Aerobic Methane-oxidizing Bacteria Research Articles

Ridge with no-tillage facilitates microbial N2 fixation associated with methane oxidation in rice soil

Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 μg 13C g−1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 μg 15N g−1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation – not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.

Linking methanotroph phenotypes to genotypes using a simple spatially resolved model ecosystem.

Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental context in laboratory settings. Laboratory-based model ecosystems offer a means to better account for environmental conditions compared with standard planktonic cultures and can help link genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs) within the methane-oxygen counter gradient typically found in the natural environment of these organisms. Culturing the methanotroph Methylomonas sp. strain LW13 in this system resulted in the formation of a distinct horizontal band at the intersection of the counter gradient, which we discovered was not due to increased numbers of bacteria at this location but instead to an increased amount of polysaccharides. We also discovered that different methanotrophic taxa form polysaccharide bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this band, we identified genes upregulated within the band and validated their involvement in growth and band formation within the model ecosystem using knockout strains. Notably, deletion of these genes did not negatively affect growth using standard planktonic culturing methods. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover bacterial phenotypes missing from standard laboratory conditions, and to link these phenotypes with their genetic determinants.

Warming and wetting-induced soil acidification triggers methanotrophic diversity loss and species turnover in an alpine ecosystem

Increases in temperature and precipitation have continually occurred in the past few decades, both globally and in China, which have probably impacted the dynamics of net methane (CH4) emissions by regulating soil CH4 oxidization. An alpine ecosystem is quite sensitive to climate changes, but how these two climatic factors regulate the community of soil aerobic methane-oxidizing bacteria (aMOB) remains elusive in such an ecosystem because of the lack of high-resolution soil sampling datasets. Here, we employed a hybrid approach of gridded field surveys and random forest prediction to discern the above question in the Qinghai-Tibetan Plateau (QTP). Results indicated that type Ic aMOBs exhibited a preference for drier, colder areas, while type IIa, TUSC-like and RA21-like aMOBs probably occurred in wetter and relatively warmer areas. There were no remarkable shifts in α-diversity and bacterial community compositions from the driest and coldest regions to moderate ones, while the α-diversity decreased and community compositions changed substantially from moderate arid and cold areas to wetter, relatively warmer ones. These trends were mainly regulated by soil pH, a potentially secondary effect shaped by the interactions of mean annual precipitation (MAP) and temperature (MAT) and an aridity index (AI) in the QTP. A slight decline in soil pH from the driest and coldest areas to moderate ones might regulate aMOB diversity and community structure by the stochastic extinction of individuals adapted to a higher pH and the unstable colonization of individuals preferring a moderate pH. A great decline in soil pH from the moderate arid, cold to wetter, relatively warmer areas might lead to the deterministic exclusion of species with a high pH adaptability and the stable colonization of species preferring the acidic habitat. This study implies that soil acidification probably induces aMOB diversity loss and species turnover in the arid, cold areas of the QTP under climatic warming and wetting, shedding a new light on projecting the impact of climate changes on an alpine ecosystem’s structure and function on unprecedented spatial scales.

Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR.

Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating methane emissions from paddy fields. In this study, we developed a differential quantification method for the copy number of pmoA genes of type Ia, Ib, and IIa MOB in paddy field soil using chip-based digital PCR. Three probes specific to the pmoA of type Ia, Ib, and IIa MOB worked well in digital PCR quantification when genomic DNA of MOB isolates and PCR-amplified DNA fragments of pmoA were examined as templates. When pmoA genes in the surface soil layer of a flooded paddy were quantified by digital PCR, the copy numbers of type Ia, Ib, and IIa MOB were 105 -106 , 105 -106 , and 107 copies g-1 dry soil, respectively, with the highest values in the top 0-2-mm soil layer. Especially, the copy numbers of type Ia and Ib MOB increased by 240% and 380% at the top layer after soil flooding, suggesting that the soil circumstances at the oxic-anoxic interfaces were more preferential for growth of type I MOB than type II MOB. Thus, type I MOB likely play an important role in the methane consumption at the surface paddy soil.

