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Paddy fields are recognized as significant sources of methane ( CH4) emissions, playing a pivotal role in global climate change. Elevated atmospheric carbon dioxide ( C02) concentrations ( e [ C02 ] ) exert a profound influence on the carbon cycling of paddy fields. Understanding the effects of e[C02] on CH2 emissions, as well as the underlying microbial processes, is crucial for enhancing carbon sequestration and reducing emissions in paddy fields. We reviewed the impacts of e[C02] on CH2 emission in paddy fields, focusing on the activity, abundance, community structure, and diversity of carbon-cycling-related microbes. We also delineated the roles of various microbial processes in mitigating CH2 emissions under e[C02], as well as the primary environmental determinants. Overall, the type of e [ C02 ] experimental platforms, duration of fumigation, concentration gradients, and the methods of C02 enrichment all influence CH4 emissions from paddy fields. e[C02] initially stimulates CH2 emissions, which may decrease over time, indicating an adaptability of the methane-emitting microbial community to e [ C02 ]. This response exhibits a trend of initial attenuation followed by an intensification of the positive effects on CH2 emissions. Experiments with abrupt increase of C02 concentration might overestimate CH2 emissions. The impact of e[C02] on microbial processes is predominantly characterized by enhanced activities and abundance of methanogens, aerobic and anaerobic methanotrophs. It significantly alters the community composition and diversity of methanotrophs, with minimal effects on methanogens and anaerobic methanotrophic communities. Finally, we outlined future research directions: 1) Integrated investigations into the effects of e [ C02 ] on CH4 emissions, methanogenesis, and both aerobic and anaerobic methanotrophs in paddy fields could elucidate the mechanisms underlying the impacts of climate change on CH4 emissions; 2) Long-term studies are essential to understand the mechanisms of e [ C02 ] on CH2 emissions and associated microbial processes more accurately and realistically; 3) Multi-scale (temporal and spatial), multi-factorial ( C02 concentration, temperature, atmospheric nitrogen deposition, and water management practices), and multi-methodological (observational, data, and model integration) research is necessary to effectively reduce the uncertainties in assessing the response of CH4 emissions in paddy fields and related microbial processes to e[C02] under future climate change scenarios. [ABSTRACT FROM AUTHOR]

Aerobic methane oxidation (MOx) mediated by methanotrophs is a crucial mechanism in controlling methane emissions from the surface ocean to the atmosphere. Coastal waters dominate global oceanic methane emissions, but the dynamics, controls and roles of MOx remain largely unconstrained in the marginal seas around China. Here, we conducted a variety of biogeochemical analyses to investigate the controls of methane cycling and the dynamics of methanotrophic activity in the East China Sea and Yellow Sea. Methane was supersaturated in the surface seawater and the concentrations ranged from 2.8 to 19.8 nM. The distribution of methane was regulated by the sources and sinks, which were influenced largely by hydrological and biogeochemical factors. Methane was turned over rapidly with high rates (k: 5 × 10−4–0.04 d−1), indicating the enzymatic capability of methanotrophic biomass to metabolize methane. Rates of MOx varied significantly between sites (1 × 10−3–0.60 nM d−1) and relatively high MOx rates were observed in shallow waters. MOx exhibited the Michaelis‐Menten kinetics with the Vmax of 0.30 nM d−1 and a Km of 78.3 nM. Methanotrophic activity was impacted by environmental factors such as methane availability, nutrient levels, bacterial production and temperature. Nutrient addition experiments demonstrated that phosphate elevated MOx rates, while the activity was largely inhibited by ammonium probably due to competitive inhibition of the methane monooxygenase by ammonia. Comparing the depth‐integrated MOx rates with the air‐sea fluxes at selected sites showed that methane consumed through microbial oxidation accounted for up to 78.1% of the total methane loss (=sum of MOx rates and air‐sea flux), highlighting the role of MOx as a microbial filter for methane emissions. Plain Language Summary: Methane is a potent greenhouse gas and aerobic methane oxidation controls methane emission from the ocean to the atmosphere. However, methane oxidation rates are poorly described in the global ocean, and the magnitude and control of aerobic methane oxidation remains largely unconstrained in marginal seas around China. We investigated methane cycling and methanotrophic activity in the East China Sea and Yellow Sea. Methane oxidation rates showed significant variability between sites, with higher rates observed in shallow coastal waters. A variety of environmental factors such as methane availability, bacterial production, nutrient levels, and temperature affected methane oxidation. Compared to air‐sea exchange, methanotrophy represented an important methane sink and contributed up to 78.1% of the total methane loss at selected sites. These results provide a supplement to the global database of methane oxidation rates and improve our current understanding of methanotrophy in coastal systems. Key Points: Methane oxidation rates varied significantly between sites and higher rates were observed in shallow watersMethanotrophic activity could be influenced by methane availability, nutrient levels and temperatureMOx exhibited the Michaelis‐Menten kinetics with the Vmax of 0.30 nM d−1 and a Km of 78.3 nM [ABSTRACT FROM AUTHOR]

