Uses and challenges of eDNA-based monitoring

March 16, 2019


The application of environmental DNA (eDNA) based monitoring could revolutionize biodiversity science and conservation. While traditional biomonitoring approaches typically depend on direct observation of targeted species (e.g., an invasive or endangered species), monitoring using eDNA relies instead on detecting the DNA shed by these same species into their environment. Basically, DNA contained in biological material such as sloughed skin cells, feces, and gametes, is extracted from water, sediment or other samples collected from the environment and analyzed to determine the source species.

The benefits of eDNA-based monitoring are many: detection of species that are rare, ephemeral or difficult to recognize visually, monitoring of organisms in entire ecosystems in near real time, reduction in the accidental transferring of invasive species, detection capability and sensitivity that is relatively high, and lower cost compared to traditional methods. Despite these advantages, there are significant issues impeding the widespread adoption of eDNA into management and research. Cristescu and Hebert (2018) reviewed the uses as well as the challenges of eDNA-based monitoring.

The majority of studies using eDNA are based on aquatic environments and among these, the focus has been on freshwater over marine habitats. Working with eDNA dissolved in water provides two advantages over eDNA in terrestrial environments where it is bound to particles. First, eDNA is relatively evenly distributed throughout aquatic habitats thereby reducing the number of field sampling locations needed to characterize a system under study and second, the process of extracting eDNA from water is easier. However, abiotic factors specific to marine habitats such as greater dilution and mixing and higher salinity compared to freshwater habitats, introduce specific challenges in using eDNA in a marine setting.    

There are important unknowns related to the application of eDNA, be it in an aquatic or terrestrial environment. Cristescu and Hebert (2018) identified gaps in our understanding of the origin, state, fate, and transportation of eDNA, as illustrated in the image above. There are also data gaps in reference libraries which are needed to accurately match an eDNA sequence with the identity of the source species.

The greatest challenges however, center around the occurrence of false positives and false negatives. False positives are problematic because they indicate potential contamination of a sample or problems with the amplification, detection, or characterization of the targeted species’ eDNA. False negatives are of concern since they can mean that an invasive or endangered species is not being detected in a location where it is in fact present. Cristescu and Hebert (2018) suggest that accurate calibration and validation of eDNA techniques and protocols are essential to reducing the likelihood of false positives and negatives.

Ultimately, the use of eDNA could expand our understanding of ecosystem-level processes through monitoring of species composition and distribution in near real time. Cristescu and Hebert (2018) stress the importance of monitoring in near real time given that the rate of human impacts on biodiversity and ecosystems currently outpaces traditional monitoring approaches.


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Cristescu ME and Hebert PDN. 2018. Uses and misuses of environmental DNA in biodiversity science and conservation. Annual Reviews of Ecology, Evolution, and Systematics. 49:209-230.