Exploring the potential of eDNA as a conservation tool

article / 10 February 2023

Exploring the potential of eDNA as a conservation tool

Environmental (DNA) has emerged as a powerful and accessible tool to non-invasively and cost-effectly identify the presence of species in an environment, used by conservationists, researchers and citizen scientists. In this article, Heather Needham introduces eDNA and explores the potential of eDNA as a conservation tool.

Heather Needham

@heatherneedham
| She/Her

Fauna & Flora

University of Oxford

Heather is a Biodiveristy Manager at the University of Oxford. She recently undertook an internship at Fauna and Flora International after completing her MSc in Biodiversity, Conservation & Management at the University of Oxford

Groups

eDNA & Genomics

What is environmental DNA (eDNA)?

Organisms naturally shed biological material, such as their skin, hair, mucus or feces, into the environment they interact with. This biological material, containing uniquely identifying genetic information such as DNA, can be collected from water, soil and even the air (Barnes & Turner, 2016). The organismal DNA that is obtained from these environments is known as ‘environmental DNA’ (eDNA). eDNA has become a powerful tool for identifying and monitoring species in their natural habitats.

Traditionally, identifying species has been expensive and time consuming, relying on expert observations and lots of funding. However, eDNA technology has emerged as a promising new tool in conservation thanks to advancements in DNA technology and decreasing costs of DNA analysis. Collecting eDNA enables researchers to non-invasively and cost-effectively determine the presence of species in an environment from a relatively small biological sample, making it a valuable tool for species monitoring and management.

In some cases, however there may not be enough eDNA in a sample to accurately identify a species due to DNA degradation. The rate at which eDNA breaks down depends on the type of environment the eDNA is shed within. There might also not have been enough pieces of DNA shed into the environment to make an accurate assessment. In addition, eDNA sampling may obtain false positive (caused by contamination or spread of eDNA away from the deposited area) or false negative results (from improper sampling strategy or procedure). Although, there are lots of specialist eDNA laboratories that can assist with estabalishing sampling sizes, provide training and eDNA testing equipment to reduce the risk of flase results.

Moreover, eDNA can only be used to identify a species if we already have a record of its DNA structure. In some cases, we can rely on open-source genetic databases, but in others, we may need to create the reference ourselves by obtaining and sequencing a verified tissue sample from the organism. This can be costly and time consuming, but without a comprehensive reference database, the identities of some species may remain unresolved. However, the eBioAtlas aims to be a comprehensive open-access global repository for eDNA-biodiversity data where eDNA data can be deposited and shared.

The use of eDNA is a simple and efficient process, it can be done with minimal training and simple tools, which makes it accessible for conservationists, researchers, and citizen scientists. So, how might eDNA be deployed as a useful tool in conservation work?

Detecting focal species presence:

eDNA can detect the presence of different species in the environment without relying on traditional methods such as physically observing or trapping them. By analysing the DNA that organisms shed into their surroundings, researchers can detect a wide range of species, including aquatic and terrestrial animals, fungi, parasites, and more. For example, a WWF study in British Columbia, detected 25% more terrestrial mammals than using camera traps by sampling the eDNA of stream water and found that many species were too small to trigger the cameras (WWF, 2022). Collecting an eDNA sample requires very little training and can be done within 20 to 30 minutes. Whereas identifying species using a camera trap can take hours, days or even weeks, since the method relies on observing the species and typically a vast network of cameras.

i) Endangered, cryptic, or rare species

Some species can be challenging to monitor due to fact that they’re hard to spot, have low population numbers, or can’t be approached safely (Bohmann et al., 2014). eDNA can reveal whether a species is present in a specific area without disturbing or even seeing the organism. Knowing if a species is present in an area can justify conservation interventions and help guide more intensive but informative monitoring efforts.

In South-eastern Liberia, for example, a team from Fauna & Flora International (FFI) used eDNA to find pygmy hippos (Choeropsis liberiensis) in water samples collected from the Sapo National Park, along with 165 other species (six of which were endangered). Pygmy hippos are hard to detect with camera traps and surveys as they are nocturnal and solitary, so eDNA provided a cost-effective solution to support local conservation efforts (NatureMetrics, 2022). Similarly, an FFI team in Cambodia used eDNA to detect Siamese crocodiles (Crocodylus siamensis) after breeding and releasing 130 of the endangered animals into the Cardamon Mountains. Using eDNA to detect Siamese Crocodiles was advantageous, as the method did not require disturbing or physically observing the species (Fauna & Flora International, 2022).

eDNA collection in Virachey National Park, north-eastern Cambodia (© Jeremy Holden / Fauna & Flora International)

ii) Invasive species

Rapid detection of invasive species is critical for implementing successful removal and control measures. Repeated eDNA sampling can detect invasive species early, enabling the quick implementation of interventions to prevent the organism's establishment and spread. For instance, eDNA has been used to detect invasive zebra and quagga mussels in the Rhine River across Germany, the Netherlands, and Switzerland, where traditional surveying methods couldn't detect them (De Ventura et al., 2017).

However, keep in mind that the detection of an organisms' DNA does not guarantee that the organism was present in the environment at the time that the sample was collected. DNA can remain in the environment for hours to years, depending on the environment into which it was deposited (DNA in water can persist for hours to days, whereas DNA in soil can persist for days-years). Moreover, eDNA can be spread away from its source. For example, if you are sampling air or water, the DNA detected may have travelled from a different source (e.g., upstream) to arrive at your sampling location.

