(M/F) PhD Position in Physical Chemistry: DNA/Clay Interfaces – Study of environmental DNA stabilization mechanisms within reconstructed terrestrial systems.

Job Description

Thesis Subject

PhD Position: Investigating the mechanisms of environmental DNA stabilization within reconstructed terrestrial systems

Abstract
This PhD project is part of the ClayMED ANR project, an ambitious initiative led by a multi- and pluridisciplinary consortium including IC2MP (Poitiers), ICGM (Montpellier), and LIEC (Nancy). The objective is to elucidate the physicochemical mechanisms governing the persistence of environmental DNA (eDNA) within mineral matrices. Rather than studying raw natural samples, the project relies on the reconstruction of model terrestrial environments to identify key parameters—such as clay mineralogy, water chemistry, and confinement effects—that promote the preservation of genetic information over long timescales. Leveraging state-of-the-art characterization techniques and molecular modeling, this thesis aims to transform the understanding of these mechanisms into a concrete lever for developing original extraction methods. These new methods must enable the quantitative and selective recovery of eDNA while ensuring optimal quality of the extracted molecules (integrity and absence of inhibitors), which is essential for the success of subsequent PCR amplification and sequencing stages for ecosystem reconstruction.

Context and Problem Statement
The rapid and ongoing decline of terrestrial biodiversity is one of the most pressing issues of our time. Recent assessments indicate that up to one million species are at risk of extinction within decades, at a rate tens to hundreds of times higher than the natural background rate. This crisis is fueled by anthropogenic disturbances such as habitat destruction, climate change, pollution, and overexploitation, leading to a widespread depletion of wild flora and fauna. These losses threaten essential ecosystem services—such as pollination, water purification, and carbon sequestration—which are the pillars of our civilizations and economic systems. A major obstacle to resolving this crisis is the persistent lack of knowledge regarding the status, spatial distribution, and historical evolution of biodiversity during past climate changes. This knowledge gap is particularly pronounced in ecosystems where monitoring has historically been limited. While traditional biodiversity assessment methods are valuable, they often provide incomplete snapshots and struggle to capture cryptic species or rapid community changes. In this context, environmental DNA (eDNA) has emerged as a revolutionary tool capable of creating a molecular footprint of biodiversity. When genetic material becomes trapped and preserved under specific environmental conditions, particularly within fine particles such as clays, it can persist for millennia. However, although clay-rich terrestrial environments are recognized as robust reservoirs, their utilization remains a major challenge due to the difficulty of extracting DNA bound to mineral surfaces.

Project Description
The doctoral research will be structured around three major objectives. The first axis is based on the idea that a "library" of complex DNA/clay structures, integrating both mineral and organic heterogeneities, is necessary to faithfully represent terrestrial micro-environments. The candidate will determine the optimal physicochemical conditions promoting DNA immobilization within complex systems. Since soil composition varies radically across climates, the project will analyze how salinity, pH, and the presence of organic matter—which can either protect DNA through coating effects or compete for binding sites—influence the formation of eDNA "hotspots." This systematic approach will provide insight into the stability of genetic information under realistic and varied environmental conditions. The second axis explores the hypothesis that the preservation capacity of clays is closely linked to confinement effects and nanoscale heterogeneities. The goal is to elucidate the molecular mechanisms of stabilization by examining how the distribution of structural charges in minerals modifies the organization of the interfacial water network and, consequently, the geometric conformation of DNA. To precisely isolate these factors, the candidate will utilize clays produced via hydrothermal synthesis, allowing for rigorous control of mineral chemistry. Finally, the third axis contends that a deep understanding of molecular organization at interfaces will overcome the technological barriers associated with extraction. The candidate will be involved in designing new methodologies for the selective recovery of trapped genetic material to enable the recovery of ancient DNA in temperate, non-permafrost environments.

Methodology
The research strategy will rely on an integrated multi-scale approach, combining rigorous mineral synthesis, advanced characterization techniques, and numerical modeling. The candidate will begin by preparing mineral phases using either the purification of natural clays or hydrothermal synthesis to obtain minerals with perfectly controlled structural properties. On this basis, adsorption isotherms will be conducted under varied physicochemical conditions to faithfully reconstruct the diversity of depositional environments found in soils. To decipher the nature of interactions, the PhD student will deploy a comprehensive analytical arsenal including X-ray diffraction (XRD), infrared spectroscopy (ATR-FTIR), and second-harmonic generation (SHG), as well as calorimetry to quantify interaction energies. These data will be systematically coupled with molecular modeling to visualize stabilization mechanisms at the atomic scale. Finally, the candidate will develop specific experimental setups to probe DNA preservation against environmental stressors and participate in the development of original extraction solvents with tunable properties to quantitatively extract DNA from clay matrices.

Candidate
Profile The candidate must hold a Master's degree (Master 2) with a specialization in materials physical chemistry, geochemistry, or environmental sciences. Beyond the academic background, a strong appetite for rigorous experimental approaches is indispensable. The candidate must demonstrate a deep interest in the mechanistic aspects of interface chemistry, with a drive to elucidate the relationships between the atomic structure of minerals and the reactivity of biomolecules. Curiosity regarding numerical modeling tools and advanced characterization methods (spectroscopy, diffraction) is also expected. Finally, the candidate must demonstrate autonomy, scientific rigor, and the ability to engage with multidisciplinary concepts. A good level of scientific English, essential for the promotion of the work and publication in international journals, is required to successfully carry out this project within the ClayMED consortium.

Your Work Environment

Recruited by the CNRS, the successful candidate will conduct their research at the Institute of Chemistry of Materials and Media of Poitiers (IC2MP), located at the University of Poitiers (France). IC2MP is an interdisciplinary research laboratory combining chemistry and geosciences, jointly supported by the CNRS and the University of Poitiers.

The candidate will join the HydrASA team, whose expertise is internationally recognized in the characterization, understanding, and modeling of clay mineral reactivity. The team notably develops original experimental and theoretical approaches that enable the multi-scale integration of interfacial phenomena.

Interested candidates are invited to submit their CV, a cover letter, M1 and M2 transcripts, and the contact information of two referees.

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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