Analysis of methane monooxygenase genes in mono lake suggests that increased methane oxidation activity may correlate with a change in methanotroph community structure

Research on aerobic oxidation of methane bacteria and its influencing factors in Chongqing central city section of the Yangtze River, China

Bacterial communities play an important role in the carbon cycle of freshwater ecosystems. In order to understand the influencing factors of bacterial community in the process of carbon cycle and search for measures to reduce carbon emissions, Chongqing central city section of the Yangtze River and its tributaries were selected to be the study area in this research. High-throughput sequencing was applied to study aerobic oxidation of methane bacteria (MOB) in sampling area. The results showed that there were spatial differences in the community diversity of aerobic MOB in the Yangtze River in central Chongqing. The Shannon index in the sediment (2.389-2.728) was higher than that in the water (1.820-2.458), and the community diversity in the middle reaches of the main river was higher than that in the upstream and the downstream. The aerobic MOB community was mainly dominated by Type II (Methylocystis). Most of operational taxonomic units (OTUs) in the top ten had high homology with MOB from river and lake sediments, and a few OTUs had high homology with MOB from paddy fields, forests and wetland soils. The main environmental factors affecting the community structure of aerobic MOB were NH4+-N, dissolved oxygen (DO), temperature (T, p ≤ 0.001), pH (p ≤ 0.05), methane (CH4) and carbon dioxide (CO2).

Species shifts induce soil organic matter priming and changes in microbial communities

Invasion of plant species with functional traits that influences the rhizosphere can have significant effects on soil organic matter (SOM) dynamics if the invasive species stimulates soil microbial communities with, for example, an enhanced supply of labile carbon and oxygen. We evaluated these effects along a Phragmites invasion chronosequence spanning over 40 years. Using a δ¹³C and δ¹⁵N enriched substrate, we separated SOM-derived and substrate-derived carbon (C) and nitrogen (N) mineralization in surface (top 15 cm), shallow (30-45 cm), and deep (65-80 cm) soils collected from established, newly invaded, and native plant communities. We found all soils were susceptible to SOM priming, but priming profiles differed between vegetation communities, being highest at the surface in native assemblage soils, whereas highest at depth under invasive plants. Changes in functional microbial community composition at depth in Phragmites soils, evidenced by an increase in relative fungal laccase abundance, explained the SOM priming in these deep invaded soils. Our results show that invasive Phragmites maintains a microbial community at depth able to degrade SOM faster than that under native vegetation, evidencing that plant species shifts can fundamentally change soil biogeochemistry, altering element cycling and decreasing SOM residence time. Furthermore, our experimental design allowed to quantify real-time SOM-C and SOM-N gross mineralization, resulting in a new model relating C and N mineralization in these wetland soils and providing new insights on how SOM decomposition impacts N availability and cycling across wetland N pools.

Salinity significantly affects methane oxidation and methanotrophic community in Inner Mongolia lake sediments

Methanotrophs oxidize methane (CH₄) and greatly help in mitigating greenhouse effect. Increased temperatures due to global climate change can facilitate lake salinization, particularly in the regions with cold semiarid climate. However, the effects of salinity on the CH₄ oxidation activity and diversity and composition of methanotrophic community in the sediment of natural lakes at a regional scale are still unclear. Therefore, we collected lake sediment samples from 13 sites in Mongolian Plateau; CH₄ oxidation activities of methanotrophs were investigated, and the diversity and abundance of methanotrophs were analyzed using real-time quantitative polymerase chain reaction and high throughput sequencing approach. The results revealed that the diversity of methanotrophic community decreased with increasing salinity, and community structure of methanotrophs was clearly different between the hypersaline sediment samples (HRS; salinity > 0.69%) and hyposaline sediment samples (HOS; salinity < 0.69%). Types II and I methanotrophs were predominant in HRS and HOS, respectively. Salinity was significantly positively correlated with the relative abundance of Methylosinus and negatively correlated with that of Methylococcus. In addition, CH₄ oxidation rate and pmoA gene abundance decreased with increasing salinity, and salinity directly and indirectly affected CH₄ oxidation rate via regulating the community diversity. Moreover, high salinity decreased cooperative association among methanotrophs and number of key methanotrophic species (Methylosinus and Methylococcus, e.g). These results suggested that salinity is a major driver of CH₄ oxidation in lake sediments and acts by regulating the diversity of methanotrophic community and accociation among the methanotrophic species.

