the middle layer of the CW, which showed higher abundance of microorganisms involved in methane (Methylobacterium and Candidatus Koribacter) and sulphur (Rhodoblastus and Thiobacillus) oxidation.

Methanotrophic denitrification in wastewater treatment: microbial aspects and engineering strategies

Anaerobic technologies are consolidated for sewage treatment and are the core processes for mining marketable products from waste streams. However, anaerobic effluents are supersaturated with methane, which represents a liability regarding greenhouse gas emissions. Meanwhile, anaerobic technologies are not capable of nitrogen removal, which is required to ensure environmental protection. Methane oxidation and denitrification processes can be combined to address both issues concurrently. Aerobic methane oxidizers can release intermediate organic compounds that can be used by conventional denitrifiers as electron donors. Alternatively, anoxic methanotrophic species combine methane oxidation with either nitrate or nitrite reduction in the same metabolism. Engineered systems need to overcome the long doubling times and low NO_x consumption rates of anoxic methanotrophic microorganisms. Another commonly reported bottleneck of methanotrophic denitrification relates to gas-liquid mass transfer limitations. Although anaerobic effluents are supersaturated with methane, experimental setups usually rely on methane supply in a gaseous mode. Hence, possibilities for the application of methane-oxidation coupled to denitrification in full scale might be overlooked. Moreover, syntrophic relationships among methane oxidizers, denitrifiers, nitrifiers, and other microorganisms (such as anammox) are not well understood. Integrating mixed populations with various metabolic abilities could allow for more robust methane-driven wastewater denitrification systems. This review presents an overview of the metabolic capabilities of methane oxidation and denitrification and discusses technological aspects that allow for the application of methanotrophic denitrification at larger scales.

Experimental analysis and modeling of the methane degradation in a three stage biofilter using composted sawdust as packing media

Methane gas is a very effective greenhouse gas and the second-largest contributor to global warming. Biofiltration is an effective technology that uses microorganisms to degrade the pollutant by oxidizing it. In this work, the performance of a biofilter with supporting filter media, consisting of composted sawdust, is evaluated at three different sampling ports. Furthermore, a transient model is developed to predict methane concentration at various heights and times. The developed model is validated with the experimental data and shows good agreement with the experimental data. The highest removal efficiency and elimination capacity was found to be 72% and 0.108 g m^-3 h^-1 respectively. The effect of parameters such as specific surface area, the reaction rate constant, biofilm thickness and airflow rate were studied on the outlet methane concentration. Under similar conditions, the simulations showed that the removal efficiency of 95% might be achieved for the height of 2 m.

Methane oxidation of residual landfill gas in a full-scale biofilter: human health risk assessment of volatile and malodours compound emissions

A human health risk assessment was performed to evaluate if a biofilter for the biological methane oxidation reduces the risk from exposure to landfill gas emissions and improves the air quality mitigating odour emissions from an aftercare landfill. Accordingly, three different scenarios of landfill gas management were defined, 9 volatile organic compounds (VOCs) (cyclohexane, n-hexane, 2-methylpentane, 3-methylpentane, benzene, xylenes, toluene, dichlorodifluoromethane, vinyl chloride) were identified and using the CALPUFF dispersion model; the pollutant concentration at eleven sensitive receptors was determined. Consequently, the risk (for cancer and non-cancer compounds) was assessed applying the methodology proposed by USEPA 2009. From one hand, to determine concentration and emission rates of VOCs and hydrogen sulphide, a sample of raw landfill gas and three air samples from the biofilter surface were collected with dynamic flux chamber method and analysed in accordance with US EPA, 1986 and USEPA TO-15, 1999. To the other hand, odour emissions were assessed based both on chemical and dynamic olfactometric measurements (EN 13725:2003). The field surveys results showed a reduction of the cancer risk on average by 79% and of the hazard quotient on average by 92%. In contrast, the results of olfactometry measurements showed a lower efficiency on odour reduction than the target value of 70%. Nonetheless, the odour concentration was always far below 300 uo_E m^-3 at the biofilter surface and odour concentration never exceed 1 uo_E m^-3 at the sensitive receptors.

