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  • 1
    Electronic Resource
    Electronic Resource
    Activity and community structure of methane-oxidising bacteria in a wet meadow soil (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 41 (2002), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The structure and activity of the methane-oxidising microbial community in a wet meadow soil in Germany were investigated using biogeochemical, cultivation, and molecular fingerprinting techniques. Both methane from the atmosphere and methane produced in anaerobic subsurface soil were oxidised. The specific affinity (first-order rate constant) for methane consumption was highest in the top 20 cm of soil and the apparent half-saturation constant was 137–300 nM CH4, a value intermediate to measured values in wetland soils versus well-aerated upland soils. Most-probable-number (MPN) counting of methane-oxidising bacteria followed by isolation and characterisation of strains from the highest positive dilution steps suggested that the most abundant member of the methane-oxidising community was a Methylocystis strain (105–107 cells g−1 d.w. soil). Calculations based on kinetic data suggested that this cell density was sufficient to account for the observed methane oxidation activity in the soil. DNA extraction directly from the same soil samples, followed by PCR amplification and comparative sequence analyses of the pmoA gene, also detected Methylocystis. However, molecular community fingerprinting analyses revealed a more diverse and dynamic picture of the methane-oxidising community. Retrieved pmoA sequences included, besides those closely related to Methylocystis spp., others related to the genera Methylomicrobium and Methylocapsa, and there were differences across samples which were not evident in MPN analyses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2002.tb00986.x
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  • 2
    Electronic Resource
    Electronic Resource
    Methanotrophic bacteria in boreal forest soil after fire (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 50 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Methane-oxidizing bacteria are the only terrestrial sink for atmospheric methane. Little is known, however, about the methane-oxidizing bacteria that are responsible for the consumption of atmospheric methane, or about the factors that influence their activity and diversity in soil. Effects of fire and its end-product, wood ash, on the activity and community of methane oxidizing bacteria were studied in boreal forest 3 months and 12 years after the treatments. Fire significantly increased the atmospheric CH4 oxidation rate. Both fire and wood ash treatments resulted in increased soil pH, but there was no correlation with methane oxidation rates. Changes in the methane-oxidizing bacterial community due to treatments were not detected by cultivation-independent recovery and comparative sequence analysis of pmoA gene products from soil. Phylogenetic analysis showed that a majority of the pmoA sequences obtained belonged to the “upland soil cluster α”, which has previously been detected in diverse forest environments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.06.013
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  • 3
    Electronic Resource
    Electronic Resource
    Isolation of a Methylocystis strain containing a novel pmoA-like gene (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 41 (2002), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: A type II methanotrophic bacterium (Methylocystis strain SC2) was isolated from a polluted aquifer and identified based on morphology and on 16S rRNA gene phylogeny. Primers targeting the particulate methane monooxygenase subunit A gene (pmoA) were used to obtain a PCR product from DNA extract of strain SC2. Denaturing gradient gel electrophoresis of this PCR product demonstrated that strain SC2 contained two very different pmoA-like genes. One gene (pmoA1) had very high sequence homology to pmoA genes of other type II methanotrophic bacteria (identical amino acid sequence to pmoA of some other Methylocystis strains). The second gene (pmoA2) possessed only 73% identity with the first gene at the nucleotide level and 68.5% identity (83% similarity) at the amino acid level. The presence of both pmoA-like genes was verified by developing specific oligonucleotide probes for each and using these in Southern hybridisation of genomic DNA. Purity of the culture was exhaustively verified with a variety of methods to ensure that both genes were present in a single genospecies. These included microscopic examination, plating on various media, denaturing gradient gel electrophoresis of PCR products of the 16S rRNA gene (universal to bacteria) and of the methanol dehydrogenase α-subunit gene mxaF (universal to methylotrophic bacteria), and whole-cell hybridisation with fluorescently labelled 16S rRNA-targeted oligonucleotide probes specific for the genera Methylosinus and Methylocystis, or specific for strain SC2. Reverse transcription PCR of extracted RNA suggested that the novel pmoA2 gene was not expressed during growth under standard conditions used for the cultivation of these bacteria. The presence of multiple, diverse pmoA-like genes in a single genospecies of methanotrophic bacteria implies that pmoA must be cautiously applied as a phylogenetic marker in cultivation-independent molecular ecology studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2002.tb00962.x
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  • 4
    Electronic Resource
    Electronic Resource
    Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia (2007)
    [s.l.] : Nature Publishing Group
    Nature 450 (2007), S. 879-882 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Aerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature06411
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  • 5