The characteristics and influencing factors of dissolved methane concentrations in Chongqing's central urban area in the Three Gorges Reservoir, China

Methane (CH₄) emissions from reservoirs have received widespread attention. The central urban area of Chongqing in the Three Gorges Reservoir area was selected as the study area in 2020. The temporal and spatial distribution of dissolved CH₄ concentration and flux, key generation pathways, and influencing factors have been studied. The dissolved CH₄ concentration in low-water-level period and impoundment period varied from 0.037~0.12 μmol·L^-1 and 0.11~0.23 μmol·L^-1, with the average values of (0.066 ± 0.0067) μmol·L^-1 and (0.13 ± 0.034) μmol·L^-1. The CH₄ flux was (0.941 ± 0.217) μmol·m^-2·h^-1 in low-water-level period and (1.915 ± 0.204) μmol·m^-2·h^-1 in impoundment period. CH₄ was produced by CO₂ reduction and acetic acid fermentation, accounting for 17.95% and 82.05% of the total CH₄ production, respectively. The dissolved CH₄ concentration was significantly positively correlated with DO and NO₃^--N, and it is opposite with dissolved inorganic carbon. The dissolved CH₄ concentration in this study area is affected by water environment (33.42%), inorganic nitrogen (29.60%), organic carbon (23.88%), and inorganic carbon (13.10%), and anthropogenic influences promoted dissolved CH₄ concentration.

Eutrophic levels and algae growth increase emissions of methane and volatile sulfur compounds from lakes

Eutrophic lakes are hot spots of CH₄ and volatile sulfur compound (VSC) emissions, especially during algal blooms and decay. However, the response of CH₄ and VSC emissions to lake eutrophication and algae growth as well as the underlying mechanisms remain unclear. In this study, the emissions of CH₄ and VSCs from four regions of Lake Taihu with different eutrophic levels were investigated in four months (i.e., March, May, August and December). The CH₄ emissions ranged from 20.4 to 126.9 mg m^-2 d^-1 in the investigated sites and increased with eutrophic levels and temperature. H₂S and CS₂ were the dominant volatile sulfur compounds (VSCs) emitted from the lake. The CH₄ oxidation potential of water ranged from 2.1 to 14.9 μg h^-1 L^-1, which had positive correlations with trophic level index and the environmental variables except for the NH₄⁺-N concentration. Eutrophic levels could increase the abundances of bacteria and methanotrophs in lake water. α-Proteobacteria methanotroph Methylocystis was more abundant than γ-Proteobacteria methanotrophs in March and May, while the latter was more abundant in August and November. The relative abundance of Cyanobacteria, including Microcystis, A. granulata var. angustissima and Cyanobium had significantly positive correlations with temperature, turbidity, SO₄^2--S, and total sulfur. Partial least squares path modelling revealed that the algal growth could promote VSC emissions, which had a positive correlation with CH₄ oxidation potential, likely due to the positive correlation between the CH₄ and VSC emissions from lakes. These findings indicate that water eutrophication and algae growth could increase the emissions of CH₄ and VSCs from lakes. Controlling algae growth might be an effective way to mitigate the emissions of CH₄ and VSCs from freshwater lakes.

Occurrence and biodegradation of hydrocarbons at high salinities

Hypersaline environments are found around the world, above and below ground, and many are exposed to hydrocarbons on a continuous or a frequent basis. Some surface hypersaline environments are exposed to hydrocarbons because they have active petroleum seeps while others are exposed because of oil exploration and production, or nearby human activities. Many oil reservoirs overlie highly saline connate water, and some national oil reserves are stored in salt caverns. Surface hypersaline ecosystems contain consortia of halophilic and halotolerant microorganisms that decompose organic compounds including hydrocarbons, and subterranean ones are likely to contain the same. However, the rates and extents of hydrocarbon biodegradation are poorly understood in such ecosystems. Here we describe hypersaline environments potentially or likely to become contaminated with hydrocarbons, including perennial and transient environments above and below ground, and discuss what is known about the microbes degrading hydrocarbons and the extent of their activities. We also discuss what limits the microbial hydrocarbon degradation in hypersaline environments and whether there are opportunities for inhibiting (oil storage) or stimulating (oil spills) such biodegradation as the situation requires.

