First genome data from uncultured upland soil cluster alpha methanotrophs provide further evidence for a close phylogenetic relationship to Methylocapsa acidiphila B2 and for high-affinity methanotrophy involving particulate methane monooxygenase

Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications

Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH₄ ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH₄ , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH₄ monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.

Unique high Arctic methane metabolizing community revealed through in situ 13CH4-DNA-SIP enrichment in concert with genome binning

Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.

Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations

Termite mounds have recently been confirmed to mitigate approximately half of termite methane (CH4) emissions, but the aerobic CH4 oxidising bacteria (methanotrophs) responsible for this consumption have not been resolved. Here, we describe the abundance, composition and CH4 oxidation kinetics of the methanotroph communities in the mounds of three distinct termite species sampled from Northern Australia. Results from three independent methods employed show that methanotrophs are rare members of microbial communities in termite mounds, with a comparable abundance but distinct composition to those of adjoining soil samples. Across all mounds, the most abundant and prevalent methane monooxygenase sequences were affiliated with upland soil cluster α (USCα), with sequences homologous to Methylocystis and tropical upland soil cluster (TUSC) also detected. The reconstruction of a metagenome-assembled genome of a mound USCα representative highlighted the metabolic capabilities of this group of methanotrophs. The apparent Michaelis-Menten kinetics of CH4 oxidation in mounds were estimated from in situ reaction rates. Methane affinities of the communities were in the low micromolar range, which is one to two orders of magnitude higher than those of upland soils, but significantly lower than those measured in soils with a large CH4 source such as landfill cover soils. The rate constant of CH4 oxidation, as well as the porosity of the mound material, were significantly positively correlated with the abundance of methanotroph communities of termite mounds. We conclude that termite-derived CH4 emissions have selected for distinct methanotroph communities that are kinetically adapted to elevated CH4 concentrations. However, factors other than substrate concentration appear to limit methanotroph abundance and hence these bacteria only partially mitigate termite-derived CH4 emissions. Our results also highlight the predominant role of USCα in an environment with elevated CH4 concentrations and suggest a higher functional diversity within this group than previously recognised.

Sulfide restrains the growth of Methylocapsa acidiphila converting renewable biogas to single cell protein

Methane-oxidizing bacteria (MOB) that can use biogas and recycled nitrogen from wastewater as a sustainable feedstock for single cell protein (SCP) synthesis are receiving increasing attention. Though promising, limited knowledge is available on the alternative strains especially the ones that can tolerant to strict environments such as acidic conditions. Furthermore, how would the hydrogen sulfide affect the MOB (especially the alternative strains) for SCP synthesis when crude biogas is used as feedstock is still unknown. In this study, the capability of an acidic-tolerant methanotrophic bacterium Methylocapsa acidiphila for SCP production using raw biogas and the associated inhibitory effect of sulfide on the bioconversion was for the first time investigated. Results showed that the inhibitory effect of sulfide on the growth of M. acidiphila was observed starting from 8.13 mg L^-1 Na₂S (equivalent to approximately 1000 ppm of H₂S in crude biogas). The total amino acid content in the dry biomass decreased more than two times due to sulfide inhibition compared with the control samples without the presence of sulfide (585.96 mg/g dry biomass), while the proportion of essential amino acids in the total amino acid was not affected when the concentration of Na₂S was lower than 5.73 mg L^-1. The performance of M. acidiphila in a sulfide-rich environment was further studied at different operational conditions. The feeding gas with a CH₄/O₂ ratio of 6:4 could help to alleviate the sulfide inhibition, compared with other ratios (4:6 and 8:2). Moreover, the sequential supply of the feed gas could also alleviate sulfide inhibition. In addition, the MOB's growth rate was higher when applying a higher mixing rate of 120 rpm, compared with 70 rpm and 0, due to a better gas-liquid mass transfer. The inoculum size of 20% and 10% resulted in a faster growth rate compared with the 5%. Furthermore, M. acidiphila could assimilate either NH₄⁺ or NO₃^- as nitrogen source with a similar growth rate, giving it the potential to recycle nitrogen from a wide range of wastewaters. The results will not only create new knowledge for better understanding the role of hydrogen sulfide in the assimilation of raw biogas by acid-tolerant M. acidiphila but also provide technical insights into the development of an efficient and robust process for the waste-to-protein conversion.

Widespread soil bacterium that oxidizes atmospheric methane

The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and 13C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2 Its estimated specific affinity for CH4 (a0s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

Methanotrophy across a natural permafrost thaw environment

The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ¹³C-CH₄ isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.

