Introduction to eDNA
Before we can manage any species, we have to find it – and that’s often easier said than done. Traditional survey methods require experienced biologists to go into the field to capture, identify, and count organisms that are often elusive. It’s a process that’s not for the faint of heart. Field days and nights can be long and uncomfortable, and proficiency in locating and identifying species comes only after months or years of training and on the ground experience. Some species may be so hard to detect that we can’t have a lot of confidence that we know whether they’re present or absent in a particular area. Others, like disease-causing bacteria and viruses, can’t be seen with the naked eye. Trying to find a rare species can be like searching for a needle in a haystack.
The difficulties of finding any kind of organism are compounded in aquatic environments. We’re terrestrial animals, after all. We don’t see or hear well underwater. When we want to find animals or plants in rivers, lakes, wetlands, or oceans, we have to be especially ingenious. Fortunately, we now have an ingenious sampling tool to help us find aquatic species: environmental DNA.
Aquatic organisms continuously deposit DNA in their environment by sloughing skin cells, excreting waste, reproducing, and eventually dying and decomposing. This environmental DNA (eDNA for short) may remain in the water for several weeks after the organism has traveled through the pond, lake or stream. By taking a small sample of water, researchers can use genetic methods to detect small pieces of the target species’ DNA in the sample. This allows them to determine whether the species has recently been present in the water body — without ever having to see, hear, or capture individuals.
What is eDNA?
We define eDNA as genetic material that can be extracted from environmental samples without any visible evidence of the organism itself. While DNA can be found in many kinds of environmental samples (soil, ice, aquatic sediments, or even air), this website focuses on DNA that’s found in water. Moreover, our definition excludes biological material that we can see, like hair, scat, or skin – because we already know something about the kind of species it came from, the methods for handling these samples are a bit different. When we have a mix of DNA in a water sample, we don’t know anything about whose DNA it is until we analyze it with genetic methods.
Some of the DNA we can detect is dissolved, freely floating DNA that’s broken out of the tissue cells in which it originated. We’re learning, however, that most eDNA is larger than this, maybe still contained within cells, or in clusters of cells, and isn’t evenly distributed in a water body. These clumps can move away from the organism producing them, or even settle out of the water column, and eDNA researchers are trying to learn more about how eDNA moves in the environment and where a species might have been when its DNA was shed.
How do we use eDNA?
There are two approaches for using eDNA. The first is to confirm the presence or absence of a single (or a few) species in which we’re interested. This approach can be a powerful tool for finding specific plants or animals we want to conserve (like threatened or endangered species) or species we want to control (such as invasive species or disease-causing pathogens).
The other approach tries to describe the entire aquatic community by identifying every species whose DNA is in the water sample. This can give us a good idea of the biodiversity of the water body, which can help guide conservation efforts.
Many rare species (including threatened and endangered species) are at risk of population decline or even extinction from threats such as habitat loss, predation, invasive species, or disease. They might occur in low densities or at only a few locations, which can make them hard to find. It’s critical that we know not only where they are, but also whether any pathogens, predators, competitors, or invasive species are present, so we can address these and other factors that put them at risk. Additionally, some field survey methods such as capturing animals with nets can put a lot of stress on sensitive animals or damage their habitat. Because we can use eDNA to detect species at very low densities, it’s an effective tactic for finding rare species without disturbing them.
Aquatic invasive species, often called aquatic nuisance species, are plants and animals that invade ecosystems outside of their natural, historic ranges and threaten the diversity and abundance of native species and ecosystems. Invasive species initially occur in low densities, but once they gain a foothold they can disrupt commercial, recreational, and agricultural activities that depend on intact ecosystems. Environmental DNA methods can detect invasive species even when only a few individuals are present and provide an early warning that an invasion is underway, allowing us to implement control methods before the invasive species can become abundant.
Bacteria, viruses, fungi, and other micro-organisms in aquatic environments can cause diseases in fish, amphibians, marine mammals, semi-aquatic reptiles, and invertebrates. However, we often don’t know that the disease-causing pathogens are present until we discover a lot of sick, dying, or dead animals. If we can find a pathogen’s DNA in water samples before a disease outbreak, we can get ahead of the curve for preventing the disease from spreading.
One measure of the biodiversity of an ecosystem is species richness, or the number of species that occur in the ecosystem. It’s exceedingly difficult to identify all of the species in a pond, stream, lake, or ocean, though, because different groups of species require specific field survey methods to confirm that the species are there, and some species are hard to find with any survey method. Methods are being developed to use environmental DNA to identify all of the taxonomic groups present in a set of water samples, which will be a cost-effective alternative to multispecies field survey strategies.
What are the advantages of eDNA?
Environmental DNA technology can be highly cost efficient and effective for monitoring populations of rare species. In some systems, eDNA methods can actually be more sensitive to species presence than traditional field surveys. Using water samples instead of field surveys can shorten field search time, eliminate stress to sensitive species, and minimize disturbance of sensitive habitats. One big advantage of eDNA methods is that multiple species can be identified from a single water sample, so eDNA sampling can be much more efficient than conducting field surveys for multiple species that require different survey methods.
If we don’t know where and when aquatic species are found, we might waste time and money on conservation and management programs in the wrong place or at the wrong time. Environmental DNA gives us accurate information about the location of aquatic species and the makeup of aquatic communities, and helps focus conservation and management actions where they’re most likely to protect rare species or prevent the spread of invasive species.
An excellent introduction to DNA can be found here: https://ghr.nlm.nih.gov/primer
Information on different DNA extraction techniques (not specific to eDNA) can be found here: https://www.qiagen.com/us/resources/molecular-biology-methods/dna/