Thesis subject

Exploring microbial DNA resources for bioremediation of sites contaminated with chlorinated compounds for development of rehabilitation technologies

Environmental concern of widely used chlorinated compounds has stimulated the research of relatively unknown anaerobic organisms and communities that determine the fate of these halogenated compounds in anaerobic environments.

To develop optimal conditions for bioremediation processes, reliable and efficient methods to follow the fate, distribution and activity of the relevant dehalogenating microorganisms are needed. Current microbiological culture techniques often capture only a minor fraction of the bacteria present in the environment and, in addition, require extended incubation periods. Increasing efforts are currently being made to develop novel ecogenomics tools for the monitoring of bioremediation processes, and the identification and isolation of yet unknown dehalogenating microorganisms.

Aim

The aim of this project will be to explore and characterise the dehalogenating microbial communities at contaminated sites.

Practical Approach

Soil and Groundwater samples from sites in The Netherlands contaminated with chlorinated ethenes will be retrieved. Phylogenetic diversity of microbial communities from these contaminated sites will be determined based on SSU rRNA- and catabolic gene-specific PCR-amplification, cloning and sequence analysis. Quantitative PCR-based assays will be used to assess expression of dehalogenase genes (bioremediation functional loci) and correlations determined between physical/chemical conditions in the subsurface and the presence and expression of bioremediation functional loci.

Techniques and Methods

Molecular Methods

  • DNA and RNA isolation
  • DGGE (Denaturant gradient gel electrophoresis)
  • Quantitative PCR
  • Gene specific PCR
  • Cloning
  • Sequencing and Sequence Analysis
  • Primer Design

Physiological Methods

  • Growing anaerobic dechlorinating bacteria under different environmental conditions
  • Following the contaminant and substrate concentrations via measurements in GC, HPLC, GC-MS, Dionex, Chlor-o-counter

More information

Supervisors: Farai Maphosa, Hauke Smidt
Contact info: farai.maphosa@wur.nl
Tel: 0317-483486
Laboratory of Microbiology
Microbiology building, room 020
Duration: 4-6.5 months

This project is mainly designed for an MSc thesis (6 months), yet it is possible to have a short term (4 months) project. This project aims to give students experience with growing cultures in anaerobic conditions, working with different molecular techniques and data analysis. Please do not hesitate to contact us for further information.