Using eDNA to Monitor Fish Dispersal

Environmental DNA is a hot topic in biomonitoring. But what is it exactly, and how can it be used to monitor the dispersal of a reintroduced fish species? (Image credit: Gunnar Jacobs, CC BY-SA 2.0, Image Cropped).

Guest post by Christopher Hempel

Using environmental DNA to monitor the reintroduction success of the Rhine sculpin (Cottus rhenanus) in a restored stream (2019) Hempel et al., PeerJ,

The Crux

The term “environmental DNA (eDNA)” is currently booming in molecular ecology. But what exactly is this technological marvel? Essentially, eDNA comprises all DNA released by organisms into their environment, and originates from mucus, scales, faeces, epidermal cells, saliva, urine, hair, feathers – basically anything an organism might get rid of during its life. The eDNA can be collected from the environment, extracted, and analyzed to detect species using molecular approaches. As this is a very sensitive and non-invasive approach, it is a very hot topic for biomonitoring.

eDNA can be collected from any animal (in theory), but aquatic organisms in particular have been shown to be good target individuals (as eDNA is easiest to handle in water samples). Consequently, there are many studies using eDNA to monitor the activity of fish, reaching from the presence of invasive species to the effects of aquaculture. Here, we applied eDNA analysis to monitor a reintroduced fish species, the Rhine sculpin. The sculpin’s poor swimming ability make it useful as a bioindicator of the passability of streams and rivers. We wanted to investigate the potential of using eDNA to monitor the dispersal of the species in a remediated stream on a fine spatial and temporal scale.

What We Did

We reintroduced 118 individuals of the Rhine sculpin into a small German stream. The stream has been used as an open sewer system for wastewater disposal from the 19th century on, but recent conservation work has left the stream partially restored (or ‘remediated’) and it now represents a near-natural ecosystem. We installed a barrier downstream of the reintroduction sites and took water samples every 50 meters upstream of the sites, up to 550 meters. 300 meters beyond the last sampling site upstream there was a loose stone dam, which was expected to represent a dispersal barrier for the fish.

We sampled every third day for ten days, then once a month for three months. After one year, we took additional samples, and also carried out electrofishing (temporarily stunning fish with electroshocks) to visually validate our findings. Due to unexpected findings, we again sampled after one more month.

We filtered the water samples and processed the filters in the laboratory to extract eDNA. We then analyzed the eDNA in the laboratory to detect eDNA of the Rhine sculpin, which indicated the presence of the fish.

Did You Know: The Fate of Stream and River eDNA

Although eDNA is supposed to be fragile and only present as single molecules, it persists surprisingly well in freshwater, and shows an incredible transportation potential. These fragile molecules are able to survive up to one month in aquatic environments, and were shown to be transported up to 130 kilometer downstream in rivers. There are hence attempts to establish eDNA as a biomonitoring tool for whole ecosystems, taking advantage of its long persistence and travel distances. The aim is to detect all species of an ecosystem by taking water samples from terminal lakes, in which all streams and rivers flow into, accumulating eDNA from every animal that got in contact with those streams and rivers. If this idea is feasible needs to be seen.

What We Found

We found that the fish dispersed qickly initially (200 meters within the first five days) makign it to the last sampling site within the first ten days. This is almost eight ties as fast as previously observed behaviour. Most likely, the high number of reintroduced individuals led to high competition between individuals and hence to rapid dispersal in upstream direction.

We also found that within the first 104 days, the dispersal stopped at the potential dispersal barrier 300 meters upstream. One year later, we still did not find the species upstream of the barrier using electrofishing. However, we surprisingly detected eDNA of the fish upstream of the barrier. To make sure this was not due to sample contamination, we collected water samples after one more month and again detected Rhine sculpin eDNA, validating the presence of the species upstream of the barrier. We only guess as to how the fish was able to cross the barrier. Maybe small individuals were able to swim through the lose stone dam, or the fish were able to swim over the dam during rare flooding events. It is also possible that children, who frequently play at the stream, transferred individuals into the section upstream of the barrier.

Finally, we found a much higher detection rate of Rhine sculpin eDNA at every single sampling site downstream of the barrier after one year, and also visually detected several individuals at every sampling site via electrofishing, including juveniles. This confirms the successful establishment of the species in the remediated stream.


Production (top) and collection (bottom) of environmental DNA, shown for the Rhine sculpin (Image Credit: Christopher Hempel, CC BY-SA 2.0)


In theory, a single DNA molecule is enough to be detected using molecular approaches, but in practice bias can be introduced at several steps during the molecular sample processing. We failed to detect eDNA at times, even when we’d previously detected it in the same place before. We need to keep in in mind that no eDNA detection of the species does not mean it is not there.

So What?

So how does science benefit from knowing that the dispersal of a reintroduced fish species could be monitored using eDNA? Well, our results represent two scientifically new insights. Number one is that eDNA analysis is not only applicable for large-scale dispersal monitoring as has been shown in previous studies, but also on a smaller, more detailed scale. This implies that eDNA analysis is applicable for detailed dispersal monitoring of reintroduced or invasive species, at least in freshwater.

It also means that eDNA analysis can be a useful tool to investigate remediation processes, as it validated the good passability of the remediated stream section, even for a fish with poor swimming abilities. This was not possible within this study using traditional electrofishing. eDNA has the potential for being used as an ecosystem monitoring tool for future water management.

Christopher Hempel is a PhD Candidate at the University of Guelph. You can follow his work on Twitter here.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s