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ABSTRACT: Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil contaminated aquifer by Pyro-SIP

PROVIDER: PRJNA133811 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR073680.fastq.gz	Fastqsanger.gz
	SRR073681.fastq.gz	Fastqsanger.gz

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Similar Datasets

Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil contaminated aquifer by Pyro-SIP

Project description:Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil contaminated aquifer in Germany, where a specialized community of contaminant degraders co-dominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase alpha-subunit, bssA) genes detected in situ appeared more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with 13C7-toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae for sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This, and the absence of 13C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy amongst anaerobic toluene degraders on site. 2 samples examined from the different electron-acceptors (sulphate or ferric iron) incubates at the time point of maximal toluene degradation.

2011-03-18 | E-GEOD-25449 | biostudies-arrayexpress

Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil contaminated aquifer by Pyro-SIP

2011-03-18 | GSE25449 | GEO

Transcriptome-SIP of hydrocarbon degrader adaption under dual electron acceptor availability in aquifer sediments

Project description:We demonstrate the feasibility of total RNA-SIP in experiments where microbes from a hydrocarbon-contaminated aquifer were studied in microcosms with 13C-labelled-toluene to understand their adaptation to the simultaneous availability of low levels of different electron acceptors. SIP successfully resolved the involvement of microaerobic vs. aerobic and anaerobic populations. Under microoxic, nitrate-amended conditions hydrocarbon degradation was actually stimulated, but transcripts of denitrification showed no signs of 13C-labelling. The expression of distinct oxygenase-based catabolic pathways for toluene degradation was clearly apparent in 13C-labelled mRNA. We discuss how these direct insights into the gene expression and adaptation mechanisms within complex degrader communities can guide more integrated approaches in monitoring and restoration of contaminated sites.

2019-11-08 | GSE140055 | GEO

Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into hypoxic pollutant-degrading aquifer microbiota

Project description:We investigated a contaminant-degrading microbial community by sequencing total RNA (without rRNA depletion) from microcosms containing sediment from a hypoxic contaminated aquifer fed with isotopically labeled toluene.

2018-09-07 | GSE119644 | GEO

Gene expression patterns under conditions of oxidative stress in Geobacter uraniumreducens

Project description:Previous analysis of gene transcript levels of Geobacter species in groundwater during in situ bioremediation of a uranium-contaminated aquifer detected expression of genes encoding superoxide dismutase (sodA) and cytochrome d ubiquinol oxidase (cydA), proteins known to be involved in the response to oxidative stress in other microorganisms. In order to further elucidate gene expression patterns that could be attributed to oxygen exposure, G. uraniumreducens was grown with acetate as the electron donor and fumarate as the electron acceptor in the presence of oxygen and compared to non-oxygen treated cultures.

2009-06-04 | GSE12455 | GEO

Expression analysis in anaerobic Hanford 100H aquifer flow-through columns receiving lactate and chromate

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2014-04-08 | GSE56554 | GEO

Expression analysis in anaerobic Hanford 100H aquifer flow-through columns receiving lactate and chromate

Project description:Columns containing Hanford 100H aquifer sediment continuously infused with 5 mM lactate, 5 uM Cr(VI), and either 7.5 mM sulfate or 12 mM nitrate as an electron acceptor. A two-chip study using total RNA extracted from unfiltered effluent from columns (nitrate or sulfate infused).

2014-04-08 | E-GEOD-56554 | biostudies-arrayexpress

Transcriptome-SIP of hydrocarbon degrader adaption under dual electron acceptor availability in aquifer sediments

Project description:Transcriptome-SIP of hydrocarbon degrader adaption under dual electron acceptor availability in aquifer sediments

| PRJNA588156 | ENA

Analysis of the physiological status of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

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2008-10-20 | GSE10920 | GEO

Transcriptional Response of Rhodococcus aetherivorans I24 to Polychlorinated Biphenyl-Contaminated Sediments.

Project description:We analyzed the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 to biphenyl and polychlorinated biphenyls (PCBs). This species has not been extensively exposed to PCBs, as it was first isolated from a toluene contaminated aquifer, rather than a site contaminated with polychlorinated hydrocarbons. Using a microarray targeting 3524 genes, we assessed gene expression in minimal medium supplemented with various substrates (e.g. PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were up-regulated in the various treatments. In medium and in sediment, PCBs elicited the up-regulation of a common set of 100 genes, including chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were up-regulated in response to PCBs or biphenyl. This study is one of the first which utilizes microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions which more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism. In addition, the identification of numerous genes expressed in contaminated soil specifically may have implications for the development of biosensors. Finally, comparative genomic and transcriptomic analyses suggest that the mere presence of orthologs of the required enzymes may not be sufficient to confer a vigorous biphenyl/PCB metabolism.

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