7.12 Single cell microbial physiology to monitor the water quality in treatment processes and water distribution systems

Drinking water companies are constantly monitoring the quality of the water in their distribution networks. The companies are mainly interested in the fast detection of deviations in water quality. Whatever the origin of the contamination, rapid identification is needed to ensure water quality and subsequent consumer safety and satisfaction. Despite a wide and ever-increasing variety of molecular techniques available in the microbiologist’s toolbox of analytical methods, their use for the routine microbiological examination of drinking water is still limited and restricted to the presence or absence of (specific) microorganisms. The methods (Q-PCR, PCR, FISH) are mostly used for the detection of specific bacteria (Legionella species) or confirmation of the microbial identity of colonies grown on specific agar plates (coliforms, Clostridia, Aeromonads etc.). Lack of sensitivity, complexity, and the relative costs of molecular, compared to traditional, methods and regulatory restrictions are factors that have limited the acceptance of molecular techniques by water utilities and drinking water testing laboratories. The decrease in costs for equipment, DNA/RNA-sequencing, synthesis of DNA probes, user-friendly bioinformatics software might change this situation rapidly in the future.

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.

We are looking for a candidate with an MSc degree in the field of molecular microbiology (microbial genetics, bio-informatics, microbial physiology) with excellent experimental and theoretical skills and experience with handling very small volumes. Affinity of bioinformatics is essential.
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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Wetsus, Leeuwarden, The Netherlands

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