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Claudia Luke - One of the best experts on this subject based on the ideXlab platform.
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methylotetracoccus oryzae strain c50c1 is a novel type ib gammaproteobacterial methanotroph adapted to freshwater environments
mSphere, 2019Co-Authors: Mohammad Ghashghavi, P. Frenzel, Daan R Speth, Paul L. E. Bodelier, Svetlana E. Belova, Sebastian Lucker, Claudia LukeAbstract:Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial Methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II Methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib Methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib Methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib Methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "Methylotetracoccus oryzae" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C 16:1 ω9c as the major membrane phospholipid fatty acid, which has not been found in other Methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.
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gammaproteobacterial Methanotrophs dominate cold methane seeps in floodplains of west siberian rivers
Applied and Environmental Microbiology, 2014Co-Authors: Igor Y Oshkin, Claudia Luke, Werner Liesack, Carleric Wegner, M V Glagolev, I V Filippov, Nikolay Pimenov, Svetlana N. DedyshAbstract:A complex system of muddy fluid-discharging and methane (CH4)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH4 h−1, while some seeps emitted up to 5.54 g CH4 h−1. The δ13C value of methane released from these seeps varied between −71.1 and −71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH4 ml−1 day−1) were measured in mud samples. Fluorescence in situ hybridization detected 107 methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of Methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting Methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant Methanotrophs, thereby providing a challenge for future isolation studies.
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macroecology of methane oxidizing bacteria the β diversity of pmoa genotypes in tropical and subtropical rice paddies
Environmental Microbiology, 2014Co-Authors: Claudia Luke, Peter Frenzel, Dian Fiantis, Peter Schad, Bellinda Schneider, Lorenz Schwark, Sri Rahayu UtamiAbstract:Studies addressing microbial biogeography have increased during the past decade, but research on microbial distribution patterns is still in its infancies, and many aspects are only poorly understood. Here, we compared the methanotroph community in paddy soils sampled in Indonesia, Vietnam, China and Italy, focusing on the distance-decay relationship. We used the pmoA gene as marker for methanotroph diversity in terminal restriction fragment length polymorphism, microarray and pyrosequencing approaches. We could observe a significant increase of -diversity with geographical distance across continents (12000km). Measured environmental parameters explained only a small amount of data variation, and we found no evidence for dispersal limitation. Thus, we propose historical contingencies being responsible for the observed patterns. Furthermore, we performed an in-depth analysis of type II methanotroph pmoA distribution at the sequence level. We used ordination analysis to project sequence dissimilarities into a three-dimensional space (multidimensional scaling). The ordination suggests that type II Methanotrophs in paddy fields can be divided into five major groups. However, these groups were found to be distributed in all soils independent of the geographic origin. By including tropical field sites (Indonesia and Vietnam) into the analysis, we further observed the first paddy fields harbouring a methanotroph community depleted in type II Methanotrophs.
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aerobic methanotroph diversity in riganqiao peatlands on the qinghai tibetan plateau
Environmental Microbiology Reports, 2013Co-Authors: Claudia Luke, Yongcui Deng, Marc G DumontAbstract:Summary The Zoige Plateau is characterized by its high altitude, low latitude and low annual mean temperature of approximately 1°C and is a major source of atmos- pheric methane in the Qinghai-Tibetan Plateau. Meth- anotrophs play an important role in the global cycling of CH 4 , but the diversity, identity and activity of meth- anotrophs in this region are poorly characterized. Soils were collected from hummocks and hollows in the Riganqiao peatland and the methanotroph com- munity was analysed by qPCR and sequencing methane monooxygenase (pmoAandmmoX) genes. ThepmoAgenes ranged between 10 7 and 10 8 cop- ies g -1 fresh soil, with a somewhat greater abundance in hummocks than hollows. ThepmoAgenes were analysed by amplicon pyrosequencing and themmoX genes by cloning and sequencing.Methylocystis species were found to be the most abundant meth- anotrophs, but numerous clades were present includ- ing three novelpmoAand three novelmmoXclusters. There were differences between the methanotroph communities in the hummocks and hollows, with the most significant being an increased abundance of uncultivated type Ib Methanotrophs in the hollows. The results indicate that aerobic Methanotrophs are abundant in Riganqiao peatland and include previ- ously undetected clades in this geographically iso- lated and distinctive environment.
