All living things shed genetic material like hair, scales, skin and faeces into their local environment. This is known as environmental DNA (eDNA).
For example, an earthworm wiggling through the soil leaves behind skin cells and mucus. This soil sample will also have genetic material from plants and other organisms – from microbes to mammals. The same thing happens in aquatic ecosystems – fish, plants and other life forms shed fragments of themselves into their watery habitat.
Sampling aquatic ecosystems using eDNA
Would you be able to identify all of the species in this image – even those too small to be seen without a microscope? eDNA – traces of DNA released into the environment – provides a quick and accurate way to sample and monitor ecosystems.
The image is from Lake Wānaka. The common bully is easy to spot. What else can you see?
Image sourced from iNaturalistNZ.
These tiny, discarded bits give us a picture of what’s living in an ecosystem. Scientists can get an insight into the existing populations from the DNA fragments shed over recent days. Scientists can also create pictures of past populations. Sediment cores from peat bogs and lakes and ice cores from the Arctic and Antarctic regions have eDNA in them. Information from eDNA provides evidence of environmental changes in timescales from a few months to thousands of years!
Genetic barcoding and eDNA
DNA is in the cell of every living thing. It is the genetic information that acts like the blueprints for an organism. Each piece of DNA has two long strands that contain a combination of four chemical bases: Adenine, Thymine, Guanine and Cytosine. These four chemicals (A, T, G and C) are repeated in different orders again and again in each strand of DNA. The order (sequence) in which these bases are arranged creates a unique genetic code.
Segments of this unique sequence are used to create a barcode for the species. Just like we scan barcodes to identify a product in our shopping trolley, scientists use DNA barcodes to identify individual organisms. Advances in technology mean that, instead of scanning one item at a time, scientists can identify the whole trolley-load – all the species within a habitat – from a single sample of sediment, water or air!
Creating a DNA barcode
DNA barcoding uses a short section of DNA from an organism to create a unique barcode. The DNA barcodes, or sequences, are stored in databanks and used to identify organisms.
This scheme is similar to the barcodes placed on items we purchase from the supermarket.
Note: this is a simulated example of a DNA barcode.
Longfin tuna illustration by Bruce Mahalski, courtesy of Te Ara The Encyclopedia of New Zealand.
The eDNA process
The process begins by collecting a sample from an area of interest. The DNA from the sample of sediment, water or air is extracted and purified. The DNA is amplified using a technique called polymerase chain reaction (PCR). The individual DNA sequences are identified and then matched to known sequences (barcodes) from worldwide databases. From this, a list of species is produced – similar to a receipt of your shopping trolley items.
Collecting and analysing eDNA
This diagram shows the steps in the eDNA process. Advances in technology have made this process potentially faster, less expensive and more thorough than traditional identification methods.
Diagram: Schallenberg, L., Wood, S., Pochon, X. & Pearman, J. (2020) What Can DNA in the Environment Tell Us About an Ecosystem?. Frontiers for Young Minds. 8:150. doi: 10.3389/frym.2019.00150. Released under CC BY4.0.
Download a PDF of this image.
Why use eDNA?
Environmental DNA is used to monitor or detect species within an ecosystem. Traditional monitoring practices usually involve visiting an area to observe, identify and count species numbers. The people doing the monitoring need to be able to identify a lot of different species – from invertebrates to animals like fish or birds! Some species, like kōura, are difficult to monitor because they are good at hiding. Other species might be rare, so we might miss them. Using eDNA to monitor species means there is no need to capture or disturb the living things, so it is less disruptive or destructive. Another advantage of using eDNA is the cost – physically monitoring species can take lots of time, especially when scientists are looking for rare species.
There are limits to using eDNA testing. Once the genetic material is shed in aquatic environments, it may get washed away. Sunlight and other natural processes can also cause eDNA to break down. Environmental DNA identifies which species are present, but it cannot necessarily identify the number of individual members or if the members are male or female or young or old. Databases are not yet complete because there are still a lot of species that haven’t been sequenced.
Lakes380
Lakes380 – Our lakes’ health: past, present, future is a research programme that has sampled about 10% of the lakes in Aotearoa New Zealand. The team has collected and analysed lake sediments and water samples, making field visits and interweaving scientific data with mātauranga Māori. Environmental data provides evidence (alongside other methods) of when and why changes occurred in lake ecosystems. This information will help with restoration goals as well as identifying lakes that need our protection. The team has used bacterial eDNA to estimate the health of lakes across Aotearoa New Zealand. This data shows that about 45% of our lakes are in poor condition or worse.
The team has also developed new eDNA methods to detect precious taonga species such as kākahi and tuna – this is allowing the current and historical distribution of these species to be monitored. As well as detecting species that live in the lakes, eDNA from the surrounding land washes into the lake – this has enabled the team to track changes in animals and birds that live on the land around the lakes. For example, working on a lake on the West Coast, the team has been able to identify DNA from now extinct moa and the likely extinct South Island kōkako!
Nature of science
eDNA provides information about what’s living in an environment, including organisms that shouldn’t be living there. It can help us track ecosystem changes through time such as the negative impacts of climate change or positive changes due to restoration actions. It can detect invasive species before their populations grow, helping to stop their spread.
Related content
Find out how students used DNA barcodes to identify food sources in wētā frass (poo). Schools are using this information to create wētā-friendly habitats!
The Hub's eDNA collection has background information and activities to help students learn more about DNA collection and processing, and how eDNA helps scientists build a better picture of the biodiversity and resilience of an ecosystem.
Activity ideas
Finding out what’s in our lake using eDNA is an energetic activity that simulates the collection of eDNA to identify some of the organisms living in a lake system – aka a container of water on the field.
Use this activity to extract DNA from a tomato.
Useful links
Lakes380 – Our lakes’ health: past, present, future is a 5-year research project that has enriched our understanding of the environmental, social and cultural histories of lakes in Aotearoa New Zealand. The project involved collecting and analysing lake sediments and water samples as well as interviews and field visits.
Visit the Environmental Protection Authority’s Wai Tuwhera o te Taiao – Open Waters Aotearoa programme. The programme provides eDNA testing kits and resources to community groups, iwi, hapū, school and kura.
New Zealand’s Biological Heritage National Science Challenge uses eDNA for environmental monitoring. It has supported the creation of a nationwide database to integrate and share eDNA data.
Wilderlab provides lab testing services for eDNA monitoring in Aotearoa. Wilderlab has an interactive map with publicly available eDNA data. This is a useful resource for scientists, conservationists, educators and anyone else with an interest in Aotearoa New Zealand’s biodiversity, water quality and biosecurity.
When University of Otago geneticist Professor Neil Gemmell wanted to showcase the science of eDNA, he went big – the Loch Ness Monster big! The world was fascinated by the hunt and saddened by the results.
Aorere College students are using eDNA to monitor the impacts of their local stream restoration efforts – as reported in this Education Gazette article.
This The Conversation article looks at the application of eDNA to develop a new index to measure river health using the Taxon-Independent Community Index.
Acknowledgement
This resource has been developed in collaboration with Lakes380 – Our lakes’ health: past, present, future (C05X1707), Cawthron Institute and GNS Science.
Lakes380 – Our lakes’ health: past, present, future
Lakes380 is a national project to gain in-depth understanding of the current and historical health of lakes in Aotearoa New Zealand. The project was co-led by GNS Science and Cawthron Institute and funded by the New Zealand Ministry of Business, Innovation and Employment (C05X1707; Lakes380.com).
