Environmental DNA (eDNA) is nuclear or mitochondrial DNA that is released from an organism into the environment. Sources of eDNA include secreted faeces, mucous, gametes, shed skin, hair and carcasses. In this article, Sarah Kuppert introduces eDNA and discusses the potential conservation applications for this technology in the future.
eDNA is a molecular tool that can be used to detect species presence in samples taken from the environment. To date, eDNA has been used for species detection, biomass estimation, diet analysis, reconstruction of past flora and fauna, and wildlife disease detection. Species detection relies on the presence of extracellular DNA present in the environment. The extracellular DNA comes from cell lysis, excretions and secretions (Valentini, Pompanon, & Taberlet, 2009). eDNA has proven to be a non-invasive, sensitive and reliable tool. This is ideal for detecting secretive species, or species that occur in low numbers, such as invasive and endangered species. eDNA surveys are also valuable as they allow for positive species identification and because they require less effort and man power for field sampling compared to many traditional survey methods.
In addition, DNA stays in the environment even after the animals have left. In pond ecosystems, for example, DNA can last from two weeks (Thomsen, Kielgast, Iversen, Wiuf, et al., 2012) up to a month (Dejean et al., 2011). In streams DNA persists for up to one hour (Pilliod, Goldberg, Arkle, & Waits, 2014). Studies have confirmed its application for species detection in different environmental samples, such as streams (Goldberg, Sepulveda, Ray, Baumgardt, & Waits, 2013), ponds (Dejean et al., 2012), marine environments (Thomsen, Kielgast, Iversen, Møller, et al., 2012), snow (Doyle, Alistair, 2014), feces (Pompanon et al., 2012), and even air (Bartlett et al., 1997). This method can be used to detect the presence of a single species or multiple species at once (Simmons, Tucker, Chadderton, Jerde, & Mahon, 2015), depending on the primers that are used. Primers are a short strand of short nucleic acid sequences that serves as a starting point for DNA synthesis.
The amount of DNA found in a sample, has been successfully correlated with the biomass of animals surveyed (Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012). However, this method cannot give researchers an idea of the age demographics of the surveyed population. For some studies, it is important to know whether there are a few large adults or many small juveniles. Overall, eDNA may facilitate a great number of monitoring efforts, if the limitations of this tool are kept in mind when designing a study.
Since the application of eDNA for vertebrates is relatively new, a lot of potential usages remain to be explored. There is a great need in the conservation community. Monitoring of endangered and invasive species, understanding the diet of species with eDNA surveys can be a valuable addition or replacement of traditional monitoring methods. The eDNA method can improve the current understanding of species distributions.
eDNA also has the potential to be used as a tool for a citizen science project (Biggs et al., 2015), because sampling is easy and can be done by non-biologists with minimal training.
Another possibility for future application is the usage of eDNA as a forensic tool for illegal activities in fisheries, logging or poaching. If the DNA of illegally obtained species is detected on fishing vessels, shipping containers or other equipment, it can be used to build a case against the violators.
This method is also ideal to monitor the spread of diseases in the environment, such as chytrid fungus (Batrachochytrium dendrobatidis), which is the most significant current threat to the world's amphibian populations. eDNA surveys allow for early detection in the environment, it may be preferable to waiting until animals or plants show symptoms.
The potential for innovative research using the eDNA method is vast. Since its application for vertebrate and plant species is relatively new, however, there are numerous challenges that need to be solved.
Challenges that could stall future uptake
As DNA sequencing technologies are evolving quickly and allowing for evermore base pair reads in a shorter time, a major challenge will involve bioinformatics. Some of the bioinformatics challenges include increasing computing power, data storage, and improving and tailoring data analysis tools. In addition, eDNA is difficult to use in remote areas, where the need for species surveys may be the greatest. This difficulty is due to the requirement of storing the samples or filters storage on ice, which slows the degradation of DNA.
False positives and false negatives are other common issues with this species detection method. False positives can occur due to contamination or the spread of DNA through movement by predator's. False negatives can have numerous causes, such as improper sample sizes or replications, incorrect sampling location or period, and mistakes with sample storage or extraction. Nevertheless, many of these issues can be avoided by having high-quality field and lab protocols and hygiene.
Another challenge is that DNA found in the environment is highly degraded, which makes it difficult to work with. Also, many questions that can be answered with molecular tools may not be answerable with eDNA. Short pieces of DNA, which are found in environmental samples, are not able to identify individuals or gender, for example. Because of the high degradation rates of DNA, it is also crucial to process samples as quickly as possible and use filtering, Transportation and extraction protocols that limit this problem.
Furthermore, for a broad usage of eDNA in conservation, it will take a lot of time to verify protocols for monitoring of each species or group of species. As of now there is also no existing reference database for working primers and protocols exists, such as the Barcode of Life database for barcoding.
