Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1067199 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27671243_1.fastq.gz | Fastqsanger.gz | |||
| SRR27671243_2.fastq.gz | Fastqsanger.gz | |||
| SRR27671244_1.fastq.gz | Fastqsanger.gz | |||
| SRR27671244_2.fastq.gz | Fastqsanger.gz | |||
| SRR27671245_1.fastq.gz | Fastqsanger.gz |
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Project description:Positive-ionization DDA metabolomics data of anaerobic SDC-9 cultures, which perform dechlorination of chlorinated ethenes for bioremediation
2022-07-21 | MSV000089937 | GNPS
Project description:Negative-ionization DDA metabolomics data of anaerobic SDC-9 cultures, which perform dechlorination of chlorinated ethenes for bioremediation
2022-07-20 | MSV000089928 | GNPS
Project description:Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 106 cells or M-bM-^HM-<1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing M-bM-^HM-<10% and M-bM-^HM-<1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low. The genomic DNA (gDNA) of each culture or sorted and amplifed DNA was analyzed in triplicate.
2015-01-31 | E-GEOD-54040 | biostudies-arrayexpress
Project description:Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ~1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ~10% and ~1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.
2015-01-31 | GSE54040 | GEO
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
Project description:Organohalide respiration is an environmentally relevant type of anaerobic respiration. We show that Sulfurospirillum halorespirans undergoes the same type of downregulation of the organohalide respiratory genes as had been overserved before in S. multivorans when cultivated without chlorinated ethenes for a long period of time. We compared the proteomes and acetylomes of S. halorespirans cells cultivated in the presence of PCE with those of cells long- and short-term cultivated with nitrate as sole electron acceptor.
2018-04-05 | PXD008953 | Pride
Project description:Microbial degradation of chlorinated ethenes
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Project description:Evaluation of temperature dependence on sequential chlorinated ethenes dechlorination and the dynamics of dechlorinating microorganisms
| PRJDB11653 | ENA
Project description:The organohalide-respiring Sulfurospirillum multivorans uses chlorinated ethenes as electron acceptors for growth under anoxic conditions. However, little is known about the interaction of these substrates with proteins. Here, we apply thermal proteome profiling (TPP) to analyze enzyme-trichloroethene interactions. TPP is commonly used to investigate protein-ligand binding through protein melting curve shifts. Several modifications in the protocol, e.g. performing the incubation under anaerobic conditions and increasing the temperature range up to 97°C, improved the detection range and allowed the investigation of oxygen-sensitive proteins. Enzymatic reductive dehalogenation was prevented by omitting the electron donor during incubations. This enabled detecting the interaction of the tetrachloroethene reductive dehalogenase PceA with trichloroethene and confirms the enzyme’s specificity for this substrate. Another 19 proteins showed significant melting curve shifts with trichloroethene, pointing to other proteins directly or indirectly interacting with trichloroethene. Interestingly, a putative response regulator reacted similarly towards trichloroethene, which is potentially in line with its proposed role in regulating trichloroethene respiration. The TPP approach is here proven to facilitate the identification of substrate-enzyme interactions of strictly anaerobic reductive dehalogenases and probably their regulators. This strategy can be used to identify yet unknown substrate specificities and potential signal-sensing proteins in other difficult to study bacteria.
2018-06-06 | PXD009308 | Pride