Exploring simultaneous nitrous oxide and methane sink in wetland sediments under anoxic conditions

Methane (CH₄) and nitrous oxide (N₂O) are the most powerful greenhouse gases globally; recent emissions exceed previous estimates. The potential link between N₂O reduction and CH₄ oxidation in anoxic wetland sediments would be a sink for both gases, which has attracted broad attention. To explore the simultaneous N₂O and CH₄ biotransformation, wetland sediments were used to inoculate an enrichment reactor, continuously fed with CH₄ and N₂O for 500 days. After enrichment, the CH₄ oxidation rate reached 2.8 μmol·g^-1_dw·d^-1, which was 800-fold higher than the rate of the wetland sediments used as inoculum. Moreover, stable isotopic tracing proved CH₄ oxidation was driven by N₂O consumption under anoxic conditions. Genomic sequencing showed that the microbial community was dominated by methanotrophs. Species of Methylocaldum genus, belonging to γ-Proteobacteria class, were significantly enriched, and became the predominant methanotrophs. Quantitative analysis indicated methane monooxygenase and nitrous oxide reductase increased by 38- and 8-fold compared to the inoculum. As to the potential mechanisms, we propose that N₂O-driven CH₄ oxidation was mediated by aerobic methanotrophs solely or along with denitrifying bacteria under hypoxia. Electrons and energy are generated and transferred in the oxidative phosphorylation pathway. Our findings expand the range of electron acceptors associated with CH₄ oxidation as well as elucidate the significant role of methanotrophs relative to both carbon and nitrogen cycles.

Manipulation of soil methane oxidation under drought stress

Drought events are predicted to occur more frequently, but comprehensive knowledge of their effects on methane (CH₄) oxidation by soil methanotrophs in upland ecosystems remains elusive. Here, we put forward a new conceptual model in which drought influences soil CH₄ oxidation through a direct pathway (i.e., positive effects of soil CH₄ oxidation via increasing soil aeration) and through an indirect pathway (i.e., negative effects of in planta ethylene (C₂H₄) production on soil CH₄ oxidation). Through measuring soil CH₄ efflux along a gradient of drought stress, we found that drought increases soil CH₄ oxidation, as the former outweighs the latter on soil CH₄ oxidation, based on a mesocosm experiment employing distinct levels of watering and a long-term drought field trial created by rainfall exclusion in a subtropical evergreen forest. Moreover, we used aminoethoxyvinylglycine (AVG), a C₂H₄ biosynthesis inhibitor, to reduce in planta C₂H₄ production under drought, and found that reducing in planta C₂H₄ production increased soil CH₄ oxidation under drought. To confirm these findings, we found that inoculation of plant growth-promoting rhizobacteria containing the 1-aminocyclopropane-1-carboxylate deaminase alleviated the negative effects of drought-induced in planta C₂H₄, thus increasing soil CH₄ oxidation rates. All these results provide strong evidence for the hypothesis that in planta C₂H₄ production inhibits soil CH₄ oxidation under drought. To our knowledge, this is the first study to manipulate the negative feedback between C₂H₄ production and CH₄ oxidation under drought stress. Given the current widespread extent of arid and semiarid regions in the world, combined with the projected increased frequency of drought stress in future climate scenarios, we provide a reliable means for increasing soil CH₄ oxidation in the context of global warming.

Lack of methane hotspot in the upstream dam: Case study in a tributary of the Three Gorges Reservoir, China

River damming has seen a growing trend in demand worldwide and the impounded reaches are considered hotspots of greenhouse gas emissions. However, it remains unclear how the spatial distribution of C-gas in sediments and methane (CH₄) emissions of dammed tributary changes under different operation periods of the Three Gorges reservoir (TGR). We measured CH₄ and carbon dioxide (CO₂) concentrations in sediment and CH₄ emissions from a dammed river of the TGR, and evaluated the effect of damming on the spatial variability of carbon in the sediment and on CH₄ flux. It was found that damming led to a distinct spatial pattern of total organic carbon (TOC) in the sediment, which resulted in higher CH₄ and CO₂ in upstream sediment compared to the downstream. During the TGR impounding period, the upstream CH₄ diffusive flux (0.253-0.427 mg m^-2 h^-1) across the water-air interface was higher than in the downstream (0.093 mg m^-2 h^-1), which was consistent with the spatial variation of CH₄ in the sediments. However, the CH₄ emission was predominantly by ebullition and the flux in the downstream (169.173 mg m^-2 h^-1) was significantly higher than upstream (12.23-123.05 mg m^-2 h^-1) in the discharging period. This can be attributed to a sharp increase in TOC in downstream sediment due to riparian zone soil erosion on both banks, which was caused by periodic large fluctuation in the water level, and a shallow water depth in the downstream. This study adds to our understanding of effects of the TGR's operation on CH₄ emissions from a dammed tributary and suggests that the water level fluctuation of tributaries which has direct influence on ebullition and methane oxidation caused by manipulation of the TGR should not be overlooked.

