The following elements will have their visibility changed, please review the list before confirming the visibility change

Study

Study Name: Enriched contaminated groundwater dechlorinating microbial communities from synthetic mineral medium in Toronto, Ontario, Canada (KB-1)

Projects

Biosamples

Organisms

Biosamples: 1 Seq. Projects: 1
STUDY NAME
GOLD Study ID Gs0056622
Study Name Enriched contaminated groundwater dechlorinating microbial communities from synthetic mineral medium in Toronto, Ontario, Canada (KB-1)
Other Names Dechlorinating community KB-1
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
Legacy ER Study ID 11622
Legacy GOLD ID Gm00048
Added By Nikos Kyrpides on 2007-11-27
Last Modified By Michelle Isbandi on 2014-12-16
STUDY DESCRIPTION
PI Elizabeth Edwards
Description A shotgun metagenome microarray was created and used to investigate gene transcription during vinyl chloride (VC) dechlorination by a microbial enrichment culture called KB1. The array was constructed by spotting genomic fragments amplified from short-insert libraries of KB1 metagenomic DNA. Subsequently, the microarrays were interrogated with RNA extracted from KB1 during VC dechlorination (VC+methanol), and in the absence of VC (methanol-only). The most differentially expressed spots, and spots with the highest intensities, were then chosen to be sequenced. Sequencing revealed that Dehalococcoides (Dhc) genes involved in transcription, translation and energy generation were up-regulated during VC degradation. Furthermore, the results indicated that the reductive dehalogenase homologous (RDH) gene KB1rdhA14 is the only RDH gene up-regulated upon VC degradation, and that multiple RDH genes were more highly transcribed in the absence of VC. Numerous hypothetical genes from Dehalococcoides were also more highly transcribed in methanol only treatments and indicate that many uncharacterized proteins are involved in cell maintenance in the absence of chlorinated substrates. Spots with genes from Spirochaetes, Chloroflexi, Geobacter, Methanogens and phage organisms were differentially expressed and sequencing provided information from these uncultivated organisms that can be used to design primers for more targeted studies. This array format is powerful, as it does not require a priori sequence knowledge. This study provides the first report of such arrays being used to investigate transcription in a mixed community, and shows that this array format can be used to screen metagenomic libraries for functionally important genes. Overall design: 2 Biological replicate experimens conducted 1 month apart. In the first there were 2 dye-swapped duplicates (total 4) of VC+MeOH versus MeOH only. In the second experiment there was one set of dye swapped arrays. Thus 6 arrays were performed including biological replicates, dye swapped replicates and technical duplicates.
Relevance
Study Information Link
Study Information Link URL
Study Information Visibility Public
GOLD CLASSIFICATION
Ecosystem Engineered
Ecosystem Category Bioremediation
Ecosystem Type Tetrachloroethylene and derivatives
Ecosystem Subtype Chloroethene
Specific Ecosystem Bioreactor
Metagenomic Study Yes
STUDY COMPOSITION
Number of Biosamples 1
Number of Organisms 0
Number of Seq Projects 1
Number of Analysis Projects 1
Number of Related Studies 0

 

 

  You are going to add the following user to ALL Sequencing Projects, Biosamples and Analysis Projects that
sit under this study (a cascading permission update).

 

Contact Name/Email:

Do you want to continue?

 

 

  You are going to remove permissions for the following user to all Sequencing Projects,
Biosamples and Analysis Projects under this study.

 

Contact Name/Email:

Do you want to continue?