National Research Institute for Agriculture, Food and the Environment

INRAE logo

INRAE is the France's National Research Institute for Agriculture, Food and Environment, created in January 2020 from the merger of 2 leading research institutes in these fields (INRA and Irstea). INRAE uses research, innovation, and support for public policies as tools to guide the emergence of sustainable agricultural and food production systems. INRAE aims to carry out science dedicated to life, humans, and the Earth that uncovers solutions to our most pressing concerns.

Pharm-ERA will mobilize 4 Research Units respectively belonging to the ‘AQUA’ (RiverLy, Lyon; EABX, Bordeaux), and ‘AgroEcoSystem’ (Agroécologie, Dijon; EcoSys, Palaiseau) Divisions of INRAE.

RiverLy - Interdisciplinary research unit for the management and restoration of river systems and their catchment

Visit RiverLy website

Research interests & main objectives

  • The Research Group on Aquatic Microbial Ecotoxicology carries out research to provide knowledge and develop innovative tools and approaches to describe how micropollutants affect the vulnerability and resilience of benthic microbial biodiversity and to evaluate the ecological quality of contaminated aquatic ecosystems through the study of natural periphytic and sediment microbial communities.
  • The Aquatic Environment Chemistry Laboratory carries out researches to provide knowledge and develop innovative methodologies to characterize sources, transfer routes and exposure to contaminants, understand their behaviour in aquatic environments and characterise their bioavailability. .

Principal investigator

Stéphane PESCE – Senior scientist (Director of Research) in aquatic microbial ecotoxicology

Staff involved in Pharm-ERA

  • Research Group on Aquatic Microbial Ecotoxicology
    • Bernadette VOLAT – Engineer in Aquatic Microbial Ecotoxicology
  • Aquatic Environment Chemistry Laboratory:
    • Cécile MIEGE – Senior scientist (Director of Research) in Environmental Chemistry  
    • Christelle MARGOUM – Senior scientist (Research Engineer) in Environmental Chemistry

Equipment and processes

The laboratory of Aquatic Microbial Ecotoxicology is eqquiped with facilities for microbial function assessment (PhytoPAM, I-PAM, micro gas chromatography, molecular biology lab…)  and microcosm experiments (including indoor artificial channels and sediment columns).  as well as long-term experimental study sites in agroecosystems and urban rivers. The staff also has all the equipment and experience needed to carry out sampling campaigns (water, periphyton and sediment) in lotic and lake environments.

The Aquatic Environment Chemistry Laboratory has equipment for :
- sampling: spot and integrative environmental samples, i.e. sediment traps and passive samplers ;
- characterising solids (suspended particles, sediment) in the aquatic environment: laser granulometer, organic and total carbon content, N and S, dry and volatile matter
- analysing major chemical elements (anions, cations, organic matter), trace metals (ICP-OES, ICP-MS, GC-ICP-MS), and organic contaminants (LC-MSMS triple quadrupole, LC or APGC-HRMS QTOF) in waters, river sediments, biota.

EMA-Artifical chanel
Microcosm experiments (artificial channels) in the laboratory of Aquatic Microbial Ecotoxicology
Non-targeted analysis of organic micropollutants in water by ultra-high performance liquid chromatography coupled with high-resolution mass spectrometer & gas chromatography coupled with high-resolution mass spectrometer
LAMA team. Non-targeted analysis of organic micropollutants with ultra-high performance liquid chromatography coupled to a high-resolution mass spectrometer. © Grégoire Maisonneuve
LAMA team. Data processing of organic micropollutants analysis using ultra-high performance liquid chromatography coupled to a quadrupole tandem mass spectrometer. © Grégoire Maisonneuve
LAMA team. Target analysis of organic micropollutants with ultra-high performance liquid chromatography coupled to a quadrupole tandem mass spectrometer. © Grégoire Maisonneuve