ABSTRACT: Large amounts of gas hydrate are distributed in the northern slope of the South China Sea, which is a potential threat of methane leakage. Aerobic methane oxidation by methanotrophs, significant methane biotransformation that occurs in sediment surface and water column, can effectively reduce atmospheric emission of hydrate-decomposed methane. To identify active aerobic methanotrophs and their methane oxidation potential in sediments from the Shenhu Area in the South China Sea, multi-day enrichment incubations were conducted in this study. The results show that the methane oxidation rates in the studied sediments were 2.03–2.36 μmol/gdw/d, which were higher than those obtained by sediment incubations from other areas in marine ecosystems. Thus the authors suspect that the methane oxidation potential of methanotrophs was relatively higher in sediments from the Shenhu Area. After the incubations family Methylococcaea (type I methanotrophs) mainly consisted of genus Methylobacter and Methylococcaea_Other were predominant with an increased proportion of 70.3%, whereas Methylocaldum decreased simultaneously in the incubated sediments. Collectively, this study may help to gain a better understanding of the methane biotransformation in the Shenhu Area.©2022 China Geology Editorial Office.

Aerobic methane oxidation (MOx) depends critically on the availability of copper (Cu) as a crucial component of the metal centre of particulate methane monooxygenase, one of the main enzymes involved in MOx. Some methanotrophs have developed Cu acquisition strategies, in which they exude Cu‐binding ligands termed chalkophores under conditions of low Cu availability. A well‐characterised chalkophore is methanobactin (mb), exuded by the microaerophilic methanotroph Methylosinus trichosporium OB3b. Aerobic methanotrophs generally reside close to environmental oxic–anoxic interfaces, where the formation of Cu sulphide phases can aggravate the limitation of bioavailable Cu due to their low solubility. The reactivity of chalkophores towards such Cu sulphide mineral phases has not yet been investigated. In this study, a combination of dissolution experiments and equilibrium modelling was used to examine the dissolution and solubility of bulk and nanoparticulate Cu sulphide minerals in the presence of mb as influenced by pH, oxygen and natural organic matter. In general, we show that mb is effective at increasing the dissolved Cu concentrations in the presence of a variety of Cu sulphide phases that may potentially limit Cu bioavailability. More Cu was mobilised per mole of mb from Cu sulphide nanoparticles compared with well‐crystalline bulk covellite (CuS). In general, the efficacy of mb at mobilising Cu from Cu sulphides is pH‐dependent. At lower pH, e.g. pH 5, mb was ineffective at solubilizing Cu. The presence of mb increased dissolved Cu concentrations between pH 7 and 8.5, where the solubility of all Cu sulphides is generally low, both in the presence and absence of oxygen. These results suggest that chalkophore‐promoted Cu mobilisation from sulphide phases is an effective extracellular mechanism for increasing dissolved Cu concentrations at oxic–anoxic interfaces, particularly in the neutral to slightly alkaline pH range. This suggests that aerobic methanotrophs may be able to fulfil their Cu requirements via the exudation of mb in natural environments where the bioavailability of Cu is constrained by very stable Cu sulphide phases. [ABSTRACT FROM AUTHOR]

Aims: Aerobic methane oxidation coupled to denitrification (AME‐D) is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. This study used RNA stable isotope probing (RNA‐SIP) and high‐throughput sequencing to identify the micro‐organisms that are actively involved in aerobic methane oxidation within a denitrifying biofilm. Methods and Results: Two RNA‐SIP experiments were conducted to investigate labelling of RNA and methane monooxygenase (pmoA) transcripts when exposed to 13C‐labelled methane over a 96‐hour time period and to determine active bacteria involved in methane oxidation in a denitrifying biofilm. A third experiment was performed to ascertain the extent of 13C labelling of RNA using isotope ratio mass spectrometry (IRMS). All experiments used biofilm from an established packed bed reactor. IRMS confirmed 13C enrichment of the RNA. The RNA‐SIP experiments confirmed selective enrichment by the shift of pmoA transcripts into heavier fractions over time. Finally, high‐throughput sequencing identified the active micro‐organisms enriched with 13C. Conclusions: Methanotrophs (Methylovulum spp. and Methylocystis spp.), methylotrophs (Methylotenera spp.) and denitrifiers (Hyphomicrobium spp.) were actively involved in AME‐D. Significance and Impact of the Study: This is the first study to use RNA‐SIP and high‐throughput sequencing to determine the bacteria active within an AME‐D community. [ABSTRACT FROM AUTHOR]

