Environmental DNA

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.

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!

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.

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!