EABX - Aquatic ecosystems and global change

Visit EABX website

Research interests & main objectives

  • The research conducted by the ECOVEA team (Ecology of Aquatic Plant Communities and Impact of Multiple Pressures, focuses on understanding the biodiversity and functioning of plant communities (macrophytes, phytoplankton, phytobenthos) in freshwater ecosystems, as well as their responses to natural and anthropogenic disturbances. By crossing the disciplinary fields of ecology and ecotoxicology, at complementary study scales ranging from molecules to communities (phytoplankton, biofilms, and macrophytes), the team addresses the following questions:
  • Interspecific regulation capacities through molecules released into the environment by aquatic organisms, effects, and ecological role of allelopathic relationships
  • Spatio-temporal dynamics of aquatic plant biodiversity in the context of global changes (artificialization of natural habitats, eutrophication of waters, biological invasions, and climate change)
  • Structure and response of aquatic plant communities to physical and chemical alterations of hydrosystems
  • Ecotoxicological risks for organisms at the basis of trophic networks and impacts on key ecological functions
  • Intracellular mechanisms involved in the response to toxic stress and altered metabolic pathways (including lipids).
  • Biomarkers discovery for water quality biomonitoring purpose

Principal investigators

Chloé Bonnineau – Researcher in aquatic microbial ecotoxicology

Staff involved in Pharm-ERA

  • Nicolas Creusot - Researcher in biofilm metabolomics  
  • Soizic Morin – Senior scientist (Director of Research) in aquatic microbial ecotoxicology  
  • Nicolas Mazzella -  Senior scientist (Research engineer) in environmental chemistry/lipidomics  

Equipement and processes

The ECOVEA team carries out in situ and experimental research activities within two platforms: the Aquatic Vegetation Service and Bordeaux Metabolome.

  • The laboratories of the Aquatic Vegetation Service have facilities and equipments to perform experiments on microalgal cultures (e.g. thermostatic chambers ) or complex microbial communities (e.g. indoor artificial channels), to measure microbial functions (Phyto-PAM, I-PAM) and to perform microscope observations of fresh and fixed samples (7 microscopes equipped with phase contrast and DIC, with lenses range from X4 to X100, digital camera, image acquisition and processing software Archimed). The Aquatic Vegetation Service is managed by experienced Ecovea team members, this service is also part of the national Collective Scientific Infrastructure XPO platform (eXPérimentation et d'Observation sur les Écosystèmes Aquatiques) and of the national LIFE (Living In Freshwaters and Estuaries) Research Infrastructure and of AnaEE France.

Microalgal exposure experiment (Scenedesmus costatus) within the Aquatic Vegetation Service of Ecovea © Emma Barcelo
Microcosm experiment (artificial channels) within the Aquatic Vegetation Service of Ecovea © Chloé Bonnineau
Sample preparation room at Ecovea’s biomarkers laboratory


  • The Bordeaux Metabolome platform is part of the national MetaboHub Infrastructure focusing on metabolomics and fluxomics activities and includes ECOVEA’s biomarkers laboratory. This laboratory is fully equipped for water quality analyses (nutriments, organic micropollutants), non-targeted metabolomics (using high-resolution time-of-flight mass spectrometry) and lipidomics (triple quadrupole tandem mass spectrometry) analyses on complex matrices including microalgae and whole microbial communities such as periphyton. The staff from biomarkers laboratory has also the experience and equipment to perform sampling in freshwater environments, sample preparation, chemical analyses and further data analyses.

More specifically, the biomarkers laboratory has :

  • Techniques and equipments for analysing main nutriments in freshwaters (anions, cations, dissolved organic carbon…) :   Ion Chromatography, TOC-VWP TOC meter (Shimadzu) equipped with a persulphate oxidation system, UV-visible spectrophotometer 1800 (Shimadzu), Flash Smart N/C soil elemental analyzer (Thermo)
  • Techniques and equipments for organic micropollutants analyses : passive samplers preparation (POCIS), liquid or gaz chromatography coupled to tandem or ToF mass spectrometry : UPLC XEVO G2-S-Tof Waters, GC/MS/MS  Thermo Scientific, Ultimate 3000 Dionex API 2000 LC/MS/MS SCIEX
  • Techniques and equipments for non-target metabolomics using high-resolution time-of-flight mass spectrometry
  • Techniques and equipments for lipidomics analyses using triple quadrupole tandem mass spectrometry
  • Techniques and equipments for sample preparation : centrifuges, water station MQ Neptune (France Water), sieve shaker, freeze dryer, multi-station evaporator SpeedVac, pressurized solid-liquid extraction system ASE 200 (Dionex) for sediments, sludges and biological matrices...
Ultimate 3000 Dionex API 2000 LC/MS/MS SCIEX at Ecovea’s biomarkers laboratory © Elsa PERRIN


