PhD position : Impact of Toxic Chemical Pressure on the Current Evolution of Invertebrate Communities in French Rivers

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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 join the RiverLy Research Unit, which combines expertise in hydrology, hydraulics, environmental chemistry, ecology, ecotoxicology, and microbiology to develop multiscale approaches for understanding the quality, functioning, and dynamics of freshwater systems. Its interdisciplinary research aims to better consider both natural and human-induced risks for improved river management and restoration. This PhD will be conducted jointly and at the interface between two RiverLy teams: Ecotoxicology (https://ecotox.riverly.inrae.fr/) and EcoFlows (https://ecoflows.inrae.fr/). The Ecotoxicology team focuses on chemical contaminant transfer in biota, understanding chronic toxicity through physiological and molecular approaches in aquatic organisms (crustaceans, fish), inter- and intra-species sensitivity differences, and the development of in situ biomonitoring tools to assess contamination and toxicity in aquatic environments. Meanwhile, the EcoFlows team addresses aquatic ecology at various spatial scales (from microhabitats to watersheds), investigating how habitat changes or degradation (e.g., hydraulic, thermal, physicochemical) affect fish and invertebrate populations and communities, especially under increasing and multiple anthropogenic pressures on freshwater ecosystems.

Research Topic and PhD Objectives
Keywords: aquatic macroinvertebrates, diversity patterns, macroecology, in situ ecotoxicology, chemical contamination, biomonitoring.
Toxic chemical pressure is considered one of the main, yet poorly characterized, drivers of ongoing aquatic biodiversity loss, and a limiting factor in the effectiveness of habitat restoration [1,2]. Focusing on invertebrates — key indicators of biodiversity crisis — this PhD aims to establish robust links between chemical contamination exposure and the evolution of species communities in French rivers. Thanks to 20 years of community data from national monitoring networks, this project will leverage a novel opportunity: access to in situ ecotoxicology indicators (caged Gammarus) recorded repeatedly over the past 5 years at several hundred stations. These indicators quantify exposure to various substances or the overall toxicity of environmental contaminant mixtures [3,4]. The main goal of the PhD is to evaluate how integrating taxonomic monitoring data with in situ ecotoxicological indicators (collected at matching spatial scales) can reveal specific impacts of chemical contamination on macroinvertebrate diversity patterns in national river systems. Building on earlier "proof of concept" studies [5–8], the PhD will rely on large datasets to support statistical modeling at various spatial scales (national, hydro-eco-regional, watershed). It will examine different chemical pressures (agricultural, industrial, urban, geochemical) in multiple contexts (e.g., warming, trophic dynamics, habitat diversity) to assess how exposure levels influence biodiversity metrics (species richness, abundance, % sensitive or exotic species, etc.). The thesis will explore diversity patterns (beta-diversity) and processes (species turnover, homogenization/differentiation) at large spatial scales (e.g., watersheds) in relation to these exposure gradients. This multiscale, national-level approach will also help reinterpret unexplained biodiversity changes observed in local observatory stations, particularly in the Rhône river system (RhonEco program [9]). In addition to taxonomic diversity, the PhD will analyze changes in functional diversity (trait-based approach) to assess the functional vulnerability of communities exposed to chemical contamination under current environmental changes.
REFERENCES : [1] doi.org/10.1111/gcb.16689; [2] doi.org/10.1038/s41586-023-06400-1; [3] doi.org/10.14758/SET-REVUE.2021.4.15; 
[4] doi.org/10.14758/SET-REVUE.2021.4.16; [5] doi.org/10.1021/acs.est.9b01271; [6] doi.org/10.1016/j.envpol.2022.119565; [7] doi.org/10.1016/j.watres.2021.117546; [8] doi.org/10.1016/j.scitotenv.2024.178328; [9] hal.science/hal-04680015v1;

The PhD candidate will develop a strong background in community ecology, with a unique focus on environmental chemical contamination, gaining deep knowledge in ecotoxicology, advanced biomonitoring tools, and diagnostic indicators of toxic chemical pressure in aquatic ecosystems. The candidate will be trained in managing and analyzing large datasets and geographic information systems. They will acquire robust theoretical and technical skills in statistical modeling using a wide array of methods. He/She will also gain in-depth understanding of taxonomic and functional diversity metrics and community assembly processes, integrating knowledge from biogeography, functional ecology, and macroecology.
Supervisors: Arnaud Chaumot (Ecotox) & David Eme (EcoFlows)
         Emails: arnaud.chaumot@inrae.fr ; david.eme@inrae.fr
This PhD is co-funded (50%) by INRAE’s AQUA department and is central to a strategic axis within the RiverLy unit, aiming to bridge work between the ecotoxicology and ecology fields. It also aligns with broader initiatives involving Lyon-based research groups (especially UMR LEHNA) within the RhonEco project (2024–2028), which has monitored the ecological restoration of the Rhône River for the past 30 years [9]. RhonEco will co-fund the PhD (50%).
 

Training and skills

Recommended training: Master’s (MSc or equivalent) in Ecology or Biostatistics
Desired knowledge: Data analysis methods, ecological modeling, community ecology
Appreciated experience (but not-required): Internship/expertise in hydrobiology, biodiversity pattern analysis, statistical modeling of ecological/environmental relationships
Skills: Strong interest in data analysis and biodiversity, intellectual curiosity, openness to interdisciplinary work, organizational skills, ability to work in a multidisciplinary team, strong scientific synthesis, writing, and communication skills

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.

How to apply

I send my CV and my motivation letter