Bioassessment

Alternatively, eDNA can be used as a “bioindicator” of ecosystem health. You might recognize well-known indicator species, such as mayflies, lichens, and the northern spotted owl, which can act as a proxy for the condition and integrity of the environment and, consequently, for other species. For example, eDNA sampling of small insect species in the Engiadina Val Müstair, Switzerland, has been used to infer the integrity of protected alpine springs (Blattner et al., 2021).

Biodiversity assessments and environmental baselines

Documenting entire wildlife communities can be difficult work due to the cost and time required for alternative methods such as observational surveys, drones, or camera traps, as well as the need for expert knowledge. For example, Kay et al. (2020) found that even with camera traps it can take several weeks to accurately estimate the local detection rate of mammals.

eDNA survey techniques can offer a more efficient solution for broad-scale biodiversity mapping and monitoring. eDNA can identify all species that have left traces of DNA in an environmental sample, such as water or soil, using a process known as 'metabarcoding.' This information is used to determine species richness, establish biodiversity inventories or baselines for ongoing monitoring, or monitor conservation efforts (Deiner et al., 2017).

Chimanimani National Park in Mozambique was designated in 2020 and is known for its high levels of biodiversity. The park’s vast area and high levels of unqiue and endemic species, made cost-effective and efficient monitoring a major challenge. The FFI team in Mozambique used eDNA sampling to establish baseline data on freshwater biodiversity, providing information on new species that was critical to support conservation decision making for the park.

The different applications and uses of eDNA (Ruppert, Kline & Rahman, 2019)

In conclusion, eDNA has emerged as valuable tool for species identification and biodiversity assessment for conservation work. Its non-invasive and cost-effective method of identifying species in their natural habitat, makes the tool highly accessible to researchers, conservationists, and citizen scientists. The ability to detect endangered, cryptic, or rare species, invasive species, and use it as a bioindicator of ecosystem health are just some of the ways eDNA is making a significant impact in the field of conservation. Although eDNA has limitations, such as the need for a comprehensive reference database, it provides a simple and efficient solution for species detection that can be done with minimal training. With continued advancements in DNA technology and decreasing costs, eDNA will continue to play an important role in conservation work alongisde the use of other technologies such as drones and camera traps, allowing us to better understand and protect our natural world.

If you're interested to learn more about eDNA make sure to join the WildLabs eDNA and Geonmics Group.

Literature Cited

Barnes, M.A. and Turner, C.R., 2016. The ecology of environmental DNA and implications for conservation genetics. Conservation genetics, 17(1), pp.1-17.
Deiner, K. et al. (2017) “Environmental DNA Metabarcoding: Transforming how we survey animal and Plant Communities,” Molecular Ecology, 26(21), pp. 5872–5895. Available at: https://doi.org/10.1111/mec.14350.
Blattner, L. et al. (2021) “Targeted non-invasive bioindicator species detection in Edna water samples to assess and monitor the integrity of vulnerable alpine freshwater environments,” Ecological Indicators, 129, p. 107916. Available at: https://doi.org/10.1016/j.ecolind.2021.107916.
Bohmann, K., Evans, A., Gilbert, M.T.P., Carvalho, G.R., Creer, S., Knapp, M., Douglas, W.Y. and De Bruyn, M., 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends in ecology & evolution, 29(6), pp.358-367.
De Ventura, L. et al. (2017) “Tracing the quagga mussel invasion along the Rhine river system using Edna markers: Early detection and surveillance of invasive zebra and quagga mussels,” Management of Biological Invasions, 8(1), pp. 101–112. Available at: https://doi.org/10.3391/mbi.2017.8.1.10.
FFI detects pygmy hippos in southeast Liberia (2022) NatureMetrics. Available at: https://www.naturemetrics.co.uk/case-study/ffi-detects-pygmy-hippo-in-southeast-liberia/ (Accessed: February 11, 2023).
How scientists use eDNA to monitor biodiversity (2022) WWF. World Wildlife Fund. Available at: https://www.worldwildlife.org/magazine/issues/summer-2022/articles/how-scientists-use-edna-to-monitor-biodiversity (Accessed: February 11, 2023).
Kays, R. et al. (2020) “An empirical evaluation of Camera Trap Study Design: How many, how long and when?,” Methods in Ecology and Evolution, 11(6), pp. 700–713. Available at: https://doi.org/10.1111/2041-210x.13370.
Return of the croc – snapshots of a rare reptile reintroduction in Cambodia (2022) Fauna & Flora International. Available at: https://www.fauna-flora.org/news/return-of-the-croc-snapshots-of-a-rare-reptile-reintroduction-in-cambodia/ (Accessed: February 11, 2023).
Ruppert, K.M., Kline, R.J. and Rahman, M.S. (2019) “Past, present, and future perspectives of environmental DNA (Edna) metabarcoding: A systematic review in methods, monitoring, and applications of Global Edna,” Global Ecology and Conservation, 17. Available at: https://doi.org/10.1016/j.gecco.2019.e00547.

Add the first post in this thread.

Want to share your own conservation tech experiences and expertise with our growing global community? Login or register to start posting!

article / 10 February 2023