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 NOx 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. [ABSTRACT FROM AUTHOR]

Methanobactins (MBs) are ribosomally synthesized and posttranslationally modified peptides (RiPPs) produced by methanotrophs for copper uptake. The posttranslational modification that defines MBs is the formation of two heterocyclic groups with associated thioamines from X-Cys dipeptide sequences. Both heterocyclic groups in the MB from Methylosinus trichosporium OB3b (MB-OB3b) are oxazolone groups. The precursor gene for MB-OB3b is mbnA, which is part of a gene cluster that contains both annotated and unannotated genes. One of those unannotated genes, mbnC, is found in all MB operons and, in conjunction with mbnB, is reported to be involved in the formation of both heterocyclic groups in all MBs. To determine the function of mbnC, a deletion mutation was constructed in M. trichosporium OB3b, and the MB produced from the #916;mbnC mutant was purified and structurally characterized by UV-visible absorption spectroscopy, mass spectrometry, and solution nuclear magnetic resonance (NMR) spectroscopy. MB-OB3b from the ΔmbnC mutant was missing the C-terminal Met and was also found to contain a Pro and a Cys in place of the pyrrolidinyl-oxazolone-thioamide group. These results demonstrate MbnC is required for the formation of the C-terminal pyrrolidinyl-oxazolone-thioamide group from the Pro-Cys dipeptide, but not for the formation of the N-terminal 3-methylbutanol-oxazolone-thioamide group from the N-terminal dipeptide Leu-Cys. [ABSTRACT FROM AUTHOR]

Methanobactins (MBs) are small (,1,300-Da) posttranslationally modified copper-binding peptides and represent the extracellular component of a copper acquisition system in some methanotrophs. Interestingly, MBs can bind a range of metal ions, with some being reduced after binding, e.g., Cu2+ reduced to Cu1. Other metal ions, however, are bound but not reduced, e.g., K1. The source of electrons for selective metal ion reduction has been speculated to be water but never empirically shown. Here, using H2 18O, we show that when MBs from Methylocystis sp. strain SB2 (MB-SB2) and Methylosinus trichosporium OB3+ (MB-OB3) were incubated in the presence of either Au31, Cu2, or Ag+, 18,18O2 and free protons were released. No 18,18O2 production was observed in the presence of either MB-SB2 or MB-OB3b alone, gold alone, copper alone, or silver alone or when K1 or Mo2+ was incubated with MB-SB2. In contrast to MB-OB3b, MB-SB2 binds Fe31 with an N2S2 coordination and will also reduce Fe31 to Fe2+. Iron reduction was also found to be coupled to the oxidation of 2H2O and the generation of O2. MB-SB2 will also couple Hg2+, Ni2+, and Co2+ reduction to the oxidation of 2H2O and the generation of O2, but MB-OB3+ will not, ostensibly as MB-OB3+ binds but does not reduce these metal ions. To determine if the O2 generated during metal ion reduction by MB could be coupled to methane oxidation, 13CH4 oxidation by Methylosinus trichosporium OB3+ was monitored under anoxic conditions. The results demonstrate that O2 generation from metal ion reduction by MB-OB3+ can support methane oxidation. [ABSTRACT FROM AUTHOR]

Aerobic methane (CH4) oxidation plays a significant role in marine CH4 consumption. Temperature changes resulting from, for example, global warming, have been suggested to be able to influence methanotrophic communities and their CH4 oxidation capacity. However, exact knowledge regarding temperature controls on marine aerobic methane oxidation is still missing. In this study, CH4 consumption and the methanotrophic community structure were investigated by incubating sediments from shallow (Bohai Bay) and deep marine environments (East China Sea) at 4, 15, and 28 °C for up to 250 days. The results show that the abundance of the methanotrophic population, dominated by the family Methylococcaceae (type I methanotrophs), was significantly elevated after all incubations and that aerobic methane oxidation for both areas had a strong temperature sensitivity. A positive correlation between the CH4 oxidation rate and temperature was witnessed in the Bohai Bay incubations, whereas for the East China Sea incubations, the optimum temperature was 15 °C. The systematic variations of pmoA OTUs between the Bohai Bay and East China Sea incubations indicated that the exact behaviors of CH4 oxidation rates with temperature are related to the different methanotrophic community structures in shallow and deep seas. These results are of great significance for quantitatively evaluating the biodegradability of CH4 in different marine environments.

