eDNA: learning from the molecule that’s always left behind

Think of the last time you went for a swim. Before walking away from the shore, you probably gathered up all your things: your towel, sandals, sunglasses, hat, sunscreen, and perhaps a book or magazine. Yet despite your careful attention there was still something you left behind. Did you know you left some of your very own DNA in the water? It’s true, and it’s natural for organisms to shed DNA into the environment. In fact, there is a lot we can learn using this environmental DNA, known as eDNA.

You may think you brought everything home with you, but you left some of your DNA behind! Illustration by Kayla Martin.
An environmental sample containing eDNA can tell us about the organisms present in an area. Graphic by Kayla Martin.

What is eDNA?

Though too small to be seen by the naked eye, DNA looks like long strands made up of a sequence of many smaller molecules. The sequence that these molecules are arranged in is different for individual organisms and species. This means that DNA can be used to identify different species and even individuals of the same species. Nearly every cell in an organism’s body contains DNA. Organisms shed cells into the environment through skin, hair, mucus, pollen, leaves, and even excrement (which contains cells from the stomach and intestines). These cells, which contain the organism’s DNA, are scattered and distributed throughout the environment as eDNA.

As a simple definition, eDNA refers to pieces of DNA that an organism sheds into the environment. The “e” in eDNA stands for environmental; and DNA, as you may recall from biology class, stands for deoxyribonucleic acid. DNA is the molecule that contains the genetic “instructions” for organisms. These instructions support the development and maintenance of an organism’s body. DNA is also passed down from generation to generation (in other words, it is hereditary), which is why offspring have similar traits to their parents.

What can we learn from eDNA?

The use of eDNA has become more popular within the past decade. It’s now used in a variety of fields, including ecology, biological monitoring, conservation biology, and paleontology.

Recall that the sequence of molecules in DNA strands are unique to an individual organism. From studying the sequence of molecules in DNA, we can identify the species and individual that the DNA came from. We can use eDNA to check an area for a single target species, or to assess a community of different species. Repeated sampling over time helps monitor how species composition changes in an area over time, making it a good tool for understanding ecosystem diversity.

Image: Researchers use a battery-powered pump to collect a water sample containing eDNA. Photo credit: USGS.

The process of eDNA sampling and analysis

eDNA can be sampled with equipment as simple as a hand pump, flask, and filter. Illustration by Kayla Martin.

The general process for analyzing eDNA is to collect samples, extract and purify the eDNA, and then use a process called quantitative PCR to detect and identify DNA.

Let’s start with sample collection. eDNA is collected through environmental samples (e.g. soil, sediment, water). This differs from traditional sampling methods, which typically involve temporarily trapping and/or handling an organism to collect a physical sample (e.g. blood, hair, skin). Sampling for eDNA is far less invasive to an organism since the organism is not approached or handled. Timing is important when sampling; once DNA is shed, it spreads out as it is moved around farther from its original location (e.g. by water or wind). It also naturally degrades over time due to heat, acidity, solar radiation (UVB rays), and other factors (e.g. still vs flowing water). The eDNA must be collected before it completely degrades.

After collection, the samples are sent to a lab to extract and purify DNA from the sample. This releases DNA from organic chemicals such as humic acid, which is common in soil and sediment. Extraction and purification ensure that the DNA can be detected during the next step in the process.

The final step, which also takes place in the lab, is to detect DNA. The most common technique is called PCR, which stands for polymerase chain reaction. During PCR, DNA is replicated and amplified. This makes the DNA easier to detect and analyze, so researchers can tell whether the DNA from a particular species is present in the sample. The PCR analysis can be targeted to detect a single species, or it can be a general assessment of all the species whose DNA is in the sample. The latter approach, called metabarcoding, is a good way to assess an entire community of species in an ecosystem. Metabarcoding, however, is less sensitive than a targeted single-species PCR and may miss a rare species.

The PCR analysis can take as little as one week if testing for a single target species. The analysis takes longer – up to several months – if testing for multiple species using the metabarcoding approach.

Is eDNA the optimal method?

As with any method for sampling and analysis, using eDNA has advantages and limitations.

eDNA is a valuable tool for detecting species, and even stronger when paired with conventional sampling methods. It has applications in multiple fields, including conservation biology and ecosystem management. The in-lab analyses may increase the cost of eDNA methods compared to traditional sampling methods; however, using eDNA can still be more cost-effective when dealing with rare, endangered, or invasive species. In some cases it is also less labour-intensive. Researchers continue to improve the methods, sampling procedures, and analyses used for eDNA. With these improvements comes a wider range of applications in conservation and species management.

eDNA can be used to distinguish similar-looking species and species complexes, such as the Jefferson salamander and the Unisexual Ambystoma salamander complex. Photo credit: Kayla Martin.

References

Bourque, Danielle. 2019. “Taking Biodiversity Monitoring to the next Level: Environmental DNA as a Predictor of Aquatic Organism Abundance.” Biodiversity Resilience Network. January 11, 2019. https://www.biodiversityresilience.com/research-spotlight/taking-biodiversity-monitoring-to-the-next-level-environmental-dna-as-a-predictor-of-aquatic-organism-abundance.

“Frequently Asked Questions.” n.d. EDNA RESOURCES. Accessed September 21, 2021. https://ednaresources.science/faqs.

Harrison, Jori B., Jennifer M. Sunday, and Sean M. Rogers. 2019. “Predicting the Fate of EDNA in the Environment and Implications for Studying Biodiversity.” Proceedings of the Royal Society B: Biological Sciences 286 (1915): 20191409. https://doi.org/10.1098/rspb.2019.1409.

Laramie, Matthew B., David S. Pilliod, Caren S. Goldberg, and Katherine M. Strickler. 2015. “Environmental DNA Sampling Protocol—Filtering Water to Capture DNA from Aquatic Organisms.” In U.S. Geological Survey Techniques and Methods, 15. Techniques and Methods, book 2. https://pubs.usgs.gov/tm/02/a13/tm2a13.pdf.

Wilson, C, A Welsh, C Jerde, M Docker, and B Locke. n.d. “Environmental DNA: A Sensitive Tool for Species Detection.” Fisheries Management, 4.