Environmental DNA for fish biodiversity monitoring

Finding Fish

By Molly Czachur

Marine biodiversity is a rich and colourful display of what the natural world has to offer. Whilst large whale sharks are gliding through the oceans, the nearby coastal mangrove forests are acting as a vital nursery ground that is teeming with the microscopic larvae of future fish generations. The closer we look, the more we see of the staggering diversity of life in the oceans.

Across the globe, we govern diverse fish resources to reap the ecological and economic benefits. We want to understand ‘which fish live where’ in order to approach the daunting task of managing them. There are ~2,000 fish species in South Africa, many of which are commercially and ecologically important. For lots of South Africans, recreational fishing is a popular pass time that also requires healthy fish populations. The more we know about the distribution of fishes, the better equipped we are to make well-informed management decisions.


To understand where different fishes are living, we currently look at which fish have been caught, and carry out visual surveys. These methods rely on ‘seeing’ the fishes, and require a certain level of expertise to correctly identify them. The results are incredibly informative but obtaining this information is costly on time and resources. There is also a ‘hidden diversity’ of life in the oceans, comprised of many rare and cryptic species that simply can’t be captured with traditional methods. We now need to utilise emerging new technologies to describe the biodiversity of fishes, even those that can’t be ‘seen’.

Environmental DNA

Fish shed their DNA into the environment as they pass through the water. This means that the oceans are a big soup of free-floating DNA, known as environmental DNA. Different fishes have slightly different genetic makeup, so we can look at the free-floating DNA and work out which species the DNA has come from.

eDNA (1)

Here in the von der Heyden lab at Stellenbosch University, we have received funding from the National Research Foundation to develop this environmental DNA technology in South Africa.

We collect DNA from coastal waters, and bring it back to our laboratories for further analyses. We can match the DNA that we find in the seawater with known DNA sequences that are available in online databases. In many ways, we are completing a complicated puzzle by matching the environmental DNA to its original owner. Once we have matched the DNA to different fishes, we can make conclusions about which fish have recently been swimming in that area of the coast.


We are beginning the exciting first steps of using environmental DNA for biodiversity monitoring in South Africa. This research will allow us to generate contemporary information about fish biodiversity that compliments the current survey methods in the region. More up-to-date and representative data will enhance the management of fishes as we enter the ever-changing future.

All illustrations were created by the author. See www.zoologymolly.com for more information.

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