eDNA metabarcoding makes it possible to map the entire populations in one sample. The technique is similar to a normal eDNA test, but instead of species specific primers, universal primers are used. The DNA sequence of the amplified product is then read (next geneneration sequencing), resulting in a list of all fish occurring in the sampled water.
One sample (1 liter) was filtrated from the Hunze near Gieterveen (The Netherlands). The sample was taken at the surface in the main stream of the river. After sampling, the sample was immediately taken to the lab
After arriving at the lab, the DNA was isolated for analysis. A PCR was performed using universal primers to obtain multiple copies of a specific DNA region from all fish species present. A total of one million reads (read DNA molecules) was obtained from this PCR product via Next generation sequening. The reads were compared with the fish DNA database of Sylphium and a species list was generated from this.
The generated species list consisted of 17 different fish species (see figure). In about the same sampling period, the entire fish population was mapped in the same area via traditional monitoring. This resulted in a species list of 14 different fish. This revealed that all fish species detected via traditional monitoring also appeared in the species list obtained via eDNA metabarcoding.