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enzymatic
removal of exogeneous dna for profiling of live drinking water microbiomes

Type of project: MSc thesis
Duration: 6 months
Location: Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, the Netherlands
Salary: The maximum Wetsus allowance for this internship is 425 € per month.  Grant holding students (i.e. Erasmus or other) receiving financial support of less than 425 € per month can apply for a top-up supplement to the maximum allowance.

Background

When water is treated for consumption, disinfection processes further reduce biomass by partial killing of the microbiome. As DNA sequencing does not distinguish DNA from live and dead cells, treated water microbiomes are prone to inaccurate representation when dead cell DNA is not first effectively removed. DNA sequencing technologies facilitate the study of microbiomes and their functions. As the reliability of microbiome data strongly depends on the quality and quantity of DNA extracted from a sample, a challenge arises for low biomass ecosystems, such as drinking water. Here, collected samples often yield little DNA and are prone to contamination that causes bias away from the ecosystem’s true microbiome. Enzymatic breakdown of free DNA using Benzonase has been shown to degrade unprotected DNA of dead cells and other free contaminant DNA. For the specific purpose of accurate microbiome profiling of treated water, in this project you will develop a benzonase-based sample pre-treatment protocol for precise live microbiome quantification and profiling.

Research goals

The main goal of this MSc project is to demonstrate the efficacy of benzonase treatment in removing exogenous and dead cell DNA prior to DNA extraction from drinking water and develop an optimized protocol. A series of experiments will be conducted using bacterial cultures with varying live and dead proportions and spiked with exogenous DNA. The presence and absence of live and dead cell DNA will be assessed using nucleic acid coupled to flow cytometry and qPCR, followed by statistical analysis and data visualization.

Your responsibilities

  • Carry out lab experiments using microbial cultures and drinking water
  • Test the enzymatic DNA degradation efficacy of benzonase with various bacterial live:dead ratios
  • Perform DNA extraction, qPCR and flow cytometry
  • Record and interpret experimental data
  • Write an MSc thesis / article manuscript
  • Present data according to conventional standards

 

Our requirements

  • EU citizen or international student registered at a Dutch university enrolled in a relevant MSc studies (e.g. Biology, Biochemistry, Biotechnology)
  • Overall interest in microbiology and/or molecular biology
  • Previous experience in molecular biology techniques such as DNA extraction and PCR is a plus.
  • Good verbal and written communication skills in English
  • Precise, organized, and reliable

Your benefits

Supervision team: Pieter van Veelen, Denise van de Pol, Adel Bou Alia

Submit a CV (max. 2 A4 pages), motivation letter (max. 1 A4 page) and a list of attended courses via the application form bellow (in English).
Feel free to contact Pieter van Veelen (pieter.vanveelen@wetsus.nl) if you have further questions or need more information.

Application form: Enzymatic removal of exogeneous DNA for profiling of live drinking water microbiomes

  • Max. bestandsgrootte: 1 GB.
  • Max. bestandsgrootte: 1 GB.

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