CH4 oxidation in a boreal lake during the development of hypolimnetic hypoxia

Freshwater ecosystems represent a significant natural source of methane (CH₄). CH₄ produced through anaerobic decomposition of organic matter (OM) in lake sediment and water column can be either oxidized to carbon dioxide (CO₂) by methanotrophic microbes or emitted to the atmosphere. While the role of CH₄ oxidation as a CH₄ sink is widely accepted, neither the magnitude nor the drivers behind CH₄ oxidation are well constrained. In this study, we aimed to gain more specific insight into CH₄ oxidation in the water column of a seasonally stratified, typical boreal lake, particularly under hypoxic conditions. We used ¹³CH₄ incubations to determine the active CH₄ oxidation sites and the potential CH₄ oxidation rates in the water column, and we measured environmental variables that could explain CH₄ oxidation in the water column. During hypolimnetic hypoxia, 91% of available CH₄ was oxidized in the active CH₄ oxidation zone, where the potential CH₄ oxidation rates gradually increased from the oxycline to the hypolimnion. Our results showed that in warm springs, which become more frequent, early thermal stratification with cold well-oxygenated hypolimnion delays the period of hypolimnetic hypoxia and limits CH₄ production. Thus, the delayed development of hypolimnetic hypoxia may partially counteract the expected increase in the lacustrine CH₄ emissions caused by the increasing organic carbon load from forested catchments.

Microbial mechanism underlying high and stable methane oxidation rates during mudflat reclamation with long-term rice cultivation: Illumina high-throughput sequencing-based data analysis

This study aimed to determine the methane oxidation rates (MOR), pmoA gene abundance and diversity, and microbial community composition using Illumina high-throughput sequencing. Mudflats located within Yancheng City, divided into different plots with 0-, 11-, and 20-year successive rice planting histories, were selected and sampled. The study found that the relative MOR (normalized with the 16S rRNA gene) increased dramatically after 11-year cultivation and remained stable in 20-year treatment, indicating that long-term rice cultivation in mudflats promoted MOR. The sequencing data analysis revealed that high MOR was related to the synergistic growth of methane-producing archaea (MPA) and aerobic and facultative methane-consuming bacteria (MCB) mainly belonging to Proteobacteria. Redundancy and correlation analyses showed that Methylophilaceae and Methylococcaceae affiliated within β- and γ-Proteobacterial methanotrophs were closely related to the relative MOR. Methane-oxidizing archaea (MOA) coupled to sulfate and nitrite reductions contributed more to the high and stable MOR compared with Proteobacterial MCB. Chloroflexi and Geobacter were the potential hydrogen donors for hydrogenotrophic MPA. The results showed that long-term rice cultivation in mudflats promoted the relative MOR. The unknown MOA coupled to sulfate and nitrite reductions, besides the necessary hydrogenotrophic MPA and their hydrogen donors (Chloroflexi and Geobacter) collectively contributed to methane cycling.

Eutrophication influences methanotrophic activity, abundance and community structure in freshwater lakes

Lake is an important natural source of methane, a potential greenhouse gas, in the atmosphere. Aerobic methanotrophs can consume a notable proportion of the methane produced in lacustrine ecosystems. However, previous studies mainly focused on aerobic methanotrophs in deep and oligotrophic lakes, while little is known about these organisms in shallow and eutrophic lakes. Lake eutrophication leads to more abundant substrates for methanogenesis, and a subsequent higher methane flux. Therefore, the methanotrophs in eutrophic lakes might play a more important role in mediating lacustrine methane emission. In the current study, aerobic methanotrophs in the sediments of two adjacent shallow freshwater lakes at different trophic status (mesotrophic and eutrophic, respectively) were investigated. Abundant methanotrophs and active aerobic methane oxidation were observed in both lakes. While the eutrophic lake harbored a higher abundance of methanotrophs. The result of pmoA-based high-throughput sequencing suggested that methanotrophic communities in the two studied lakes were dominated by unique groups (Type Ib and Type II), dependent on lake and season. But generally, eutrophication might lead to a higher proportion of Type II methanotrophs. The abundance and uniqueness of methanotrophic community could be attributed to lake eutrophication, and were regulated by environmental variables of both sediment and overlying water. This work provides a new insight towards methanotrophs in shallow freshwater lake impacted by eutrophication.

Microbial diversity associated with the anaerobic sediments of a soda lake (Mono Lake, California, USA)

Soda lakes are inhabited by important haloalkaliphilic microbial communities that are well adapted to these extreme characteristics. The surface waters of the haloalkaline Mono Lake (California, USA) are alkaline but, in contrast to its bottom waters, do not present high salinity. We have studied the microbiota present in the shoreline sediments of Mono Lake using next-generation sequencing techniques. The statistical indexes showed that Bacteria had a higher richness, diversity, and evenness than Archaea. Seventeen phyla and 8 “candidate divisions” were identified among the Bacteria, with a predominance of the phyla Firmicutes, Proteobacteria, and Bacteroidetes. Among the Proteobacteria, there was a notable presence of Rhodoplanes and a high diversity of sulfate-reducing Deltaproteobacteria, in accordance with the high sulfate-reducing activity detected in soda lakes. Numerous families of bacterial fermenters were identified among the Firmicutes. The Bacteroides were represented by several environmental groups that have not yet been isolated. Since final organic matter in anaerobic environments with high sulfate contents is mineralized mainly by sulfate-reducing bacteria, very little methanogenic archaeal biodiversity was detected. Only 2 genera, Methanocalculus and Methanosarcina, were retrieved. The species similarities described indicate that a significant number of the operational taxonomic units identified may represent new species.

