Marine biodiversity assessment using eDNA sequencing

We apply molecular ecology tools to study biodiversity and genetic diversity in the marine ecosystem.

We are constantly developing new tools and methods to enable rapid and affordable diversity monitoring, many of which are based on environmental DNA (eDNA) sampling and metabarcoding. The use of eDNA analysis enables non-invasive monitoring of marine biodiversity. We couple eDNA analysis with Nanopore DNA sequencing, which makes it a very powerful and portable technique, which we can fit in a suitcase and deploy anywhere (see for example the (Dutch) Resource article CSI at Sea). Currently, the focus is on developing more efficient metabarcoding primers for the North Sea ecosystem and building a bioinformatics pipeline which streamlines data-analysis and visualisation (see the Biorxiv preprint).

Furthermore, we have developed autonomous eDNA sampling approaches, which for instance allow for sampling timeseries offshore via a Fish Sensing Box.

Next to that, we are exploring the option of skipping the metabarcoding approach completely and instead sequencing all DNA in the sample, and use the bioinformatic tools available and developed in house to extract the information required for the question that needs answering.

Eventually, the combination of these developments will allow for the development of remote biodiversity monitoring stations that can use eDNA to in real time monitor the marine biodiversity (see the (Dutch) Bionieuws article on expectations for eDNA).

Fish sensing box
Fish sensing box

Other resources