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eDNA : Unveiling life

The eDNA revolution

Everywhere we go, we leave traces of ourselves: our DNA. DNA is a universal molecule, shared by all the living world. When a living being passes through a forest, a lake or a reef, he leaves bits of saliva, urine, or skin… a unique signal of his presence in an ecosystem.

Every species has its own DNA sequence. By sampling DNA in an environment, it becomes possible to reveal most species in a given place. That method is called environmental DNA, or eDNA. From viruses to whales, including insects, birds or amphibians, eDNA allows us to unveil the biodiversity present in an ecosystem using only a few samples of water, dirt, honey or feces.

DNA is a molecule shared by all living beings, and eDNA allows us to discover biodiversity as a whole, from small to big animals. On the left, Antillean crested hummingbird (Orthorhyncus cristatus). On the top right, a grouper on a reef in Ponto do Ouro, Mozambique. On the bottom right, a western honey bee (Apis mellifera).
Photo credit: Raphaël Seguin.

We face a massive erosion of biodiversity, where human activities impact all ecosystems on earth. Confronted with the immense challenge of halting biodiversity loss and climate change, our ability to monitor and understand ecosystem changes has never been more important.

Environmental DNA is a revolution in our ability to survey biodiversity.  For instance, eDNA allowed us to detect species that we rarely see with our own eyes, such as the Short-finned Pilot Whale (Globicephala macrorhynchus) in the AGOA Sanctuary of Guadeloupe. It also overcomes bias towards studying only the species we like – like marine mammals – as it reveals indiscriminately popular species such as dolphins or pandas as well as invisible species (viruses, bacteria), or long ignored species (blennies, insects).

eDNA unveils biodiversity undiscriminately, from the ignored and unseen such as the Tompot blenny (Parablennius gattorugine) on the left to the massive and popular humpback whale, on the right.
Photo credit: Loïc Sanchez (photo on the left) and Nacim Guellati (Photo on the right).

In the marine environment, monitoring biodiversity can be highly challenging. Methods such as visual counts during dives or underwater videos often hide some species that are afraid of humans, hidden in the reef or at unreachable depths. However, all of those species, such as sharks or blennies, release DNA in the environment that will be detectable for days.

Be it to study how ecosystems respond to pollution, exploitation, or how species will change their home range facing climate change, eDNA allows us to better understand biodiversity, and helps us to protect it. However, eDNA also has its limits: from this technique we cannot know the number of species in an ecosystem, their age or their sex. That’s why it’s important to combine eDNA with other biodiversity monitoring techniques.

Coastal ecosystems and eDNA

For the MaCoBioS project, we sample multiple habitats using eDNA, from kelp forests to seagrass, coral reefs or salt marshes, all across Europe and the Caribbean Sea.    Our first fieldwork mission took place in Martinique, where we sampled coral reefs and seagrass using eDNA. We sampled while diving: that allows us to filter water close to the bottom and detect hidden species in the reef. Using “eDNA pumps”, we filtrate the water for 30 minutes. The water goes through a filter that keeps all the little fragments of DNA contained in the water. This filter is then sent to Spygen, a laboratory that takes care of analyses and assigns the DNA to a given species. 
In Martinique, eDNA sampling was performed while diving (Top picture) with an eDNA pump. The water goes through a filter that collects the DNA fragments in the water (Bottom picture).
Photo credit: Renaud Leroux.

Monitoring two essential habitats

Seagrass beds are vast underwater prairies composed of long, green leaves. But they’re not algae, they’re flowering plants, just like the ones we find on earth!
Seagrass ecosystems are a nursery for juvenile fish, a food source for herbivores and act as carbon sink.
Photo credit: Umeed Mistry / Ocean Image Bank on the left, and Raphaël Seguin on the right

Coral reefs only cover 0.1% of the oceans…but shelter more than 6000 species of fish. They are among the most threatened ecosystems by climate change.

Coral bleaching are one of the most vulnerable ecosystems in the face of climate change. Raising ocean temperatures are causing widespread bleaching of reefs.
Photo credit: The Ocean Agency / Ocean Image Bank

Humanity has an intricate and interwoven relationship with coral reefs, a relationship that has lasted for thousands of years. This interdependence rests on the functioning of reefs, which depend on the species they shelter. That’s why it’s so important to monitor their biodiversity!

Humanity has a strong relationship with coral reefs.
Photo credit: Grant Thomas / Ocean Image Bank

Facing this crucial challenge, in which the future of millions of human lives is connected to the future of seagrass, corals and the living beings they host, eDNA offers a standardized and easily reproducible universal method thus opening a door to international collaboration on the science of coastal ecosystems. This technique will allow us to understand how these marine and coastal ecosystems respond to climate change, overfishing, and how these pressures affect their functioning and humanity. Understanding these ecosystems will also give us the tools to appropriately choose how to protect them: where to establish marine protected areas? What degree of restrictions should we choose? Which extractive activities are the most destructive to coral reefs?

The MaCoBioS project aims to understand how coastal ecosystems in Europe and the Caribbean respond to human pressures such as climate change, and how to effectively manage them. Environmental DNA, by allowing long-term monitoring of these ecosystems, will help us understand the dynamics of these ecosystems and guide their protection and recovery through this period of planetary warming, in the midst of the Anthropocene.

Text by : Raphael Seguin

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