Ammonia removal through combined methane oxidation and nitrification-denitrification and the interactions among functional microorganisms

It would be highly beneficial to use the methane produced by anaerobic digestion, which is low cost and accessible, as the carbon source in the removal of nitrogenous contaminants in wastewater. However, there is a knowledge gap regarding coupling systems that entail methane oxidation, nitrification, and denitrification, which restricts their industrial application. In this study, we acclimated a mixed culture to deal with simultaneous nitrification-denitrification coupled to methane oxidation in a laboratory-scale hollow-fiber membrane biofilm reactor, which achieved a steady ammonia removal rate of 38.09 mg N/(L•d). Furthermore, a series of batch experiments were conducted to test methane oxidation coupled to nitrate denitrification (AME-D3), nitrite denitrification (AME-D2), and simultaneous nitrification and denitrification (ME-SND). The molar ratio between methane consumed and nitrate reduced (C/N) equals 10 and 5 mol CH₄C mol^-1 NO₃N in AME-D3 and AME-D2, averagely and respectively. Without methane injection, the removal of nitrates and nitrites was very low, indicating that the coupling of nitrate/nitrite denitrification and methane oxidation was beneficial. The average ammonia removal rates in the 20% O₂ and 25% O₂ groups were 20.06 and 22.03 mg N/(L•d) in the ME-SND system, respectively. Without methane, the ammonia oxidation rate declined, and large amounts of nitrite accumulated. As traditional ammonia and nitrite oxidation approaches are autotrophic, we proposed the possibility of heterotrophic nitrification-aerobic denitrification (HN-AD). To study the coupling systems, the microbial communities and functional bacteria were analyzed. The results indicated that the system contained a guild of methanotrophs (mainly Methylobacter) and HN-AD bacteria (mainly Chrysobacterium and Comamonas).

Filamentous green algae Spirogyra regulates methane emissions from eutrophic rivers

Excessive growth of filamentous green algae in rivers has attracted much attention due to their functional importance to primary production and carbon cycling. However, comprehensive knowledge of how filamentous green algae affect carbon cycling, especially the CH₄ emissions from river ecosystems, remains limited. In this study, incubation experiments were conducted to examine the factors regulating CH₄ emissions from a eutrophic river with dense growth of filamentous green algae Spirogyra through combinations of biogeochemical, molecular biological, and stable carbon isotope analyses. Results showed that although water dissolved oxygen (DO) in the algae+sediment (A+S) incubation groups increased up to 19 mg L^-1, average CH₄ flux of the groups was 13.09 μmol m^-2 day^-1, nearly up to two times higher than that from sediments without algae (S groups). The significant increase of sediment CH₄ oxidation potential and methanotroph abundances identified the enhancing sediment CH₄ oxidation during Spirogyra bloom. However, the increased water CH₄ concentration was consistent with depleted water [Formula: see text] and decreased apparent fractionation factor (α_app), suggesting the important contribution of Spirogyra to the oxic water CH₄ production. It can thus be concluded that high DO concentration during the algal bloom promoted the CH₄ consumption by enhancing sediment CH₄ oxidation, while algal-linked oxic water CH₄ production as a major component of water CH₄ promoted the CH₄ emissions from the river. Our study highlights the regulation of Spirogyra in aquatic CH₄ fluxes and will help to estimate accurately CH₄ emissions from eutrophic rivers with dense blooms of filamentous green algae. Graphical abstract.

Biologically mediated release of endogenous N2O and NO2 gases in a hydrothermal, hypoxic subterranean environment

The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO₂-rich fluids. Anomalous concentrations of N₂O and NO₂ were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO₂ and CH₄ during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O₂, temperature, and GHG concentration. Both the N₂O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N₂O and NO₂ emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH₂OH, NO, and NO₂^- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla.