Methane Monooxygenase Research Articles

Iron Oxide Clusters as Electron Donors Under Light Enhance Oxygen Reduction Kinetics at Atomically Dispersed Fe for Photocatalytic CH4 Partial Oxidation.

Photocatalytic CH4 oxidation to CH3OH emerges as a promising strategy to sustainably utilize natural gas and mitigate the greenhouse effect. However, there remains a significant challenge for the synthesis of methanol by using O2 at low temperature. Inspired by the catalytic structure in soluble methane monooxygenase (MMO) and the corresponding reaction mechanism, we prepared a biomimetic photocatalysts with the decoration of Fe2O3 nanocluster and satellite Fe single atom immobilized on carbon nitride. The catalyst demonstrates an excellent CH3OH productivity of 5.02 mmol·gcat-1·h-1 with methanol selectivity of 98.5%. Mechanism studies reveal that the synergy between Fe2O3 nanocluster and Fe single atom establishes a dual-Fe site as MMO for O2 activation and subsequent CH4 partial oxidation. Moreover, the light excitation of Fe2O3nanoclusters with a relative narrow bandgap could deliver the electrons and protons to atomic Fe that facilitating the oxygen reduction kinetics for the robust of methanol synthesis.

A bis-Phenolate Carbene-Supported bis-μ-Oxo Iron(IV/IV) Complex with a [FeIV(μ-O)2FeIV] Diamond Core Derived from Dioxygen Activation.

The diiron(II) complex, [(OCO)Fe(MeCN)]2 (1, MeCN = acetonitrile), supported by the bis-phenolate carbene pincer ligand, 1,3-bis(3,5-di-tert-butyl-2-hydroxyphenyl)benzimidazolin-2-ylidene (OCO), was synthesized and characterized by single-crystal X-ray diffraction, 1H nuclear magnetic resonance, infrared (IR) vibrational, ultraviolet/visible/near-infrared (UV/vis/NIR) electronic absorption, 57Fe Mössbauer, X-band electron paramagnetic resonance (EPR) and SQUID magnetization measurements. Complex 1 activates dioxygen to yield the diferric, μ-oxo-bridged complex [(OCO)Fe(py)(μ-O)Fe(O(C═O)O)(py)] (2) that was isolated and fully characterized. In 2, one of the iron-carbene bonds was oxidized to give a urea motif, resulting in an O(CNHC═O)O binding site, while the other Fe(OCO) unit remained unchanged. When the reaction is performed at -80 °C, an intensively colored, purple intermediate is observed (INT, λmax = 570 nm; ε = 5600 mol L-1 cm-1). INT acts as a sluggish oxidant, reacting only with easily oxidizable substrates, such as PPh3 or 2-phenylpropionic aldehyde (2-PPA). The identity of INT can be best described as a dinuclear complex containing a closed diamond core motif [(OCO)FeIV(μ-O)2FeIV(OCO)]. This proposal is based on extensive spectroscopic [UV/vis/NIR electronic absorption, 57Fe Mössbauer, X-band EPR, resonance Raman (rRaman), X-ray absorption, and nuclear resonance vibrational (NRVS)] and computational studies. The conversion of the diiron(II) complex 1 to the oxo diiron(IV) intermediate INT is reminiscent of the O2 activation process in soluble methane monooxygenases (sMMO). Most importantly, the low reactivity of INT supports the consensus that the [FeIV(μ-O)2FeIV] diamond core in sMMO is kinetically inert and needs to open up to terminal FeIV═O cores to react with the strong C-H bonds of methane.

Effects of Fallow Season Water and Straw Management on Methane Emissions and Associated Microorganisms

The effects of fallow season water and straw management on methane (CH4) emissions during the fallow season and the subsequent rice-growing season are rarely reported, and the underlying microbial mechanisms remain unclear. A field experiment was conducted with four treatments: (1) fields flooded in both the fallow and rice seasons (FF), (2) fields drained in the fallow season and flooded in the rice season (DF), (3) FF with straw retention (FFS), and (4) DF with straw retention (DFS). The CH4 emissions in fields under different water and straw treatments were monitored using the static closed chamber method. Methanogenic and methanotrophic communities in these fields were examined using terminal restriction fragment length polymorphism (T-RFLP) analysis based on the mcrA gene and pmoA gene encoding methyl coenzyme M reductase and particulate methane monooxygenase, respectively. The results showed that CH4 emissions were significantly affected by water management, straw retention, season, and their interactions. Over 80% of CH4 emissions occurred during the rice season. Field drainage during the fallow season reduced CH4 emissions by 47.0% and 53.8% with and without straw during the rice season, respectively. Water management altered the abundance and composition of methanogens and methanotrophs, whereas the effects of straw retention were less pronounced. The quantitative polymerase chain reaction (qPCR) assay revealed that field drainage in the fallow season decreased the mcrA gene abundance by 30.0% and 23.2% with and without straw in rice season, respectively, and increased the pmoA gene abundance by 108.9% and 213.7% with and without straw in rice season, respectively. CH4 flux was significantly positively associated with mcrA gene copy number and the ratio of mcrA to pmoA gene copy number, whereas it was significantly negatively correlated with the pmoA gene copy number. Results indicated that fallow drainage greatly decreased CH4 emission not only during the fallow season but also during the subsequent rice season by altering the community composition of methanogens and methanotrophs. These findings provide scientific insight into the role of water and straw management in controlling CH4 emissions through microbial community dynamics.

Methane-driven microbial nitrous oxide production and reduction in denitrifying anaerobic methane oxidation cultures

Methane (CH4) and nitrous oxide (N2O) are two important greenhouse gases (GHGs), and it is very important to achieve the reduction of both gases in the case of increasingly serious climate change. The study confirms the simultaneous mitigation of potent GHGs N2O and CH4 in denitrifying anaerobic methane oxidation (DAMO) enrichment, supplementing the understanding that DAMO microorganisms do not produce and reduce N2O. We observed rapid accumulation and consumption of N2O in DAMO cultures subjected to high nitrate and nitrite loadings. Moreover, when N2O served as the sole electron acceptor, a significant correlation was found between the flux of N2O reduction and CH4 oxidation. Inhibition of the particulate methane monooxygenase (pMMO) led to a notable decrease of 95% in N2O reduction and 50% in CH4 oxidation. Metagenomic analysis revealed that Candidatus Methanoperedens and Candidatus Methylomirabilis were the dominant genera, with all functional genes related to denitrification and methane oxidation identified, including NO reductase (nor) of Ca. Methylomirabilis. Transcriptomic analysis further confirmed that the transcripts of nor were one order of magnitude higher than other functional genes. These results indicate that when the substrate NO2- surpasses the dismutation capacity of NO dismutase (nod), DAMO bacteria can alternatively induce nor to reduce NO to N2O. However, considering that N2O reductase (nosZ) is still missing in Ca. Methylomirabilis, the partner Methyloversatilis may be responsible for N2O reduction. Our results provide new insights into the link between GHG emissions in DAMO systems under anaerobic conditions.

Quantum refinement in real and reciprocal space using the Phenix and ORCA software.

X-ray and neutron crystallography, as well as cryogenic electron microscopy (cryo-EM), are the most common methods to obtain atomic structures of biological macromolecules. A feature they all have in common is that, at typical resolutions, the experimental data need to be supplemented by empirical restraints, ensuring that the final structure is chemically reasonable. The restraints are accurate for amino acids and nucleic acids, but often less accurate for substrates, inhibitors, small-molecule ligands and metal sites, for which experimental data are scarce or empirical potentials are harder to formulate. This can be solved using quantum mechanical calculations for a small but interesting part of the structure. Such an approach, called quantum refinement, has been shown to improve structures locally, allow the determination of the protonation and oxidation states of ligands and metals, and discriminate between different interpretations of the structure. Here, we present a new implementation of quantum refinement interfacing the widely used structure-refinement software Phenix and the freely available quantum mechanical software ORCA. Through application to manganese superoxide dismutase and V- and Fe-nitrogenase, we show that the approach works effectively for X-ray and neutron crystal structures, that old results can be reproduced and structural discrimination can be performed. We discuss how the weight factor between the experimental data and the empirical restraints should be selected and how quantum mechanical quality measures such as strain energies should be calculated. We also present an application of quantum refinement to cryo-EM data for particulate methane monooxygenase and show that this may be the method of choice for metal sites in such structures because no accurate empirical restraints are currently available for metals.

Simultaneously reducing methane emissions and arsenic mobility by birnessite in flooded paddy soil: Overlooked key role of organic polymerisation

Flooding of paddy fields enhances methane (CH4) emissions and arsenic (As) mobilisation, which are crucial issues for agricultural greenhouse gas emissions and food safety. Birnessite (δ-MnO2) is a common natural oxidant and scavenger for heavy metals. In this study, birnessite was applied to As-contaminated paddy soil. The capacity for simultaneously alleviating CH4 emissions and As mobility was explored. Soil microcosm incubation results indicated that birnessite addition simultaneously reduced CH4 emissions by 47 %–54 % and As release by 38 %–85 %. The addition of birnessite decreased the dissolved organic carbon (DOC) contents and altered its chemical properties. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) results showed that birnessite reduced the labile fractions of proteins, carbohydrates, lignins, tannins, and unsaturated hydrocarbons, however, increased the abundance of condensed aromatic structures, suggesting the polymerisation of dissolved organic matter (DOM) by birnessite. The degradation of labile fractions and the polymerisation of DOM resulted in an inventory of recalcitrant DOM, which is difficult for microbes to metabolise, thus inhibiting methanogenesis. In contrast, birnessite addition increased CH4 oxidation, as the particulate methane monooxygenase (pmoA) gene abundance increased by 30 %. The enhanced polymerisation of DOM by birnessite also increased As complexation with organics, leading to the transfer of As to the organic bound phase. In addition, the decrease in ferrous ion [Fe(II)] concentrations with birnessite indicated that the reductive dissolution of Fe oxides was suppressed, which limited the release of arsenite [As(III)] under reducing conditions. Furthermore, birnessite decreased As methylation and shaped the soil microbial community structure by enriching the metal-reducing bacterium Bacillus. Overall, our results provide a promising method to suppress greenhouse gas emissions and the risk of As contamination in paddy soils, although further studies are needed to verify its efficacy and effectiveness under field conditions.

Exploring modes of microbial interactions with implications for methane cycling.

Methanotrophs are the sole biological sink of methane. Volatile organic compounds (VOCs) produced by heterotrophic bacteria have been demonstrated to be a potential modulating factor of methane consumption. Here, we identify and disentangle the impact of the volatolome of heterotrophic bacteria on the methanotroph activity and proteome, using Methylomonas as model organism. Our study unambiguously shows how methanotrophy can be influenced by other organisms without direct physical contact. This influence is mediated by VOCs (e.g. dimethyl-polysulphides) or/and CO2 emitted during respiration, which can inhibit growth and methane uptake of the methanotroph, while other VOCs had a stimulating effect on methanotroph activity. Depending on whether the methanotroph was exposed to the volatolome of the heterotroph or to CO2, proteomics revealed differential protein expression patterns with the soluble methane monooxygenase being the most affected enzyme. The interaction between methanotrophs and heterotrophs can have strong positive or negative effects on methane consumption, depending on the species interacting with the methanotroph. We identified potential VOCs involved in the inhibition while positive effects may be triggered by CO2 released by heterotrophic respiration. Our experimental proof of methanotroph-heterotroph interactions clearly calls for detailed research into strategies on how to mitigate methane emissions.

An investigation of soil and groundwater metagenomes for genes encoding soluble and particulate methane monooxygenase, toluene-4-monoxygenase, propane monooxygenase and phenol hydroxylase.

Soil and groundwater were investigated for the genes encoding soluble and particulate methane monooxygenase/ammonia monooxygenase (sMMO, pMMO/AMO), toluene 4-monooxygenase (T4MO), propane monooxygenase (PMO) and phenol hydroxylase (PH). The objectives were (1) to determine which subunits were present, (2) to examine the diversity of the phylotypes associated with the biomarkers and (3) to identify which metagenome associated genomes (MAGs) contained these subunits. All T4MO and PH subunits were annotated in the groundwater metagenomes, while few were annotated in the soil metagenomes. The majority of the soil metagenomes included only four sMMO subunits. Only two groundwater metagenomes contained five sMMO subunits. Gene counts for the pMMO subunits varied between samples. The majority of the soil metagenomes were annotated for all four PMO subunits, while three out of eight groundwater metagenomes contained all four PMO subunits. A comparison of the blast alignments for the sMMO alpha chain (mmoX) indicated the phylotypes differed between the soil and groundwater metagenomes. For the pMMO/AMO alpha subunit (pmoA/amoA), Nitrosospira was important for the soil metagenomes, while Methylosinus and Methylocystis were dominant for the groundwater metagenomes. The majority of pmoA alignments from both metagenomes were from uncultured bacteria. High quality MAGs were obtained from the groundwater data. Four MAGs (Methylocella and Cypionkella) contained sMMO subunits. Another three MAGs, within the order Pseudomonadales, contained all three pMMO subunits. All PH subunits were detected in seven MAGs (Azonexus, Rhodoferax, Aquabacterium). In those seven, all contained catechol 2,3-dioxagenase, and Aquabacterium also contained catechol 1,2-dioxygenase. T4MO subunits were detected in eight MAGs (Azonexus, Rhodoferax, Siculibacillus) and all, except one, contained all six subunits. Four MAGs (Rhodoferax and Azonexus) contained all subunits for PH and T4MO, as well as catechol 2,3-dixoygenase. The detection of T4MO and PH in groundwater metagenomes and MAGs has important implications for the potential oxidation of groundwater contaminants.

Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA.

We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.

Effects of exogenous thermophilic bacteria and ripening agent on greenhouse gas emissions, enzyme activity and microbial community during straw composting

This research examined the impact of exogenous thermophilic bacteria and ripening agents on greenhouse gas (GHG) emission, enzyme activity, and microbial community during composting. The use of ripening agents alone resulted in a 30.9 % reduction in CO2 emissions, while the use of ripening agents and thermophilic bacteria resulted in a 50.8 % reduction in N2O emissions. Pearson’s analysis showed that organic matter and nitrate nitrogen were the key parameters affecting GHG emissions. There was an inverse correlation between CO2 and CH4 releases and methane monooxygenase α subunit and N2O reductase activity (P<0.05). Additionally, N2O emissions were positively related to β-1, 4-N-acetylglucosaminidase, and ammonia monooxygenase activity (P<0.05). Deinococcota, Chloroflexi, and Bacteroidota are closely related to CO2 and N2O emissions. Overall, adding thermophilic bacteria represents an effective strategy to mitigate GHG emissions during composting.

Mechanisms for Methane and Ammonia Oxidation by Particulate Methane Monooxygenase.

Particulate MMO (pMMO) catalyzes the oxidation of methane to methanol and also ammonia to hydroxylamine. Experimental characterization of the active site has been very difficult partly because the enzyme is membrane-bound. However, recently, there has been major progress mainly through the use of cryogenic electron microscopy (cryoEM). Electron paramagnetic resonance (EPR) and X-ray spectroscopy have also been employed. Surprisingly, the active site has only one copper. There are two histidine ligands and one asparagine ligand, and the active site is surrounded by phenyl alanines but no charged amino acids in the close surrounding. The present study is the first quantum chemical study using a model of that active site (CuD). Low barrier mechanisms have been found, where an important part is that there are two initial proton-coupled electron transfer steps to a bound O2 ligand before the substrate enters. Surprisingly, this leads to large radical character for the oxygens even though they are protonated. That result is very important for the ability to accept a proton from the substrates. Methods have been used which have been thoroughly tested for redox enzyme mechanisms.

Synthetic Copper-(Di)oxygen Complex Generation and Reactivity Relevant to Copper Protein O2-Processing.

Synthetic copper-dioxygen complex design, generation and characterization, play a crucial role in elucidating the structure/function of copper-based metalloenzymes, including dopamine β-monooxygenase, lytic polysaccharide monooxygenases, particulate methane monooxygenase, tyrosinase, hemocyanin, and catechol oxidase. Designing suitable ligands to closely mimic the variable active sites found in these enzymes poses a challenging task for synthetic bioinorganic chemists. In this review, we have highlighted a few representative ligand systems capable of stabilizing various copper-dioxygen species such as CuII-(O2 •-)(superoxide), Cu2 II-(μ-η 1:η 1-O2 2-) (trans/cis-peroxide), Cu2 II-(μ-η 2:η 2-O2 2-)(side-on peroxide) and Cun II--OOH (hydroperoxide) species. Here, we discuss the ligand type utilized, syntheses, and spectroscopic characterization of these species. We also delineate reactivity patterns, particularly electrophilic arene hydroxylation by a side-on peroxo species which occurs via a "NIH shift" mechanism and thermodynamic-kinetic relationships among Cu2-(O2 •-)/O2 2-/-OOH moieties.

Detection of Thermoacidophiles from Yellowstone Hot Spring

Aerobic methanotrophic bacteria maintain an unrivalled capability of utilizing methane as their sole carbon and energy source and have been retrieved from various environments. Phylogenetically, true aerobic thermoacidophilic methane oxidizers capable of growing below pH 3 have hitherto been associated only with the phylum Verrucomicrobia. In this report, the initial detection of a moderately thermoacidophilic Methylococcus-like Type Ib methanotroph of the class Gammaproteobacteria from an acidic thermal spring (50oC and pH 2.8) in the Yellowstone National Park, USA is presented. The isolate, termed YT-MC, was identified in a methane enrichment (55°C), which may represent a novel strain in the family Methylococcaceae Type Ib. The existence of this bacterium in the enrichments was demonstrated by the detection of pmoA gene, Southern blotting technique, phase-contrast, and electron microscopy. The coccus-typed cells showed tubular membranes instead of intracytoplasmic membrane systems (ICM). The soluble methane monooxygenase (sMMO) was not detected by PCR, indicating that the biotransformation of methane to methanol is oxidized by the particulate methane monooxygenase (pMMO). Moreover, YT-MC performs in a formerly undiscovered active biological methane sink in geothermal acidic environments, magnifying our knowledge of its ecological role in methane cycling, diversity, and coexistence of aerobic methanotrophy. Furthermore, the present study also reports the isolation and identification of an alphaproteobacterial heterotroph (strain YT-AC) and a verrucomicrobial methanotroph (strain YT-VM) from the same environment. Bangladesh J Microbiol, Volume 40, Number 2, December 2023, pp 86-94

Single Dispersion of Fe(H2O)2-Based Polyoxometalate on Polymeric Carbon Nitride for Biomimetic CH4 Photooxidation.

Direct methane conversion to value-added oxygenates under mild conditions with in-depth mechanism investigation has attracted wide interest. Inspired by methane monooxygenase, the K9Na2Fe(H2O)2{[γ-SiW9O34Fe(H2O)]}2·25H2O polyoxometalate (Fe-POM) with well-defined Fe(H2O)2 sites is synthesized to clarify the key role of Fe species and their microenvironment toward CH4 photooxidation. The Fe-POM can efficiently drive the conversion of CH4 to HCOOH with a yield of 1570.0µmol gPOM -1 and 95.8% selectivity at ambient conditions, much superior to that of [Fe(H2O)SiW11O39]5- with Fe(H2O) active site, [Fe2SiW10O38(OH)]2 14- and [P8W48O184Fe16(OH)28(H2O)4]20- with multinuclear Fe-OH-Fe active sites. Single-dispersion of Fe-POM on polymeric carbon nitride (PCN) is facilely achieved to provide single-cluster functionalized PCN with well-defined Fe(H2O)2 site, the HCOOH yield can be improved to 5981.3µmol gPOM -1. Systemic investigations demonstrate that the (WO)4-Fe(H2O)2 can supply Fe═O active center for C-H activation via forming (WO)4-Fea-Ot···CH4 intermediate, similar to that for CH4 oxidation in the monooxygenase. This work highlights a promising and facile strategy for single dispersion of ≈1-2 Å metal center with precise coordination microenvironment by uniformly anchoring nanoscale molecular clusters, which provides a well-defined model for in-depth mechanism research.

A rationally designed miniature of soluble methane monooxygenase enables rapid and high-yield methanol production in Escherichia coli

Soluble methane monooxygenase (sMMO) oxidizes a wide range of carbon feedstocks (C1 to C8) directly using intracellular NADH and is a useful means in developing green routes for industrial manufacturing of chemicals. However, the high-throughput biosynthesis of active recombinant sMMO and the ensuing catalytic oxidation have so far been unsuccessful due to the structural and functional complexity of sMMO, comprised of three functionally complementary components, which remains a major challenge for its industrial applications. Here we develop a catalytically active miniature of sMMO (mini-sMMO), with a turnover frequency of 0.32 s−1, through an optimal reassembly of minimal and modified components of sMMO on catalytically inert and stable apoferritin scaffold. We characterise the molecular characteristics in detail through in silico and experimental analyses and verifications. Notably, in-situ methanol production in a high-cell-density culture of mini-sMMO-expressing recombinant Escherichia coli resulted in higher yield and productivity (~ 3.0 g/L and 0.11 g/L/h, respectively) compared to traditional methanotrophic production.

Nitrous oxide respiration in acidophilic methanotrophs

Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.

Origin of Unprecedented Formation and Reactivity of FeIV═O Species via Oxygen Activation: Role of Noncovalent Interactions and Magnetic Coupling.

Emulating the capabilities of the soluble methane monooxygenase (sMMO) enzymes, which effortlessly activate oxygen at diiron(II) centers to form a reactive diiron(IV) intermediate Q, which then performs the challenging oxidation of methane to methanol, poses a significant challenge. Very recently, one of us reported the mononuclear complex [(cyclam)FeII(CH3CN)2]2+ (1), which performed a rare bimolecular activation of the molecule of O2 to generate two molecules of FeIV═O without the requirement of external proton or electron sources, similar to sMMO. In the present study, we employed the density functional theory (DFT) calculations to investigate this unique mechanism of O2 activation. We show that secondary hydrogen-bonding interactions between ligand N-H groups and O2 play a vital role in reducing the energy barrier associated with the initial O2 binding at 1 and O-O bond cleavage to form the FeIV═O complex. Further, the unique reactivity of FeIV═O species toward simultaneous C-H and O-H bond activation process has been demonstrated. Our study unveils that the nature of the magnetic coupling between the diiron centers is also crucial. Given that the influence of magnetic coupling and noncovalent interactions in catalysis remains largely unexplored, this unexplored realm presents numerous avenues for experimental chemists to develop novel structural and functional analogues of sMMO.

Isolation of a facultative methanotroph Methylocystis iwaonis SD4 from rice rhizosphere and establishment of rapid genetic tools for it.

Methanotrophs of the genus Methylocystis are frequently found in rice paddies. Although more than ten facultative methanotrophs have been reported since 2005, none of these strains was isolated from paddy soil. Here, a facultative methane-oxidizing bacterium, Methylocystis iwaonis SD4, was isolated and characterized from rhizosphere samples of rice plants in Nanjing, China. This strain grew well on methane or methanol but was able to grow slowly using acetate or ethanol. Moreover, strain SD4 showed sustained growth at low concentrations of methane (100 and 500ppmv). M. iwaonis SD4 could utilize diverse nitrogen sources, including nitrate, urea, ammonium as well as dinitrogen. Strain SD4 possessed genes encoding both the particulate methane monooxygenase and the soluble methane monooxygenase. Simple and rapid genetic manipulation methods were established for this strain, enabling vector transformation and unmarked genetic manipulation. Fast growth rate and efficient genetic tools make M. iwaonis SD4 an ideal model to study facultative methanotrophs, and the ability to grow on low concentration of methane implies its potential in methane removal.