The hunt for the most-wanted chemolithoautotrophic spookmicrobes

Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane-Oxidizing Upland Soil Cluster α

Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. The 16S rRNA gene sequence recovered was distinctive and suggests this crucial group as a new genus within the Beijerinckiaceae, close to Methylocapsa. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high-affinity activity of methane oxidation to USCα cells in situ. Analysis of the global biogeography of this group further revealed its presence in previously unrecognized habitats, such as subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane.

Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows

The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.

An active atmospheric methane sink in high Arctic mineral cryosols

Methane (CH4) emission by carbon-rich cryosols at the high latitudes in Northern Hemisphere has been studied extensively. In contrast, data on the CH4 emission potential of carbon-poor cryosols is limited, despite their spatial predominance. This work employs CH4 flux measurements in the field and under laboratory conditions to show that the mineral cryosols at Axel Heiberg Island in the Canadian high Arctic consistently consume atmospheric CH4. Omics analyses present the first molecular evidence of active atmospheric CH4-oxidizing bacteria (atmMOB) in permafrost-affected cryosols, with the prevalent atmMOB genotype in our acidic mineral cryosols being closely related to Upland Soil Cluster α. The atmospheric (atm) CH4 uptake at the study site increases with ground temperature between 0 °C and 18 °C. Consequently, the atm CH4 sink strength is predicted to increase by a factor of 5-30 as the Arctic warms by 5-15 °C over a century. We demonstrate that acidic mineral cryosols are a previously unrecognized potential of CH4 sink that requires further investigation to determine its potential impact on larger scales. This study also calls attention to the poleward distribution of atmMOB, as well as to the potential influence of microbial atm CH4 oxidation, in the context of regional CH4 flux models and global warming.

Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils

The oxidation of atmospheric CH₄ in upland soils is mostly mediated by uncultivated groups of microorganisms that have been identified solely by molecular markers, such as the sequence of the pmoA gene encoding the β-subunit of the particulate methane monooxygenase enzyme. The objective of this work was to compare the activity and diversity of methanotrophs in Amazonian Dark Earth soil (ADE, Hortic Anthrosol) and their adjacent non-anthropic soil. Secondly, the effect of land use in the form of manioc cultivation was examined by comparing secondary forest and plantation soils. CH₄ oxidation potentials were measured and the structure of the methanotroph communities assessed by quantitative PCR (qPCR) and amplicon pyrosequencing of pmoA genes. The oxidation potentials at low CH₄ concentrations (10 ppm of volume) were relatively high in all the secondary forest sites of both ADE and adjacent soils. CH₄ oxidation by the ADE soil only recently converted to a manioc plantation was also relatively high. In contrast, both the adjacent soils used for manioc cultivation and the ADE soil with a long history of agriculture displayed lower CH₄ uptake rates. Amplicon pyrosequencing of pmoA genes indicated that USCα, Methylocystis and the tropical upland soil cluster (TUSC) were the dominant groups depending on the site. By qPCR analysis it was found that USCα pmoA genes, which are believed to belong to atmospheric CH₄ oxidizers, were more abundant in ADE than adjacent soil. USCα pmoA genes were abundant in both forested and cultivated ADE soil, but were below the qPCR detection limit in manioc plantations of adjacent soil. The results indicate that ADE soils can harbor high abundances of atmospheric CH₄ oxidizers and are potential CH₄ sinks, but as in other upland soils this activity can be inhibited by the conversion of forest to agricultural plantations.

Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USCα clade

Forest soils are a major biological sink for atmospheric methane, yet the identity and physiology of the microorganisms responsible for this process remain unclear. Although members of the upland soil cluster α (USCα) are assumed to represent methanotrophic bacteria adapted to the oxidation of the trace level of methane in the atmosphere and to be an important sink of this greenhouse gas, so far they have resisted isolation. In particular, the question of whether the atmospheric methane oxidizers are able to obtain all their energy and carbon solely from atmospheric methane still waits to be answered. In this study, we performed stable-isotope probing (SIP) of RNA and DNA to investigate the assimilation of (13) C-methane and (13) C-acetate by USCα in an acidic forest soil. RNA-SIP showed that pmoA mRNA of USCα was not labelled by (13) C of supplemented (13) C methane, although catalysed reporter deposition - fluorescence in situ hybridization (CARD-FISH) targeting pmoA mRNA of USCα detected its expression in the incubated soil. In contrast, incorporation of (13) C-acetate into USCαpmoA mRNA was observed. USCαpmoA genes were not labelled, indicating that they had not grown during the incubation. Our results indicate that the contribution of alternative carbon sources, such as acetate, to the metabolism of the putative atmospheric methane oxidizers in upland forest soils might be substantial.