Jeremy D Semrau - One of the best experts on this subject based on the ideXlab platform.
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the origin of aerobic methanotrophy within the proteobacteria
Fems Microbiology Letters, 2019Co-Authors: Christina S Kang, Peter F. Dunfield, Jeremy D SemrauAbstract:: Aerobic Methanotrophs play critical roles in the global carbon cycle, but despite their environmental ubiquity, they are phylogenetically restricted. Via bioinformatic analyses, it is shown that methanotrophy likely arose from methylotrophy from the lateral gene transfer of either of the two known forms of methane monooxygenase (particulate and soluble methane monooxygenases). Moreover, it appears that both known forms of pyrroloquinoline quinone-dependent methanol dehydrogenase (MeDH) found in Methanotrophs-the calcium-containing Mxa-MeDH and the rare earth element-containing Xox-MeDH-were likely encoded in the genomes before the acquisition of the methane monooxygenases (MMOs), but that some Methanotrophs subsequently received an additional copy of Xox-MeDH-encoding genes via lateral gene transfer. Further, data are presented that indicate the evolution of methanotrophy from methylotrophy not only required lateral transfer of genes encoding for methane monooxygenases, but also likely the pre-existence of a means of collecting copper. Given the emerging interest in valorizing methane via biological platforms, it is recommended that future strategies for heterologous expression of methane monooxygenase for conversion of methane to methanol also include cloning of genes encoding mechanism(s) of copper uptake, especially for expression of particulate methane monooxygenase.
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methanotrophy environmental industrial and medical applications
Current Issues in Molecular Biology, 2019Co-Authors: Jeremy D Semrau, Alan A. DispiritoAbstract:Aerobic Methanotrophs are an intriguing group of microbes with the singular ability to consume methane as their sole source of carbon and energy. As such, Methanotrophs are receiving increased attention to control methane emissions to limit future climate change. Methanotrophs have a wide range of other applications, including pollutant remediation and methane valorization (e.g. conversion of methane to protein, bioplastics, and biodiesel amongst other products). Methanotrophs also produce a novel copper-binding compound, methanobactin, that has significant potential for the treatment of copper-related human pathologies. Here we provide an overview of aerobic methanotrophy, describe current and future applications of these unique microbes, as well as discuss various strategies one can consider to better realize the opportunities these microbes present.
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bioremediation via methanotrophy overview of recent findings and suggestions for future research
Frontiers in Microbiology, 2011Co-Authors: Jeremy D SemrauAbstract:Microbially mediated bioremediation of polluted sites has been a subject of much research over the past 30 years, with many different compounds shown to be degraded under both aerobic and anaerobic conditions. Aerobic-mediated bioremediation commonly examines the use of Methanotrophs, microorganisms that consume methane as their sole source of carbon and energy. Given the diverse environments in which Methanotrophs have been found, the range of substrates they can degrade and the fact that they can be easily stimulated with the provision of methane and oxygen, these microorganisms in particular have been examined for aerobic degradation of chlorinated hydrocarbons. The physiological and phylogenetic diversity of methanotrophy, however, has increased substantially in just the past 5 years. Here in this review, the current state of knowledge of methanotrophy, particularly as it applies to pollutant degradation is summarized, and suggestions for future research provided.
