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Kevin Beentjes

Kevin Beentjes - PhD, DNA waterscan


Email: kevin.beentjes@naturalis.nl
Phone: 071-5271911
Room number: Leiden, Sylvius e06.04.18a


After working in the molecular laboratories of Naturalis for close to five years, I started doing my PhD in the DNA Waterscan project. My background lies in molecular and forensic biology. During my time as a research technician at

Naturalis I worked on the FES-funded Dutch DNA barcoding campaign, on many different projects dealing with vertebrates, invertebrates, plants and fungi. As of 2017, I started my PhD in the field of metabarcoding and environmental DNA, with a focus on macroinvertebrates communities in Dutch freshwater systems.


Research interest

My main research interest at the moment is the application of molecular techniques in the monitoring of freshwater macroinvertebrates. These monitoring programs are part of the European Water Framwork Directive, which have been interpreted in the Netherlands by the Kader Richtlijn Water. Integrating molecular strategies may allow for better and more standardized inventories of macroinvertebrate communities. The ultimate goal is to adapt environmental DNA techniques for the detection and identification of freshwater species with non-invasive sampling.


environmental dna, freshwater, metabarcoding, invertebrates

Current research topics

My current research entails the molecular part of the DNA Waterscan project, funded by the Gieskes-Strijbis Fonds

This PhD project is supervised by Prof. Dr. Menno Schilthuizen and Dr. Arjen Speksnijder. In order to adapt molecular tools for the detection, identification and monitoring of macroinvertebrate species in freshwater, several sub-projects have been created, dealing with the various questions that arise when working with molecular data, such as;

  • How to optimize metabarcoding strategies and sequencing pipelines for the successful bulk identification of complex samples
  • How to use environmental DNA to detect and identify macroinvertebrate species
  • Temporal and spatial patterns of environmental DNA signals
  • Differences in measured communities with morphological monitoring versus molecular tools
  • The creation of a reference library with DNA sequence data


Within this project, there are multiple collaborations with partners such as the Institute of Environmental Sciences (CML) of Leiden University, Hoogheemraadschap van Rijnland, Aquon, and Staatsbosbeheer. The creation of the DNA reference library is a follow-up project of the FES-funded DNA Barcoding project, in which I work closely with the amateur taxonomist network of Stichting EIS.



I’ve assisted in several courses, including the first-year’s field course “Excursies Flora & Fauna”, and provided guest lectures both in and outside Leiden. I regularly supervise BSc and MSc research projects and internships. Check the Naturalis website for available projects, or send me an email to discuss possibilities.

Supervision MSc Students

2016 Supervisor - Visser J. - Optimal sampling time and methods for environmental DNA detection of aquatic beetles

Supervision BSc Students

2018 Supervisor - Groen S. - Metabarcoding van eDNA-samples voor de detectie van algen
2018 Supervisor - Ocké K. - Community analysis of environmental DNA in WFD samples
2018 Supervisor - Mankoe R. - Identification of fish communities with environmental DNA
2017 Supervisor - Feiner F. - DNA barcoding van aquatische referentie specimens
2017 Supervisor - Pelkmans J. - Onderzoek naar het gedrag van eDNA in stilstaande wateren
2017 Supervisor - Tijs W. - Species identification through mass sequencing as an alternate method for the determination of ecological state within aquatic systems
2016 Supervisor - Gil Cantero D. - Optimization of DNA isolation for NGS taxonomic studies in water quality monitoring
2016 Supervisor - Suttie R. - Molecular identification of complex macrofauna samples
Available student projects

Public outreach

Both the DNA Barcoding and the DNA Waterscan projects have given me ample opportunity to talk about the work I and my colleagues do at Naturalis. Some examples:



Journals SCI, peer-reviewed

Beentjes K.K., Speksnijder A.G.C.L., Schilthuizen M., Schaub B.E.M., Hoorn B.B. van der 2018. The influence of macroinvertebrate abundance on the assessment of freshwater quality in The Netherlands. Metabarcoding and Metagenomics 2: e26744.
Go to website (DOI)