Community structure and network interaction of aerobic methane-oxidizing bacteria in Chongqing’s central urban area in the Three Gorges Reservoir, China

A reservoir is an important source of methane (CH4), which is consumed by aerobic methane-oxidizing bacteria (MOB), representing the main CH4 sink in water. The central urban area of Chongqing in the Three Gorges Reservoir (TGR) area was selected as the study area in 2021. High-throughput sequencing was used to analyze the community structure and abundance of MOBs. The results showed that Methylocystis (Type II) was the dominant MOB in water, whereas Methylococcus (Type I) and Methylocystis co-dominated the sediments. High water temperature in the study area largely accounted for the predominance of Type II MOBs in the two habitats. Moreover, the influence of environmental factors on MOB community and its interspecific relationship were significantly regulated by the operation of the TGR. In the low-water-level period, NO2--N and CO2 concentration significantly correlated with Methylocystis, whereas in the high-water-level period, the higher discharge and velocity weakened the influence of all environmental factors on Methylocystis. In addition, the scouring of sediments by increasing discharge in the high-water-level period caused a significant decrease in dissolved CH4 concentration. The decrease in substrate increased interspecific competition within the MOB community, especially between different types of MOBs, in the high-water-level period.

Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.

Aerobic and denitrifying methanotrophs: Dual wheels driving soil methane emission reduction

The greenhouse gas methane in soils has been considered to be consumed mainly by aerobic methane-oxidizing bacteria for a long time. In the last decades, the discovery of anaerobic methanotrophs greatly complemented the methane cycle, but their contribution rates and ecological significance in soils remain undescribed. In this work, the soil samples from forest, grassland and cropland in four different climatic regions were collected to investigate these conventional and novel methanotrophs. A dual-core microbial methane sink, responsible for over 80 % of soil methane emission reduction, was unveiled. The aerobic core was performed by aerobic methanotrophic bacteria in topsoil, who played important roles in stabilizing bacterial communities. The anaerobic core was denitrifying methanotrophs in anoxic soils, including denitrifying methanotrophic bacteria from NC10 phylum and denitrifying methanotrophic archaea from ANME-2d clade. They were ubiquitous in terrestrial soils and potentially led to around 50 % of the total methane removal. Human activities such as livestock farming and rice cultivation further promoted the contribution rates of these denitrifying methanotrophs. This work elucidated the emission reduction contribution of different methanotrophs in the continental setting, which would help to reduce uncertainties in the estimations of the soil methane emission.

Characterization and genome analysis of a psychrophilic methanotroph representing a ubiquitous Methylobacter spp. cluster in boreal lake ecosystems

Lakes and ponds are considered as a major natural source of CH4 emissions, particularly during the ice-free period in boreal ecosystems. Aerobic methane-oxidizing bacteria (MOB), which utilize CH4 using oxygen as an electron acceptor, are one of the dominant microorganisms in the CH4-rich water columns. Metagenome-assembled genomes (MAGs) have revealed the genetic potential of MOB from boreal aquatic ecosystems for various microaerobic/anaerobic metabolic functions. However, experimental proof of these functions, i.e., organic acid production via fermentation, by lake MOB is lacking. In addition, psychrophilic (i.e., cold-loving) MOB and their CH4-oxidizing process have rarely been investigated. In this study, we isolated, provided a taxonomic description, and analyzed the genome of Methylobacter sp. S3L5C, a psychrophilic MOB, from a boreal lake in Finland. Based on phylogenomic comparisons to MAGs, Methylobacter sp. S3L5C represented a ubiquitous cluster of Methylobacter spp. in boreal aquatic ecosystems. At optimal temperatures (3–12 °C) and pH (6.8–8.3), the specific growth rates (µ) and CH4 utilization rate were in the range of 0.018–0.022 h−1 and 0.66–1.52 mmol l−1 d−1, respectively. In batch cultivation, the isolate could produce organic acids, and the concentrations were elevated after replenishing CH4 and air into the headspace. Up to 4.1 mM acetate, 0.02 mM malate, and 0.07 mM propionate were observed at the end of the test under optimal operational conditions. The results herein highlight the key role of Methylobacter spp. in regulating CH4 emissions and their potential to provide CH4-derived organic carbon compounds to surrounding heterotrophic microorganisms in cold ecosystems.

Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction.

Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitrogen-free M2 medium. The methanotroph labeled as MO3_YZ.1 had a size of 3.83 Mb, GC content of 65.6%, and 3442 gene-coding regions. Based on phylogeny of pmoA gene and genome and the genomic average nucleotide identity, we confirmed its affiliation to the MO3 lineage and a close relationship to Methylocapsa. MO3_YZ.1 contained mxaF- and xoxF-type methanol dehydrogenase. MO3_YZ.1 used the serine cycle to assimilate carbon and regenerated glyoxylate through the glyoxylate shunt as it contained isocitrate lyase and complete tricarboxylic acid cycle-coding genes. The ethylmalonyl-CoA pathway and Calvin–Benson–Bassham cycle were incomplete in MO3_YZ.1. Three acetate utilization enzyme-coding genes were identified, suggesting its potential ability to utilize acetate. The presence of genes for N2 fixation, sulfur transformation, and poly-β-hydroxybutyrate synthesis enable its survival in heterogeneous habitats with fluctuating supplies of carbon, nitrogen, and sulfur.

Diversity and Effect of Increasing Temperature on the Activity of Methanotrophs in Sediments of Fildes Peninsula Freshwater Lakes, King George Island, Antarctica.

Global warming has a strong impact on polar regions. Particularly, the Antarctic Peninsula and nearby islands have experienced a marked warming trend in the past 50 years. Therefore, higher methane (CH4) emissions from this area could be expected in the future. Since mitigation of these emissions can be carried out by microbial oxidation, understanding this biological process is crucial since to our knowledge, no related studies have been performed in this area before. In this work, the aerobic CH4 oxidation potential of five freshwater lake sediments of Fildes Peninsula (King George Island, South Shetland Islands) was determined with values from 0.07 to 10 μmol CH4 gdw–1 day–1 and revealed up to 100-fold increase in temperature gradients (5, 10, 15, and 20°C). The structure and diversity of the bacterial community in the sediments were analyzed by next-generation sequencing (Illumina MiSeq) of 16S rRNA and pmoA genes. A total of 4,836 ASVs were identified being Proteobacteria, Actinobacteriota, Acidobacteriota, and Bacteroidota the most abundant phyla. The analysis of the pmoA gene identified 200 ASVs of methanotrophs, being Methylobacter Clade 2 (Type I, family Methylococcaceae) the main responsible of the aerobic CH4 oxidation. Moreover, both approaches revealed the presence of methanotrophs of the classes Gammaproteobacteria (families Methylococcaceae and Crenotrichaceae), Alphaproteobacteria (family Methylocystaceae), Verrucomicrobia (family Methylacidiphilaceae), and the candidate phylum of anaerobic methanotrophs Methylomirabilota. In addition, bacterial phospholipid fatty acids (PLFA) biomarkers were studied as a proxy for aerobic methane-oxidizing bacteria and confirmed these results. Methanotrophic bacterial diversity was significantly correlated with pH. In conclusion, our findings suggest that aerobic methanotrophs could mitigate in situ CH4 emissions in a future scenario with higher temperatures in this climate-sensitive area. This study provides new insights into the diversity of methanotrophs, as well as the influence of temperature on the CH4 oxidation potential in sediments of freshwater lakes in polar regions of the southern hemisphere.

Demethylation-The Other Side of the Mercury Methylation Coin: A Critical Review.

The public and environmental health consequences of mercury (Hg) methylation have drawn much attention and considerable research to Hg methylation processes and their dynamics in diverse environments and under a multitude of conditions. However, the net methylmercury (MeHg) concentration that accumulates in the environment is equally determined by the rate of MeHg degradation, a complex process mediated by a variety of biotic and abiotic mechanisms, about which our knowledge is limited. Here we review the current knowledge on MeHg degradation and its potential pathways and mechanisms. We describe detoxification by resistant microorganisms that employ the Hg resistance (mer) system to reductively break the carbon-mercury (C-Hg) bond producing methane (CH4) and inorganic mercuric Hg(II), which is then reduced by the mercuric reductase to elemental Hg(0). Very recent research has begun to elucidate a mechanism for the long-recognized mer-independent oxidative demethylation, likely involving some strains of anaerobic bacteria as well as aerobic methane-oxidizing bacteria, i.e., methanotrophs. In addition, photochemical and chemical demethylation processes are described, including the roles of dissolved organic matter (DOM) and free radicals as well as dark abiotic demethylation in the natural environment about which little is currently known. We focus on mechanisms and processes of demethylation and highlight the uncertainties and known effects of environmental factors leading to MeHg degradation. Finally, we suggest future research directions to further elucidate the chemical and biochemical mechanisms of biotic and abiotic demethylation and their significance in controlling net MeHg production in natural ecosystems.