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake

We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at five depths that captured the major redox zones of the lake during the onset of meromixis. The prokaryotic community was dominated by bacteria from the phyla Proteobacteria, Firmicutes, and Bacteroidetes, while the picoeukaryotic chlorophyte Picocystis dominated the eukaryotes. Most (80%) of the abundant (>1% relative abundance) OTUs recovered as amplicons of 16S rRNA genes have been reported in previous surveys, indicating that Mono Lake's microbial community has remained stable over 12 years that have included periods of regular, annual overturn interspersed by episodes of prolonged meromixis that result in extremely reducing conditions in bottom water. Metatranscriptomic sequences binned predominately to the Gammaproteobacteria genera Thioalkalivibrio (4–13%) and Thioalkalimicrobium (0–14%); and to the Firmicutes genera Dethiobacter (0–5%) and Clostridium (1–4%), which were also abundant in the 16S rRNA gene amplicon libraries. This study provides insight into the taxonomic affiliations of transcriptionally active communities of the lake's water column under different redox conditions.

Salinity Affects the Composition of the Aerobic Methanotroph Community in Alkaline Lake Sediments from the Tibetan Plateau

Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied. The quantitative PCR, terminal restriction fragment length polymorphism, and 454-pyrosequencing methods were used to target the pmoA genes. The pmoA gene copies ranged 10⁴-10⁶ per gram fresh sediment. Type I methanotrophs predominated in Tibetan lake sediments, with Methylobacter and uncultivated type Ib methanotrophs being dominant in freshwater lakes and Methylomicrobium in saline lakes. Combining the pmoA-pyrosequencing data from Tibetan lakes with other published pmoA-sequencing data from lake sediments of other regions, a significant salinity and alkalinity effect (P = 0.001) was detected, especially salinity, which explained ∼25% of methanotroph community variability. The main effect was Methylomicrobium being dominant (up to 100%) in saline lakes only. In freshwater lakes, however, methanotroph composition was relatively diverse, including Methylobacter, Methylocystis, and uncultured type Ib clusters. This study provides the first methanotroph data for high-altitude lake sediments (>4000 m) and shows that salinity is a driving factor for the community composition of aerobic methanotrophs.

Methane Oxidation and Molecular Characterization of Methanotrophs from a Former Mercury Mine Impoundment

The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO₂ with some CH₄ present. The δ¹³CH₄ value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively ¹²C-enriched CO₂ suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria. An enrichment culture was established that grew in an acidic (pH 4.5) medium via methane oxidation.

High phylogenetic diversity of glycosyl hydrolase family 10 and 11 xylanases in the sediment of Lake Dabusu in China

Soda lakes are one of the most stable naturally occurring alkaline and saline environments, which harbor abundant microorganisms with diverse functions. In this study, culture-independent molecular methods were used to explore the genetic diversity of glycoside hydrolase (GH) family 10 and GH11 xylanases in Lake Dabusu, a soda lake with a pH value of 10.2 and salinity of 10.1%. A total of 671 xylanase gene fragments were obtained, representing 78 distinct GH10 and 28 GH11 gene fragments respectively, with most of them having low homology with known sequences. Phylogenetic analysis revealed that the GH10 xylanase sequences mainly belonged to Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes and Verrucomicrobia, while the GH11 sequences mainly consisted of Actinobacteria, Firmicutes and Fungi. A full-length GH10 xylanase gene (xynAS10-66) was directly cloned and expressed in Escherichia coli, and the recombinant enzymes showed high activity at alkaline pH. These results suggest that xylanase gene diversity within Lake Dabusu is high and that most of the identified genes might be novel, indicating great potential for applications in industry and agriculture.