    Electronic Resource
    Electronic Resource
    Organic matter, heterotrophic activity, and NO· consumption in soils (1998)
    Oxford, UK : Blackwell Science Ltd
    Global change biology 4 (1998), S. 0 
    Details
    ISSN: 1365-2486
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Notes: When the effect of water content was minimized, soil CO2 evolution and soil organic matter content were good predictors of aerobic NO. uptake rate constants across a wide range of soil types. Field manure application to a Gleysol stimulated NO. uptake rate constants and lowered NO. compensation points compared to unfertilized or NH4NO3-fertilized soil. This effect lasted for months after manure application. In a laboratory experiment, addition of manure reduced the NO. efflux associated with nitrification of NH4 Cl fertilizer, and manured soils had a greater capacity to remove NO. from polluted air. Evidence is presented that these observations result from NO. oxidation during heterotrophic microbial activity in soil.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2486.1998.00123.x
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  • 6
    Electronic Resource
    Electronic Resource
    Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 32 (2000), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The aim of this study was to examine whether the terminal restriction fragment length polymorphism (T-RFLP) analysis represents an appropriate technique for monitoring highly diverse soil bacterial communities, i.e. to assess spatial and/or temporal effects on bacterial community structure. The T-RFLP method, a recently described fingerprinting technique, is based on terminal restriction fragment length polymorphisms between distinct small-subunit rRNA gene sequence types. This technique permits an automated quantification of the fluorescence signal intensities of the individual terminal restriction fragments (T-RFs) in a given community fingerprint pattern. The indigenous bacterial communities of three soil plots located within an agricultural field of 110 m2 were compared. The first site was planted with non-transgenic potato plants, while the other two were planted with transgenic GUS and Barnase/Barstar potato plants, respectively. Once prior to planting and three times after planting, seven parallel samples were taken from each of the three soil plots. The T-RFLP analysis resulted in very complex but highly reproducible community fingerprint patterns. The percentage abundance values of defined T-RFs were calculated for the seven parallel samples of the respective soil plot. A multivariate analysis of variance was used to test T-RFLP data sets for significant differences. The statistical treatments clearly revealed spatial and temporal effects, as well as space×time interaction effects, on the structural composition of the bacterial communities. T-RFs which showed the highest correlations to the discriminant factors were not those T-RFs which showed the largest single variations between the seven-sample means of individual plots. In summary, the T-RFLP technique, although a polymerase chain reaction-based method, proved to be a suitable technique for monitoring highly diverse soil microbial communities for changes over space and/or time.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2000.tb00717.x
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  • 7
    Electronic Resource
    Electronic Resource
    Archaeal community structures in rice soils from different geographical regions before and after initiation of methane production (2001)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 37 (2001), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The methane production potential of rice soils, which are situated in different geographical regions, shows inherent variations and is catalyzed by archaeal methanogens. We therefore investigated the archaeal community structure in 11 rice field soils which represent a range of climatic conditions (temperate to subtropical zones) and soil properties. Retrieval of environmental partial SSU rDNA sequences from the rice soils of Shenyang (China) and Gapan (The Philippines) showed that the communities were different from each other. However, despite the differences in soil properties and geographical region the sequences clustered in similar phylogenetic groups to those obtained earlier from rice fields of Vercelli (Italy). The archaeal community structure in the other rice field soils was compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the SSU rRNA gene and the methyl-coenzyme M reductase α-subunit gene (mcrA). The relative abundance of each terminal restriction fragment (T-RF) was determined by fluorescence peak area integration. The 182-bp SSU rDNA T-RF (representing members of Methanosarcinaceae and rice cluster (RC) VI) was dominant (40–80% contribution) in Chinese soils (Zhenjiang, Changchun, Jurong, Beiyuan, Shenyang) and the Philippine soil of Gapan. The other Philippine soils (Luisiana, Guangzhou, Pila) and the Italian soils (Vercelli, Pavia) showed a dominant 389-bp T-RF (35–40% contribution), representing mainly the novel methanogenic RC-I. All the other T-RF (80, 88, 280, 375 and 〉800 bp) contributed 〈20%. Prolonged anoxic incubation (30–200 days) of the air-dried soils resulted in the production of CH4, which was in some soils preceded by a characteristic halt phase. T-RFLP analysis revealed that the soils with a methanogenic halt phase also showed dramatic archaeal population dynamics which were related to the length of the halt phase. Our results show that the archaeal communities in rice field soils of different geographical origin are highly related, but nevertheless exhibit individual patterns and dynamics, thus providing evidence for the active participation of the community members in energy and carbon flow.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2001.tb00865.x
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  • 8