Carbon and hydrogen isotope fractionation during aerobic oxidation of short-chain alkanes in experimental incubations of vent fluids

Aerobic oxidation of short-chain alkanes was observed in gas samples from the Lutao intertidal hydrothermal vents in Taiwan, during storage at 20 °C for up to 29 months without adding bacterial strains and replenishing substrates. The carbon isotope fractionation factors (εC) of methane (C1), ethane (C2), and propane (C3), were calculated using the Rayleigh fractionation equation to be −37.1 ± 7.5‰, −14.8 ± 4.8‰, and −4.7 ± 5.2‰, respectively. The hydrogen isotope fractionation factor (εH) of methane was determined to be −281 ± 187‰. DNA sequencing of the 16S rRNA gene in the vent fluids suggests that aerobic oxidation is dominated by methanotrophs of the genera Methylomicrobium and Methylophaga, which use the ribulose monophosphate pathway (RuMP). The degrees of isotope fractionation (εC and εH values) herein are larger than previously reported values, possibly due to the limited O2 supply and low abundance of aerobic methane-oxidizing bacteria in the experiments. Since the fractionation factor of methane is higher than those of ethane and propane, the aerobic oxidation of thermogenic or microbial alkanes could produce a carbon isotope reversal, which is frequently noted as a trait of abiotic hydrocarbons. This work demonstrates that in addition to anaerobic microbial oxidation, aerobic oxidation with a low cell density can also produce significant isotope fractionation of alkanes in geological closed/semi-closed environments and open flow reaction systems that are characterized by moderate temperatures and a limited supply of substrates and O2; these environments include cold seeps, mud volcanoes, and low-temperature hydrothermal plumes/aquifers/reservoirs.

Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island

The genus Methylobacter is considered an important and often dominant group of aerobic methane-oxidizing bacteria in many oxic ecosystems, where members of this genus contribute to the reduction of CH4 emissions. Metagenomic studies of the upper oxic layers of geothermal soils of the Favara Grande, Pantelleria, Italy, revealed the presence of various methane-oxidizing bacteria, and resulted in a near complete metagenome assembled genome (MAG) of an aerobic methanotroph, which was classified as a Methylobacter species. In this study, the Methylobacter sp. B2 MAG was used to investigate its metabolic potential and phylogenetic affiliation. The MAG has a size of 4,086,539 bp, consists of 134 contigs and 3955 genes were found, of which 3902 were protein coding genes. All genes for CH4 oxidation to CO2 were detected, including pmoCAB encoding particulate methane monooxygenase (pMMO) and xoxF encoding a methanol dehydrogenase. No gene encoding a formaldehyde dehydrogenase was present and the formaldehyde to formate conversion follows the tetrahydromethanopterin (H4MPT) pathway. “Ca. Methylobacter favarea” B2 uses the Ribulose-Mono-Phosphate (RuMP) pathway for carbon fixation. Analysis of the MAG indicates that Na+/H+ antiporters and the urease system might be important in the maintenance of pH homeostasis of this strain to cope with acidic conditions. So far, thermoacidophilic Methylobacter species have not been isolated, however this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments.

Aerobic methanotrophs in an urban water cycle system: Community structure and network interaction pattern

Aerobic methane-oxidizing bacteria (MOB) play an important role in reducing methane emissions in nature. Most current researches focus on the natural habitats (e.g., lakes, reservoirs, wetlands, paddy fields, etc.). However, methanotrophs and the methane-oxidizing process remain essentially unclear in artificial habitat, such as the urban water cycle systems. Here, high-throughput sequencing and qPCR were used to analyze the community structure and abundance of MOB. Six different systems were selected from Yunyang City, Chongqing, China, including the raw water system (RW), the water supply pipe network system (SP), the wastewater pipe network system (WP), the hospital wastewater treatment system (HP), the municipal wastewater treatment plant system (WT) and the downstream river system (ST) of a wastewater treatment plant. Results clearly showed that the MOB community structure and network interaction patterns of the urban water cycle system were different from those of natural water bodies. Type I MOB was the dominant clade in HP. Methylocysis in Type II was the most abundant genus among the whole urban water cycle system, indicating that this genus had a high adaptability to the environment. Temperature, dissolved oxygen, pH and concentration significantly affected the MOB communities in the urban water cycle system. The network of MOB in WT was the most complicated, and there were competitive relationships among species in WP. The structure of the network in HP was unstable, and therefore, it was vulnerable to environmental disturbances. Methylocystis (Type II) and Methylomonas (Type I) were the most important keystone species in the entire urban water cycle system. Overall, these findings broaden the understanding of the distribution and interaction patterns of MOB communities in an urban water cycle system and provide valuable clues for ecosystem restoration and environmental management.

Detoxification, Active Uptake, and Intracellular Accumulation of Chromium Species by a Methane-Oxidizing Bacterium.