Methane oxidation coupled to selenate reduction has been suggested as a promising technology to bio-remediate selenium contaminated environments. However, the effect of dissolved oxygen (DO) on this process remained unclear. Here, we investigate the feasibility of selenate removal at two distinct DO concentrations. A membrane biofilm reactor (MBfR) was initially fed with ∼5 mg Se/L and then lowered to ∼1 mg Se/L of selenate, under anoxic condition containing ∼0.2 mg/L of influent DO. Selenate removal reached approximately 90% without selenite accumulation after one-month operation. Then 6–7 mg/L of DO was introduced and showed no apparent effect on selenate reduction in the subsequent operation. Electron microscopy suggested elevated oxygen exposure did not affect microbial shapes. 16S rDNA sequencing showed the aerobic methanotroph Methylocystis increased, while possible selenate reducers, Ignavibacterium and Bradyrhizobium , maintained stable after oxygen boost. Gene analysis indicated that nitrate/nitrite reductases positively correlated with selenate removal flux and were not remarkably affected by oxygen addition. Reversely, enzymes related with aerobic methane oxidation were obviously improved. This study provides a potential technology for selenate removal from oxygenated environments in a methane-based MBfR. Image 1 • Influent 6–7 mg/L DO had no inhibition on selenate reduction in a CH 4 -based MBfR. • Aerobic methanotroph Methylocystis remarkably increased after DO elevating. • Likely selenate reducers Ignavibacterium and Bradyrhizobium weren't affected by DO. [ABSTRACT FROM AUTHOR]

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

Methanotrophy of arable soils is affected by N fertilization, but the knowledge about the effect of oxygen level is poorly understood; soil aeration can fluctuate and zones of low oxygen are widespread in soil. We monitored CH4 oxidation in three mineral soils (Eutric Cambisol, Haplic Podzol, Mollic Gleysol) under laboratory conditions by varying the O2 level (from 20 to 2% O2), with or without NH4+ (100 mg N kg−1). In controls (without NH4+), CH4 was oxidized completely in the O2 range from oxia (20% O2) to high hypoxia (5% O2), while the process was inhibited under microoxia (2% O2). Ammonium application decreased CH4 consumption in all soils. This negative effect was stronger at 20% and 2% O2 than under hypoxia. The highest CH4 oxidation rates and the shortest initial (lag) phases in both control and NH4+-amended soils were observed under high (5% O2) and low (10% O2) hypoxia. [ABSTRACT FROM AUTHOR]

Mangrove forests are one of the important ecosystems in tropical coasts because of their high primary production, which they sustain by sequestering a substantial amount of CO2 into plant biomass. These forests often experience various levels of inundation and play an important role in CH4 emissions, but the taxonomy of methanotrophs in these systems remains poorly understood. In this study, DNA-based stable isotope probing showed significant niche differentiation in active aerobic methanotrophs in response to niche differentiation in upstream and downstream mangrove soils of the Tamsui estuary in northwestern Taiwan, in which salinity levels differ between winter and summer. Methylobacter and Methylomicrobium-like Type I methanotrophs dominated methane-oxidizing communities in the field conditions and were significantly 13C-labeled in both upstream and downstream sites, while Methylobacter were well adapted to high salinity and low temperature. The Type II methanotroph Methylocystis comprised only 10–15% of all the methane oxidizers in the upstream site but less than 5% at the downstream site under field conditions. 13C-DNA levels in Methylocystis were significantly lower than those in Type I methanotrophs, while phylogenetic analysis further revealed the presence of novel methane oxidizers that are phylogenetically distantly related to Type Ia in fresh and incubated soils at a downstream site. These results suggest that Type I methanotrophs display niche differentiation associated with environmental differences between upstream and downstream mangrove soils.

The O2:CH4 ratio significantly effects nitrogen removal in mixed cultures where aerobic methane oxidation is coupled with denitrification (AME-D). The goal of this study was to investigate nitrogen removal of the AME-D process at four different O2:CH4 ratios [0, 0.05, 0.25, and 1 (v/v)]. In batch tests, the highest denitrifying activity was observed when the O2:CH4 ratio was 0.25. At this ratio, the methanotrophs produced sufficient carbon sources for denitrifiers and the oxygen level did not inhibit nitrite removal. The results indicated that the synergy between methanotrophs and denitrifiers was significantly improved, thereby achieving a greater capacity of nitrogen removal. Based on thermodynamic and chemical analyses, methanol, butyrate, and formaldehyde could be the main trophic links of AME-D process in our study. Our research provides valuable information for improving the practical application of the AME-D systems.

