PhD position: Single cell microbial physiology to monitor the water quality in treatment processes and water distribution systems, the Netherlands

Research challenge

Microbial cells use their environment to translate a part of their DNA into proteins that lead to metabolic activity. RNA is the intermediate between the DNA and the proteins. Sensitive RNA analysis is possible because known technologies are available to amplify the number of RNA molecules to such an extent that allows detection and identification of the RNA molecule by sequencing. This allows, in principle, the detection of a single RNA molecule in a single microbial cell. In this project, the focus will be on the in-situ quantification of RNA expression patterns at single cell level. RNA patterns give information on the metabolic state of the microbial community and give an indication on the identity and concentration of bio-active substances in the water and which reactions/changes will take place in the water column and associated biofilm.

In this project, the PhD candidate will work on:

• Isolation of single cells at affordable costs (FACS, microfluidic cell-sorting)

• Isolation and amplification of RNA from a single cell

• Direct sequencing of isolated RNA

• Annotate RNA without annotated DNA genomes being present (bioinformatics)

• Handle the cell to cell variation of single cells in relation to changes in the environment (correlation statistics, principal component analysis, Big data)

• Design technological principles for automated water quality monitoring systems based on the metabolic activity of the endogenous microbial community


  • excellent experimental and theoretical skills and experience with handling very small volumes. Affinity of bioinformatics is essential

Specific Requirements

  •  MSc degree in the field of molecular microbiology (microbial genetics, bio-informatics, microbial physiology)

The research project is part of the Wetsus research theme Genomics-based water quality monitoring. The following companies are part of the theme: Vitens (, Biotrack (, Evides ( en Vereniging Participanten Waterketen Noord Nederland.

Promotor: Prof. dr. J. Kok (University of Groningen, Faculty of Science and Engineering, Molecular Genetics)

Co-promotor: Prof. dr. G.J.W. Euverink (University of Groningen, Faculty of Science and Engineering, Products and Processes for Biotechnology)

Wetsus supervisor: Dr. Inez Dinkla

For more information contact

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