eDentity: a national eDNA infrastructure

Janus G3 robot

Imagine a world where we can quickly and cost-effectively identify all species in a single environmental sample.

Naturalis's eDentity program unlocks the power of eDNA analysis for advanced biomonitoring by integrating scalable DNA metabarcoding solutions with high-quality reference databases. This innovative approach makes it possible to analyze large quantities of soil, water, and air samples quickly and affordably—essential for policy makers, research institutes, nature and environmental organizations, and businesses that rely on accurate biodiversity data for conservation and environmental management.

This project is currently managed by Reinier van der Geest. 
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Naturalis' scientific director Vincent Merckx is also heavily involved with eDentity.

 

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Leaflet © OpenStreetMap contributors © CARTO

Why
eDentity?

Traditional methods for species identification are time-consuming and require specialized expertise. Using powerful technology, it is now possible to detect different species in a single sample - for example, a scoop of soil or a tube of water. This is done by using DNA traces they leave behind in their environment, called environmental DNA (eDNA).  eDentity streamlines this process, enabling large-scale and virtually real-time biodiversity monitoring in the Netherlands. With the goal of collecting 75,000 samples within three years, we are building a national reference database of Dutch eDNA biodiversity.

Planned
timeline

By 2028, we will deliver a research infrastructure capable of analysing large quantities of eDNA samples with standardised procedures. The infrastructure is capable of facilitating all steps of the analysis process; from sampling to data analysis, data interpretation and reporting. The data meet predefined quality requirements, we have a fast turnaround time and the eDNA metabarcoding facility is able to process very high numbers of samples with minimal downtime.

  • By mid-2025, all necessary equipment for our lab facility will be operational.
  • Naturalis's digital infrastructure for analyzing and processing all acquired data will be completed by the end of 2025. After 2025, this digital infrastructure will be further developed to implement a fully automated process.
  • We also aim to have the first data available by the end of 2025. 

We are
looking for partners

Collecting tens of thousands of samples is quite a challenge! We are therefore looking for partners who, like Naturalis, feel the need to conduct large-scale biodiversity research. Initially, we will talk to governments, implementing organisations and site managers with ongoing monitoring programmes.

Do you want to become a participant?

Put me on your mailing list!

Minister Dijkgraaf taking a soil sample
Samples in IJmuiden

Information &
documentation

If you are a partner already, you'll appreciate this page with all our documentation, instruction and other materials that will help you make the most of eDentity. 

Information for participants

eDentity sampling kit
small tube with soil sample

Frequently Asked
Questions

What exactly is eDentity?
eDentity uses environmental DNA (eDNA) technology to collect and analyse biodiversity data in a non-invasive and highly efficient way. This approach provides valuable insights into the flora and fauna of the Netherlands, without disturbing ecosystems. With support from the Ministry of Economic Affairs and Climate, eDentity is developing a state-of-the-art facility capable of processing thousands of samples per year. This initiative provides a solid foundation for data-driven policy decisions and nature conservation.

What happens to the data. 
The data we collect through soil, water and air samples are carefully stored and processed by Naturalis. All data are shared according to the FAIR principle: Findable, Accessible, Interoperable and Reusable. This means that they are made available in a transparent and structured way. We anonymise data where necessary. The insights contribute to a better understanding of biodiversity in the Netherlands - and are thus of value to everyone working with nature and the living environment.

How is my location selected?
To get a representative picture of biodiversity in the Netherlands, we aim for the fullest possible geographical distribution as well as a wide variety. We actively approach partners in different regions and ecosystems - from nature reserves and agricultural land to urban zones and wetlands. Together, we determine whether and how your location fits into eDentity's national network.

Can I participate as an individual?
At the moment, participation is only possible for organisations and not for private individuals. We are focusing at this stage on setting up a solid digital infrastructure and establishing a laboratory facility capable of processing 75,000 samples from all over the Netherlands. In doing so, the focus is on building a representative network of analysis sites in cooperation with partners. Still interested as an individual? Let us know - we are happy to think along with you or refer you to related initiatives.

What will eDentity not do?
Because we use a small amount of soil or air within eDentity, we cannot give 100% certainty about the presence or absence of a species. To minimise this so-called sampling effect, we try to take multiple samples in a given area, at different times. Metabarcoding technology also cannot say anything about the absolute number of individuals of a species in an environmental sample or the functions of species in the ecosystem.

What good is a new infrastructure if we can only name about half of the species by DNA analysis?
Naturalis is busy expanding the DNA reference database of Dutch (eukaryotic) species on a daily basis. We do this with ARISE but also with our extensive natural history reference collection that includes many Dutch species. But we will also be able to monitor species we cannot (yet) name with this infrastructure.

Are you only looking at multicellular species? Those are a minority!
That's true. eDentity does not as yet focus on analysis of bacteria and viruses. Other institutes, such as the RIVM, use metabarcoding to analyse these groups. In this regard, the data generated by both Naturalis and the RIVM are complementary.