Despite the wide-ranging proscription of hexavalent chromium, chromium(VI) remains among the major polluting heavy metals worldwide. Aerobic methane-oxidizing bacteria are widespread environmental microorganisms that can perform diverse reactions using methane as the feedstock. The methanotroph Methylococcus capsulatus Bath, like many other microorganisms, detoxifies chromium(VI) by reduction to chromium(III). Here, the interaction of chromium species with M. capsulatus Bath was examined in detail by using a range of techniques. Cell fractionation and high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS) indicated that externally provided chromium(VI) underwent reduction and was then taken up into the cytoplasmic and membranous fractions of the cells. This was confirmed by X-ray photoelectron spectroscopy (XPS) of intact cultures that indicated negligible chromium on the surfaces of or outside the cells. Distribution of chromium and other elements within intact and sectioned cells, as observed via transmission electron microscopy (TEM) combined with energy-dispersive X-ray spectroscopy (EDX) and electron energy loss spectroscopy (EELS), was consistent with the cytoplasm/membrane location of the chromium(III), possibly as chromium phosphate. The cells could also take up chromium(III) directly from the medium in a metabolism-dependent fashion and accumulate it. These results indicate a novel pattern of interaction with chromium species distinct from that observed previously with other microorganisms. They also suggest that M. capsulatus and similar methanotrophs may contribute directly to chromium(VI) reduction and accumulation in mixed communities of microorganisms that are able to perform methane-driven remediation of chromium(VI).IMPORTANCEM. capsulatus Bath is a well-characterized aerobic methane-oxidizing bacterium that has become a model system for biotechnological development of methanotrophs to perform useful reactions for environmental cleanup and for making valuable chemicals and biological products using methane gas. Interest in such technology has increased recently owing to increasing availability of low-cost methane from fossil and biological sources. Here, it is demonstrated that this versatile methanotroph can reduce the toxic contaminating heavy metal chromium(VI) to the less toxic form chromium(III) while accumulating the chromium(III) within the cells. This is expected to diminish the bioavailability of the chromium and make it less likely to be reoxidized to chromium(VI). Thus, M. capsulatus has the capacity to perform methane-driven remediation of chromium-contaminated water and other materials and to accumulate the chromium in the low-toxicity chromium(III) form within the cells.

Research progress of aerobic methane oxidation process in inland waters

内陆水体是全球碳循环的关键组成部分，是大气中甲烷（CH₄）的重要来源，每年从内陆淡水与自然湿地排放进入大气的CH₄约为185~357 Tg/a.通常，内陆水体中CH₄主要由分布于水层底部的厌氧区或沉积层内的产甲烷菌介导产生，其向水层表面传输的过程中易被甲烷氧化菌所氧化.甲烷氧化菌可分为好氧甲烷氧化菌和厌氧甲烷氧化菌，有氧条件下，由好氧甲烷氧化菌介导的好氧甲烷氧化过程是水体中甲烷氧化过程的主要形式，湖泊底部产生的CH₄总量中约有99%可以被上覆水体中的好氧甲烷氧化过程所消耗.本文收集文献综合分析阐明，好氧甲烷氧化过程是由水环境因子、水文条件以及不同内陆水体的生态系统特征共同调控，同时也表现在了好氧甲烷氧化菌的生境偏好上.复杂的调控过程构建了内陆水体向大气输送CH₄的动态平衡，并最终反映在内陆水体对全球CH₄循环、碳循环作出的贡献上.;Inland waters are important parts in global carbon biogeochemial cycles. It is also one of the main sources of methane. Annual emissions of CH₄ from inland freshwaters and natural wetlands into the atmosphere is 185-357 Tg/a. Methane is mainly produced by the reactions between bottom organic sediments and methanogenic bacteria in anoxic zone of inland waters. Methane is then consumed by methane-oxidizing bacteria during its upsurge to surface water. Methane-oxidizing bacteria can be divided into aerobic methane-oxidizing bacteria and anaerobic methane-oxidizing bacteria. Under aerobic conditions, the aerobic methane oxidation process mediated by aerobic methane-oxidizing bacteria is the main form of methane oxidation process in water, and about 99% of the total CH₄ produced at the bottom of the lake can be consumed by the aerobic methane oxidation process in the overlying water. According to the comprehensive analysis of literature collected in this paper, the process of aerobic methane oxidation is controlled by water environmental factors, hydrological conditions and ecosystem characteristics of different inland waters, and also reflected in the habitat preference of aerobic methane-oxidizing bacteria. The complex regulation process constructs the dynamic balance of the total amount of CH₄ transported from inland waters to the atmosphere, which is reflected in the contribution of inland waters to the global CH₄ cycle and carbon cycle.