EcoSys - Functional ecology and ecotoxicology of agroecosystems), Soil&Tox Research Group

Research interests & main objectives

The Soil&Tox Research Group of the JRU EcoSys conducts research through experimental and modelling approaches to study the role of soils in agroecosystems facing external constraints related to global changes, according to six main research lines: 

  • Optimization of organic waste recycling in agriculture
  • Understanding the fate, dispersion and impacts of pesticides and other organic contaminants in agricultural soils
  • Understanding the soil organic matter dynamics
  • Understanding the complex influences of the soil matrix on the exposition on organisms
  • Understanding the long-term impacts of the contaminants on the organisms and their functions, integrating the notion of resilience
  • Assessing the ecosystem services provided by soils at different scales.

Principal investigators

Laure MAMY – Senior scientist (Director of Research) in soil science
Pierre BENOIT - Senior scientist (Director of Research) in soil science

Equipement and processes

The main input of EcoSys will be to use and improve the TyPol tool. This tool is able to classify organic compounds by combining molecular descriptors, and fate and effect parameters. It was developed by several scientists: Pierre BENOIT and Laure MAMY from EcoSys, and Eric LATRILLE, Dominique PATUREAU, Virginie ROSSARD and Rémi SERVIEN from the Laboratory of Environmental Biotechnology (LEB) of INRAE in Narbonne. TyPol is accessible in EcoSys, and there is a close and constant collaboration with the scientists of the LBE to continue to update and improve the tool. The calculation of molecular descriptors, which have to be inputted in TyPol for each studied compound, requires the use of several softwares (such as Dragon) which are available in EcoSys as well as the use of a supercomputing system (CALMIP - CALcul en MIdi Pyrénées) which is accessible thanks to a close collaboration with the University of Toulouse (Fabienne BESSAC, Sophie HOYAU).

Ecosys-AgroParisTech Campus
AgroParisTech Campus - University of Paris-Saclay
TyPol tool and methods of molecular descriptors calculation



The Agroecology laboratory is aiming at developing sustainable agriculture, enabling production that meets food requirements in terms of quality and quantity, while respecting the environment. The aim of Agroecology laboratory is to increase our knowledge of biotic interactions (in particular plant-plant and plant-micro-organism interactions) within agroecosystems, in order to design innovative cropping systems that respect the environment. Researches are conducted at different levels of integration and spatio-temporal scales. It draws on complementary expertises in agronomy, ecology, biology, genetics, microbiology and modelling.

Research interests & main objectives

Microbiomes and ecosystemic functions of soils-MICSOL department of Agroecology lab is conducting its researches along four principal questions:

  1. Analysing the spatial and temporal structuring of soil microbial communities in order to understand the biotic and abiotic determinants,
  2. Evaluate and understand the impact of agricultural practices on soil microbial communities and their functions in the context of climate change,
  3. Understand and make the most of biotic interactions between microorganisms and with plants in agroecosystems,
  4. Mobilising microbial communities as levers to accelerate ecological transition.

Principal investigators

Fabrice Martin-Laurent – Senior scientist (Director of Research) in soil microbial ecotoxicology

Staff involved in Pharm-ERA

Aymé Spor, Senior Researcher in soil microbial ecology, INRAE
Marion Devers, Engineer in microbial ecology, INRAE
Jérémie Béguet, Engineer in molecular biology, INRA

Equipement and processes

The Agroecology laboratory is fully equipped with facilities for microbial ecology and microbial ecotoxicology with all the equipment’s required to incubate soil under control conditions, extract and analyze nucleic acid from soils to study the abundance, structure and diversity of microbial communities, measure microbial activities using a range of methods among which radiorespirometry allowing the measurement 14C-compound transformation to 14CO2. It has also equipment and method to characterize soil physicochemical properties.

Agroeco - lab to field ecotox
Lab-to-field ecotoxicology of xenobiotics.

See also

Modification date : 29 March 2024 | Publication date : 06 March 2024 | Redactor : Emilie EGEA