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Researchers use DNA from streams for biodiversity monitoring

Why spend time wading through streams and rivers to catch insects and other small animals with finely meshed nets, when all you need is their DNA in a water sample to check the biodiversity in the watercourse? Using this method, which is called environmental DNA (eDNA), researchers from Aarhus University have detected 212 different species of invertebrates in five Danish watercourses. Twelve of these are entirely new species, never detected in Denmark before.

2021.05.25 | Peter F. Gammelby

Link to larger version of photo

Mads Reinholdt Jensen is taking water samples south of Aarhus. In the background are children from a kindergarten on a field trip. Photo: Eva Egelyng Sigsgaard, AU.

Among other things, the researchers found eDNA from stonefly larvae. The picture shows an adult stage stonefly found in the Store Hansted Å stream. Stoneflies are often found near freshwater streams. They require an aquatic environment with high water quality and are therefore a good indicator of the state of the aquatic environment. Photo: Philip Francis Thomsen, AU

Biologists will still have to use their wellies in future to monitor biodiversity in aquatic environments, however. Sharp eyes and wet hands are still needed to get a true picture of the biology of Danish watercourses.

We will return to this later.

However, by sequencing DNA from water samples, researchers can get a "second opinion" and additional information for their databases of species in the watercourses being monitored.

We have to monitor our watercourses, just as we have to monitor our lakes and all other areas with surface water. That is what the EU Water Framework Directive says. The goal is for all water bodies to have a "good ecological status" by 2027, and this is assessed on the basis of the composition of insect species in water bodies, for example.

Less demanding

However, collecting and identifying insects is demanding and time-consuming. In their larval stages, in particular, the species of insect can be difficult to identify for anyone other than very experienced taxonomists.

Once the method and technology have been scaled up, it will be much easier and faster to take water samples, filter them for eDNA, sequence the eDNA found, and compare the results with a database containing DNA sequences from hundreds of thousands of identified species from around the world.

"We know from several eDNA studies, for example of soil, fertilizer and flowers, that the technique is very effective at detecting species, and it's already being widely used for biomonitoring. Our new study is yet more proof that the method works in a Danish context," says Associate Professor Philip Francis Thomsen from the Department of Biology, Aarhus University.

He is co-author of the study, which has just been published in the journal Environmental DNA.

Twelve species from neighbouring countries

The researchers were rather surprised about the number of species they were able to identify using the eDNA method. They identified a total of 212 species, including DNA traces from 12 species otherwise only known to exist in neighbouring countries, but which may very well also be present in Denmark.

"These animals represent groups that have not been studied particularly thoroughly in Denmark, and they may easily have gone unnoticed hitherto," explains the main author of the study, PhD student Mads Reinholdt Jensen.

eDNA provides the broader picture

The study also revealed that there is a big difference between the number and the composition of species in samples taken in the spring and autumn, respectively.

Watercourses in Denmark are monitored during spring. However, in view of the major changes in species composition between the spring and autumn samples, the researchers believe it would be relevant to study Danish watercourses throughout the year. Otherwise, species that are affected differently by climate and seasonal factors may not be represented in the monitoring data.


Furthermore, using eDNA, the researchers also find DNA traces from species that are not included in the monitoring programme. With data from eDNA, you get an objective picture, so to speak, of the diversity of arthropods on these sites, because the researchers do not differentiate between species that are useful or not useful to monitor, and because they avoid problems of having to distinguish very similar species.

Still somewhat demanding

However, the eDNA method cannot fully replace traditional monitoring. This is because you have to examine whether the species you find traces of actually live in the areas where you found their DNA, and, if so, in what numbers. The DNA may be transported over long distances before it decomposes or is caught in your water sample, although this is more often the exception than the rule.

Additional information

We strive to ensure that all our articles live up to the Danish universities' principles for good research communication (scroll down to find the English version on the web-site). Because of this the article will be supplemented with the following information:

FinansieringCarlsberg Foundation
CollaboratorsThomas Pape, Martin Vinther Sørensen and Reinhardt Møbjerg Kristensen from the Museum of Natural History, University of Copenhagen. Novogene in Cambridge sequenced the DNA.    
Read moreonlinelibrary.wiley.com/doi/full/10.1002/edn3.193
ContactMads Reinholdt Jensen, PhD student, Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, email: mrj@bio.au.dk, mobile: +45 2168 3618
Philip Francis Thomsen, Associate Professor, Section for Genetics, Ecology and Evolution, Department of Biology, Aarhus University, email: pfthomsen@bio.au.dk, mobile: + 45 2714 2046     

Department of Biology, Sustainability