When metagenomics meets stable-isotope probing: progress and perspectives

The application of metagenomics, the culture-independent capture and subsequent analysis of genomic DNA from the environment, has greatly expanded our knowledge of the diversity of microbes and microbial protein families; however, the metabolic functions of many microorganisms remain largely unknown. DNA stable-isotope probing (DNA-SIP) is a recently developed method in which the incorporation of stable isotope from a labelled substrate is used to identify the function of microorganisms in the environment. The technique has now been used in conjunction with metagenomics to establish links between microbial identity and particular metabolic functions. The combination of DNA-SIP and metagenomics not only permits the detection of rare low-abundance species from metagenomic libraries but also facilitates the detection of novel enzymes and bioactive compounds.

The global methane cycle: recent advances in understanding the microbial processes involved

The global budget of atmospheric CH4 , which is on the order of 500-600 Tg CH4 per year, is mainly the result of environmental microbial processes, such as archaeal methanogenesis in wetlands, rice fields, ruminant and termite digestive systems and of microbial methane oxidation under anoxic and oxic conditions. This review highlights recent progress in the research of anaerobic CH4 oxidation, of CH4 production in the plant rhizosphere, of CH4 serving as substrate for the aquatic trophic food chain and the discovery of novel aerobic methanotrophs. It also emphasizes progress and deficiencies in our knowledge of microbial utilization of low atmospheric CH4 concentrations in soil, CH4 production in the plant canopy, intestinal methanogenesis and CH4 production in pelagic water.

The quest for atmospheric methane oxidizers in forest soils

Aerobic methanotrophs in forest soils are the largest biological sink for atmospheric methane (CH4 ). Community structures in 53 soils from Europe, Russia, North and South America, Asia and New Zealand located in boreal, temperate and tropical forests were analysed and maximal abundances of 2.1 × 10(7) methanotrophs g(-1)   DW were measured. In acidic soils, the most frequently detected pmoA genotypes were Upland Soil Cluster α (USCα) and Methylocystis spp. Phospholipid fatty acids that were labelled by consumption of (14/13) CH4 suggested the activity of type II methanotrophs. Cluster 1 (Methylocystaceae), USCγ and Methylocystis spp. were frequently detected genotypes in pH-neutral soils. Genotypes with ambiguous functional affiliation were co-detected (Clusters MR1, RA21, 2) and may represent aerobic methanotrophs, ammonia oxidizers or enzymes with an unknown function. The physiological traits of atmospheric CH4 oxidizers are largely unknown because organisms possessing the key forest soil pmoA genotypes (USCα, USCγ, Cluster 1) have not been cultivated. Some methanotrophic strains belonging to the family Methylocystaceae have been shown to oxidize CH4 at atmospheric mixing ratios. Methylocystis strain SC2 was found to have an alternative particulate CH4 monooxygenase responsible for CH4 oxidation at atmospheric mixing ratios. pH, forest type and temperature might be environmental factors that shape methanotrophic communities in forest soils. However, specific effects on individual species are largely unknown, and only a limited number of studies have addressed environmental controls of methanotrophic diversity, pointing to the need for future research in this area.

Links between methanotroph community composition and CH oxidation in a pine forest soil

The main gap in our knowledge about what determines the rate of CH(4) oxidation in forest soils is the biology of the microorganisms involved, the identity of which remains unclear. In this study, we used stable-isotope probing (SIP) following (13)CH(4) incorporation into phospholipid fatty acids (PLFAs) and DNA/RNA, and sequencing of methane mono-oxygenase (pmoA) genes, to identify the influence of variation in community composition on CH(4) oxidation rates. The rates of (13)C incorporation into PLFAs differed between horizons, with low (13)C incorporation in the organic soil and relatively high (13)C incorporation into the two mineral horizons. The microbial community composition of the methanotrophs incorporating the (13)C label also differed between horizons, and statistical analyses suggested that the methanotroph community composition was a major cause of variation in CH(4) oxidation rates. Both PLFA and pmoA-based data indicated that CH(4) oxidizers in this soil belong to the uncultivated 'upland soil cluster alpha'. CH(4) oxidation potential exhibited the opposite pattern to (13)C incorporation, suggesting that CH(4) oxidation potential assays may correlate poorly with in situ oxidation rates. The DNA/RNA-SIP assay was not successful, most likely due to insufficient (13)C-incorporation into DNA/RNA. The limitations of the technique are briefly discussed.

Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the Lena Delta, Siberia

With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.

Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands

Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

Soluble and particulate methane monooxygenase gene clusters in the marine methanotroph Methylomicrobium sp. strain NI

Soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO) gene clusters in the marine methanotroph Methylomicrobium sp. strain NI were completely sequenced and analysed. Degenerated primers were newly designed and used to amplify the gene fragments containing intergenic mmoX-Y and mmoD-C regions and a partial pmoC region. Phylogenetic analysis of amino acid sequences deduced from mmoX and pmoA, as well as of 16S rRNA gene sequences, indicated that this strain was most closely related to the halotolerant methanotroph Methylomicrobium buryatense. There were putative sigma(54)- and sigma(70)-dependent promoter sequences upstream of the sMMO and pMMO genes, respectively, and mmoG, which is known to be related to the expression and assembly of sMMO, existed downstream of the sMMO genes. These findings suggest that the major components and regulation of MMOs in this marine methanotroph are quite similar to those in freshwater methane oxidizers, despite the difference in their habitats.

Diversity of the active methanotrophic community in acidic peatlands as assessed by mRNA and SIP-PLFA analyses

The active methanotroph community was investigated for the first time in heather (Calluna)-covered moorlands and Sphagnum/Eriophorum-covered UK peatlands. Direct extraction of mRNA from these soils facilitated detection of expression of methane monooxygenase genes, which revealed that particulate methane monooxygenase and not soluble methane monooxygenase was probably responsible for CH(4) oxidation in situ, because only pmoA transcripts (encoding a subunit of particulate methane monooxygenase) were readily detectable. Differences in methanotroph community structures were observed between the Calluna-covered moorland and Sphagnum/Eriophorum-covered gully habitats. As with many other Sphagnum-covered peatlands, the Sphagnum/Eriophorum-covered gullies were dominated by Methylocystis. Methylocella and Methylocapsa-related species were also present. Methylobacter-related species were found as demonstrated by the use of a pmoA-based diagnostic microarray. In Calluna-covered moorlands, in addition to Methylocella and Methylocystis, a unique group of peat-associated type I methanotrophs (Gammaproteobacteria) and a group of uncultivated type II methanotrophs (Alphaproteobacteria) were also found. The pmoA sequences of the latter were only distantly related to Methylocapsa and also to the RA-14 group of methanotrophs, which are believed to be involved in oxidation of atmospheric concentrations of CH(4). Soil samples were also labelled with (13)CH(4), and subsequent analysis of the (13)C-labelled phospholipid fatty acids (PLFAs) showed that 16:1 omega 7, 18:1 omega 7 and 18:1 omega 9 were the major labelled PLFAs. The presence of (13)C-labelled 18:1 omega 9, which was not a major PLFA of any extant methanotrophs, indicated the presence of novel methanotrophs in this peatland.

Molecular characterization of methanotrophic communities in forest soils that consume atmospheric methane

Methanotroph abundance was analyzed in control and long-term nitrogen-amended pine and hardwood soils using rRNA-targeted quantitative hybridization. Family-specific 16S rRNA and pmoA/amoA genes were analyzed via PCR-directed assays to elucidate methanotrophic bacteria inhabiting soils undergoing atmospheric methane consumption. Quantitative hybridizations suggested methanotrophs related to the family Methylocystaceae were one order of magnitude more abundant than Methyloccocaceae and more sensitive to nitrogen-addition in pine soils. 16S rRNA gene phylotypes related to known Methylocystaceae and acidophilic methanotrophs and pmoA/amoA gene sequences, including three related to the upland soil cluster Alphaproteobacteria (USCalpha) group, were detected across different treatments and soil depths. Our results suggest that methanotrophic members of the Methylocystaceae and Beijerinckiaceae may be the candidates for soil atmospheric methane consumption.

Novel facultative anaerobic acidotolerant Telmatospirillum siberiense gen. nov. sp. nov. isolated from mesotrophic fen

Three facultative anaerobic acidotolerant Gram-negative motile spirilla strains designated 26-4b1, 26-2 and K-1 were isolated from mesotrophic Siberian fen as a component of methanogenic consortia. The isolates were found to grow chemoorganotrophically on several organic acids and glucose under anoxic and low oxygen pressure in the dark, tolerant up to 5kPa of oxygen. At low oxygen supply, faint autotrophic growth on the H(2):CO(2) mixture was also observed. All three isolates were able to fix N(2). Major cellular fatty acids were 18:1 omega7c, 17:0 cyclopropane and 16:0. Phylogenetic analyses of the 16S rRNA gene sequences revealed that they formed a deep branch within the family Rhodospirillaceae of the Alphaproteobacteria with the highest similarity of 90.9-92.5% with members of genera Phaeospirillum and Magnetospirillum. Phylogenetic study of nifH (nitrogenase) and cbbL (RuBisCO) amino acid sequence identities confirmed that the new isolates represent a novel group. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strains 26-4b1, 26-2 and K-1 represent a new species of a novel genus for which the name Telmatospirillum siberiense gen. nov. sp. nov. is proposed.