Solid phase speciation controls copper mobilisation from marine sediments by methanobactin

Although marine environments represent huge reservoirs of the potent greenhouse gas methane, they currently contribute little to global net methane emissions. Most of the methane is oxidized by methanotrophs, minimizing escape to the atmosphere. Aerobic methanotrophs oxidize methane mostly via the copper (Cu)-bearing enzyme particulate methane monooxygenase (pMMO). Therefore, aerobic methane oxidation depends on sufficient Cu acquisition by methanotrophs. Because they require both oxygen and methane, aerobic methanotrophs reside at oxic-anoxic interfaces, often close to sulphidic zones where Cu bioavailability can be limited by poorly soluble Cu sulphide mineral phases. Under Cu-limiting conditions, certain aerobic methanotrophs exude Cu-binding ligands termed chalkophores, such as methanobactin (mb) exuded by Methylosinus trichosporium OB3b. Our main objective was to establish whether chalkophores can mobilise Cu from Cu sulphide-bearing marine sediments to enhance Cu bioavailability.Through a series of kinetic batch experiments, we investigated Cu mobilisation by mb from a set of well-characterized sulphidic marine sediments differing in sediment properties, including Cu content and phase distribution. Characterization of solid-phase Cu speciation included X-ray absorption spectroscopy and a targeted sequential extraction. Furthermore, in batch experiments, we investigated to what extent adsorption of metal-free mb and Cu-mb complexes to marine sediments constrains Cu mobilisation.Our results are the first to show that both solid phase Cu speciation and chalkophore adsorption can constrain methanotrophic Cu acquisition from marine sediments. Only for certain sediments did mb addition enhance dissolved Cu concentrations. Cu mobilisation by mb was not correlated to the total Cu content of the sediment, but was controlled by solid-phase Cu speciation. Cu was only mobilised from sediments containing a mono-Cu-sulphide (CuSx) phase. We also show that mb adsorption to sediments limits Cu acquisition by mb to less compact (surface) sediments. Therefore, in sulphidic sediments, mb-mediated Cu acquisition is presumably constrained to surface-sediment interfaces containing mono-Cu-sulphide phases.

Divergent effects of copper oxide nanoparticles on methanotrophs: Stimulation at low concentrations and inhibition at high concentrations

Methanotrophs represent pivotal microorganisms, integral to the regulation of global methane emissions. Upon introduction into the environment, copper oxide nanoparticles (CuO NPs), a frequently employed category of inorganic nanomaterials, possess the potential to exert influences on methanotrophs. This study investigated the impact of CuO NPs on methanotrophs, showing a clear concentration-dependent response. Under high concentrations, exposure of methanotrophs to CuO NPs induced the production of reactive oxygen species, compromised cell membrane integrity, and resulted in the substantial release of lactate dehydrogenase. The expressions of genes encoding methane monooxygenase were obviously down-regulated. Whereas under low concentrations, a distinct enhancement of bacterial growth and metabolism was observed. The presence of methanotrophs facilitated the release of Cu2+ from CuO NPs, and the Cu2+ stimulated the biosynthesis of particulate methane monooxygenase reversely. Compared to the cellular toxicity of CuO NPs as nanoparticles, the released Cu2+ exerted a more pronounced promoting effect on methanotrophs growth, resulting in an overall strengthened methane metabolism. Significant alterations were observed in genes encoding copper uptake and resistance, cytochrome-related and heme-related proteins. This study provides novel insights into interactions between methanotrophs and nanoparticles, thereby advancing our comprehension of the impact of CuO NPs on methane emissions within an environmental context.