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CERC’s eDNA Crew Blog - 2020

By Columbia Environmental Research Center

The Environmental DNA Section in the Biochemistry and Physiology Branch at the Columbia Environmental Research Center uses environmental DNA (eDNA) to detect invasive and rare native species and study how eDNA behaves in the environment. 

CERC's eDNA crew blog 2021

What is eDNA?

by Dannise Ruiz, November 2020

Identifying the wild animal and plant species that live in a place is an important step in conservation biology, but traditional methods for species surveys can be inefficient, labor-intensive, harmful to the sampled animals, and can require costly expertise. That’s why the CERC eDNA crew uses the invisible genetic traces left by animals in water to positively identify them.

We refer to environmental DNA (eDNA) as all DNA that is obtained from the environment instead of directly from the organisms. DNA is left behind by the organism in the form of shed cellular material, for example, dead leaves, hair, feces, mucus, pollen, or gametes. This DNA material can travel through air or water and accumulate in soils and sediments. That means that we can collect samples from the environment: soil, water, or air (Rees et al. 2014), and obtain evidence of the organisms living in or visiting that environment. 

eDNA shedding
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Schematic showing the shedding of DNA into the environment.

How do we detect eDNA?

To detect an animal’s DNA, we extract all the DNA from the environmental sample and amplify the target DNA. DNA amplification is accomplished using Polymerase Chain Reaction (PCR). For this the extracted DNA (template) is added to a mixture of buffers, deoxynucleotides, primers specific for the target species and Taq polymerase. This mix is cycled at specific temperatures to replicate the DNA many times.

Polymerase Chain Reaction
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Schematic showing the steps of the Polymerase Chain Reaction. Denaturation: DNA strand are separated at high temperature denaturation. Annealing or hybridization: Temperature is decreased and complementary primer sequences that flank the target sequences anneal to the target. Extension: Complementary nucleotides are added into the growing strand by the DNA polymerase enzyme. Extension usually continues until the template sequence has been completely copied. This process is repeated between 25-40 times, to generate a large number of copies from the original DNA template.

Depending on our objectives, we can use specific primers to search for a species of interest in our sample or use universal primers to identify all the members of targeted taxonomic groups contributing DNA present in that sample (metabarcoding). In metabarcoding samples are then sequenced using high-throughput DNA sequencing.

 

Why use eDNA?

Species surveys and monitoring are an integral part of conservation, allowing us to identify populations and track species recovery or invasions. But traditional surveys may lack sensitivity to detect rare species, and taxonomical expertise is needed to identify the species. Environmental DNA is a useful tool in conservation because it does not require observation or identification of the organism in the field, which speeds the data collection and reduces sampling effort. Environmental DNA also reduces the stress on the study organisms being surveyed, as they are not directly handled or manipulated. This is particularly important in the case of rare or endangered species. However, we still need taxonomic expertise to corroborate species observations and add information that must be measured directly, such as population age structures. So, eDNA is a valuable complement to traditional species monitoring and biodiversity surveys. 

Examples of eDNA applications

For rare species, eDNA can be used alongside camera traps to increase the number of observations of target species (Jerde et al. 2013; Boussarie et al. 2018). For invasive species, the detection of DNA can give away the presence of the species before the species takes residence in the place (Rees et al. 2014; Hunter et al. 2015). eDNA is also used to study species distribution and community composition (Thomsen et al. 2012; Klymus et al. 2017).  

Here in the lab, we are using eDNA to: 

  • Investigate invasive species
  • Monitor rare or threatened species       
  • Assess restoration efforts       
  • Understand eDNA transport dynamics

 

References:

Boussarie, G., Bakker, J., Wangensteen, O.S., Mariani, S., Bonnin, L., Juhel, J.-B., Kiszka, J.J., Kulbicki, M., Manel, S., Robbins, W.D., Vigliola, L., and Mouillot, D., 2018, Environmental DNA illuminates the dark diversity of sharks: Science Advances, v. 4, no. 5, p. eaap9661. 

Hunter, M.E., Oyler-McCance, S.J., Dorazio, R.M., Fike, J.A., Smith, B.J., Hunter, C.T., Reed, R.N., and Hart, K.M., 2015, Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons: PLOS ONE, v. 10, no. 4, p. e0121655. 

L., J.C., Lindsay, C.W., R., M.A., A., R.M., Joel, C., L., B.M., Sagar, M., and M., L.D., 2013, Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program: Canadian Journal of Fisheries and Aquatic Sciences, v. 70, no. 4, p. 522-526.

Klymus, K.E., Richter, C.A., Thompson, N., and Hinck, J.E., 2017, Metabarcoding of environmental DNA samples to explore the use of uranium mine containment ponds as a water source for wildlife: Diversity, v. 9, no. 4, p. 54

Rees, H.C., Maddison, B.C., Middleditch, D.J., Patmore, J.R.M., and Gough, K.C., 2014, The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology: Journal of Applied Ecology, v. 51, no. 5, p. 1450-1459.

Thomsen, P.F., Kielgast, J., Iversen, L.L., Wiuf, C., Rasmussen, M., Gilbert, M.T.P., Orlando, L., and Willerslev, E., 2012, Monitoring endangered freshwater biodiversity using environmental DNA: Molecular Ecology, v. 21, no. 11, p. 2565-2573.