Finally, it is also important to consider the policy challenges that may arise with a new understanding of species distributions. For a species listed under the Endangered Species Act, for example, it could mean de-listing and loss of protection, if eDNA surveys suggested a larger range than previously known. However, the range of a species may not be the correct indicator used for evaluating its status.
About the Author
Sarah M. Kuppert was born and raised in the Black Forest in Southern Germany. She received her Bachelor of Arts in English and American Culture and Business Studies (English, Business, and Economics) from the University of Kassel, Germany in 2012. For her Bachelor's Thesis she studied reptile and amphibian communication for seven months at the Smithsonian National Zoo in Washington, D.C. She holds a Master's degree in Environmental Science and Policy, with a focus on conservation, from George Mason University. Her graduate research focused on developing the protocols and primers for detecting two-lined salamanders (Eurycea bislineata) in a stream.
- Bartlett, M. S., Vermund, S. H., Jacobs, R., Durant, P. J., Shaw, M. M., Smith, J. W., … Lee, C. H. (1997). Detection of Pneumocystis carinii DNA in air samples: likely environmental risk to susceptible persons. Journal of Clinical Microbiology, 35(10), 2511–2513.
- Biggs, J., Ewald, N., Valentini, A., Gaboriaud, C., Dejean, T., Griffiths, R. A., … Dunn, F. (2015). Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biological Conservation. http://doi.org/10.1016/j.biocon.2014.11.029
- Bohmann, K., Evans, A., Gilbert, M. T. P., Carvalho, G. R., Creer, S., Knapp, M., … de Bruyn, M. (2014). Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution, 29(6), 358–367. http://doi.org/10.1016/j.tree.2014.04.003
- Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P., & Miaud, C. (2011). Persistence of Environmental DNA in Freshwater Ecosystems. PLoS ONE, 6(8), e23398. http://doi.org/10.1371/journal.pone.0023398
- Dejean, T., Valentini, A., Miquel, C., Taberlet, P., Bellemain, E., & Miaud, C. (2012). Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. Journal of Applied Ecology, 49(4), 953–959. http://doi.org/10.1111/j.1365-2664.2012.02171.x
- Doyle, Alistair. (2014). Polar Bear DNA Found from Tracks in Snow in Conservation Step. Retrieved October 10, 2015, from http://www.scientificamerican.com/article/polar-bear-dna-found-from-tracks-in-snow-in-conservation-step/
- Goldberg, C. S., Sepulveda, A., Ray, A., Baumgardt, J., & Waits, L. P. (2013). Environmental DNA as a new method for early detection of New Zealand mudsnails ( Potamopyrgus antipodarum ). Freshwater Science, 32(3), 792–800. http://doi.org/10.1899/13-046.1
- Herder, J., Valentini, A., Bellemain, E., Dejean, T., van Delft, Jeroen, Thomsen, Phillip Francies, & Taberlet, Pierre. (2014). Environmental DNA- a review of the possible applications for the detection of (invasive) species. RAVON.
- Pilliod, D. S., Goldberg, C. S., Arkle, R. S., & Waits, L. P. (2014). Factors influencing detection of eDNA from a stream-dwelling amphibian. Molecular Ecology Resources, 14(1), 109–116. http://doi.org/10.1111/1755-0998.12159
- Pompanon, F., Deagle, B. E., Symondson, W. O. C., Brown, D. S., Jarman, S. N., & Taberlet, P. (2012). Who is eating what: diet assessment using next generation sequencing: NGS diet analysis. Molecular Ecology, 21(8), 1931–1950. http://doi.org/10.1111/j.1365-294X.2011.05403.x
- Simmons, M. M., Tucker, D. A., Chadderton, M. W. L., Jerde, D. C. L., & Mahon, D. A. R. (2015). Active and passive environmental DNA surveillance of aquatic invasive species [research-article]. Retrieved October 18, 2015, from http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2015-0262#.ViOyXGtuoqJ
- Takahara, T., Minamoto, T., Yamanaka, H., Doi, H., & Kawabata, Z. ’ichiro. (2012). Estimation of Fish Biomass Using Environmental DNA. PLoS ONE, 7(4), e35868. http://doi.org/10.1371/journal.pone.0035868
- Thomsen, P. F., Kielgast, J., Iversen, L. L., Møller, P. R., Rasmussen, M., & Willerslev, E. (2012). Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples. PLoS ONE, 7(8), e41732. http://doi.org/10.1371/journal.pone.0041732
- Thomsen, P. F., Kielgast, J., Iversen, L. L., Wiuf, C., Rasmussen, M., Gilbert, M. T. P., … Willerslev, E. (2012). Monitoring endangered freshwater biodiversity using environmental DNA: Species Monitoring by Environmental DNA. Molecular Ecology, 21(11), 2565–2573. http://doi.org/10.1111/j.1365-294X.2011.05418.x
- Valentini, A., Pompanon, F., & Taberlet, P. (2009). DNA barcoding for ecologists. Trends in Ecology & Evolution, 24(2), 110–117. http://doi.org/10.1016/j.tree.2008.09.011
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