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Monitoring vissen met eDNA metabarcoding
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Fish monitoring in large rivers using eDNA metabarcoding

Field research on the boat
Mini laboratory on board

In 2018, Bureau Waardenburg carried out a research pilot for Rijkswaterstaat to investigate whether eDNA metabarcoding is an effective and reliable method for monitoring fish species in riverine waters. 

For this purpose, water samples were taken at various locations in three large rivers (the Rhine, Nieuwe Waterweg and Haringvliet) over a period of 6 months and analyzed in the laboratory.

Within the selected water bodies, it has been investigated if species lists can be generated using eDNA metabarcoding and if the way of sampling (such as sample type, location and time of the year) influences the eDNA detection of river fish.

Using eDNA metabarcoding, more species are detected than with traditional methodologies. There is a cumulative effect on species richness when sampling different habitats and when taking multiple water samples. Applying multiple primers, for both 12s and 16s DNA target regions, also has a cumulative effect on species richness.


In conclusion, eDNA metabarcoding is well applicable and suitable to obtain a qualitative picture of the fish species in national waters.

A good and reliable reference database is essential. The method is complementary to traditional fish monitoring: both methods yield both similar and unique species. However, it must be taken into account that eDNA metabarcoding provides a fundamentally different type of data: since eDNA does not necessarily originate from the sampling site, the geographic scale to which this qualitative picture applies must be further defined. Also, it is not yet possible to reliably map species abundance.

The research was conducted in collaboration with Datura Molecular Solutions and KWR Water Cycle research.


The report can be downloaded here (only in Dutch): 'Effectiviteit van eDNA metabarcoding voor vismonitoring rijkswateren'.
An article about the study was also published in Water Matters (December 2020).  This English version of the article can be read online here.