Journals non-SCI, peer-reviewed

Smit J.T., Dijkstra K.D.B., Beentjes K., Miller J., Madden H., Hoorn B. van der 2018. First records of Odonata from Sint Eustatius, Dutch Lesser Antilles. Notulae Odonatologicae 9: 78-82.
Go to website (DOI)


Journals SCI, peer-reviewed

Schilthuizen M., Santos Pimenta L.P., Lammers Y., Steenbergen P.J., Flohil M., Beveridge N.G.P., Duijn, P.T. van, Meulblok M.M., Sosef N., Ven R. van de, Werring R., Beentjes K.K., Meijer K., Vos R.A., Vrieling K., Gravendeel B., Choi Y., Verpoorte R., Smit C., Beukeboom L.B. 2016. Incorporation of an invasive plant into a native insect herbivore food web. PeerJ 4: e1954.
Go to website (DOI)


Journals SCI, peer-reviewed

Karremans A.P., Pupulin F., Grimaldi D., Beentjes K.K., Butôt R., Fazzi G.E., Kaspers K., Kruizinga J., Roessingh P., Smets E.F., Gravendeel B. 2015. Pollination of Specklinia by nectar-feeding Drosophila: the first reported case of a deceptive syndrome employing aggregation pheromones in Orchidaceae. Annals of Botany 116: 437-455.
Go to website (DOI)

Merckx V.S.F.T., Hendriks K.P., Beentjes K.K., Mennes C.B., Becking L.E., Peijnenburg K.T.C.A., Afendy A., Arumugam N., de Boer H., Biun A., Buang M.M., Chen P.-P., Chung A.Y.C., Dow R., Feijen F.A.A., Feijen H., Feijen-van Soest C, Geml J., Geurts R., Gravendeel B., Hovenkamp P., Imbun P., Ipor I., Janssens S.B., Jocqué M. Kappes H., Khoo E., Koomen P., Lens F., Majapun R.J., Morgado L.N., Neupane S., Nieser N., Pereira J.T., Rahman H., Sabran S., Sawang A., Schwallier R.M., Shim P.-S., Smit H., Sol N., Spait M., Stech M., Stokvis F., Sugau J.B., Suleiman M., Sumail S., Thomas D.C., van Tol J., Tuh F.Y.Y., Yahya B.E., Nais J., Repin R., Lakim M. & Schilthuizen M. 2015. Evolution of endemism on a young tropical mountain. Nature 524: 347-350.
Go to website (DOI)


Journals SCI, peer-reviewed

Miller J.A., MillerJ.H., Pham D-S., Beentjes K.K. 2014. Cyberdiversity: improving the informatic value of diverse tropical arthropod inventories. PLOS ONE 9: e115750.
Go to website (URI)


Journals SCI, peer-reviewed

Miller J.A., Beentjes K.K., Helsdingen P. van, IJland S. 2013. Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol. ZooKeys 365: 245-261.
Go to website (URI)

Aliabadian M., Beentjes K.K, Roselaar C.S., Brandwijk H. van, Nijman V., Vonk R. 2013. DNA barcoding of Dutch birds. ZooKeys 365: 25-48.

Gravendeel B., Groot A. de, Kik M., Beentjes K.K., Bergman H., Caniglia R., Cremers H., Fabbri E., Groenenberg D., Grone A., Groot Bruinderink G., Font L., Hakhof J., Harms V., Jansman H., Janssen R., Lammertsma D., Laros I., Linnartz L., Marel D. van der, Mulder J.L., Mije S. van der, Nieman A.M., Nowak C., Randi E., Rijks M., Speksnijder A., Vonhof H.B. 2013. The first wolf found in the Netherlands in 150 years was the victim of a wildlife crime. Lutra 56: 93-109.

Journals non-SCI, peer-reviewed

Miller J., Belgers J., Beentjes K., Zwakhals K., Helsdingen P. van 2013. Spider hosts (Arachnida, Araneae) and wasp parasitoids (Insecta, Hymenoptera, Ichneumonidae, Ephialtini) matched using DNA barcodes. Biodiversity Data Journal 1: 1-20.
Go to website (URI)