The O2:CH4 ratio significantly effects nitrogen removal in mixed cultures where aerobic methane oxidation is coupled with denitrification (AME-D). The goal of this study was to investigate nitrogen removal of the AME-D process at four different O2:CH4 ratios [0, 0.05, 0.25, and 1 (v/v)]. In batch tests, the highest denitrifying activity was observed when the O2:CH4 ratio was 0.25. At this ratio, the methanotrophs produced sufficient carbon sources for denitrifiers and the oxygen level did not inhibit nitrite removal. The results indicated that the synergy between methanotrophs and denitrifiers was significantly improved, thereby achieving a greater capacity of nitrogen removal. Based on thermodynamic and chemical analyses, methanol, butyrate, and formaldehyde could be the main trophic links of AME-D process in our study. Our research provides valuable information for improving the practical application of the AME-D systems. [ABSTRACT FROM AUTHOR]

Aerobic oxidation of methane plays a major role in reducing the amount of methane emitted to the atmosphere from freshwater and marine settings. We cultured an aerobic methanotroph, Methylococcus capsulatus (Bath) at 30 and 37 °C, and determined the relative abundance of 12 CH 4 , 13 CH 4 , 12 CH 3 D, and 13 CH 3 D (a doubly-substituted, or “clumped” isotopologue of methane) to characterize the clumped isotopologue effect associated with aerobic methane oxidation. In batch culture, the residual methane became enriched in 13 C and D relative to starting methane, with D/H fractionation a factor of 9.14 ( D ε/ 13 ε) larger than that of 13 C/ 12 C. As oxidation progressed, the Δ 13 CH 3 D value (a measure of the excess in abundance of 13 CH 3 D relative to a random distribution of isotopes among isotopologues) of residual methane decreased. The isotopologue fractionation factor for 13 CH 3 D/ 12 CH 4 was found to closely approximate the product of the measured fractionation factors for 13 CH 4 / 12 CH 4 and 12 CH 3 D/ 12 CH 4 (i.e., 13 C/ 12 C and D/H). The results give insight into enzymatic reversibility in the aerobic methane oxidation pathway. Based on the experimental data, a mathematical model was developed to predict isotopologue signatures expected for methane in the environment that has been partially-oxidized by aerobic methanotrophy. Measurement of methane clumped isotopologue abundances can be used to distinguish between aerobic methane oxidation and alternative methane-cycling processes. [ABSTRACT FROM AUTHOR]

Hydrothermal vents are an important contributor to marine biogeochemistry, producing large volumes of reduced fluids, gasses, and metals and housing unique, productive microbial and animal communities fueled by chemosynthesis. Methane is a common constituent of hydrothermal vent fluid and is frequently consumed at vent sites by methanotrophic bacteria that serve to control escape of this greenhouse gas into the atmosphere. Despite their ecological and geochemical importance, little is known about the ecophysiology of uncultured hydrothermal vent-associated methanotrophic bacteria. Using metagenomic binning techniques, we recovered and analyzed a near-complete genome from a novel gammaproteobacterial methanotroph (B42) associated with a white smoker chimney in the Southern Lau basin. B42 was the dominant methanotroph in the community, at ~80x coverage, with only four others detected in the metagenome, all on low coverage contigs (7x - 12x). Phylogenetic placement of B42 showed it is a member of the Methylothermaceae, a family currently represented by only one sequenced genome. Metabolic inferences based on the presence of known pathways in the genome showed that B42 possesses a branched respiratory chain with A- and B-family heme copper oxidases, cytochrome bd oxidase and a partial denitrification pathway. These genes could allow B42 to respire over a wide range of oxygen concentrations within the highly dynamic vent environment. Phylogenies of the denitrification genes revealed they are the result of separate horizontal gene transfer from other proteobacteria and suggest that denitrification is a selective advantage in conditions where extremely low oxygen concentrations require all oxygen to be used for methane activation.

