Marine biodiversity is declining at an alarming rate. Between overfishing, habitat degradation and global warming, as well as pollution and invasive species, coastal ecosystems are under increasing anthropogenic pressure. Extensive and robust data are needed to monitor marine species and guide the implementation of planning and protection measures. At the University of Montpellier, Simon Bettinger is combining environmental DNA and artificial intelligence to assess the impact of marine heatwaves on coastal marine biodiversity. This innovation could guide marine life protection strategies in sensitive areas such as the Mediterranean and the Mayotte lagoon.
By Carole Saoul-Grit and Laurie Henry
Cover photo: Sampling campaign on the Rhône © S. Bettinger
Heat waves disrupting the oceans
Global warming is not limited to land. Coastal seas also experience sudden temperature rises during marine heatwaves. These increasingly frequent events disrupt ecological balances and threaten species that are struggling to adapt.
In the face of these challenges, it is becoming crucial to observe, understand and anticipate changes in marine ecosystems. Far from traditional counting or visual monitoring approaches, new methods based on the analysis of genetic traces in the environment are opening up unprecedented access to marine biodiversity. In Montpellier, scientists are using these innovative tools to better predict the state of coastal ecosystems and guide conservation decisions.
The Mediterranean, an endangered ecosystem
The Mediterranean coastline is a striking example of the fragility of marine ecosystems. Despite its exceptional richness, this region is under pressure: intensive fishing, rapid urbanisation and global warming are endangering its coastal habitats.
While 9% of Mediterranean waters are now designated Marine Protected Areas (source: Marine Conservation Institute), an assessment carried out in 2020 by the Mediterranean Network of Marine Protected Area Managers (MedPAN) and the Regional Activity Centre for Marine Protected Areas (SPA/RAC) found that the cumulative area of MPA prohibition, catch prohibition or fishing prohibition areas only represents 0.04% of the total area of the region. The protection of Mediterranean waters therefore remains largely insufficient given the urgency of the situation.
To better understand and protect these environments, Simon Bettinger, a PhD student at the University of Montpellier, is combining environmental DNA (eDNA) and artificial intelligence to assess the impact of heat waves on marine biodiversity and guide protection strategies in sensitive areas.
Specific wealth map obtained from DNA sampling in 2023 © Martin Paquet, MARBEC
DNA databases have been accumulating for several years, but remain underutilised. How can this raw, often incomplete data be analysed? How can sequences that are not referenced in genetic databases be interpreted, especially in poorly understood areas such as deep-sea habitats? This is the focus of Simon’s new research.
A thesis at the crossroads of science
Simon’s thesis, which began in 2024, uses innovative tools to analyse ADNe data. The aim is to better classify species, model their distribution and understand their seasonal dynamics. His field of study covers areas that are particularly vulnerable to heat waves, such as the calanques of Marseille and the deep reefs of Mayotte.
One of the major challenges of this work is identifying DNA fragments that do not correspond to any species listed in current databases. To do this, Simon uses artificial intelligence methods, originally designed to analyse text, which he adapts to DNA. These tools make it possible to recognise genetic ‘words’ or ‘phrases’, even from very short or incomplete sequences.
Simon Bettinger during a campaign in Palavas © S. Bettinger
Deep habitats, potential refuges for biodiversity
Mesophotic and rariphotic reefs, located at depths where light is scarce, could play a key role in protecting marine biodiversity. These habitats, which are less exposed to heat waves, could potentially serve as refuges for certain coastal species. However, in order for this to happen, it is essential to identify, study and protect them effectively.
Simon analyses temporal variations in marine communities in relation to seasons, marine heatwaves and human activity. Using eDNA samples collected since 2021 in the calanques, he is studying changes in species composition both inside and outside marine reserves. This research could confirm the hypothesis that deep habitats serve as climate refuges.
An alliance between ecology and technology
This thesis, conducted at the UMR MARBEC at the University of Montpellier, is part of the objectives of the Priority Research Programme (PPR) Ocean & Climate. It aims to anticipate the effects of climate change on marine ecosystems. Co-supervised by David Mouillot (MARBEC) and Rodolphe Devillers (ESPACE-DEV – IRD), this research combines ecology, artificial intelligence and underwater robotics, using autonomous vehicles and ADNe pumping systems.
The ambition is clear: to support the development of marine protected areas that are more resilient and better adapted to current and future threats. Thanks to this innovative approach, marine biodiversity protection could enter a new era.
3 Questions to Simon Bettinger
Why did you decide to pursue a thesis in marine science?
I have always been very curious about the ocean, and for as long as I can remember, I have wanted to make it the focus of my career. This curiosity and thirst for knowledge about the environments I have been exposed to since childhood initially drew me to research. Throughout my training, my awareness of environmental issues and climate and biological emergencies reinforced my choice and made me want to contribute to conservation through the study of marine environments. Being part of a new generation of researchers is an opportunity for me to help advance our understanding and conservation of biodiversity, at sea and elsewhere.
What made you want to apply for this thesis topic? What were your motivations?
During my M2 internship, I worked extensively with environmental DNA data. The speed of implementation and comprehensiveness of this method struck me as essential qualities for implementing effective conservation protocols, which require good coverage and information on key but cryptic species. The proposed thesis topic addresses this issue precisely, as it draws on the full potential of eDNA inventories, particularly through modelling.
How do you envision your future after completing your thesis?
After completing my thesis, I hope to have the opportunity to apply the knowledge I have acquired about marine biodiversity to conservation efforts. I would like to go beyond basic research and become more directly involved in environmental protection.
Référence : Simon Bettinger, « Protecting Mediterranean and tropical mesophotic and rariphotic reefs as a solution for mitigating the effects of climate change on marine biodiversity », phD 2024-2027
Contact : sbettinger33@gmail.com