Changes in the planktonic microbial community during residence in a surface flow constructed wetland used for tertiary wastewater treatment

Suspended particles are a major constituent of municipal wastewater and generally contain high levels of bacteria, including human pathogens. Discharge of these particles of anthropogenic nature can have profound effects on receiving aquatic ecosystems and mitigation of these effects requires additional polishing of treated municipal wastewater. Previously it was shown that surface flow constructed wetlands are effective in improving water quality by reducing the numbers of fecal indicator organisms. However, fecal indicator organisms represent only a minor fraction of the total planktonic bacterial community and knowledge on the effects of these constructed wetlands on the composition and functioning of the entire planktonic bacterial community is limited. The aim of this descriptive study was therefore to identify changes in the planktonic bacterial community during residence of secondary treated municipal wastewater in a full-scale surface flow constructed wetland. To this purpose water samples were taken in which the bacterial community composition and functioning were analyzed using FISH, DGGE and BIOLOG. Surprisingly, the bacterial abundance at the inflow of the constructed wetland was relatively low compared with more natural surface waters. However, the inflowing bacterial community showed high metabolic activity and functional diversity. During residence in the surface flow constructed wetland the bacterial abundance doubled, but decreased in metabolic activity and functional diversity. Shifts in the community composition indicate that these changes are related to turn-over of the bacterial community. The planktonic bacterial community in the effluent of the constructed wetland closely resembled natural bacterial communities in urban and agricultural ditches. Based on these observations we conclude that constructed wetlands are capable to mitigate possible impacts of the particle load in treated wastewaters by transforming the anthropological bacterial community to a bacterial community resembling more "natural" surface waters.

Microbiology of Lonar Lake and other soda lakes

Soda lakes are saline and alkaline ecosystems that are believed to have existed throughout the geological record of Earth. They are widely distributed across the globe, but are highly abundant in terrestrial biomes such as deserts and steppes and in geologically interesting regions such as the East African Rift valley. The unusual geochemistry of these lakes supports the growth of an impressive array of microorganisms that are of ecological and economic importance. Haloalkaliphilic Bacteria and Archaea belonging to all major trophic groups have been described from many soda lakes, including lakes with exceptionally high levels of heavy metals. Lonar Lake is a soda lake that is centered at an unusual meteorite impact structure in the Deccan basalts in India and its key physicochemical and microbiological characteristics are highlighted in this article. The occurrence of diverse functional groups of microbes, such as methanogens, methanotrophs, phototrophs, denitrifiers, sulfur oxidizers, sulfate reducers and syntrophs in soda lakes, suggests that these habitats harbor complex microbial food webs that (a) interconnect various biological cycles via redox coupling and (b) impact on the production and consumption of greenhouse gases. Soda lake microorganisms harbor several biotechnologically relevant enzymes and biomolecules (for example, cellulases, amylases, ectoine) and there is the need to augment bioprospecting efforts in soda lake environments with new integrated approaches. Importantly, some saline and alkaline lake ecosystems around the world need to be protected from anthropogenic pressures that threaten their long-term existence.

Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane

Agriculture has marked impacts on the production of carbon dioxide (CO(2)) and consumption of methane (CH(4)) by microbial communities in upland soils-Earth's largest biological sink for atmospheric CH(4). To determine whether the diversity of microbes that catalyze the flux of these greenhouse gases is related to the magnitude and stability of these ecosystem-level processes, we conducted molecular surveys of CH(4)-oxidizing bacteria (methanotrophs) and total bacterial diversity across a range of land uses and measured the in situ flux of CH(4) and CO(2) at a site in the upper United States Midwest. Conversion of native lands to row-crop agriculture led to a sevenfold reduction in CH(4) consumption and a proportionate decrease in methanotroph diversity. Sites with the greatest stability in CH(4) consumption harbored the most methanotroph diversity. In fields abandoned from agriculture, the rate of CH(4) consumption increased with time along with the diversity of methanotrophs. Conversely, estimates of total bacterial diversity in soil were not related to the rate or stability of CO(2) emission. These combined results are consistent with the expectation that microbial diversity is a better predictor of the magnitude and stability of processes catalyzed by organisms with highly specialized metabolisms, like CH(4) oxidation, as compared with processes driven by widely distributed metabolic processes, like CO(2) production in heterotrophs. The data also suggest that managing lands to conserve or restore methanotroph diversity could mitigate the atmospheric concentrations of this potent greenhouse gas.

Temporal bacterial diversity and detection of putative methanotrophs in surface mats of Lonar crater lake

