Monitoring a seagrass bed at a seascape level: Overcoming challenges with technology

Monitoring a seagrass bed at a seascape level: Overcoming challenges with technology

Posidonia oceanica seagrass beds are the most important marine ecosystems along the relatively shallow waters of the Mediterranean coast. These meadows can be found from the shore up to 30-35 m of depth and spread along a considerable distance. The French cartographic database of Posidonia distribution and health status is quite complete. However, the monitoring of this ecosystem is often done under the same conditions, i.e., in the centre of the meadow at an average depth of 15 m. Yet, to study biodiversity patterns and assess the services provided by this ecosystem at the seascape level, we need to monitor seagrass beds at various points from the upper to the lower depth limit, including the interfaces with other habitats. While monitoring meadows is easily achieved on land, it becomes very challenging underwater. According to the choice of the study area, such monitoring allows to study the global health status of Posidonia ecosystem under different levels of human pressures. Our fieldwork last month (July 2021) at Cap Sicié in the South of France aimed at monitoring this ecosystem using novel approaches to overcome those challenges. This specific site of Cap Sicié presents a strong gradient of habitat quality from healthy to degraded which offers the advantage to explore the ecological responses in terms of biodiversity and produced ecosystem services.
Posidonia meadow. Photo credit: Rémy Simide
Because most fish and invertebrates are hidden inside the canopy formed by Posidonia leaves that can reach up to 1 meter in length, they are very difficult to observe using traditional visual censuses. We used novel techniques like bioacoustics to characterise the associated benthic fauna. This method allows us to listen to the environment within hundreds of meters in all directions. Many marine invertebrate species produce sounds when eating, moving or communicating. We are then able to hear all these sounds as long as we have a highly sensitive hydrophone to record them and a skilful set of ears and software to interpret this biophony.
The hydrophone deployed underwater to record the biophony. Photo credit: Rémy Simide
However, to evaluate the ecosystem and its services at a precise spatial scale, direct observation by divers is still a very accurate option. Since we are not aquatic species, it is hard to spend a lot of time underwater, moving fast, being located in this 3D environment or see far away. These limitations explain why monitoring at a seascape level can be difficult to achieve. Fortunately, thanks to innovative tools these challenges can be overcome. Indeed, using close circuit rebreather (CCR), dry suits and waterproof scooters, we were able to spend more time in the water and to move faster between each sampling point. Underwater navigation between sampling points was further facilitated by wireless geolocated waterproof tablets. We were pretty heavy underwater with this complete set of tools, but we still had space to carry our sampling materials. At each sampling point, we characterised the structural complexity of the habitat by 3D photogrammetry, made in situ samplings, evaluation of benthic communities and assessment of fish diversity that will be complimentary to the biodiversity assessed through bioacoustics.
One of our divers with his complete equipment (close circuit rebreather, dry suit, waterproof scooters, wireless geolocated waterproof tablets) doing in situ sampling. Photo credit: Rémy Simide
During our first round of fieldwork this summer, we monitored a 3 km long seagrass bed with a strong gradient of health conditions due to wastewater flow. The first part of the mission included an adjustment period to master all the material and complete multiple sampling protocols in only a few minutes per sampling point. In the end, we obtained an excellent ecological overview of this large area. We are excited and impatient to sample the next station in the National Park of Port Cros and to analyse the data.

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eDNA : Unveiling life

Screen Shot 2021-05-11 at 11.50.50

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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