The detection of rare and cryptic aquatic species with conventional methods, such as electrofishing, is often time-consuming, affects the organisms and their habitats and cannot always be applied on a larger scale due to economic reasons. This can be remedied by eDNA barcoding (environmental-DNA), in which a species is detected by its DNA in the water. In a project of the GMO laboratory and the Fachabteilung Oberflächengewässer of the Umweltbundesamt, methods for sampling of eDNA, fixing of samples, transport, storage, DNA extraction, and amplification of DNA were established.

The competencies gained were tested within the scope of a biological monitoring at the March River from 2017 – 2019 using the weatherfish, Misgurnus fossilis, as study species. One of the main challenges was the high content of organic substances in the waters of the March floodplains, which makes the extraction of useful DNA material more difficult. Nevertheless, it could be shown that the detection of the weatherfish using eDNA is as reliable as the detection using the more elaborating electrofishing. Although the use of eDNA has still limitations – neither the number (abundance) can be estimated exactly nor the vitality, sex, weight, and length of the individuals nor their willingness to spawn can be determined – it is a promising method. Thanks to the established “Standard Operating Procedures” (SOPs), the application of the eDNA approach is ready to use for routine surveys at the Umweltbundesamt for future studies.