A brief definition of a genetic method that is really taking off
Every living organism, whether animal or plant, is characterised by its very own DNA sequence. This sequence contains all the genetic information for living beings and so makes it possible to distinguish between both species and individuals. In terms of biodiversity, DNA is therefore a very rich source of information and knowledge, hence the development of methods such as environmental DNA or eDNA.
This non-invasive method of genetic analysis involves taking environmental samples, such as water or soil, and studying the DNA traces left by the animal and plant species that have frequented these environments. These traces come from urine, faeces, saliva etc. and tell us about the presence of organisms, both currently and in the past. In other words, from a simple sample of water or soil, we are able to detect the presence or passage of a species in or through a given environment.
One technique, two levels of analysis: eDNA barcoding and eDNA metabarcoding
While environmental DNA can detect traces of species in a targeted environment, there are two main levels of analysis: barcoding and metabarcoding. But before looking at the difference between these two levels, it is important to understand how environmental DNA works.
How does eDNA work?
An environmental DNA analysis involves 4 steps. It all starts with taking samples of water or soil from the natural environment. Back in the laboratory, the DNA must be recovered and amplified to ensure that there are sufficient quantities to sequence it. DNA sequencing is a technique that consists of determining the DNA sequence of a species, in other words the fragment that is specific to it and that distinguishes it from others. These fragments are then entered into international databases to make them easier to detect in the future.
In 2003, Paul Hebert came up with a new principle for analysing samples faster and more effectively, which involves listing DNA sequences in a large database in the form of barcodes. This means that species can be detected automatically in a sample just by comparing the DNA collected with the samples in the database. This is called molecular barcoding.
These different methods have undergone extraordinary advances since they were introduced, advances that are still making remarkable progress today thanks to current technologies.
What’s the difference between eDNA barcoding and eDNA metabarcoding?
So barcoding involves creating a unique barcode for each species, in the form of a DNA sequence. But what is the difference between simple barcoding and metabarcoding? Their names actually say a lot:
With simple barcoding, the aim is to search for the DNA of a very specific species. For example, the presence of a fish species in water from a river.
With metabarcoding, it is more a question of analysing a complete taxonomic group, in other words a set of living beings. The taxonomic ranks refer to the different levels of classification of the living world. It’s about studying the presence of all the species of fish living in a lake for example.
What can we use environmental DNA for?
This innovative technique has many applications. Here is a non-exhaustive list:
Inventorying the species present in aquatic or terrestrial environments
Monitoring rare or protected species
Detecting invasive alien species
Studying honey samples to characterise their floristic composition
Analysing faeces to determine an animal’s diet
Identifying pathogens in the environment (e.g. detecting traces of SARS-CoV-2 in wastewater during the Covid-19 crisis)
And many more besides…
E-BIOM, a consultancy office and laboratory specialising in environmental DNA
As a spin-off from the University of Namur, we are the only Belgian provider to offer this technique, and one of only a few in Europe. Thanks to a wide range of services, we work tirelessly to conserve biodiversity and protect the environment alongside universities, associations, NGOs and public authorities, as well as companies, architects and landscape designers.