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Facultative methanotrophy: false leads, true results, and suggestions for future research
FEMS microbiology letters, 2011Co-Authors: Jeremy D Semrau, Alan A. Dispirito, Stéphane VuilleumierAbstract:Methanotrophs are a group of phylogenetically diverse microorganisms characterized by their ability to utilize methane as their sole source of carbon and energy. Early studies suggested that growth on methane could be stimulated with the addition of some small organic acids, but initial efforts to find facultative Methanotrophs, i.e., Methanotrophs able to utilize compounds with carbon-carbon bonds as sole growth substrates were inconclusive. Recently, however, facultative Methanotrophs in the genera Methylocella, Methylocapsa, and Methylocystis have been reported that can grow on acetate, as well as on larger organic acids or ethanol for some species. All identified facultative Methanotrophs group within the Alphaproteobacteria and utilize the serine cycle for carbon assimilation from formaldehyde. It is possible that facultative Methanotrophs are able to convert acetate into intermediates of the serine cycle (e.g. malate and glyoxylate), because a variety of acetate assimilation pathways convert acetate into these compounds (e.g. the glyoxylate shunt of the tricarboxylic acid cycle, the ethylmalonyl-CoA pathway, the citramalate cycle, and the methylaspartate cycle). In this review, we summarize the history of facultative methanotrophy, describe scenarios for the basis of facultative methanotrophy, and pose several topics for future research in this area.
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Pollutant degradation by a Methylocystis strain SB2 grown on ethanol: bioremediation via facultative methanotrophy
FEMS Microbiology Letters, 2011Co-Authors: Jeremy D SemrauAbstract:A facultative methanotroph, Methylocystis strain SB2, was examined for its ability to degrade chlorinated hydrocarbons when grown on methane or ethanol. Strain SB2 grown on methane degraded vinyl chloride (VC), trans-dichloroethylene (t-DCE), trichloroethylene (TCE), 1,1,1-trichloroethane (1,1,1-TCA), and chloroform (CF), but not dichloromethane (DCM). Growth on methane was reduced in the presence of any chlorinated hydrocarbon. Strain SB2 grown on ethanol degraded VC, t-DCE, and TCE, and 1,1,1-TCA, but not DCM or CF. With the exception of 1,1,1-TCA, the growth of strain SB2 on ethanol was not affected by any individual chlorinated hydrocarbon. No degradation of any chlorinated hydrocarbon was observed when acetylene was added to ethanol-grown cultures, indicating that this degradation was due to particulate methane monooxygenase (pMMO) activity. When mixtures of chlorinated alkanes or alkenes were added to cultures growing on methane or ethanol, chlorinated alkene degradation occurred, but chlorinated alkanes were not, and growth was reduced on both methane and ethanol. Collectively, these data indicate that competitive inhibition of pMMO activity limits methanotrophic growth and pollutant degradation. Facultative methanotrophy may thus be useful to extend the utility of Methanotrophs for bioremediation as the use of alternative growth substrates allows for pMMO activity to be focused on pollutant degradation.
Richard S Hanson - One of the best experts on this subject based on the ideXlab platform.
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soluble methane monooxygenase component b gene probe for identification of Methanotrophs that rapidly degrade trichloroethylene
Applied and Environmental Microbiology, 1992Co-Authors: Hsienchyang Tsien, Richard S HansonAbstract:Restriction fragment length polymorphisms, Western blot (immunoblot) analysis, and fluorescence-labelled signature probes were used for the characterization of methanotrophic bacteria as well as for the identification of Methanotrophs which contained the soluble methane monooxygenase (MMO) gene and were able to degrade trichloroethylene (TCE). The gene encoding a soluble MMO component B protein from Methylosinus trichosporium OB3b was cloned. It contained a 2.2-kb EcoRI fragment. With this cloned component B gene as probe, methanotroph types I, II, and X and environmental and bioreactor samples were screened for the presence of the gene encoding soluble MMO. Among twelve pure or mixed cultures, DNA fragments of seven Methanotrophs hybridized with the soluble MMO B gene probe. When grown in media with limited copper, all of these bacteria degraded TCE. All of them are type II Methanotrophs. The soluble MMO component B gene of the type X methanotroph, Methylococcus capsulatus Bath, did not hybridize to the M. trichosporium OB3b soluble MMO component B gene probe, although M. capsulatus Baath also produces a soluble MMO.