    Electronic Resource
    Electronic Resource
    Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2 (2005)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 58 (2005), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The molecular regulation of methane oxidation in the first fully authenticated facultative methanotroph Methylocella silvestris BL2 was assessed during growth on methane and acetate. Problems of poor growth of Methylocella spp. in small-scale batch culture were overcome by growth in fermentor culture. The genes encoding soluble methane monooxygenase were cloned and sequenced, which revealed that the structural genes for soluble methane monooxygenase, mmoXYBZDC, were adjacent to two genes, mmoR and mmoG, encoding a σ54 transcriptional activator and a putative GroEL-like chaperone, located downstream (3′) of mmoC. Transcriptional analysis revealed that the genes were all cotranscribed from a σ54-dependent promoter located upstream (5′) of mmo X. The transcriptional start site was mapped. Transcriptional analysis of soluble methane monooxygenase genes and expression studies on fermentor grown cultures showed that acetate repressed transcription of sMMO in M. silvestris BL2. The possibility of the presence of a particulate, membrane-bound methane monooxygenase enzyme in M. silvestris BL2 and the copper-mediated regulation of soluble methane monooxygenase was investigated. Both were shown to be absent. A promoter probe vector was constructed and used to assay transcription of the promoter of the soluble methane monoxygenase genes of M. silvestris BL2 grown under various conditions and with different substrates. These data represent the first insights into the molecular physiology of a facultative methanotroph.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2958.2005.04861.x
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  • 9
    Electronic Resource
    Electronic Resource
    Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 43 (2003), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Based on an extensive 16S rRNA sequence database for type II methanotrophic bacteria, a set of 16S rRNA-targeted oligonucleotide probes was developed for differential detection of specific phylogenetic groups of these bacteria by fluorescence in situ hybridisation (FISH). This set of oligonucleotides included a genus-specific probe for Methylocystis (Mcyst-1432) and three species-specific probes for Methylosinus sporium (Msins-647), Methylosinus trichosporium (Msint-1268) and the recently described acidophilic methanotroph Methylocapsa acidiphila (Mcaps-1032). These novel probes were applied to further characterise the type II methanotroph community that was detected in an acidic Sphagnum peat from West Siberia in a previous study (Dedysh et al. (2001) Appl. Environ. Microbiol. 67, 4850–4857). The largest detectable population of indigenous methanotrophs simultaneously hybridised with a group-specific probe targeting all currently known Methylosinus/Methylocystis spp. (M-450), with a genus-specific probe for Methylocystis spp. (Mcyst-1432), and with an additional probe (Mcyst-1261) that had been designed to target a defined phylogenetic subgroup of Methylocystis spp. The same subgroup of Methylocystis was also detected in acidic peat sampled from Sphagnum-dominated wetland in northern Germany. The population size of this peat-inhabiting Methylocystis subgroup was 2.0±0.1×106 cells g−1 (wet weight) of peat from Siberia and 5.5±0.5×106 cells g−1 of peat from northern Germany. This represented 60 and 95%, respectively, of the total number of methanotroph cells detected by FISH in these two wetland sites. Other major methanotroph populations were M. acidiphila and Methylocella palustris. Type I methanotrophs accounted for not more than 1% of total methanotroph cells. Neither M. trichosporium nor M. sporium were detected in acidic Sphagnum peat.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2003.tb01070.x
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  • 10
    Electronic Resource
    Electronic Resource
    Effect of nitrogen fertilizers and moisture content on CH4 and N2O fluxes in a humisol: Measurements in the field and intact soil cores (1995)
    Springer
    Biogeochemistry 29 (1995), S. 199-222 
    Details
    ISSN: 1573-515X
    Keywords: diffusion limitation ; humisol ; methane oxidation ; nitrogen fertilizers ; nitrous oxide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Geosciences
    Notes: Abstract Field and laboratory studies were conducted to determine effects of nitrogen fertilizers and soil water content on N2O and CH4 fluxes in a humisol located on the Central Experimental Farm of Agriculture Canada, Ottawa. Addition of 100 kg N ha−1 as either urea or NaNO3 had no significant effect on soil CH4 flux measured using chambers. Fertilization with NaNO3 resulted in a significant but transitory stimulation of N2O production. Inorganic soil N profiles and the potential nitrification rate suggested that much of the NH 4 + from urea hydrolysis was rapidly nitrified. CH4 fluxes measured using capped soil cores agreed well with fluxes measured using field chambers, and with fluxes calculated from soil gas concentration gradients using Fick's diffusion law. This humisol presents an ideal, unstructured, vertically homogeneous system in which to study gas diffusion, and the influence of gas-filled porosity on CH4 uptake. In soil cores gradually saturated with H2O, the relationship of CH4 flux to gas-filled porosity was an exponential rise to a maximum. Steepening CH4 concentration gradients partially compensated for the decreasing diffusion coefficient of CH4 in soil matrix air as water content increased, and diffusion limitation of CH4 oxidation occurred only at water contents 〉 130% (dry weight), or gas-filled porosities 〈 0.2.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02186048
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