Biogéochimie moléculaire

The Molecular Biogeochemistry research team specializes in the detailed molecular analysis of complex organic mixtures derived from modern and ancient sediments, soils, microbial and plant biomass, as well as archaeological artifacts. It is part of the Doctoral School of Chemical Sciences (ED 222) and serves as a host laboratory for the Master’s programs in Analytical Sciences, Molecular & Supramolecular Chemistry, Chemistry, Biology & Drug Design.

Furthermore, in the context of growing antimicrobial resistance, the development of new therapeutic targets has become essential. The MEP pathway, which is specific to bacteria and absent in humans, is a prime target in this regard. Thus, the CBMB group, affiliated with the Molecular Biogeochemistry team since January 2026 (https://cbmb.chimie.unistra.fr/), is developing innovative strategies that combine the synthesis of inhibitors with the study of bacterial communication, using an interdisciplinary approach that integrates organic synthesis and microbiology.

Research topics

The research topics of the Molecular Biogeochemistry team lie at the intersection of analytical (bio)organic chemistry, synthetic chemistry, and the chemistry of natural products.

Main areas of research

The research conducted by the Molecular Biogeochemistry team focuses on four main areas:

1. Organic Geochemistry: Development of new molecular and isotopic tools to study the functioning of modern ecosystems and reconstruct ancient environments. This involves studying how these environments have evolved over geological time in response to climatic or biological changes and anthropogenic influences.

2. Molecular Archaeology: Molecular and isotopic analysis of organic substances from archaeological sites and artifacts (balms, amber, etc.) to trace the origin of these substances, their methods of use, and past practices and lifestyles.

3. Experimental Archaeology: Study of the fate of food residues in archaeological ceramics. This component is based on an experimental approach conducted in collaboration with archaeologists. It involves analyzing samples obtained from controlled cooking experiments using precisely defined ingredients, in order to assess the nature of the molecular signatures of the original ingredients preserved within the porosity of the ceramics, and their representativeness depending on the cooking methods.

4. Biogeochemistry of microbial lipids: Study of changes in the composition of membrane lipids in cultured bacteria and archaea in relation to their adaptive strategies to their environment and to the physicochemical changes these microorganisms may undergo, for example, in terms of salinity stress. This research also focuses on the identification of new biomarkers of biogeochemical processes, such as specific hopanoids synthesized by bacteria involved in the biogeochemical nitrogen cycle.

The specific molecular approach used by the team to develop these various research areas is based on the identification of molecular markers using mass spectrometry (GC-MS, LC-MS). In some cases, the structure of new substances is identified either after isolating the compounds of interest and conducting NMR studies, or through the organic synthesis of reference compounds. This work is carried out within the framework of numerous collaborations (both national and international).

List of equipment and instruments

Three gas chromatographs (flame ionization detector, GC-FID)
One preparative HPLC module (detection: refractive index)
Two gas chromatographs coupled with mass spectrometers (triple and single quadrupole, respectively; GC-MS(-MS)). Ionization modes: EI and CI (NH₃, i-Bu, CH₄)
One gas chromatograph coupled with an isotope ratio mass spectrometer (¹²C/¹³C, H/D; GC-IRMS)
Two HPLC modules coupled with ion trap mass spectrometers (with APCI, ESI, APPI, and DAD detection)

Recent publications

A. Fradet, P. Schaeffer, L.-P. Magnin, L. Lenen, J. Pańczak, B. Gomez, V. Grossi, P Adam
The widespread occurrence and wide structural diversity of sulfurized diterpenoids in ambers.
Organic Geochemistry, 2026, 213, 105127.
https://doi.org/10.1016/j.orggeochem.2026.105127

M. Saracco, P. Schaeffer, M. Tourte, S.V. Albers, Y. Louis, J. Peters, B. Demé, S. Fontanay, P. Oger.
Bilayer-forming lipids enhance archaeal monolayer membrane stability.
International Journal of Molecular Sciences, 2025, 26, 3045. (hal-05007477v1)
https://doi.org/10.3390/ijms26073045 ⟨hal-05007477⟩.

L. Bourmancé, A. Marie, R. Puppo, S. Brûlé, P. Schaeffer, M. Toupet, R. Notsche, A. Elsaesser, A. Kish.
The salty tango of brine composition and UV photochemistry effects on Halobacterium salinarum cell envelope biosignature preservation.
Communications Biology, 2025, 8, 602.
https://doi.org/10.1038/s42003-025-08007-w ⟨mnhn-05033856⟩.

M. Mauger, I. Makarchuk, Y. Molter, A. Sansone, F. Melin, P. Chaignon, P. Schaeffer, P. Adam, V. Schünemann, P. Hellwig, C. Ferreri, C. Chatgilialoglu, M. Seemann.
Towards bacterial resistance via the membrane strategy: enzymatic, biophysical and biomimetic studies of the lipid cis-trans isomerase of Pseudomonas aeruginosa.
ChemBioChem, 2025, 26, e202400844.
https://doi.org/10.1002/cbic.202400844 (hal-04886367).