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soluble methane monooxygenase component b gene probe for identification of Methanotrophs that rapidly degrade trichloroethylene
Applied and Environmental Microbiology, 1992Co-Authors: Hsienchyang Tsien, Richard S HansonAbstract:Restriction fragment length polymorphisms, Western blot (immunoblot) analysis, and fluorescence-labelled signature probes were used for the characterization of methanotrophic bacteria as well as for the identification of Methanotrophs which contained the soluble methane monooxygenase (MMO) gene and were able to degrade trichloroethylene (TCE). The gene encoding a soluble MMO component B protein from Methylosinus trichosporium OB3b was cloned. It contained a 2.2-kb EcoRI fragment. With this cloned component B gene as probe, methanotroph types I, II, and X and environmental and bioreactor samples were screened for the presence of the gene encoding soluble MMO. Among twelve pure or mixed cultures, DNA fragments of seven Methanotrophs hybridized with the soluble MMO B gene probe. When grown in media with limited copper, all of these bacteria degraded TCE. All of them are type II Methanotrophs. The soluble MMO component B gene of the type X methanotroph, Methylococcus capsulatus Bath, did not hybridize to the M. trichosporium OB3b soluble MMO component B gene probe, although M. capsulatus Baath also produces a soluble MMO.
Yongcui Deng - One of the best experts on this subject based on the ideXlab platform.
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salinity affects the composition of the aerobic methanotroph community in alkaline lake sediments from the tibetan plateau
Microbial Ecology, 2017Co-Authors: Yongcui Deng, Marc G Dumont, Ralf ConradAbstract: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.
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aerobic methanotroph diversity in sanjiang wetland northeast china
Microbial Ecology, 2015Co-Authors: Hongxun Zhang, Yongcui Deng, Yanfen WangAbstract:Aerobic Methanotrophs present in wetlands can serve as a methane filter and thereby significantly reduce methane emissions. Sanjiang wetland is a major methane source and the second largest wetland in China, yet little is known about the characteristics of aerobic Methanotrophs in this region. In the present study, we investigated the diversity and abundance of Methanotrophs in marsh soils from Sanjiang wetland with three different types of vegetation by 16S ribosomal RNA (rRNA) and pmoA gene analysis. Quantitative polymerase chain reaction analysis revealed the highest number of pmoA gene copies in marsh soils vegetated with Carex lasiocarpa (109 g−1 dry soil), followed by Carex meyeriana, and the least with Deyeuxia angustifolia (108 g−1 dry soil). Consistent results were obtained using Sanger sequencing and pyrosequencing techniques, both indicating the codominance of Methylobacter and Methylocystis species in Sanjiang wetland. Other less abundant methanotrophy, including cultivated Methylomonas and Methylosinus genus, and uncultured clusters such as LP20 and JR-1, were also detected in the wetland. Methanotroph diversity was almost the same in three different vegetation covered soils, suggesting that vegetation types had very little influence on the methanotroph diversity. Our study gives an in-depth insight into the community composition of aerobic Methanotrophs in the Sanjiang wetland.
