Identifying eDNA to understand aquatic biodiversity

Edwin Kardinaal PhD

  • Start date
    01 Jan 2014
  • End date
    30 Jun 2016
  • collaborating partners
    BASECLEAR, Hogeschool Leiden, Koeman en Bijkerk BV, KWR, Naturalis and Royal HaskoningDHV

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. Drawing on DNA techniques, a new method can now be developed that provides an alternative to regular monitoring techniques.


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


Translating (e)DNA to water management practice is the ultimate result.

The intended partial results of the project 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, which have been 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. It is expected that the screening of surface water will produce new insights concerning the species composition of a number of organisms. Based on these insights, water quality will have to be redefined. This project provides an impulse for such a definitional change.

The two-year project began in 2014. The initial steps regarding the collection of missing species have been taken, and a number of them have been added to the list. Several target organisms have been delivered to KWR Watercycle Research Institute and the design of the eDNA primers has begun. For Myriophyllum, Naturalis has 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 initial NGS analysis. The results were subsequently interpreted by Baseclear and Naturalis, which led to the development of good species lists. These lists are now being further interpreted, and set against the WFD yardsticks, by RoyalHaskoningDHV.