In the Mediterranean, an innovative method to protect millennia-old underwater cities and their unique biodiversity
Between Marseille and Montpellier, marine biologist Louis Troussé is seeking to understand the impact of environmental upheavals on certain endemic communities and habitats in the Mediterranean basin. His PhD research, funded for three years by the Ocean and Climate Priority Research Programme, is enabling the development of an innovative method to optimise the targeting of measures for the protection and management of ecosystems in the Mediterranean.
by Carole Saout-Grit for Connected Oceans – 09 October 2026
Born in the french Normandy region, Louis Troussé travelled during his higher education to pursue his passion for marine ecology, from La Rochelle to Costa Rica via Montpellier and Nantes. This enabled him to deepen his knowledge of marine ecology and coastal environment management. The research he has been conducting since 2024 as part of his PhD focuses in particular on the study of communities and habitats typical of the Mediterranean Sea: coralligenous habitats.
A unique biodiversity and ancient cities threatened by environmental upheavals
In the Mediterranean Sea, at depths of between 20 and 120 metres, certain habitats have existed for millennia, like small cities teeming with life and featuring small structures to shelter them. These so-called coralligenous cities are mainly formed in low-light conditions by corallines – small, stone-hard pink algae that attach themselves, along with other organisms, to rocky walls. For centuries, these organisms have piled up on top of one another, like living bricks, helping to form extremely complex structures. In a remarkable balance, these coralligenous habitats are now home to nearly 10 per cent of the species in the Mediterranean Sea, which both shape and inhabit them.
But this age-old balance is under threat from environmental changes and new pressures caused by human activities. Within these coral-based communities, certain areas close to the surface can, for example, collapse rapidly under the weight of a falling anchor or a fishing net that tears everything away in its path. An excessive rise in water temperature can also disrupt the ecological balance of certain species and their habitats: in 2026, extreme marine heatwave events affected the entire Mediterranean basin from east to west, covering an area five times larger than those observed over the previous decade. These exceptional marine heat , which are increasingly affecting the Mediterranean, have been accompanied by episodes of mass mortality among many species, particularly in coralligenous habitats.
An innovative approach to assessing communities and habitats
In the Mediterranean, Louis Troussé is therefore setting out to find new clues to identify the inhabitants of coral-built cities, as well as the structures in which they live. The aim is to try to understand why they live there and how they will react to external pressures. To this end, he has an idea based on a simple principle: why not virtually bring all these cities to the surface in order to reconstruct them more effectively?
He therefore organised his work in three stages: first, carrying out a real-life dive in the field to take thousands of photographs in these neighbourhoods under pressure, at depths of between 30 and 45 metres; second, assembling these thousands of photographs using a computer and reconstructing these cities in 3D by visualising the architecture of each neighbourhood; finally, he programmed an artificial intelligence system to scan through the thousands of images and learn to recognise species, in order to describe the population and link each inhabitant to their respective neighbourhood, thereby carrying out a massive census.
Photogrammetry and deep learning
How can we shed light on the ecological relationships between the many species present within coralligenous cities and the complex structure of their habitats, against a backdrop of global change and shifts in their three-dimensional structure? This is the central focus of Louis’s research, which, in a pioneering approach, simultaneously studies mobile communities (fish, molluscs and crustaceans), sessile communities and the three-dimensional structure of these Mediterranean habitats.
To achieve these scientific objectives, Louis initially uses photogrammetric modelling: he compiles thousands of underwater images to digitally reconstruct the habitats in 3D, thereby enabling him to analyse their spatial structure, topography and complexity. At the same time, Louis characterises mobile communities using visual counting methods applied to these Mediterranean habitats. Finally, he is developing an artificial intelligence model based on deep learning to facilitate the recognition, analysis and monitoring of sessile species present in these coral-rich cities.
Thus, the combination of these innovative methods enables Louis to deepen his understanding of the relationships between the variations observed in visible communities of organisms and the spatial structure of their habitats within these coralligenous cities.
Louis’s PhD is funded as part of the Ocean and Climate Priority Research Programme (PPR), led by the CNRS and Ifremer. His research is jointly supervised by three organisations: the Septentrion Environnement association; the Marbec Joint Research Unit (UMR) at the University of Montpellier; and the Biological and Biotechnological Sciences Unit (US2B) at the University of Nantes. As such, Louis is co-supervised by Bastien Mérigot, a marine biologist and senior lecturer at the University of Montpellier; Stéphane Télectchéa, a bioinformatician and senior lecturer at Nantes University; and Marjorie Roscian and Adrien Cheminée from Septentrion Environnement.
More broadly, this study forms part of the SEASCAPE project, which specifically aims to investigate the relationships between the spatial structure of coralligenous habitats in the Mediterranean and the species living there, in the face of climate change and human pressures.
By drawing on multidisciplinary approaches in marine ecology, computer science and image analysis, the methods developed and the knowledge gained during this PhD research should provide a more integrated understanding of coralligenous habitats, thereby helping to better guide the associated protection and management measures. For the balance of these millennia-old underwater cities is crucial to that of the Mediterranean Sea – a major reservoir of global biodiversity – and to that of humanity itself.
three questions for Louis Troussé
Why did you decide to do a PhD in marine sciences?
My first experiences with the marine world began in childhood, as I explored the organisms of the intertidal zone in Brittany and Normandy, and later through diving. For as long as I can remember, a passion for discovering the underwater world has driven me and fuelled my desire to keep learning more about it.
Driven by a curiosity about the environment around us, I steered my studies towards general ecology, and then marine ecology. For me, undertaking a PhD in marine sciences is an opportunity to devote myself fully to the study of these ecosystems, which have always fascinated me.
What made you want to apply for this PhD topic? What were your motivations?
Following my end-of-Master’s placement in marine ecology, I was captivated by coral-rich habitats, both for their biodiversity and their complex architecture. I then wanted to help improve their study and monitoring, particularly by incorporating new technologies and analysing their three-dimensional structure.
Setting up a PhD project on this topic seemed to me to be the best way to achieve this. I therefore helped to develop this PhD project alongside Adrien Cheminée, Bastien Mérigot and Stéphane Téletchéa, whilst also studying for a second Master’s degree, which enabled me to strengthen my IT skills.
What I like most about this PhD is its multidisciplinary and integrated nature. It allows me to draw on my skills in ecology and computer science, whilst working at the interface between academic research, fieldwork and collaboration with marine protected area managers.
How do you imagine your future after completing this PhD?
I wish to pursue a career in marine ecosystem research, combining my passion for exploring these ecosystems with the challenges of management and conservation. I would like to continue developing my technical skills in order to gain a better understanding of the underwater world, both in the field and at the computer. Finally, I wish to combine research and teaching, as I would like to pass on my passion to future generations.
Reference : Louis Troussé, « Underwater landscape-scale analysis of the three-dimensional structure of coralligenous habitats and its links with associated communities, using photogrammetry and deep learning », PhD thesis 2024-2027
Contact : louistrousse@gmail.com
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