Identifying eDNA to understand aquatic biodiversity

Preserving biodiversity is high on the (political) agenda worldwide. The theme has been given quite high priority at both the European level (EU Biodiversity Strategy to 2020) and the global level (UN Convention on Biological Diversity). In the Netherlands and Europe this has led to the necessary legal and regulatory framework, within which it is important that biodiversity be regularly monitored. Such monitoring requires specialised knowledge and expertise and usually involves capturing target organisms. Monitoring programmes are generally extensive and, consequently, expensive. A fast, alternative monitoring approach would be desirable. Moreover, the current inventory methods can often miss less commonly occurring (rare) organisms. Biodiversity is in this way underestimated, or organisms’ habitats might be unjustifiably disturbed. DNA techniques can provide an alternative to regular monitoring techniques.


The main objective of this project was to arrive at a demonstrably functional alternative monitoring method for inventorizing aquatic biodiversity. To develop such a method, use was made of generic (e)DNA methods to inventory the aquatic biodiversity of target species. The methods applied included meta barcoding and next generation sequencing. The target species focused on were groups of macrofauna and macroflora, which are referred to in the Water Framework Directive (WFD).


The final outcome is the translation of (e)DNA to water management practice.

Specifically, the project’s results are:

  • DNA barcodes of both well-identified collections of the Naturalis Biodiversity Center and newly collected material, with first priority for macrofauna and macroflora.
  • Optimised primer sets (=DNA tools) for meta-barcoding analysis of the prioritised macrofauna groups.
  • Developed specific eDNA methods, validated under field conditions, for a number of target species within the prioritised macrofauna groups and water plants that are of importance within the European legal and regulatory framework.
  • A guide for the interpretation of DNA information in the current legal and regulatory framework. The screening of surface water produced new insights concerning the species composition of a number of organisms.

The project began in 2014 and concluded in 2016. Steps were taken in the project towards the collection of missing species and a number of them were added to the list; the lists are however not yet complete. Several target organisms were delivered to KWR Water Research Institute and the eDNA primers were tested. For Myriophyllum, Naturalis designed special primers for Sanger sequencing of museum collections. The water samples collected by Koeman and Bijkerk were processed in the KWR lab. The pre-processed samples were then sent to Baseclear for NGS analysis. The results were subsequently jointly interpreted by Baseclear and Naturalis, which led to the development of good species lists which partly matched other species lists like those produced by existing techniques. The correspondences between the lists were clearer at the genus level. A study by RoyalHaskoningDHV demonstrated that the KWR scores, based on genera, do not show significant disparities compared to the KWR scores based on species.