Membrane biofilm (MBf) technology is a promising biological water treatment process that combines membrane aeration with biofilms. To expand its application in the treatment of toxic organic wastewater, methane/air gas mixture-MBfs ((CH 4 + Air)-MBfs) and air-MBfs were coupled to enhance the treatment of p -nitroaniline (PNA) wastewater. Based on exploration of the membrane permeability of methane and oxygen, a hybrid MBf reactor was constructed, and the degradation characteristics of PNA and the coupling effects of (CH 4 + Air)-MBfs and air-MBfs were studied. The permeation flux of methane was found to be 1.114 g/(m2 d) when using a methane/air gas mixture at an aeration pressure of 10 kPa, and this result was better than that when methane was used as the aeration gas alone. Aeration with a methane/air gas mixture provided conditions for realizing aerobic methane oxidation; the aerobic methane oxidation that occurred in the (CH 4 + Air)-MBfs promoted the reduction of PNA, and the intermediates of PNA degradation were further degraded by the air-MBfs. At an influent PNA membrane area load of 1.67 g/(m2 d), the PNA removal load reached 187.30 g/(m3 d). The coupling of MBfs took advantage of different matrix-based MBfs and promoted the degradation of PNA by utilizing the synergistic effects of various functional microorganisms. [Display omitted] • Coupling of (CH 4 + Air)-MBfs and air-MBfs was used for PNA wastewater treatment. • Aerobic methane oxidation provided electrons for the reduction of PNA. • The coupling of MBfs utilized the synergistic effect of functional microorganisms. • Methane from WWTPs can be fully utilized to reduce greenhouse gas emissions. • The achieved PNA removal load was higher than that previously reported. [ABSTRACT FROM AUTHOR]

We examined the potential for CH4 oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate or via chlorite (ClO2-) dismutation. Although dissimilatory reduction of ClO4- and ClO3- could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO2- amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO2-. We also observed complete removal of 0.2 kPa CH4 in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO2-. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although a link between ClO2- and CH4 consumption was established in soils and cultures, no upstream connection with either ClO4- or ClO3- was discerned. This result suggests that the release of O2 during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs.

The influence of hydrodynamic events on the distribution of methane and its microbial turnover was investigated during the period from August 2011 to August 2013 along a transect from the eastern (EGB) to the western Gotland Basin (WGB), central Baltic Sea. The water column was characterized by a pronounced methane concentration gradient between the methane-rich deep anoxic and the methane-poor upper oxic water layer. In both basins, enhanced vertical turbulent diffusivities in fall (November 2011) and winter (February 2012) lead to an enhanced flux of methane from the deep anoxic water towards the oxic–anoxic transition zone (redox zone). In both basins, the increased vertical transport of methane in fall/winter was mirrored by reduced methane turnover times measured within the redox zone. Moreover, specific biomarkers indicative for aerobic methanotrophic bacteria implied an increase in the microbial population size from August 2011 till February 2012, indicating a methanotrophic community adapting to the variable methane fluxes. The deep water methane inventory of the EGB showed a seasonal pattern, with concentrations increasing during spring (May) and summer (August) and decreasing during fall (November) and winter (February) as a direct result of the seasonality of the vertical turbulent diffusivity. In contrast, the WGB showed no clear correlation between the seasons and the observed deep water methane variability. Here, the impact of lateral weak intrusions penetrating the deep water layer was identified as the main factor controlling the variability of the deep water methane concentration. Moreover, methane concentration and carbon stable isotopic data (δ 13 C CH 4 ) demonstrate that the previously reported production of methane in the oxic water column below the thermocline occurs in the entire central Baltic Sea from May through November, and despite the large methane pool in the underlying anoxic deep water, might govern the moderate methane flux to the atmosphere in this area in summer. [ABSTRACT FROM AUTHOR]

Microbial oxidation of organic compounds can promote arsenic release by reducing soil-associated arsenate to the more mobile form arsenite. While anaerobic oxidation of methane has been demonstrated to reduce arsenate, it remains elusive whether and to what extent aerobic methane oxidation (aeMO) can contribute to reductive arsenic mobilization. To fill this knowledge gap, we performed incubations of both microbial laboratory cultures and soil samples from arsenic-contaminated agricultural fields in China. Incubations with laboratory cultures showed that aeMO could couple to arsenate reduction, wherein the former bioprocess was carried out by aerobic methanotrophs and the latter by a non-methanotrophic bacterium belonging to a novel and uncultivated representative of Burkholderiaceae . Metagenomic analyses combined with metabolite measurements suggested that formate served as the interspecies electron carrier linking aeMO to arsenate reduction. Such coupled bioprocesses also take place in the real world, supported by a similar stoichiometry and gene activity in the incubations with natural paddy soils, and contribute up to 76.2% of soil-arsenic mobilization into pore waters in the top layer of the soils where oxygen was present. Overall, this study reveals a previously overlooked yet significant contribution of aeMO to reductive arsenic mobilization.

