Groundwater metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA143085 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE28606: Monitoring of functional gene responses to ERD (enhanced reductive dechlorination) from four TCE-contaminated sites GSE28608: Monitoring of functional gene responses to biostimulation from a TCE-contaminated site Refer to individual Series
2012-04-02 | E-GEOD-28609 | biostudies-arrayexpress
Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene diversity present in four trichloroethylene (TCE) contaminated sites under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 2 µg of labelled gDNA from 30 groundwater samples were hybridized on the microarrays.
2012-04-03 | GSE28606 | GEO
Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene diversity present in four trichloroethylene (TCE) contaminated sites under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 2 M-BM-5g of labelled gDNA from 30 groundwater samples were hybridized on the microarrays. A 30-chip study was performed, each chip corresponding to hybridization with 2 M-BM-5g of labelled gDNA retrieved from a monitoring well from one of the four contaminated sites. Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise. Groundwater samples were collected from four contaminated sites (B, F, G and H), four monitoring wells per site (P1, P2, P3 and P4). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 and P4: wells located downstream to the contamination source. For site B, the monitoring of ERD demonstration was performed through a total of 5 sampling campaigns: C1 (T=0), C2 (T=104 days), C3 (T=231 days), C4 (T=291 days) and C5 (T=378 days). For the three other sites (F, G and H), only one sampling campaign was performed after the treatment.
2012-04-02 | E-GEOD-28606 | biostudies-arrayexpress
Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene expression in a contaminated site (site B) under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 4 M-BM-5g of labelled antisense mRNA from 3 groundwater samples were hybridized on the microarray. A 3-chip study was performed, each corresponding to hybridization with 4 M-BM-5g of labelled antisense mRNA retrieved from a monitoring well of a contaminated site (site B). Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise. Groundwater samples were collected from a contaminated site (site B) from three monitoring wells (P1, P2 and P3). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 : well located downstream to the contamination source.
2012-04-02 | E-GEOD-28608 | biostudies-arrayexpress
Project description:Polybrominated diphenyl ethers (PBDEs) are persistent, highly toxic, and widely distributed environmental pollutants. The microbial populations and functional reductive dehalogenases (RDases) responsible for PBDEs debromination in anoxic systems remain poorly understood, which confounds bioremediation of PBDE-contaminated sites. Here we report a PBDE-debrominating enrichment culture dominated by a previously undescribed Dehalococcoides mccartyi population. A D. mccartyi strain, designated TZ50, whose genome contains 25 putative RDase encoding genes was isolated from the debrominating enrichment culture. Strain TZ50 dehalogenated a mixture of penta- and tetra-BDE congeners (total BDEs 1.48 uM) to diphenyl ether within two weeks (0.58 uM Br- /d) via ortho- and meta- bromine elimination; strain TZ50 also dechlorinated tetrachloroethene (PCE) to vinyl chloride and ethene (260.2 M Cl- /d). Native-PAGE, proteomic profiling, and in vitro enzymatic activity assays implicated the involvement of three RDases in PBDEs and PCE dehalogenation. Two RDases, TZ50_0172 (PteATZ50) and TZ50_1083 (TceATZ50), were responsible for debromination of penta- and tetra-BDEs to di-BDE. TZ50_0172 and TZ50_1083 were also implicated in dechlorination of PCE to TCE and of TCE to vinyl chloride/ethene, respectively. The other expressed dehalogenase, TZ50_0090, was associated with debromination of di-BDE to diphenyl ether, but its role in PCE dechlorination was unclear. Comparatively few RDases are known to be involved in PBDE debromination and the identification of PteATZ50, TceATZ50, and TZ50_0090 provides additional information for evaluating debromination potential at contaminated sites. Moreover, the bifunctionality of the PteATZ50 and TceATZ50 in both PBDEs and PCE dehalogenation makes strain TZ50 a suitable candidate for remediation of co-contaminated sites.
2021-06-16 | PXD024983 | Pride
Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene expression in a contaminated site (site B) under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 4 µg of labelled antisense mRNA from 3 groundwater samples were hybridized on the microarray.
2012-04-03 | GSE28608 | GEO
Project description:Microbial reductive dechlorination of trichloroethene (TCE) in groundwater often results in the accumulation of dichloroethenes (DCEs). Dehalococcoides mccartyi (Dhc) are the only known bacteria capable of dechlorination beyond DCE to non-toxic ethene. In this study, two newly isolated Dhc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE, 1,1-DCE, cis-DCE, trans-DCE, and vinyl chloride (VC) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC. Each of these dechlorination reactions are coupled to growth by these strains. The VC dechlorination rate of strain 11a occurs at a rate of 258 nmol per min per mg of protein, about two times faster than previously reported stains. Strain 11a possesses the vcrA gene while strain 11a5 contains the tceA gene. Strains 11a and 11a5 share 100% 16S rRNA gene sequence identity with previously sequenced Dhc strains BAV1 and CBDB1, placing it within the Pinellas subgroup, and 85.4% and 89.5% of all genes present in the CBDB1 and BAV1 genomes were detected in strains 11a and 11a5, respectively, using a custom-designed microarray targeting four sequenced Dhc strains. Genes that were not detected in strains 11a and 11a5 are mostly within the high plasticity regions or integrated elements of the sequenced strains. This study reports the functional description and comparative genomics of two additional Dhc isolates and provides evidence that the observed functional incongruence between the activity and core genome phylogenies of Dhc strains is likely driven by the horizontal transfer of key reductive dehalogenase-encoding genes.
2013-03-01 | GSE27611 | GEO
Project description:Monitoring of functional gene responses to biostimulation from a TCE-contaminated site
| PRJNA143087 | ENA
Project description:<p>Ultra-high performance liquid chromatography-high resolution mass spectrometry (UPHLC-HRMS) is used to discover and monitor single or sets of biomarkers informing about metabolic processes of interest. The technique can detect thousands of molecules (i.e., metabolites) in a single instrument run and provide a measurement of the global metabolome, which could be a fingerprint of activity. Despite the power of this approach, technical challenges have hindered the effective use of metabolomics to interrogate microbial communities implicated in the removal of priority contaminants. Herein, our efforts to circumvent these challenges and apply this emerging systems biology technique to synthetic microbiomes relevant for contaminant biodegradation will be discussed. Chlorinated ethenes impact many contaminated sites, and detoxification can be achieved by organohalide-respiring bacteria, a process currently assessed by quantitative gene-centric tools (e.g., quantitative PCR). </p><p><br></p><p>This laboratory study monitored the metabolome of the SDC-9 bioaugmentation consortium during cis-1,2-dichloroethene conversion to vinyl chloride and nontoxic ethene. Untargeted metabolomics using an UPLC-Orbitrap mass spectrometer and performed on SDC-9 cultures at different stages of the reductive dechlorination process detected ~10,000 spectral features per sample arising from water-soluble molecules with both known and unknown structures. Multivariate statistical techniques including partial least squares-discriminate analysis (PLS-DA) identified patterns of measurable spectral features (peak patterns) that correlated with dechlorination (in)activity. ANOVA analyses identified 18 potential biomarkers of reductive dechlorination activity. Statistical clustering of samples with these 18 features predicted dechlorination activity more reliably than clustering of samples based only on chlorinated ethene concentration and Dhc 16S rRNA gene abundance data, highlighting the value of metabolomic workflows as an innovative site assessment and bioremediation monitoring tool.</p>
2022-09-16 | MTBLS5219 | MetaboLights