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aerobic methanotroph diversity in riganqiao peatlands on the qinghai tibetan plateau
Environmental Microbiology Reports, 2013Co-Authors: Claudia Luke, Yongcui Deng, Marc G DumontAbstract:Summary The Zoige Plateau is characterized by its high altitude, low latitude and low annual mean temperature of approximately 1°C and is a major source of atmos- pheric methane in the Qinghai-Tibetan Plateau. Meth- anotrophs play an important role in the global cycling of CH 4 , but the diversity, identity and activity of meth- anotrophs in this region are poorly characterized. Soils were collected from hummocks and hollows in the Riganqiao peatland and the methanotroph com- munity was analysed by qPCR and sequencing methane monooxygenase (pmoAandmmoX) genes. ThepmoAgenes ranged between 10 7 and 10 8 cop- ies g -1 fresh soil, with a somewhat greater abundance in hummocks than hollows. ThepmoAgenes were analysed by amplicon pyrosequencing and themmoX genes by cloning and sequencing.Methylocystis species were found to be the most abundant meth- anotrophs, but numerous clades were present includ- ing three novelpmoAand three novelmmoXclusters. There were differences between the methanotroph communities in the hummocks and hollows, with the most significant being an increased abundance of uncultivated type Ib Methanotrophs in the hollows. The results indicate that aerobic Methanotrophs are abundant in Riganqiao peatland and include previ- ously undetected clades in this geographically iso- lated and distinctive environment.
Werner Liesack - One of the best experts on this subject based on the ideXlab platform.
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unexpected metabolic versatility among type ii Methanotrophs in the alphaproteobacteria
Biological Chemistry, 2020Co-Authors: Anna Hakobyan, Werner LiesackAbstract:Aerobic methane-oxidizing bacteria, or Methanotrophs, play a crucial role in the global methane cycle. Their methane oxidation activity in various environmental settings has a great mitigation effect on global climate change. Alphaproteobacterial Methanotrophs were among the first to be taxonomically characterized, nowadays unified in the Methylocystaceae and Beijerinckiaceae families. Originally thought to have an obligate growth requirement for methane and related one-carbon compounds as a source of carbon and energy, it was later shown that various alphaproteobacterial Methanotrophs are facultative, able to grow on multi-carbon compounds such as acetate. Most recently, we expanded our knowledge of the metabolic versatility of alphaproteobacterial Methanotrophs. We showed that Methylocystis sp. strain SC2 has the capacity for mixotrophic growth on H2 and CH4. This mini-review will summarize the change in perception from the long-held paradigm of obligate methanotrophy to today's recognition of alphaproteobacterial Methanotrophs as having both facultative and mixotrophic capabilities.
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thriving in wetlands ecophysiology of the spiral shaped methanotroph methylospira mobilis as revealed by the complete genome sequence
Microorganisms, 2019Co-Authors: Igor Y Oshkin, Olga V Danilova, Anna Hakobyan, Kirill K Miroshnikov, Werner LiesackAbstract:Candidatus Methylospira mobilis is a recently described spiral-shaped, micro-aerobic methanotroph, which inhabits northern freshwater wetlands and sediments. Due to difficulties of cultivation, it could not be obtained in a pure culture for a long time. Here, we report on the successful isolation of strain Shm1, the first axenic culture of this unique methanotroph. The complete genome sequence obtained for strain Shm1 was 4.7 Mb in size and contained over 4800 potential protein-coding genes. The array of genes encoding C1 metabolic capabilities in strain Shm1 was highly similar to that in the closely related non-motile, moderately thermophilic methanotroph Methylococcus capsulatus Bath. The genomes of both Methanotrophs encoded both low- and high-affinity oxidases, which allow their survival in a wide range of oxygen concentrations. The repertoire of signal transduction systems encoded in the genome of strain Shm1, however, by far exceeded that in Methylococcus capsulatus Bath but was comparable to those in other motile gammaproteobacterial Methanotrophs. The complete set of motility genes, the presence of both the molybdenum–iron and vanadium-iron nitrogenases, as well as a large number of insertion sequences were also among the features, which define environmental adaptation of Methylospira mobilis to water-saturated, micro-oxic, heterogeneous habitats depleted in available nitrogen.
