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4.2 Status of Amphibians
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Section 4.3

Methods Spotlight: Amphibian eDNA

Summary of the collection and analysis of environmental DNA, and monitoring results for four of Alberta's amphibian species

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Banner credit: ABMI
image Andrew DuBois

Tiger Salamanders (Ambystoma mavortium) are difficult to survey, but can be detected through eDNA sampling.

  • Environmental DNA (eDNA) refers to DNA fragments that organisms shed into the environment through tissue (e.g., skin, scales, waste). These fragments can be collected and analyzed to detect the presence of one or more species.
  • The analysis of eDNA allows researchers to monitor species without having to collect or observe specimens directly, which can save time and money while reducing stress on target species.
  • This project was initiated to develop protocols for collecting amphibian eDNA in open water wetlands, and to compare the detection ability of eDNA collection to that of methods currently in use.

Background

Kris Kendell

Environmental DNA (eDNA) refers to DNA fragments that organisms shed into the environment. These fragments can be collected and analyzed to determine what species are present.

Environmental DNA (eDNA) sampling is a new and promising method with the potential to increase the efficiency of monitoring a wide array of taxa. eDNA sampling may serve to complement or modernize some of our current sampling protocols by:

  • detecting species without having to actually collect or observe specimens—this can reduce field time and the impact of field activities on target species and habitats,
  • identifying the presence of species that are difficult to survey using other methods, including rare and elusive species, 
  • detecting species at any life stage (e.g., egg, larvae, adult), and
  • providing more reliable trend data.

In the spring of 2020, we initiated a pilot project with InnoTech Alberta to explore the effectiveness of eDNA technology for monitoring amphibians in wetland habitats. The objectives of the project were to:

  • develop field protocols to collect amphibian DNA in open water wetlands, 
  • develop and test DNA primers (short, species-specific DNA sequences) for target amphibian species, and 
  • compare the detection ability of eDNA to the current monitoring methods employed by the ABMI (autonomous recording units [ARUs]). 
Kris Kendell

Amphibian eggs, such as these from a Tiger Salamander, can be detected in eDNA samples.

How is Environmental DNA Sampled?

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Water samples are collected in the field and...

...DNA fragments are extracted and processed in the lab to identify species.

  • A variety of habitat elements can be sampled to collect eDNA, such as water[1,2], flower petals[3] and topsoil[4,5]; we collected water samples in the pilot project. 
  • Once the environmental sample is collected, the DNA is extracted and matched to known species-specific DNA sequences (primers).
  • Primers are either designed from genetic information published in previous work or held in public databases. Their functionality is tested and optimized using tissue from target species and assessed for specificity using DNA from non-target species by looking for cross reactions.  
  • Depending on the collection methods, eDNA can be used to answer questions about species occurrence[1,6,7] and the population structure of species and communities[8].
  • To read more about eDNA sampling, see the field protocols developed for this project[9]. To read more about this project, see the final report[10] or this news article.