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How is eDNA shedding light on marine biodiversity?
24 October 2024
PML’s Dr Karen Tait discusses the role of eDNA in advancing our understanding of marine life

The urgent need to monitor and protect marine ecosystems and organisms is in focus this week at the UN Biodiversity Conference (COP16) in Cali, Colombia. PML scientists are playing an active role in the event (read more here), presenting and supporting events on the challenges to biodiversity and the technological advances in monitoring which are helping provide critical data to support improved decision-making.
Dr Karen Tait shares her thoughts on eDNA and the opportunities it presents.
Can you explain what environmental DNA (eDNA) is?
eDNA stands for environmental DNA. It refers to any DNA found in the environment, such as skin cells, faecal matter, reproductive material, or even the bodies of smaller animals. Essentially, it’s DNA from any biological material that’s out in the environment.
In marine ecosystems, this DNA can be extracted from water samples. This provides us with a powerful and non-invasive tool for detecting the presence of species and monitoring any changes in biodiversity.
Why is eDNA important, and why are we hearing more about it now?
The methodology has been used for a long time to identify bacteria in the oceans. Since many bacteria are difficult to identify, molecular biology has always been critical for studying them. Now, these techniques are being applied to larger organisms, including phytoplankton, zooplankton, fish and other animals. eDNA methods can be used in the water column but can also be used to study benthic environments – the sediments at the bottom of the ocean.
It provides a non-invasive way to gather data on biodiversity without harming any organisms. It is hugely sensitive and can detect species that are difficult to observe or catch, including endangered species, invasive organisms, or those living in hard-to-reach habitats.
What’s more, it doesn’t require a specialist to collect samples, which makes data collection much more accessible. This simplicity also means that with the right training, citizen scientists can participate in marine monitoring programs, expanding the potential scale of biodiversity surveys.
How do scientists collect eDNA samples?
For a water column sample, here at PML, we routinely take up to five litres of water from our visits to the Western Channel Observatory. The water is filtered through a special membrane that captures smaller organisms and any free-living DNA. The sample is then taken to the lab, frozen until we’re ready to work with it, and then we extract both DNA and RNA. DNA shows what organisms were present, and RNA tells us what was active at the time the sample was taken. Both are hugely informative.
What can we learn from eDNA?
We can detect a much higher diversity of life than what we can observe with the naked eye, especially smaller, understudied organisms. eDNA is shedding so much light on marine biodiversity. For example, identifying fish larvae and eggs under a microscope can be challenging, but with eDNA techniques, we can easily identify species without needing that expertise.
Another example of this has been in our work on harmful algal blooms (HABs). In comparing our morphological data with DNA analysis of harmful algae, we found we could better identify species like Alexandrium, which is hard to identify through a microscope. This is significant because Alexandrium can cause Paralytic Shellfish Poisoning, and their presence in the water column signifies a potential danger to shellfish fisheries in local areas. eDNA therefore offers huge advantages for marine management which we’re only just starting to make the most of.
Can you tell us about some of the projects you’re involved with using eDNA?
At the Western Channel Observatory, we have a long-term series of both phytoplankton and zooplankton measurements. Traditionally, samples were collected and analysed through microscope techniques by taxonomists, who could identify species visually. Now, every time we take a sample, we also collect an eDNA sample. This allows us to ground-truth our findings, comparing what we can identify with DNA to what we see with traditional morphological techniques. Sometimes one method is superior to the other, so it’s about understanding how best to use the data in complementary ways.
We’re also capturing eDNA as part of the Atlantic Meridional Transect (AMT) – the annual PML-led research voyage from UK waters to South America which began in 1995. In addition to traditional sampling, scientists began molecular sampling on the AMT around 15 years ago, so we now have a huge wealth of historical data that is ripe for exploration.
How do you determine the age or origin of the DNA in the water?
That’s a good question. DNA in the water doesn’t stay in one place because of tides and currents. So, part of the process involves some detective work to figure out where the DNA came from and how far it has travelled. Researchers are studying how many samples need to be taken from a specific geographic area to get an accurate picture of the organisms present. We also know that naked DNA is nutrient rich and so it rapidly taken up by bacteria. But DNA that is still associated to cellular material may survive a little longer in the environment: a day to several weeks.
How can eDNA complement traditional biodiversity monitoring?
eDNA is incredibly complementary to traditional methods. It gives us a more complete picture of marine biodiversity and the changes taking place and provides us with an enhanced level of detail about marine ecosystems and habitats.
With the increased pressure on science to achieve net zero emissions, the other great thing about eDNA is that you don’t always have to be present to take the sample. You can use automated collection processes, for example using autonomous vessels, so the sample can be collected without human presence. Additionally, it allows for more people to get involved through citizen science projects, where people can collect samples and contribute to biodiversity research from their own backyards.
What’s next for eDNA research?
One of the big challenges we’re tackling is turning DNA traces into meaningful numbers. Right now, when we find fish DNA in a water sample, we can’t tell if it came from one huge tuna or a school of tiny juveniles. That’s why we’re developing smart machine learning tools to help us make sense of these genetic fingerprints and what they really tell us about marine populations.
We’re also starting to look into combining eDNA with computer modelling. You can think of it as adding a genetic layer to our ocean forecasting – helping us not just spot what’s there now but predict how marine communities might change over time.
As the technology gets cheaper and faster, and as genetic libraries grow, this should open up a huge amount of possibilities. For example, we could be using eDNA to do everything from checking how well marine protected areas are working, to tracking how sea life bounces back after environmental disasters, and even monitoring how whole communities of marine species are responding to climate change and other stressors.