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Transcriptional analysis of a Dehalococcoides-containing microbial consortium reveals prophage activation. | LitMetric

Transcriptional analysis of a Dehalococcoides-containing microbial consortium reveals prophage activation.

Appl Environ Microbiol

Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.

Published: February 2012

AI Article Synopsis

  • A shotgun metagenome microarray was created to analyze gene transcription in the KB-1 microbial enrichment culture during VC degradation and starvation conditions, leading to the identification of differentially expressed genes.
  • Results showed that during VC degradation, genes related to metabolism and energy generation in Dehalococcoides were more active, and multiple RDH genes were upregulated in starvation, suggesting many unidentified proteins play roles in cell maintenance without chlorinated compounds.

Article Abstract

Chlorinated solvents are among the most prevalent groundwater contaminants in the industrialized world. Biodegradation with Dehalococcoides-containing mixed cultures is an effective remediation technology. To elucidate transcribed genes in a Dehalococcoides-containing mixed culture, a shotgun metagenome microarray was created and used to investigate gene transcription during vinyl chloride (VC) dechlorination and during starvation (no chlorinated compounds) by a microbial enrichment culture called KB-1. In both treatment conditions, methanol was amended as an electron donor. Subsequently, spots were sequenced that contained the genes most differentially transcribed between the VC-degrading and methanol-only conditions, as well as spots with the highest intensities. Sequencing revealed that during VC degradation Dehalococcoides genes involved in transcription, translation, metabolic energy generation, and amino acid and lipid metabolism and transport were overrepresented in the transcripts compared to the average Dehalococcoides genome. KB-1 rdhA14 (vcrA) was the only reductive dehalogenase homologous (RDH) gene with higher transcript levels during VC degradation, while multiple RDH genes had higher transcript levels in the absence of VC. Numerous hypothetical genes from Dehalococcoides also had higher transcript levels in methanol-only treatments, indicating that many uncharacterized proteins are involved in cell maintenance in the absence of chlorinated substrates. In addition, microarray results prompted biological experiments confirming that electron acceptor limiting conditions activated a Dehalococcoides prophage. Transcripts from Spirochaetes, Chloroflexi, Geobacter, and methanogens demonstrate the importance of non-Dehalococcoides organisms to the culture, and sequencing of identified shotgun clones of interest provided information for follow-on targeted studies.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273020PMC
http://dx.doi.org/10.1128/AEM.06416-11DOI Listing

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