Taking biodiversity monitoring to the next level: Environmental DNA as a predictor of aquatic organism abundance

January 11, 2019

By Danielle Bourque, M.Sc. Student


Left photo: For this experiment, it is important to prevent the target organism, Daphnia magna, from landing on the environmental DNA (eDNA) capture filter. Here, Limnotron water samples are vacuum filtered initially  through a 40 micron mesh to remove D. magna and their eggs from the sample, and then a much finer 1.2 micron filter to capture D. magna eDNA. Right photo: Glass fibre eDNA filters are carefully removed from the vacuum manifold and placed in sterile, labelled Petri dishes for long-term - 80 °C storage until DNA extraction.

Environmental DNA (eDNA) refers to genetic material that has been shed from a host organism into soil, water, or air [1]. The possibility of detecting a species without seeing or handling the host organisms themselves has led to an exponential interest in using eDNA for population and biodiversity monitoring [2]. Despite this surge in application, knowledge gaps still exist concerning both how eDNA interacts with the aquatic environment and what ecological information can be inferred from its signal [3]. For example, the relationship between an eDNA signal and organism abundance is not completely understood and has been explored in a diversity of aquatic settings such as tanks (20 L [4], 80 L [5]), study ponds [6], or large (~4.5 million L) multi-species aquaria [7]. 

Under the advisory of Dr. Robert Hanner and Dr. John Fryxell, the aim of my M.Sc. thesis project is to add novel insights to the eDNA-abundance relationship. My study system is located in the Limnotron [8], a facility containing six 26,000 L lentic mesocosms located within the Biodiversity Institute of Ontario at the University of Guelph. The Limnotron provides a unique opportunity to examine the eDNA-abundance relationship in a controlled aquatic setting. For my study, four tanks equipped with 18 spatially-explicit sampling ports were set-up to contain simple communities of Daphnia magna (consumer) and Chlorella vulgaris (resource). The tanks  were regularly sampled over a four month period in 2017 for both D. magna abundance and their eDNA. To quantify D. magna eDNA in this system, a small fragment of the COI-5P gene region (a gene involved in energy production) of D. magna was used to design a novel species-specific real-time quantitative PCR (qPCR) molecular assay.

Preliminary data suggests a positive correlation between D. magna abundance and eDNA signal through time, but not without confounding effects from DNA persistence and organism decomposition. Although all eDNA is subject to decay over time, its source—living or dead Daphnia—cannot be determined, making precise abundance measurements challenging. Estimating organism abundance from eDNA is one of the most desired applications of molecular-based biomonitoring. As such, elucidating the nature of this relationship in controlled environments is paramount for appropriate use of this tool in natural settings.


If you have questions or comments, please contact me at dbourque@uoguelph.ca. Details of my previous research in DNA barcoding and targeted qPCR assay development, including publications, can be found at:

ResearchGate: https://www.researchgate.net/profile/Danielle_Bourque2

LinkedIn: https://ca.linkedin.com/in/bourquedanielle

ORC-ID: 0000-0003-4819-3895



[1] Tarberlet P, Coissad E, Hajibabei M, Rieseberg LH. 2012. Environmental DNA. Mol. Ecol. 21:1789–1793

[2] Thomsen PF, Willerslev E. 2015. Environmental DNA—an emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv. 183:4–18

[3] Barnes MA, Turner CR. 2016. The ecology of environmental DNA and implications for conservation genetics. Conserv. Genet. 17:1–17

[4] Lacoursiere-Roussel A, Rosebal M, Bertnatchez L. 2016. Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions. Mol. Ecol. Res. 16:1401–14

[5] Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, et al. 2012. Monitoring endangered freshwater biodiversity by environmental DNA. Mol. Ecol. 21:2565–73

[6] Biggs J, Ewald N, Valentini A, Gaboriaud C, Dejean T, et al. 2015. Using eDNA to develop a national citizen science-based monitoring program for the great crested newt (Triturus cristatus). Biol. Conserv. 183:19–28

[7] Kelly RP, Port JA, Yamahara KM, Crowder LB. 2014a. Using environmental DNA to census marine fishes in a large mesocosm. PLOS ONE 9:e86175

[8] Betini GS, Avgar T, McCann KS, Fryxell JM. 2017. Daphnia inhibits the emergence of spatial pattern in a simple consumer-resource system. Ecology 98:1163–1170