The phylogenetic diversity of bacterial communities in microbial mats of two different seasons from saline and hyperalkaline Lonar Lake was investigated using 16S rRNA gene library analysis. Arthrospira (Cyanobacteria) related clones (>80% of total clones) dominated libraries of both the seasons. Clear differences were found in both the seasons as the operational taxonomic units (OTUs) related to Fusibacter (LAI-1 and LAI-59) and Tindallia magadiensis (LAI-27) found in post-monsoon were not found in the pre-monsoon library. Likewise, OTUs related to Planococcus rifietensis (LAII-67), Bordetella hinzii (LAII-2) and Methylobacterium variabile (LAII-25) found in the pre-monsoon were not found in post-monsoon. The study was extended to identify methanotrophs in the surface mats. Libraries constructed with type I and type II methanotroph specific 16S rRNA gene primers showed the presence of clones (LAMI-99 and LAMII-2) closely related to Methylomicrobium buryaticum and Beijerinckiaceae family members. Denaturing gradient gel electrophoresis (DGGE) fingerprinting based on protein-coding genes (pmoA and mxaF) further confirmed the detection of Methylomicrobium sp. Hence, we report here for the first time the detection of putative methanotrophs in surface mats of Lonar Lake. The finding of clones related to organisms with interesting functional attributes such as assimilation of C(1) compounds (LAII-25, LAMI-39, LAMI-99 and LAMII-2), non-sulfur photosynthetic bacteria (LAMII-43) and clones distantly affiliated to organisms of heavily polluted environments (LAI-59 and LAMII-52), is of significant note. These preliminary results would direct future studies on the functional dynamics of microbial mat associated food web chain in the extreme environment.

Methanotrophs and copper

Methanotrophs, cells that consume methane (CH(4)) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH(4), the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH(4) to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH(4) fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH(4) oxidation by the particulate CH(4) monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs.

Diversity of methanotrophs in Zoige wetland soils under both anaerobic and aerobic conditions

Zoige wetland is one of the most important methane emission centers in China. The oxidation of methane in the wetland affects global warming, soil ecology and atmospheric chemistry. Despite their global significance, microorganisms that consume methane in Zoige wetland remain poorly characterized. In this study, we investigated methanotrophs diversity in soil samples from both anaerobic site and aerobic site in Zoige wetland using pmoA gene as a molecular marker. The cloning library was constructed according to the pmoA sequences detected. Four clusters of methanotrophs were detected. The phylogenetic tree showed that all four clusters detected were affiliated to type I methanotrophs. Two novel clusters (cluster 1, cluster 2) were found to relate to none of the recognized genera of methanotrophs. These clusters have no cultured representatives and reveal an ecological adaptation of particular uncultured methanotrophs in Zoige wetland. Two clusters were belonging to Methylobacter and Methylococcus separately. Denaturing gradient gel electrophoresis gel bands pattern retrieved from these two samples revealed that the community compositions of anaerobic soil and aerobic soil were different from each other while anaerobic soil showed a higher metanotrophs diversity. Real-time PCR assays of the two samples demonstrated that aerobic soil sample in Zoige wetland was 1.5 times as much copy numbers as anaerobic soil. These data illustrated that methanotrophs are a group of microorganisms influence the methane consumption in Zoige wetland.

Methanotrophs and methanotrophic activity in engineered landfill biocovers

The dynamics and changes in the potential activity and community structure of methanotrophs in landfill covers, as a function of time and depth were investigated. A passive methane oxidation biocover (PMOB-1) was constructed in St-Nicéphore MSW Landfill (Quebec, Canada). The most probable number (MPN) method was used for methanotroph counts, methanotrophic diversity was assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting of the pmoA gene and the potential CH(4) oxidation rate was determined using soil microcosms. Results of the PMOB-1 were compared with those obtained for the existing landfill cover (silty clay) or a reference soil (RS). During the monitoring period, changes in the number of methanotrophic bacteria in the PMOB-1 exhibited different developmental phases and significant variations with depth. In comparison, no observable changes over time occurred in the number of methanotrophs in the RS. The maximum counts measured in the uppermost layer was 1.5x10(9) cells g dw(-1) for the PMOB-1 and 1.6x10(8) cells g dw(-1) for the RS. No distinct difference was observed in the methanotroph diversity in the PMOB-1 or RS. As expected, the potential methane oxidation rate was higher in the PMOB-1 than in the RS. The maximum potential rates were 441.1 and 76.0 microg CH(4) h(-1) g dw(-1) in the PMOB and RS, respectively. From these results, the PMOB was found to be a good technology to enhance methane oxidation, as its performance was clearly better than the starting soil that was present in the landfill site.

Abundance and activity of methanotrophic bacteria in littoral and profundal sediments of lake constance (Germany)

The abundances and activities of aerobic methane-oxidizing bacteria (MOB) were compared in depth profiles of littoral and profundal sediments of Lake Constance, Germany. Abundances were determined by quantitative PCR (qPCR) targeting the pmoA gene and by fluorescence in situ hybridization (FISH), and data were compared to methane oxidation rates calculated from high-resolution concentration profiles. qPCR using type I MOB-specific pmoA primers indicated that type I MOB represented a major proportion in both sediments at all depths. FISH indicated that in both sediments, type I MOB outnumbered type II MOB at least fourfold. Results obtained with both techniques indicated that in the littoral sediment, the highest numbers of methanotrophs were found at a depth of 2 to 3 cm, corresponding to the zone of highest methane oxidation activity, although no oxygen could be detected in this zone. In the profundal sediment, highest methane oxidation activities were found at a depth of 1 to 2 cm, while MOB abundance decreased gradually with sediment depth. In both sediments, MOB were also present at high numbers in deeper sediment layers where no methane oxidation activity could be observed.

Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway

Deep-water coral reefs are seafloor environments with diverse biological communities surrounded by cold permanent darkness. Sources of energy and carbon for the nourishment of these reefs are presently unclear. We investigated one aspect of the food web using DNA stable-isotope probing (DNA-SIP). Sediment from beneath a Lophelia pertusa reef off the coast of Norway was incubated until assimilation of 5 micromol 13CH4 g(-1) wet weight occurred. Extracted DNA was separated into 'light' and 'heavy' fractions for analysis of labelling. Bacterial community fingerprinting of PCR-amplified 16S rRNA gene fragments revealed two predominant 13C-specific bands. Sequencing of these bands indicated that carbon from 13CH4 had been assimilated by a Methylomicrobium and an uncultivated member of the Gammaproteobacteria. Cloning and sequencing of 16S rRNA genes from the heavy DNA, in addition to genes encoding particulate methane monooxygenase and methanol dehydrogenase, all linked Methylomicrobium with methane metabolism. Putative cross-feeders were affiliated with Methylophaga (Gammaproteobacteria), Hyphomicrobium (Alphaproteobacteria) and previously unrecognized methylotrophs of the Gammaproteobacteria, Alphaproteobacteria, Deferribacteres and Bacteroidetes. This first marine methane SIP study provides evidence for the presence of methylotrophs that participate in sediment food webs associated with deep-water coral reefs.

Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing

A considerable amount of methane produced during decomposition of landfill waste can be oxidized in landfill cover soil by methane-oxidizing bacteria (methanotrophs) thus reducing greenhouse gas emissions to the atmosphere. The identity of active methanotrophs in Roscommon landfill cover soil, a slightly acidic peat soil, was assessed by DNA-stable isotope probing (SIP). Landfill cover soil slurries were incubated with (13)C-labelled methane and under either nutrient-rich nitrate mineral salt medium or water. The identity of active methanotrophs was revealed by analysis of (13)C-labelled DNA fractions. The diversity of functional genes (pmoA and mmoX) and 16S rRNA genes was analyzed using clone libraries, microarrays and denaturing gradient gel electrophoresis. 16S rRNA gene analysis revealed that the cover soil was mainly dominated by Type II methanotrophs closely related to the genera Methylocella and Methylocapsa and to Methylocystis species. These results were supported by analysis of mmoX genes in (13)C-DNA. Analysis of pmoA gene diversity indicated that a significant proportion of active bacteria were also closely related to the Type I methanotrophs, Methylobacter and Methylomonas species. Environmental conditions in the slightly acidic peat soil from Roscommon landfill cover allow establishment of both Type I and Type II methanotrophs.

Methylosoma difficile gen. nov., sp. nov., a novel methanotroph enriched by gradient cultivation from littoral sediment of Lake Constance

A novel methanotroph, strain LC 2(T), was isolated from the littoral sediment of Lake Constance by enrichment in opposing gradients of methane and oxygen, followed by traditional isolation methods. Strain LC 2(T) grows on methane or methanol as its sole carbon and energy source. It is a Gram-negative, non-motile, pale-pink-coloured methanotroph showing typical intracytoplasmic membranes arranged in stacks. Cells are coccoid, elliptical or rod-shaped and occur often in pairs. Strain LC 2(T) grows at low oxygen concentrations and in counter-gradients of methane and oxygen. It can grow on medium free of bound nitrogen, possesses the nifH gene and fixes atmospheric nitrogen at low oxygen pressure. It grows at neutral pH and at temperatures between 10 and 30 degrees C. Phylogenetically, it is most closely related to the genus Methylobacter, with the type strains of Methylobacter tundripaludum and Methylobacter psychrophilus showing 94 and 93.4 % 16S rRNA gene sequence similarity, respectively. Furthermore, the pmoA gene sequence of strain LC 2(T) is most closely related to pmoA gene sequences of Methylobacter strains (92 % similar to Methylobacter sp. LW 12 by deduced amino acid sequence identity). The DNA G+C content is 49.9 mol% and the major cellular fatty acid is 16 : 1omega7c (60 %). Strain LC 2(T) (=JCM 14076(T)=DSM 18750(T)) is described as the type strain of a novel species within a new genus, Methylosoma difficile gen. nov., sp. nov.

