What is Environmental DNA (eDNA)?

You are constantly shedding skin, hair, and other things that contain your DNA so it should be no surprise that other organisms are also "losing" DNA to their environment. We call this "environmental DNA" or eDNA and we are able to take a sample from the environment and identify the species present in that sample. While we can do this with soils, snow, the air, and other environments, it should be no surprise that eDNA sampling is probably most effective in aquatic systems as DNA can remain suspended in water.

DNA is the code for life. DNA is used to create mRNA which is then translated into proteins.

Source: University of Minnesota Classroom Partners

Environmental DNA has been been widely applied in aquatic systems. It has been used in lakes (e.g. Hervé et al. 2022), wetlands (e.g. Bird et al. 2024), the shallow (e.g. Dan et al. 2024) and deep ocean (e.g. McClenaghan et al. 2024), and maybe most effectively in streams and rivers (e.g.Carraro et al. 2018). And it has been used in studies of fishes (e.g. Adrian-Kalchhauser and Burkhardt-Holm 2016), amphibians (i.e. Svenningsen et al. 2022), turtles (i.e. Davy et al. 2015), mussels (e.g. Prié et al. 2023), aquatic macrophytes (rooted plants, e.g. Jo 2024), and even fungi (e.g. Greeff-Laubscher et al. 2023) among other aquatic organisms. eDNA is particularly useful to survey species that are rare (e.g. Pfleger et al. 2016), difficult to sample (e.g. Baltazar‐Soares 2022), and in searching for potentially invading species (e.g. Stepien et al. 2019) or diseases (Greeff-Laubscher et al. 2023).

An important advantage of eDNA sampling is that the field work required to take samples is quite minimal. This saves both time and money which allows for a greater number of samples to be collected. Another significant advantage is that it is effective at sampling species that are rare and thus less likely to be captured by traditional fisheries methods (like electrofishing). It is also effective for difficult to sample species like lamprey which live embedded in stream substrates as ammocoete larva for most of their lives. This makes them difficult to sample with fisheries gear.

Smith-Root and other companies make eDNA samplers that have integrated pumps and filters that allow a small filter to be the only material needed to be "carried out" of the field.

Source: Smith-Root eDNA Sampler

Like any emerging technology, we are still trying to understand how effective the sampling method is and its limitations. There are certainly drawbacks such as that the relationship between the amount of DNA each species sheds is different so the amount of DNA may not correlate with populations (Buxton et al. 2017). We do not always have a good understanding of the scope of a sample - how far upstream in a stream is that DNA coming from? And there is always a risk of contamination - that is we can get false positives if our waders, eDNA sampling device, or other gear contains DNA of target species. DNA degrades once it enters the environment which provides some challenges but also tends to make the samples temporally-relevant (i.e. we are not sampling a species that was there weeks or months ago).

Of course, another drawback is that you need to have a pretty good understanding of genetics to make it work for you. Like most fisheries biologists, I know enough about genetics to be dangerous. Fortunately, there are many scientists we can work with that understand the advantages and how to avoid some of the potential issues with eDNA.

While I called it an emerging technology, the first use of eDNA dates back to 1999 (link) or in the genetics world, damn near a lifetime ago. The concept behind aquatic eDNA is pretty simple. A water sample is collected and ran through a filter and a small bit of DNA is extracted from the filter. Amplification techniques can turn that small bit of DNA into a larger amount of DNA. Then the DNA is sequenced and compared to a "library", a set of known DNA locations that are unique to that species. This is an oversimplification, to be sure, but do you really need to know the little details? I'm good with a little "scientific magic" once in a while. (If you do, see the links and literature at the end of this post.)

Environmental DNA is rapidly becoming a fisheries management technique that is widely used and applied. As mentioned previously, much of the monitoring of new invasive species is done through eDNA sampling. Another advantage of eDNA is that it allows for passive sampling with companies making eDNA samplers that can take samples at specific intervals (i.e. every 12 hours) or conditions (i.e. when flows exceed/are below a certain value). As in the video from Shenandoah National Park above, it is easy to train citizen science volunteers to collect samples. This provides a snapshot in time of things like the distribution of Brook Trout in the park. Sampling 80 streams with electrofishing gear would require the better part of a summer. However, that effort would provide some information that eDNA can not - such as length-weight relationships and other population metrics. Environmental DNA sampling may or may not have a relationship with population size (Lacoursiere-Roussel et al. 2016). Standard fisheries techniques like electrofishing, capture nets, and other capture techniques likely won't be replaced but rather supplemented with eDNA sampling.

Of course, another tradeoff is that the time and effort in the field is replaced with time, effort, and costs in the laboratory. Much of the time, these samples are "sent off" to a laboratory and analyzed. The cost is largely a function of the information from the sample that you are seeking. Results may be as simple as presence / absence of a single or a couple of species or as complex as community metabarcoding where all species above a detection limit are identified. Additionally, there are some eDNA methods that allow for a greater ability to quantify the relative number of individuals in the sample. As this technology continues to be used and improved, it will continue to be more informative and less expensive. It has already come down greatly in price, one of the biggest reasons it has been increasingly popular for gaining a better understanding of the distribution of species.

This was hardly a full exploration of eDNA and its applications but doing so would have made for a much longer and harder to digest post. More about eDNA is another post, I am sure. I embedded the above video for those seeking a longer, more detailed description of eDNA sampling.