PhD position in Characterizing the chemical pressure fingerprints of streams in small watersheds: developing non-targeted analysis strategies for organic compounds

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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

The presence of numerous organic contaminants in aquatic ecosystems can lead to a degradation of the ecological status of watercourses. Small catchments with mixed land use and land cover are particularly sensitive to these pressures of contamination, with i) many and varied origins, linked to urban development and car traffic, tourism, industry and agriculture, ii) watercourses often close to the contaminant sources, sometimes intermittent or with low dilution capacities and iii) contaminants subject to transformation processes leading to a large number of substances potentially present in surface water. While point source contamination is well established, non-point source contamination is more difficult to identify because of the complexity of the transfer pathways to watercourses. The identification of organic contamination (which means here dissolved organic matter - DOM - and organic micropollutants) is particularly challenging because these compounds may be of natural or anthropogenic origin, and may result from a variety of uses over time and space.
Characterisation of DOM is usually based on measuring the concentration of dissolved organic carbon (DOC), although it is now recognised that human activities modify the composition of the DOM in watercourses, with possible impacts, as yet poorly understood, on ecosystem functioning and on the global carbon cycle (Williams et al., 2016). On the other hand, while nearly 350,000 chemical substances with a wide range of physico-chemical properties are used in industry (Wang et al., 2020), monitoring programmes follow a predetermined list of micropollutants, which makes it impossible to characterise chemical pressure in its entirety. Non-target screening (NTS) approaches based on high-resolution mass spectrometry (HRMS) are developing rapidly in the field of environmental chemistry. They allow the vast majority of the thousands of organic compounds present in a water sample to be explored without any a priori, whether they are of anthropogenic or natural origin, and they include organic micropollutants as well as the components of dissolved organic matter (Boukra 2023, González-Gaya et al. 2021).
Decision-makers (public authorities, managers, users, etc.) need in-depth knowledge of the various chemical pressures in small catchment areas to better understand the risks and impacts of human activities on watercourses. This will enable them to optimise the implementation of actions to protect water resources (protecting both the environment and human health) and to anticipate future water pressures in a context of climate change and evolution of territorial trajectories (Hernández et al., 2019).

The aim of this thesis is to improve non-targeted data acquisition and processing strategies in order to improve the characterisation of organic contamination (DOM and micropollutants) in watercourses. The purpose of this work is then to increase our knowledge of chemical pressures in catchment areas.
The main scientific objectives are: 
1.    To develop and adapt acquisition and reprocessing strategies for LC-HRMS data in order to improve the reliability of lists of organic compounds present in samples, based on the team's previous work (Rocco et al. 2022, Ducroq 2025).
2.    Design advanced statistical analysis methods to better characterise families of organic compounds (natural and anthropogenic origins).
3.    Propose new global indicators derived from HRMS analyses, to identify and characterise the chemical pressures affecting the water samples collected at the outlet of sub-catchments.

The PhD student will carry out a research project including: 
- Sampling surveys: design of the sampling campaigns and collection of surface water samples subject to different chemical pressures and of mixtures at the outlets of catchment areas (mainly in the Auvergne-Rhône-Alpes region in France);
- Analytical developments: optimisation of liquid chromatography analysis coupled with high-resolution mass spectrometry to make data acquisition more reliable and to generate an original database relating to chemical pressures;
- Exploitation of HRMS data: implementation of chemometric, statistical and data management tools for in-depth processing of HRMS data (e.g. specific HRMS analyses of the Kendricks or Van Krevelen type, multivariate analyses, machine learning) in order to define contamination typologies.

References: 
Boukra A. (2023). Caractérisation intégrée de la matière organique dissoute : recherche d’empreintes physico-chimiques pour tracer les sources de pollutions anthropiques. tel-04584694v1
Ducrocq T. (2025). Exploration des micropolluants organiques dans les sédiments du Rhône par analyse non-ciblée. In press.
González-Gaya B. et al. (2021). Suspect and non-target screening: the last frontier in environmental analysis. DOI: 10.1039/D1AY00111F
Hernández F et al. (2019): The role of analytical chemistry in exposure science: Focus on the aquatic environment. DOI: 10.1016/j.chemosphere.2019.01.118
Rocco K. et al. (2022). Enhanced database creation with in silico workflows for suspect screening of unknown tebuconazole transformation products in environmental samples by UHPLC-HRMS. DOI: 10.1016/j.jhazmat.2022.129706
Wang Z. et al. (2020). Toward a Global Understanding of Chemical Pollution: A First Comprehensive Analysis of National and Regional Chemical Inventories. DOI: 10.1021/acs.est.9b06379
Williams, C.J. et al. (2016).  Human activities cause distinct dissolved organic matter composition across freshwater ecosystems. DOI: 10.1111/gcb.13094

 

Training and skills

Recommended training: Master 2 Research degree in analytical or environmental chemistry.
Desired knowledge: solid theoretical background in environmental chemistry, knowledge in chemoinformatics concepts and statistical tools using R or another free programming language.
Appreciated experience: previous experience in non-targeted analyses (LC or GC-HRMS).
Skills: interest in environmental issues, scientific rigour and a strong attitude to teamwork.
 

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