Biomarkers Laboratory

Biomarkers Laboratory

The laboratory conducts innovative research into biomarkers in metabolomics and lipidomics. It is part of the Bordeaux Metabolome platform, which has received IBISA and ISC accreditation, and the national METABOHUB infrastructure.

Biomarker Laboratory Topics and Activities


In an era of chemical pollutions and global change, periphytic microbial communities play a key function in the characterization and understanding of how exposure to contaminants affects aquatic communities. These microbial communities are typically used because of their essential role in ecosystem functions, such as biogeochemical cycling and biomonitoring, and associated services, as well as their diversity spanning all biological kingdoms. Although laboratory studies have improved our understanding on how such organisms acclimate, adapt and resist chemical stressors, it remains challenging to better understand how environmental stressors influence organism responses. In addition, the limited representativeness of laboratory approaches can be compensated with in situ studies, which reflect the complexity of the real-world conditions and integrate numerous natural factors alongside man-made toxic chemical stress. It will also enable more appropriate environmental management solutions to be proposed for both monitoring and mitigating. Lastly, the development of descriptors that take into account microbial communities, rather than just specific components, is critical. With this goal in mind, we are working towards a more complete picture of the ecosystem, and then address how periphytic microbial communities respond to environmental stressors.

In this context, the work of the biomarker laboratory of the EABX research unit aims to propose new descriptors of exposure, and biological and ecological effects. These biomarkers, especially when compared to traditional global descriptors (i.e. growth, respiration, and photosynthesis), would improve specific and early understanding of responses to different types of stress. Non-targeted metabolomics (using high-resolution time-of-flight mass spectrometry) and lipidomics (triple quadrupole tandem mass spectrometry) with extracts from biological communities are the main methodologies developed here. These two 'omics' approaches provide an innovative way of looking at physiological changes within organisms, and then an access to the mechanisms involved in stress impacts. In particular, exposure to pollutants can alter the molecular response of biota, and certain environmental parameters, such as temperature, light or nutrients, modulate the measured responses.

In addition, our ecotoxicology research benefits from a strong earlier expertise in the development of passive sampling tools. These techniques make it possible to relate in situ exposure to observed biological effects in aquatic organisms (periphyton, plants, fish, shrimps). The use of passive integrative samplers also improves the spatio-temporal resolution of pollution measurements as part of WFD surveillance or trend monitoring. The laboratory can also measure key physicochemical parameters and nutrients, in relation with primary producers in freshwaters, to characterize the trophic level, thanks to its analytical capabilities and skills.

The works of the EABX research unit in ecology or ecotoxicology is supported by the in-depth characterization of exposure on either the field or in the laboratory (i.e. microcosms). Altogether, these approaches are enabling us to better understand the toxicokinetics and toxicodynamics of contaminants within microbial communities, leading to a higher knowledge of the link between exposure and ecological impacts.


Water chemistry laboratory equipment

Physico-chemical analyses, organic carbon and nutrient analysis

Chromatographie ionique 881 Compact IC Pro Metrohm
Chromatographie ionique 881 Compact IC Pro Metrohm © Bertrand NICOLAS
Spectrophotomètre UV-Visible-1800 Shimadzu
Spectrophotomètre UV-Visible-1800 Shimadzu © Elsa PERRIN
  • pH titrator and TAC easy plus (Mettler Toledo)
  • Compact Ion Chromatography System 881 with 858 automated sample/dilution changer and conductivity detector (Metrohm)
  • TOC-VWP TOC meter (Shimadzu) equipped with a persulphate oxidation system
  • UV-visible spectrophotometer 1800 (Shimadzu)
  • Flash Smart N/C soil elemental analyzer (Thermo)

Bio-organic analyses

  • microplate, multiskan (Thermofisher) and Synergy HT (Bioteck) readers


Dosage of organic pesticides

UPLC XEVO G2-S-Tof Waters
UPLC XEVO G2-S-Tof Waters © Bertrand NICOLAS
GC/MS/MS Thermo Scientific
GC/MS/MS Thermo Scientific © Elsa PERRIN
Ultimate 3000 Dionex API 2000 LC/MS/MS SCIEX
Ultimate 3000 Dionex API 2000 LC/MS/MS SCIEX © Elsa PERRIN
  • Gas chromatography coupled to a tandem mass spectrometer TSQ Quantum GC - GC-MS/MS (Thermo)
  • UltiMate 3000 High Performance Liquid Chromatography (Thermo) coupled to an API 2000 Tandem Mass Spectrometer (AB Sciex)
  • Ultra Performance Liquid Chromatography ACQUITY H-Class (Waters) coupled to Xevo G2-S ToF time-of-flight mass spectrometer (Waters)


Ovens and scales

Étuves et balances
Étuves et balances © Elsa PERRIN
  • Ovens (Memmert) and muffle furnace (Nabertherm)
  • Micro scale SARTORIUS MSA36P-000-DH
  • Precision scale MS 204S (Mettler)
  • Scale PB 1501 (Mettler)


Sample Preparation

Préparation d'échantillons
Salle de préparation d'échantillons
  • Extractor hoods
  • Bench mattresses
  • Mineralization ramps (total phosphorus dosage)
  • Centrifuge ST16 (Thermo)
  • Large volume centrifuge (JOUAN)
  • Water station MQ Neptune (France Water)
  • Sieve shaker AS200 (Retsch)
  • Automatic Distillation Unit B-324 (Buchi) for Kjeldahl nitrogen
  • Alpha 1/2-4 freeze dryer (CHRIST)
  • Multi-station evaporator SpeedVac SPD121P (Thermo)
  • Pressurized solid-liquid extraction system ASE 200 (Dionex) for sediments, sludges and biological matrices
  • HiSorb Agitator Incubator (Markes)


Health & Safety and miscellaneous equipment

  • Storage cabinet for acids, bases and solvents with activated carbon CAPTAIR
  • Showers and eye rinses
  • Safety refrigerators for storage of chemicals and samples
  • Safety freezers for storage of chemical products, standard solutions
  • Demineralized water (purification by resin cartridge), many points of arrival in the different parts.
  • Nitrogen generator (AirFlux)
  • Air compressor (AirFlux)
  • Outdoor room for gas cylinders: Nitrogen, Argon and Helium 6.0
  • Outdoor room for storage of solvents, acids, bases, etc.
  • Outdoor room for waste storage before recycling

Modification date : 02 February 2024 | Publication date : 24 February 2020 | Redactor : MP