Monitoring fish migration through eDNA

To bring the ecological quality of European waters up to standard, water management entities have to implement extensive sets of measures. In this way they can satisfy the requirements laid out in the Habitats Directive and particularly those in the Water Framework Directive. For fish populations, among other things, the unimpeded spatial use of the habitat is necessary. Connectivity is an important factor and therefore so too is the passability of the many dams, sluices and hydropower plants, which can be obstacles to fish migration – for instance, in the direction of spawning areas, and between areas for growth and wintering. There is still only limited monitoring of the effectiveness of the wide variety of civil engineering solutions used for a free fish migration. Traditional fish capturing techniques are relatively time-consuming and costly, and do not always provide a good picture of the actual use of river basins and fish passages by the target species. Moreover, experimental count methods do not always provide exact information on the species composition, and frequently refer only to a short time period. There is an important need for a fast, qualitative and quantitative method to assess and monitor the distribution and migration of fish populations, as well as the effectiveness of fish passages.


Fish shed so-called environmental DNA (eDNA) through their slime and faeces. This eDNA enables the identification of a species and the determination of the order of magnitude of the abundance of fish populations in various habitats (quantitative analysis of the eDNA). Differences in the abundance in space and time provide an indication of the manner in which the fish populations use the water system. If, for example, upstream from a fish passage in a stream or a river, the abundance of some fish species, on the basis of eDNA, is found to be much lower than that found downstream, this can indicate that an obstacle still exists to the migration of these species. A proper interpretation of such information of course requires appropriate knowledge of fish ecology.


The proposed research involves (1) the reliable detection of fish eDNA (DNA markers; a protocol for sampling eDNA in the field; DNA sample conservation and effective sample handling ; quantification of species-specific eDNA concentrations with qPCR for selected fish species; identification of fish species observed using meta barcoding), but, most of all (2) the validation and interpretation of the eDNA monitoring data acquired. The latter requires a simultaneous use of (3) traditional fishing methods and possibly other approaches, such as automatic counting. Moreover, (4) an effective eDNA field sampling method needs to be developed and tested (spatially, over time ), and be as robust as possible.


Proof-of-principle of a cost-effective and reliable eDNA quick-scan method to determine the distribution of fish populations over a water system; it will also enable the identification of obstacles to connectivity, which possibly hinder the development of a healthy fish community in a river basin.