Transcriptome-SIP of hydrocarbon degrader adaption under dual electron acceptor availability in aquifer sediments
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ABSTRACT:
PROVIDER: PRJNA588156 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10416360_1.fastq.gz | Fastqsanger.gz | |||
| SRR10416360_2.fastq.gz | Fastqsanger.gz | |||
| SRR10416361_1.fastq.gz | Fastqsanger.gz | |||
| SRR10416361_2.fastq.gz | Fastqsanger.gz | |||
| SRR10416362_1.fastq.gz | Fastqsanger.gz |
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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
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.
2011-03-18 | GSE25449 | GEO
Project description:The Geobacter species evolved respiratory versatility to utilize a wide range of terminal electron acceptors. To explore this adaptive mechanism, Fe(III) citrate, hydrous ferric oxide, and fumarate were selected as electron acceptors, and the methylome and metabolome of Geobacter sulfurreducens PCA grown on each electron acceptor were investigated via third-generation, single-molecule real-time DNA sequencing.Results showed that the patterns of 4-methylcytosine (m4C) and 6-methyladenine (m6A) modification were all varied in different electron acceptor cultures. Moreover, genes (e.g., GSU0466 and GSU1467) with low expression levels generally had high methylation levels. These findings suggest that m4C and m6A modifications play a role in the adaption of G. sulfurreducens to diverse electron acceptors, and DNA methylation may be involved in the adaption mainly via gene expression regulation.
2021-08-31 | GSE157224 | GEO
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.
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Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate.
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Project description:Microbially-mediated uranium bioremediation has been demonstrated in uranium contaminated aquifers when acetate was artificially supplied and growth of the natural population of Geobacteraceae was stimulated. In order to mimic the environmental response to acetate, steady-state cells of G. sulfureducens were cultured in chemostats under conditions of either 1) acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor or 2) acetate was supplied in excess with fumarate as sole electron acceptor and limiting factor. In silico fluxome modeling and transcriptome analysis were used as tools for investigating the cell response to the acetate availability. For global gene expression profiling, a DNA microarray of the complete G. sulfurreducens genome was used. Statistically significant results were obtained from two-color, dye swap hybridizations produced from a total of three biological replicates. Eight technical replicates were tested from two of the biological replicates and six technical replicates were tested from the third biological replicate. Major findings from this study are given as follows. The in silico model successfully predicted a higher TCA-cycle flux (ca. 2-fold) under acetate-excess conditions, suggesting that catabolism of acetate is favored with respect to anabolism, and thus more electrons are available for metal reduction. Transcriptome analyses offered a comprehensive picture of the regulation points subjected to the acetate availability. Under acetate-excess conditions, acetate transporters in the G. sulfurreducens genome were down-regulated. In addition the oxidation-related acetyl-CoA transferase was up-regulated approximately three-fold and the assimilatory-related acetate kinase was down-regulated approximately two-fold, respectively, indicating that the transcriptional regulation of acetate activation may be the key point for coping with the excess of acetate and increasing the TCA flux. The level of transcription for 10 c-type cytochromes was significantly increased in cells cultured with an excess of acetate. OmcS, an outer-membrane cytochrome which actively participates in electron transfer to Fe(III)-oxides and graphite electrodes from fuel cells, showed one of the highest fold increases in transcription. The integration of in silico modeling and genome-wide analysis shows for first time how G. sulffureducens adapts its metabolic flux and transcriptional network for optimizing the use of acetate as an electron donor for exocellular respiration instead of for use as a carbon source for biomass production. Keywords: Geobacter, gene expression, acetate limitation, fumarate limitation
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Project description:Geobacter sulfurreducens PCA was put under selective pressure for rapid Fe(III) oxide reduction. The resultant strain, V1, contained five confirmed mutations and reduced Fe(III) oxide 17 times faster. One of these five mutations inactivates dcuB, a fumarate/succinate antiporter necessary for growth with fumarate as an electron acceptor. V1 dcuB+ is a V1 strain containing a wild type copy of dcuB. Whole genome DNA microarray analysis was performed in order to determine which genes are up- or down-regulated in V1 dcuB+ compared to PCA, both grown with fumarate as an electron acceptor.
2011-04-12 | GSE21313 | GEO