J. Connan, J. Bonnéric, R. Perrogon, M.H. Engel, R. Gley, A. Zumberge, P. Schaeffer. Geochemical study of bitumen residues on potsherds from the al-Qusur Monastery (7th–9th c. CE): Composition and origin.
Molecules, 2025, 30, 2006.
https://doi.org/10.3390/molecules30092006

T. Liyanage, L. M van Maldegem, J. Hope, P. Schaeffer, P. Adam, H.P. Nytoft, D. Edwards, J. Brocks.
Hopanoid breakdown products (HBPs) and their influence on tetracyclic and tricyclic terpane (cheilanthane) oil-source rock parameters.
Organic Geochemistry, 2025, 210, 105085.
https://doi.org/10.1016/j.orggeochem.2025.105085 (hal-05379084).

F. Baudin, I. Jovovic, P. Adam, M. Ader, F. Arnaud, F. Gélin, V. Grossi. (2024).
Early stages of Type I−S kerogen formation revealed by Rock−Eval^® 7S analysis of sediment from a modern halo−alkaline lake (Dziani Dzaha, Mayotte).
Organic Geochemistry, 2024, 195, 104794.
https://doi.org/10.1016/j.orggeochem.2024.104794 (hal−04600490).

N. Tarifa−Mateo, R. Laborda, A. Sierra, L. Montes, P. Utrilla, M. Sana, E. Motsch, P. Schaeffer, P. Adam.
Milk production in pottery. Evidence for various exploited resources used by the first farmers in Central Pyrenees using the morphological, chemical and stable carbon isotopic composition of organic residues from ceramic vessels.
Archaeological and Anthropological Sciences, 2024, 16, 101.
https://doi.org/10.1007/s12520-024-02001-9 (hal-04788050).

S. Sallon, E. Solowey, M. R. Gostel, M. Egli, G.R. Flematti, B. Bohmazn, P. Schaeffer, P. Adam, A. Weeks.
Characterization and analysis of a Commiphora species germinated from an ancient seed suggests a possible connection to a species mentioned in the Bible.
Communications Biology, 2024, 7, 1109.
https://doi.org/10.1038/s42003-024-06721-5 (hal−04788119).

M. Michler, G. Auxiette, F. Jodry, N. Tarifa-Mateo, P. Adam, P. Schaeffer, C. Féliu, C. Véber.
Le site de l’âge du Bronze moyen de Berstett Langenberg (Bas-Rhin), approches croisées. Gallia Préhistoire – Préhistoire de la France dans son contexte européen, Varia, 2023, 63.
https://doi.org/10.4000/galliap.3554 ⟨hal-04081914⟩

R. Schwartz−Narbonne, P. Schaeffer, S.K. Lengger, J. Blewett, D.M. Jones, et al.
Bacterial physiology highlighted by the d¹³C fractionation of bacteriohopanetetrol isomers.
Organic Geochemistry, 2023, 181, 104617.
https://doi.org/10.1016/j.orggeochem.2023.104617 (hal−04107656)

M. Galmiche, E. Esslinger, O. Delhomme, P. Schaeffer, E. Motsch, et al.
Method development for the LC−MS/MS determination of C₆₀ and C₇₀ fullerenes and their functionalized derivatives in airborne particulate matter, settled dust and soot.
International Journal of Mass Spectrometry, 2023, 490, 117072.
https://doi.org/10.1016/j.ijms.2023.117072 (hal−04271655).

L. Lenen, A. Fradet, P. Schaeffer, B. Gomez, P. Adam.
Sulfurized diterpenoids in amber as diagenetic indicators of sulfate−reducing processes in past depositional environments. Organic & Biomolecular Chemistry, 2023, 21, 768−774.
https://doi.org/10.1039/D2OB02017C (hal−04271619).

J.J. Brocks, B.J. Nettersheim, P. Adam, P. Schaeffer, A.J.M. Jarrett, et al.
Lost world of complex life and the late rise of the eukaryotic crown.
Nature, 2023, 618, 767−773.
https://doi.org/10.1038/s41586-023-06170-w (hal−04273175).

Additional information

Industrial collaborations: TotalEnergies

National and international academic collaborations:
- Institut National de Recherches Archéologiques Préventives (INRAP), France.
- Archéologie Alsace, Sélestat, France.
- Laboratoire Image, Ville, Environnement (UMR 7362, CNRS, Université de Strasbourg), France.
- Equipe Microbiologie des Environnements Extrêmes (M2E), INSA Villeurbanne, France.
- Laboratoire de Géologie de Lyon: Terre, Planètes , Environnement (UMR 5276, CNRS-Université de Lyon I-ENS Lyon), Villeurbanne, France.
- Géochimie des isotopes stable, Institut de Physique du Globe de Paris (UMR 7154), France.
- Research School of Earth Sciences, The Australian University, Canberra, Australie.
- Max-Planck-Institute for Biogeochemistry, Jena, Allemagne.
- Centre de Recherche sur les Sociétés et Environnements en Méditerranée (CRESEM - UR 7397, Université de Perpignan), France.
- Archéologie des Sociétés Méditerranéennes, UMR 5140, Montpellier.
- Service régional de l’archéologie, Occitanie, Montpellier, France.
- Institut für Biologie II, Molecular Biology of Archaea, Albert-Ludwigs Universität Freiburg, Allemagne.
- Institute of Southeast Asian Studies, Singapour.
- Géosciences Rennes, Université de Rennes, France.
- Sheffield Hallam University (Biomolecular Science Research Center), Royaume Uni.
- Organic Geochemistry Unit, University of Bristol, Royaume Uni.
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Royaume Uni.
- Microbiology and Biogeochemistry Department, Netherland Institute for Sea Research, Pays-Bas.