39 research outputs found

    Methanethiol-dependent dimethylsulfide production in soil environments

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    Dimethylsulfide (DMS) is an environmentally important trace gas with roles in sulfur cycling, signalling to higher organisms and in atmospheric chemistry. DMS is believed to be predominantly produced in marine environments via microbial degradation of the osmolyte dimethylsulfoniopropionate (DMSP). However, significant amounts of DMS are also generated from terrestrial environments, for example, peat bogs can emit ~6 μmol DMS m−2 per day, likely via the methylation of methanethiol (MeSH). A methyltransferase enzyme termed ‘MddA’, which catalyses the methylation of MeSH, generating DMS, in a wide range of bacteria and some cyanobacteria, may mediate this process, as the mddA gene is abundant in terrestrial metagenomes. This is the first study investigating the functionality of MeSH-dependent DMS production (Mdd) in a wide range of aerobic environments. All soils and marine sediment samples tested produced DMS when incubated with MeSH. Cultivation-dependent and cultivation-independent methods were used to assess microbial community changes in response to MeSH addition in a grassland soil where 35.9% of the bacteria were predicted to contain mddA. Bacteria of the genus Methylotenera were enriched in the presence of MeSH. Furthermore, many novel Mdd+ bacterial strains were isolated. Despite the abundance of mddA in the grassland soil, the Mdd pathway may not be a significant source of DMS in this environment as MeSH addition was required to detect DMS at only very low conversion rates

    Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments

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    Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle

    UASB Treatment of Methanolic Pulp Wastewater with Addition of Waste Starch and Incinerated Ash

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    Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen form an anaerobic reactor fed with methanol

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    A novel thermophilic, obligately methylotrophic, methanogenic archaeon, strain L2FAWT, was isolated from a thermophilic laboratory-scale upflow anaerobic sludge blanket reactor fed with methanol as the carbon and energy source. Cells of strain L2FAWT were non-motile, irregular cocci, 0·7¿1·5 µm in diameter and usually occurred singly (sometimes forming clusters of two or four cells). The cells stained Gram-negative and lysed immediately in 0·1 % (w/v) SDS. Growth was inhibited by chloramphenicol and tetracycline, but not by penicillin, bacitracin, spectinomycin, vancomycin or kanamycin. Methanol and mono-, di- and trimethylamine were used as substrates, but H2/CO2, formate, acetate, propanol, dimethyl sulfide and methanethiol were not. The temperature range for growth was 42¿58 °C, with an optimum at 50 °C. The fastest growth was observed at a salinity below 100 mM NaCl; no growth occurred above 300 mM NaCl. The optimal pH for growth was 6·5; growth was observed from pH 5 to pH 7·5. The G+C content of the genomic DNA was 37·6 mol%. Analysis of the 16S rRNA gene sequence and the partial methyl-CoM reductase gene sequence revealed that the organism was phylogenetically closely related to Methanomethylovorans hollandica DMS1T (98 % similarity for the 16S rRNA gene sequence and 91 % similarity for the methyl-CoM reductase gene sequence). The DNA¿DNA relatedness between L2FAWT and Methanomethylovorans hollandica DMS1T was 46 %. On the basis of these results, strain L2FAWT (=DSM 17232T=ATCC BAA-1173T) represents the type strain of a novel species, for which the name Methanomethylovorans thermophila sp. nov. is proposed

    MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources

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    Here we introduce a MIxS extension to facilitate the recording and cataloguing of metadata from samples related to hydrocarbon resources. The proposed MIxS-HCR package incorporates the core features of the MIxS standard for marker gene (MIMARKS) and metagenomic (MIMS) sequences along with a hydrocarbon resources customized environmental package. Adoption of the MIxS-HCR standard will enable the comparison and better contextualization of investigations related to hydrocarbon rich environments. The insights from such standardized way of reporting could be highly beneficial for the successful development and optimization of hydrocarbon recovery processes and management of microbiological issues in petroleum production systems

    Genome sequencing of one-carbon degrading acetogenic bacteria Moorella glycerini Strain NMP

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    The genus Moorella contains, up to now, only one sequenced genome, that of M. thermoacetica. Sequencing more strains is essential in understanding their common and specific physiology. Moreover, Moorella species typically grow with one-carbon substrates, but there are differences in their ability to grow with for example carbon monoxide. By comparing the already sequenced genomes of the type strains M. thermoacetica with close related strains we can assess which genes are responsible for the physiological differences

    Formation of Dimethyl Sulfide and Methanethiol in Anoxic Freshwater Sediments

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    Concentrations of volatile organic sulfur compounds (VOSC) were measured in water and sediment columns of ditches in a minerotrophic peatland in The Netherlands. VOSC, with methanethiol (4 to 40 nM) as the major compound, appeared to be mainly of sediment origin. Both VOSC and hydrogen sulfide concentrations decreased dramatically towards the water surface. High methanethiol and high dimethyl sulfide concentrations in the sediment and just above the sediment surface coincided with high concentrations of hydrogen sulfide (correlation factors, r = 0.91 and r = 0.81, respectively). Production and degradation of VOSC were studied in 32 sediment slurries collected from various freshwater systems in The Netherlands. Maximal endogenous methanethiol production rates of the sediments tested (up to 1.44 (mu)mol per liter of sediment slurry (middot) day(sup-1)) were determined after inhibition of methanogenic and sulfate-reducing populations in order to stop VOSC degradation. These experiments showed that the production and degradation of VOSC in sediments are well balanced. Statistical analysis revealed multiple relationships of methanethiol production rates with the combination of methane production rates (indicative of total anaerobic mineralization) and hydrogen sulfide concentrations (r = 0.90) or with the combination of methane production rates and the sulfate/iron ratios in the sediment (r = 0.82). These findings and the observed stimulation of methanethiol formation in sediment slurry incubations in which the hydrogen sulfide concentrations were artificially increased provided strong evidence that the anaerobic methylation of hydrogen sulfide is the main mechanism for VOSC formation in most freshwater systems. Methoxylated aromatic compounds are likely a major source of methyl groups for this methylation of hydrogen sulfide, since they are important degradation products of the abundant biopolymer lignin. Increased sulfate concentrations in several freshwater ecosystems caused by the inflow of water from the river Rhine into these systems result in higher hydrogen sulfide concentrations. As a consequence, higher fluxes of VOSC towards the atmosphere are conceivable
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