18 November 2020

Environmental DNA: a new area in marine biodiversity monitoring?

A recent scientific publication, published in November 2020 in the international journal Environmental DNA, compares two techniques used to assess marine biodiversity: the classic underwater visual census and the study of environmental DNA, an emerging technique in this field.

The study, supported by Monaco Explorations, focuses on the census of the number of fish species living on tropical coral reefs and was carried out in Colombian marine sites. The results are part of a vast international research program: the Megafauna project, initiated among others by the researchers of the MARBEC Joint Research Unit (MARine Biodiversity, Exploitation and Conservation), which aims at carrying out an exhaustive inventory of marine biodiversity on a maximum of sites around the world. Research in which the need for knowledge is still immense given the unknowns and current environmental issues in terms of sustainable development and management of seas and oceans.

Scientific divers setting up a temporary net to take biological samples of different fish species to enrich the genetic reference base - Santa Marta, Colombia © O. Borde Monaco Explorations

A multidisciplinary team.

The authors come from various horizons such as Andrea Polanco, a researcher from the Institute of Marine and Coastal Research, INVEMAR, from Colombia; Virginie Marques, PHD student  from the University of Montpellier ; Loic Pellissier, Professor of Ecology at the ETH Zurich in Switzerland; Stéphanie Manel Professor, from the École Pratique des Hautes Études, Center for Functional and Evolutionary Ecology Department based in Montpellier in France ; Camille Albouy researcher from IFREMER Nantes; Tony Dejean director of the SPYGEN company in Le Bourget-du-Lac; and Régis Hocdé, researcher from the French National Research Institute for Sustainable Development and David Mouillot Professor at Montpellier University both based at MARBEC research unit. They demonstrate that the environmental DNA technique is a revolutionary tool for exhaustive and rapid censuses of the fish present in an ecosystem as complex as a coral reef.

Their study focused on two tropical coral reefs on the Colombian Atlantic coast: Providencia and Gayraca Bay. Visual censuses have been carried out there regularly since 1999 and environmental DNA samples were taken more recently during two missions coordinated by the Explorations de Monaco in 2018. Thanks to this technique, more than a hundred different species of fishes have been identified without any disturbance, just by filtering the water. These results are proof of a significant biodiversity that is rarely recorded by visual census or by camera. They enable the managers of these two sites to encourage the public authorities to protect these places, still full of life, which need to be monitored over time at this critical period of global change.

However, the study points out the limits of this census method and the need to continue to increment the reference genetic databases in order to be ever more precise in assigning species to all the DNA fragments collected by filtration.

More information

An ocean endangered by global change

The biodiversity of the oceans is in danger. Under the pressure of numerous man-made pollutants, such as plastic waste and industrial effluents, the underwater world is also subject to the over-exploitation of resources by fishing or deep-sea drilling. All these factors are weakening a complex ecosystem in which the diversity of species is falling drastically. This collapse endangers a whole range of life on which the human species is dependent.

Several groups of marine biologists are working in particular to identify this biodiversity in a more exhaustive, non-destructive and reliable manner in order to study it while there is still time. In doing so, they warn about the health status of an environment that they note is in a deteriorating state. The objective, beyond research, is to offer reflections to find preservation solutions compatible with sustainable management and development.

Coral reefs: hotspots of biodiversity but difficult to study

Several million years old, coral reefs represent the most diverse marine ecosystems on the planet and the most threatened. It justifies their exploration and monitoring. Due to their structural complexity, they are home to a very wide species diversity ranging from small damselfish to large migratory species such as manta rays or sharks. Because of this high diversity, life on coral reefs has always been difficult to inventory with traditional methods. Usually, the most widely used technique is the underwater visual census (UVC), for which scientific divers carry out dive counts following a very precise study protocol, limited in space and time.

Coral reefs - Santa Marta, Colombia © O. Borde Monaco Explorations.
Coral reefs - Santa Marta, Colombia © O. Borde Monaco Explorations.

Environmental DNA: a new age of census

For the past ten years or so, the census of species can be conducted using an innovative technique: the study of environmental DNA. This method is based on the fact that all living beings leave DNA traces in their environment, for example through excrement or blood or skin loss. To study the marine world, it is therefore possible to take water samples from any depth, filter them and isolate the DNA present using molecular biology techniques. In order to be able to then proceed with taxonomic identification, scientists compare the DNA sequences found with sequences already known and referenced by species in shared databases.

Encouraging results

From this study conducted in Colombian waters, the researchers were able to compare the results of several years of visual censuses (between 1999 and 2017) with the results of the environmental DNA study from water samples taken from the same sites in 2018.


A total of 113 species have been recorded in Providencia by visual technique and 31% of these species have been found by environmental DNA. In Gayraca, 57 species have been recorded by visual counting and 28% have been found by DNA. On the other hand, in both locations, environmental DNA analysis allowed new species to be identified that were not detected by visual techniques, 72 in Providencia and 85 in Gayraca.

Enriching the reference database: a necessity for the future of environmental DNA

The environmental DNA technique has been in use for about ten years, however, to reach its full potential, the database for genetic referencing of species needs to be completed. In fact, only biological sampling, such as a small piece of fin, allows the sequencing of an individual’s specific DNA and thus to find its trace in the water later on. At present, only 16% of fish species are referenced, which largely explains the differences between visual census and DNA study. An enormous amount of collection and sequencing work remains to be done. Apart from teams of scientists, it is possible to mobilize different communities such as fishermen or the international network of aquariums to carry out these samplings.

Stone fish - Santa Marta, Colombia © O. Borde Monaco Explorations.
Stone fish - Santa Marta, Colombia © O. Borde Monaco Explorations.

Providencia and Gayraca Bay: little-known areas to be protected

Located in the southwestern Caribbean Sea off the coast of Colombia, Providencia Island is a listed member of the UNESCO World Network of Biosphere Reserves (Seaflower Biosphere Reserve). From volcanic origin, a large coral reef surrounds the island and protects it from climatic hazards. Gayraca Bay is located in the Tayrona Natural National Park along the Sierra Nevada de Santa Marta. The coast is composed of different types of rocks forming bays and islets. The corals are distributed along the coast in a very diverse universe, between mangrove and seagrass.

Adjacent to relatively well known and protected terrestrial areas, the marine area of Providencia Island and Gayraca Bay are now identified as important in terms of biodiversity, which justifies studying them in greater detail in order to adapt protection measures.