Aerobic methane (CH4) oxidation plays a significant role in marine CH4 consumption. Temperature changes resulting from, for example, global warming, have been suggested to be able to influence methanotrophic communities and their CH4 oxidation capacity. However, exact knowledge regarding temperature controls on marine aerobic methane oxidation is still missing. In this study, CH4 consumption and the methanotrophic community structure were investigated by incubating sediments from shallow (Bohai Bay) and deep marine environments (East China Sea) at 4, 15, and 28 °C for up to 250 days. The results show that the abundance of the methanotrophic population, dominated by the family Methylococcaceae (type I methanotrophs), was significantly elevated after all incubations and that aerobic methane oxidation for both areas had a strong temperature sensitivity. A positive correlation between the CH4 oxidation rate and temperature was witnessed in the Bohai Bay incubations, whereas for the East China Sea incubations, the optimum temperature was 15 °C. The systematic variations of pmoA OTUs between the Bohai Bay and East China Sea incubations indicated that the exact behaviors of CH4 oxidation rates with temperature are related to the different methanotrophic community structures in shallow and deep seas. These results are of great significance for quantitatively evaluating the biodegradability of CH4 in different marine environments. [ABSTRACT FROM AUTHOR]

• Multiple indications of BHPs were evaluated in the East China Sea for the first time. • Two end-member model of R soil was applied to quantify OM source allocation. • BHT-isomer ratio of 0.20–0.45 is proposed as a threshold value to indicate hypoxia. • CH 4 oxidation markers have potential to reflect aerobic methane oxidation activity. The bacterial biomarker group of bacteriohopanepolyols (BHPs) has shown a significant potential to track terrestrial inputs and to respond to environmental changes. A total of 12 BHPs were detected in surface sediments of the East China Sea (ECS), with the contents of 3.79–361 μg/g TOC. The spatial distribution patterns and correlation analyses of bacteriohopanetetrol (BHT) and soil marker BHPs in sediments of the ECS indicate that they were mainly derived from marine autochthonous and terrestrial sources, respectively. The R soil index presented an "offshore decrease" trend, with the contribution of terrestrial organic matter (OM) decreasing from 63% in the coastal waters to 0.81% in the outer seas. This suggests that sedimentary OM in the coastal waters is mainly from terrestrial sources while that in the outer seas is dominantly from marine sources. The spatial distribution patterns and correlation analyses suggest mainly marine sources for the BHT-isomer in the ECS. Thus, although the co-eluted BHT-x and BHT-34R cannot be distinguished, the BHT-isomer in the ECS may be mainly BHT-x derived from marine bacteria rather than BHT-34R derived from terrestrial bacteria. Zones with high value of BHT-isomer ratios in sediments were consistent with the seasonal hypoxic zones in the ECS; furthermore, these ratios were negatively correlated with dissolved oxygen concentrations in the bottom waters. These results indicate that hypoxic environments are beneficial to BHT-isomer production, further confirming that the BHT-isomer can be a biomarker for marine hypoxia. Aminotetrol and aminopentol were closely related to the aerobic methane-oxidation gene pmoA and dissolved CH 4 , suggesting their potential as markers for aerobic methane oxidation. [ABSTRACT FROM AUTHOR]

• Up-to-date fundamentals of biological CH 4 oxidation are integrated and summarized. • State-of-the-art studies using CH 4 to remove oxidized contaminants are evaluated. • Opportunities and unsolved questions deserving future explorations are identified. Being an energetic fuel, methane is able to support microbial growth and drive the reduction of various electron acceptors. These acceptors include a broad range of oxidized contaminants (e.g., nitrate, nitrite, perchlorate, bromate, selenate, chromate, antimonate and vanadate) that are ubiquitously detected in water environments and pose threats to human and ecological health. Using methane as electron donor to biologically reduce these contaminants into nontoxic forms is a promising solution to remediate polluted water, considering that methane is a widely available and inexpensive electron donor. The understanding of methane-based biological reduction processes and the responsible microorganisms has grown in the past decade. This review summarizes the fundamentals of metabolic pathways and microorganisms mediating microbial methane oxidation. Experimental demonstrations of methane as an electron donor to remove oxidized contaminants are summarized, compared, and evaluated. Finally, the review identifies opportunities and unsolved questions that deserve future explorations for broadening understanding of methane oxidation and promoting its practical applications. [ABSTRACT FROM AUTHOR]

