PhD POSITION : Evaluation of estuarine restoration effects through community modeling and functional approaches

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

You will be welcomed into the Aquatic Ecosystems and Global Changes Research Unit (UR EABX: https://eabx.bordeaux-aquitaine.hub.inrae.fr/qui-sommes-nous/l-unite-eabx), located in Cestas, near the city of Bordeaux. This research unit is part of the INRAE Bordeaux–Nouvelle Aquitaine Center.

The research conducted by UR EABX aims to provide knowledge, develop methodologies, and improve tools to define and understand the status and dynamics of freshwater aquatic ecosystems (including estuaries, coastal marshes, lakes, and rivers). This is achieved by assessing the responses of these ecosystems and their key species—particularly diadromous, estuarine, and euryhaline marine fish, as well as aquatic plants—to a range of human-induced pressures (e.g., fishing, habitat fragmentation, pollution, climate change). The Functioning and Restoration of Estuarine Ecosystems and Amphihaline Migratory Populations (FREEMA) team conducts ecological research on the response of fish communities to environmental constraints and local and global human pressures. This research primarily focuses on understanding the links between the structure and dynamics of these communities and the overall ecological functioning of ecosystems under environmental constraints. Bioindication tools are widely used within the research unit to perform ecological diagnostics. Additionally, the restoration of degraded aquatic ecosystems—particularly estuaries and associated habitats like wetlands—is becoming increasingly central to FREEMA's research activities.

Estuarine ecosystems are dynamic and productive environments that provide essential habitats for many fish species. However, they are increasingly threatened by human activities, making restoration efforts crucial to maintaining their functionality and biodiversity. This PhD project aims to evaluate and predict community responses to habitat restoration actions in a context of variable environmental stress, providing crucial information on the long-term evolution of biodiversity and ecosystem functioning in estuarine habitats.

The successful candidate will assess the impacts of current estuary restoration practices on fish communities in the Gironde estuary using a joint species distribution modelling (JSDM) framework. By resampling two case studies at several restored and un-restored sites, including Île Nouvelle and Mortagne in the Gironde, the candidate will assess the current state and composition of fish communities in relation to historical data. He/she will analyze the temporal trajectory of species occurrence probabilities and quantify the main environmental and management factors influencing species responses. This shed light on the level of success of the restoration actions underway. The project will further examine the functional trajectories of fish community by analyzing changes in the functional diversity and functional rarity in relation to restoration efforts and environmental conditions. This analysis will make it possible to identify the habitat characteristics associated with the ‘hot spots’ and ‘cold spots’ of functional metrics, and to assess the resilience potential of communities in a restoration context. This understanding will shed light on the mechanisms underlying ecosystem functioning in estuarine habitats, guiding the selection of species and traits to target in restoration projects. Finally, the project aims to develop predictive models to project future dynamics of fish communities under various environmental and restoration scenarios. These predictive models will guide adaptive management and restoration planning, enhancing the resilience of fish communities to future changes.

The thesis will try to answer questions such as:

• How do restoration actions affect the assembly of estuarine fish communities, and which species benefit the most?
• Can restoration actions promote functional hotspots to preserve community resilience?
• What are the future impacts of climate change on estuarine communities and their functioning?
• Can habitat restoration mitigate the effects of climate change and contribute to community resilience?

Throughout this doctoral project, the candidate will develop a diverse skill set, enabling them to conduct a wide range of research in the field of ecology. During the sampling campaigns, they will gain hands-on experience with fish survey methods and protocols. In addition to theoretical knowledge in community and estuarine ecology, the candidate will learn to construct, analyze, and interpret hierarchical joint species distribution models, using them to make predictions based on future environmental change scenarios. These practical skills in field ecology and statistical modeling will provide a strong foundation for their postdoctoral career. Furthermore, they will develop and refine scientific writing skills to successfully publish research articles.

 

 

Training and skills

Recommended Training: The successful candidate will hold a Master's degree in ecology or a related field. During their studies and internships, they will have received training in community ecology, with a particular focus on quantitative ecology. They should be familiar with concepts related to species distribution changes and the underlying mechanisms.

Required Knowledge: The candidate will have a solid understanding of, or at least a strong interest in, statistical modeling and programming in R.

Preferred Experience: The candidate must be autonomous while also knowing how to collaborate with others to ensure the success of the project. A strong command of English is essential.

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering ;

-partial support for home/work subscription (TER, TBM...).

How to apply

Please apply on the doctoral school website:

https://adum.fr/as/ed/voirproposition.pl?site=adumR&matricule_prop=62208#version

Deadline for applications: 28.05.2025

Please note that interviews with the thesis supervisors for recommendations to the doctoral school may already be held before the deadline and hence, non-last-minute applications are preferable.