Monitoring environmental quality by analyzing environmental DNA samples

Monitoring Environmental Quality

Background and context

Classical monitoring of biodiversity is based on site visits, visual observations and identifications, and sampling/catching of organisms. Nowadays this can be supplemented by analyzing DNA from soil or water samples. Fingerprinting techniques and DNA barcodes may enable automated processing of samples for routine identifications. Nevertheless, monitoring the field remains essential, at least to validate the results of the automated process. Naturalis is currently developing a pipeline for this eDNA procedure. Multiple student projects are possible within the project, each focusing on a particular aspect of the eDNA workflow.

Objectives and goals

Naturalis is presently carrying out a large project to use DNA present in fresh water samples to monitor biodiversity and consequently water quality. Sampling of relevant water basins is now opportune (and further process these samples) as well as carrying out checks in the field. The procedure of sampling, DNA extraction and amplification, and next-generation sequencing will be optimized to work towards monitoring standards. The combined information will be used to evaluate the value and level of confidence of the eDNA procedure.

Methods, tasks and approach

Compare and evaluate DNA extraction methods for water samples. Analyze the primer bias and amplification efficiency for NGS purposes. Use the existing pipe-line system, collect water samples in the field and use traditional collecting and observation methods to have an independent check of the eDNA results. Analyze the resulting information in terms of water quality parameters.


Kevin Beentjes, Berry van der Hoorn


Period and duration

ca. 4-9 months

Study and level

Biology, BSc or MSc