Identification of Aerobic Methane-Oxidizing Bacteria in Coastal Sediments of the Crimean Peninsula

Methane oxidation rates and diversity of methane-oxidizing microorganisms in the upper sediment layers of the Crimean Peninsula coastal regions (Black Sea) were investigated. Analysis of the 16S rRNA gene sequences revealed microorganisms of the class Gammaproteobacteria, order Methylococcales. At the sites of continuous gas seepage, the percentage of methanotrophs in the bacterial community was high (up to 2.1% of the total read number), which made it possible to detect them by sequencing of the native samples. At the sites of intermittent gas seepage formed during summer and autumn, methanotrophs were minor components of the communities and could be detected only after incubation of the sediment samples in the presence of methane. Low similarity between their 16S rRNA sequences and those of the known methanotrophs indicates that some organisms probably belong to new taxa of the species and genus levels.

Diversity of amoA and pmoA Genes in Extremely Saline Alkaline Soils of the Former Lake Texcoco

Ammonia-oxidizing bacteria (AOB) and aerobic methane oxidizing-bacteria (MOB) were studied in three extreme soils of the former Lake Texcoco, Mexico, with pH ranging from 8.5 to 10.5 and electrolytic conductivity (EC) from 0.67 to 84.76 dS m−1, and in two arable soils. Soil DNA was extracted with three different methods and total DNA was used as a template to amplify the pmoA and amoA functional genes and subsequently sequenced by pyrosequencing. The amoA gene sequences clustered as uncultured AOB dominated in the Texcoco soils, while Nitrosospira was dominant in the arable soils. Sequences of MOB associated with Nitrosococcus-rel (Type I) dominated (>85%) in the Texcoco soils, but they were more diverse in the arable soils, for example, JR2, JR3, Methylocaldum USC-g (Type I), USC-a (Type II) and gp23 (pxmA). Aerobic methane oxidizing-bacteria and AOB microbial diversity were significantly related to EC and pH (p < 0.05). As such, the lower MOB and AOB microbial diversity in the Texcoco soil compared to the arable soil was determined by its higher EC and pH.

Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates.

Lake methane (CH4 ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes.

Methyl Selenol as a Precursor in Selenite Reduction to Se/S Species by Methane-Oxidizing Bacteria.

A wide range of microorganisms have been shown to transform selenium-containing oxyanions to reduced forms of the element, particularly selenium-containing nanoparticles. Such reactions are promising for the detoxification of environmental contamination and the production of valuable selenium-containing products, such as nanoparticles for application in biotechnology. It has previously been shown that aerobic methane-oxidizing bacteria, including Methylococcus capsulatus (Bath), are able to perform the methane-driven conversion of selenite (SeO32-) to selenium-containing nanoparticles and methylated selenium species. Here, the biotransformation of selenite by Mc. capsulatus (Bath) has been studied in detail via a range of imaging, chromatographic, and spectroscopic techniques. The results indicate that the nanoparticles are produced extracellularly and have a composition distinct from that of nanoparticles previously observed from other organisms. The spectroscopic data from the methanotroph-derived nanoparticles are best accounted for by a bulk structure composed primarily of octameric rings in the form Se8 -x S x with an outer coat of cell-derived biomacromolecules. Among a range of volatile methylated selenium and selenium-sulfur species detected, methyl selenol (CH3SeH) was found only when selenite was the starting material, although selenium nanoparticles (both biogenic and chemically produced) could be transformed into other methylated selenium species. This result is consistent with methyl selenol being an intermediate in the methanotroph-mediated biotransformation of selenium to all the methylated and particulate products observed.IMPORTANCE Aerobic methane-oxidizing bacteria are ubiquitous in the environment. Two well-characterized strains, Mc. capsulatus (Bath) and Methylosinus trichosporium OB3b, representing gamma- and alphaproteobacterial methanotrophs, respectively, can convert selenite, an environmental pollutant, to volatile selenium compounds and selenium-containing particulates. Both conversions can be harnessed for the bioremediation of selenium pollution using biological or fossil methane as the feedstock, and these organisms could be used to produce selenium-containing particles for food and biotechnological applications. Using an extensive suite of techniques, we identified precursors of selenium nanoparticle formation and also found that these nanoparticles are made up of eight-membered mixed selenium and sulfur rings.