Environmental DNA

Environmental DNA

Environmental DNA is the environmental monitoring equivalent of CSI, or forensic science research, where we look for bits of microscopic DNA in nature to figure out which species live there.

Living organisms constantly release bits of DNA to the environment around them in the form of skin and hair cells, saliva, faeces and the like. Environmental DNA technology can use the evidence we find in water and soil samples to monitor species diversity in nature without us ever having to see or hear the species being detected. 

Analyses of environmental DNA are often more cost-effective, and in many cases also more accurate than traditional field methods for species inventories and monitoring. Today, we use this technology to detect rare Red List species, track the unwanted spread of alien species or describe species diversity in nature.

Species-specific and species-general analyses of environmental DNA

Environmental DNA is what we call the DNA fragments we find in water and soil samples. We use two different methods to analyse these DNA bits. One is a relatively simple method where we check if DNA from a specific species is found in the sample. The other is a slightly more complicated method, where we examine the sample to see how many different species we can detect.

Species-specific analyses with a qPCR or digital PCR machine search for a genetic marker that is only found in the species we are looking for. We then get a yes or no answer in relation to whether DNA from this species is found in the sample, and we can measure the concentration of the DNA in the sample to say something about how common the species is.

Species-general analyses use a genetic marker that is found in many species, and are often used when we want to investigate a specific species group such as fish, amphibians, insects or mammals. We then use a DNA metabarcoding analysis where a machine reads millions of short DNA fragments which are then compared with a reference database to determine the species from which each DNA fragment originates. Ideally, we can then identify all the species from the species group we are interested in. We can also add up how many DNA fragments we find for each species as a measure of relative quantity, although this approach is still somewhat under debate. The DNA fragments also show a good deal of variation within species, which means we can also look at genetic variation between different areas and changes over time for each species. These analyses provide an even finer scale for studying species than a traditional species list.

Environmental DNA has a wide range of uses

Environmental DNA can allow us to describe the species diversity in an entire ecosystem using water and soil samples and more. In addition, DNA samples can be stored for a long time, which make them a historical reference sample for today's biodiversity in relation to future climate change or other impacts.

We currently use environmental DNA in a number of different projects at NINA. We analyse water and soil samples to track individual species or describe species diversity in different species groups. We also use a number of other sample types where all or part of the animals we want to examine are in the sample. We use DNA metabarcoding to analyse hundreds of insects collected in a bottle at the same time, we use stool samples from deer and wild boar to look at their diets, we analyse pollen from bumblebees and other bees to see which flower species they visit, and we analyse plankton samples from both freshwater and saltwater to look at species diversity and quantify the density of salmon lice in the sea, among other things.

Environmental DNA in water

Most people who have heard of environmental DNA associate it with water samples. By filtering water through a fine-mesh filter, we can collect DNA fragments that float water, which we can then use genetic analysis to identify species.

NINA offers a separate environmental DNA kit for sampling water samples in rivers and lakes. With this simple equipment, anyone can take environmental DNA samples which they can submit for analysis at NINA. Frode Fossøy or Rolf Sivertsgård are the contacts for people interested in kits.

We use species-specific markers to identify individual species and species-general markers to describe the species diversity of species groups in the aquatic environment. Species-specific analyses use a qPCR or a digital PCR machine to look for a genetic marker that is only found in the species we are looking for. Species-general analyses rely on a genetic marker that is found in many species, so we use this approach when we want to investigate a specific species group such as fish, amphibians, insects or mammals. This approach uses DNA metabarcoding, where a machine reads millions of short DNA fragments which are then compared to a reference database to determine which species each DNA fragment originates from.

By filtering water through a fine-mesh filter, we can collect DNA fragments that float water, which we can then use genetic analysis to identify species. Photo: Frode Fossøy / NINA

Contact

Frode Fossøy
Senior Research Scientist, Aquatic Biodiversity

Norwegian Institute for Nature Research

NINA is an independent foundation for nature research and research on the interaction between human society, natural resources and biodiversity.
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