Onderwerp scriptie

Bioremediation of sites contaminated with halogenated compounds for development of rehabilitation technologies

Environmental concern of widely used halogenated 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. The focus of our research is biodegradation and microbial ecology of halogenated organic pollutants in contaminated aquifers, sediments, soil, drinking water and aquaculture systems.

Practical Approach

We study a wide range of microbial communities involved in bioremediation of halogenated compounds in pure/enrichment cultures to microcosms/mesocosms/columns and also contaminated field sites. Phylogenetic diversity of microbial communities are determined using MiSeq analysis of 16/16S rRNA- and catabolic-genes and in some cases PCR-amplification, cloning and sequence analysis. Quantitative PCR-based assays are used to assess abundance and expression of involved microbial guilds and their catabolic genes and correlations are determined between physical/chemical conditions in the subsurface and the presence and expression of specific microbial groups/genes.

picture project Siavash.jpg

Techniques and Methods

Molecular Methods

  • DNA
    and RNA isolation
  • Quantitative
    PCR
  • Gene
    specific PCR
  • MiSeq
    sequencing
  • Cloning
  • Sanger
    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 HPLC GC-FID,
    GC-MS, Dionex …

More information

Supervisors: Dr. Siavash Atashgahi, Prof. Dr. Hauke Smidt

Contact: siavash.atashgahi@wur.nl; hauke.smidt@wur.nl

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.