Alkalilimnicola ehrlichii sp. nov., a novel, arsenite-oxidizing haloalkaliphilic gammaproteobacterium capable of chemoautotrophic or heterotrophic growth with nitrate or oxygen as the electron acceptor

A facultative chemoautotrophic bacterium, strain MLHE-1T, was isolated from Mono Lake, an alkaline hypersaline soda lake in California, USA. Cells of strain MLHE-1T were Gram-negative, short motile rods that grew with inorganic electron donors (arsenite, hydrogen, sulfide or thiosulfate) coupled with the reduction of nitrate to nitrite. No aerobic growth was attained with arsenite or sulfide, but hydrogen sustained both aerobic and anaerobic growth. No growth occurred when nitrite or nitrous oxide was substituted for nitrate. Heterotrophic growth was observed under aerobic and anaerobic (nitrate) conditions. Cells of strain MLHE-1T could oxidize but not grow on CO, while CH4 neither supported growth nor was it oxidized. When grown chemoautotrophically, strain MLHE-1T assimilated inorganic carbon via the Calvin–Benson–Bassham reductive pentose phosphate pathway, with the activity of ribulose 1,5-bisphosphate carboxylase (RuBisCO) functioning optimally at 0.1 M NaCl and at pH 7.3. Strain MLHE-1T grew over broad ranges of pH (7.3–10.0; optimum, 9.3), salinity (15–190 g l−1; optimum 30 g l−1) and temperature (13–40 °C; optimum, 30 °C). Phylogenetic analysis of 16S rRNA gene sequences placed strain MLHE-1T in the class Gammaproteobacteria (family Ectothiorhodospiraceae) and most closely related to Alkalispirillum mobile (98.5 %) and Alkalilimnicola halodurans (98.6 %), although none of these three haloalkaliphilic micro-organisms were capable of photoautotrophic growth and only strain MLHE-1T was able to oxidize As(III). On the basis of physiological characteristics and DNA–DNA hybridization data, it is suggested that strain MLHE-1T represents a novel species within the genus Alkalilimnicola for which the name Alkalilimnicola ehrlichii is proposed. The type strain is MLHE-1T (=DSM 17681T=ATCC BAA-1101T). Aspects of the annotated full genome of Alkalilimnicola ehrlichii are discussed in the light of its physiology.

Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico

Methanotrophs are ubiquitous in soil, fresh water and the open ocean, but have not been well characterized in deep-sea hydrocarbon seeps and gas hydrates, where methane is unusually abundant. Here we report the presence of new functional genes for the aerobic oxidation of methane by methanotrophs in marine sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico. Samples were collected from two hydrate locations (GC185 and GC234): one hydrocarbon-seep location at a brine pool (GC233) and one background-marine location about 1.2 miles north of the brine pool (NBP). Community DNA was extracted from each location to establish clone libraries for the pmoA functional gene using a PCR-based cloning approach. Three hundred and ninety clones were screened by sequencing and 46 operational taxonomic units were obtained. Eight operational taxonomic units were present in every sample; one of them was predominant and accounted for 22.8-25.3% of each clone library. Principal-component analysis indicated that samples GC185 and GC234 were closely related and, along with GC233, were significantly different from NBP. These results indicate that methanotrophic communities may be similarly impacted by hydrocarbons at the gas-hydrate and seep sites, and can be distinguished from methanotrophic communities in the normal marine sediment. Furthermore, cluster analysis showed that 84.8% of operational taxonomic units from all samples formed distinct clusters, which could not be grouped with any published pmoA sequences, indicating that a considerable number of novel methanotrophic species may exist in the Gulf of Mexico.

Cultivation of methanotrophic bacteria in opposing gradients of methane and oxygen

In sediments, methane-oxidizing bacteria live in opposing gradients of methane and oxygen. In such a gradient system, the fluxes of methane and oxygen are controlled by diffusion and consumption rates, and the rate-limiting substrate is maintained at a minimum concentration at the layer of consumption. Opposing gradients of methane and oxygen were mimicked in a specific cultivation set-up in which growth of methanotrophic bacteria occurred as a sharp band at either c. 5 or 20 mm below the air-exposed end. Two new strains of methanotrophic bacteria were isolated with this system. One isolate, strain LC 1, belonged to the Methylomonas genus (type I methantroph) and contained soluble methane mono-oxygenase. Another isolate, strain LC 2, was related to the Methylobacter group (type I methantroph), as determined by 16S rRNA gene and pmoA sequence similarities. However, the partial pmoA sequence was only 86% related to cultured Methylobacter species. This strain accumulated significant amounts of formaldehyde in conventional cultivation with methane and oxygen, which may explain why it is preferentially enriched in a gradient cultivation system.