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gammaproteobacterial Methanotrophs dominate cold methane seeps in floodplains of west siberian rivers
Applied and Environmental Microbiology, 2014Co-Authors: Igor Y Oshkin, Claudia Luke, Werner Liesack, Carleric Wegner, M V Glagolev, I V Filippov, Nikolay Pimenov, Svetlana N. DedyshAbstract:A complex system of muddy fluid-discharging and methane (CH4)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH4 h−1, while some seeps emitted up to 5.54 g CH4 h−1. The δ13C value of methane released from these seeps varied between −71.1 and −71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH4 ml−1 day−1) were measured in mud samples. Fluorescence in situ hybridization detected 107 methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of Methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting Methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant Methanotrophs, thereby providing a challenge for future isolation studies.
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Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2
Proceedings of the National Academy of Sciences, 2008Co-Authors: Mohamed Baani, Werner LiesackAbstract:Methane-oxidizing bacteria (Methanotrophs) attenuate methane emission from major sources, such as wetlands, rice paddies, and landfills, and constitute the only biological sink for atmospheric methane in upland soils. Their key enzyme is particulate methane monooxygenase (pMMO), which converts methane to methanol. It has long been believed that methane at the trace atmospheric mixing ratio of 1.75 parts per million by volume (ppmv) is not oxidized by the Methanotrophs cultured to date, but rather only by some uncultured Methanotrophs, and that type I and type II Methanotrophs contain a single type of pMMO. Here, we show that the type II methanotroph Methylocystis sp. strain SC2 possesses two pMMO isozymes with different methane oxidation kinetics. The pmoCAB1 genes encoding the known type of pMMO (pMMO1) are expressed and pMMO1 oxidizes methane only at mixing ratios >600 ppmv. The pmoCAB2 genes encoding pMMO2, in contrast, are constitutively expressed, and pMMO2 oxidizes methane at lower mixing ratios, even at the trace level of atmospheric methane. Wild-type strain SC2 and mutants expressing pmoCAB2 but defective in pmoCAB1 consumed atmospheric methane for >3 months. Growth occurred at 10–100 ppmv methane. Most type II but no type I Methanotrophs possess the pmoCAB2 genes. The apparent Km of pMMO2 (0.11 μM) in strain SC2 corresponds well with the Km(app) values for methane oxidation measured in soils that consume atmospheric methane, thereby explaining why these soils are dominated by type II Methanotrophs, and some by Methylocystis spp., in particular. These findings change our concept of methanotroph ecology.
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Detection and enumeration of Methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris.
Applied and Environmental Microbiology, 2001Co-Authors: Svetlana N. Dedysh, Manigee Derakshani, Werner LiesackAbstract:Two 16S rRNA-targeted oligonucleotide probes, Mcell-1026 and Mcell-181, were developed for specific detection of the acidophilic methanotroph Methylocella palustris using fluorescence in situ hybridization (FISH). The fluorescence signal of probe Mcell-181 was enhanced by its combined application with the oligonucleotide helper probe H158. Mcell-1026 and Mcell-181, as well as 16S rRNA oligonucleotide probes with reported group specificity for either type I Methanotrophs (probes M-84 and M-705) or the Methylosinus/Methylocystis group of type II Methanotrophs (probes MA-221 and M-450), were used in FISH to determine the abundance of distinct methanotroph groups in a Sphagnum peat sample of pH 4.2. M. palustris was enumerated at greater than 106 cells per g of peat (wet weight), while the detectable population size of type I Methanotrophs was three orders of magnitude below the population level of M. palustris. The cell counts with probe MA-221 suggested that only 104 type II Methanotrophs per g of peat (wet weight) were present, while the use of probe M-450 revealed more than 106 type II methanotroph cells per g of the same samples. This discrepancy was due to the fact that probe M-450 targets almost all currently known strains of Methylosinus and Methylocystis, whereas probe MA-221, originally described as group specific, does not detect a large proportion of Methylocystis strains. The total number of methanotrophic bacteria detected by FISH was 3.0 (±0.2) × 106 cells per g (wet weight) of peat. This was about 0.8% of the total bacterial cell number. Thus, our study clearly suggests that M. palustris and a defined population of Methylocystis spp. were the predominant Methanotrophs detectable by FISH in an acidic Sphagnum peat bog.