Mangrove forests are one of the important ecosystems in tropical coasts because of their high primary production, which they sustain by sequestering a substantial amount of CO2 into plant biomass. These forests often experience various levels of inundation and play an important role in CH4 emissions, but the taxonomy of methanotrophs in these systems remains poorly understood. In this study, DNA-based stable isotope probing showed significant niche differentiation in active aerobic methanotrophs in response to niche differentiation in upstream and downstream mangrove soils of the Tamsui estuary in northwestern Taiwan, in which salinity levels differ between winter and summer. Methylobacter and Methylomicrobium-like Type I methanotrophs dominated methane-oxidizing communities in the field conditions and were significantly 13C-labeled in both upstream and downstream sites, while Methylobacter were well adapted to high salinity and low temperature. The Type II methanotroph Methylocystis comprised only 10–15% of all the methane oxidizers in the upstream site but less than 5% at the downstream site under field conditions. 13C-DNA levels in Methylocystis were significantly lower than those in Type I methanotrophs, while phylogenetic analysis further revealed the presence of novel methane oxidizers that are phylogenetically distantly related to Type Ia in fresh and incubated soils at a downstream site. These results suggest that Type I methanotrophs display niche differentiation associated with environmental differences between upstream and downstream mangrove soils. [ABSTRACT FROM AUTHOR]

• The YRD wetland presents characteristics of a methane sink in the dry season. • Aerobic methane oxidation is the main contributor to the methane sink. • Methylomicrobium and Methylobacter are potential operators of methane oxidation. • The pure culture of Methylobacter confirmed its ability to form methane sinks. Recent investigations demonstrate that some coastal wetlands are atmospheric methane sinks, but the regulatory mechanisms are not clear. Here, the main pathway and operator of methane oxidation in the Yellow River Delta (YRD) wetland, a methane source in the wet season but a methane sink in the dry season, were investigated. The anaerobic oxidation of methane (AOM) and aerobic methane oxidation (AMO) abilities of wetland soil were measured, and the microbial community structure was analyzed. The experimental results showed that AMO was active throughout the year. In contrast, AOM was weak and even undetected. The microbial community analysis indicated that Methylomicrobium and Methylobacter potentially scavenged methane in oxic environments. A representative strain of Methylobacter , which was isolated from the soil, presented a strong AMO ability at high concentrations of methane and air. Overall, this study showed that active AMO performing by Methylobacter may account for methane sink in the YRD wetland during the dry season. Our research not only has determined the way in which methane sinks are formed but also identified the potential functional microbes. In particular, we confirmed the function of potential methanotroph by pure culture. Our research provides biological evidence for why some wetlands have methane sink characteristics, which may help to understand the global methane change mechanism. [ABSTRACT FROM AUTHOR]

Chromate contamination can pose a high risk to both the environment and public health. Previous studies have shown that CH 4 -based membrane biofilm reactor (MBfR) is a promising method for chromate removal. In this study, we developed a multispecies biofilm model to study chromate reduction and its interaction with nitrate reduction in a CH 4 -based MBfR. The model-simulated results were consistent with the experimental data reported in the literature. The model showed that the presence of nitrate in the influent promoted the growth of heterotrophs, while suppressing methanotrophs and chromate reducers. Moreover, it indicated that a biofilm thickness of 150 μm and an influent dissolved oxygen concentration of 0.5 mg O 2 /L could improve the reactor performance by increasing the chromate removal efficiency under the simulated conditions., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2019 Zhejiang University.)

Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria , Verrucomicrobia , and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs ( Methylococcus and Methylocaldum ) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named " Methylotetracoccus oryzae " C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C 16:1 ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems. IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions., (Copyright © 2019 Ghashghavi et al.)

The O 2 :CH 4 ratio significantly effects nitrogen removal in mixed cultures where aerobic methane oxidation is coupled with denitrification (AME-D). The goal of this study was to investigate nitrogen removal of the AME-D process at four different O 2 :CH 4 ratios [0, 0.05, 0.25, and 1 (v/v)]. In batch tests, the highest denitrifying activity was observed when the O 2 :CH 4 ratio was 0.25. At this ratio, the methanotrophs produced sufficient carbon sources for denitrifiers and the oxygen level did not inhibit nitrite removal. The results indicated that the synergy between methanotrophs and denitrifiers was significantly improved, thereby achieving a greater capacity of nitrogen removal. Based on thermodynamic and chemical analyses, methanol, butyrate, and formaldehyde could be the main trophic links of AME-D process in our study. Our research provides valuable information for improving the practical application of the AME-D systems.