Description du sujet de thèse

"Evolutionary microbiology, paleomicrobiology and biogeochemistry"

We seek a highly motivated PhD candidate to:
1. Unravel the links between heavy metal use and antibiotic resistance through metagenomic analysis of ancient and modern environmental DNA (sediment cores), focusing on:
• Detection and annotation of ARGs, HMRGs, and mobile genetic elements (MGEs).
• Taxonomic profiling and functional gene association studies.
• Time-series analysis of resistance gene dynamics.
2. Explore the evolutionary history of resistance genes
• Sequence analysis and phylogeny in relation to exposure and time
3. Uncover drivers of antibiotic resistance spread
• Apply time-series modeling to link historical pollution events with ARG emergence.
• Identify "high-risk" genetic configurations still circulating today.

We are looking for a highly motivated candidate with a Master's degree in molecular biology, bioinformatics, microbial ecology, environmental genomics, or a related field. A Master's program that combines wet-lab molecular biology with computational skills would be ideal, but applicants strong in one area and motivated to develop the other are also encouraged to apply. The candidate must be able to integrate into teams of different cultures, have a strong taste for data analysis, be autonomous and know how to take initiatives.
Expected competences:
• Molecular biology expertise : DNA extraction, metagenomic workflow, and downstream data analysis (taxonomic and functional annotation).
• Bioinformatics proficiency: ability to run and develop code in R, Python, and similar tools.
• Good understanding of microbial ecology and its applications in biogeochemical cycles.
• Communication skills: excellent command of spoken and written English.

Contexte de travail

Global biogeochemical cycles, driven by microbial activity, are critical to planetary health. Human activities—mining, industrial processes, and antibiotic use—have altered these cycles, leading to widespread pollution and the emergence of heavy metal resistance genes (HMRGs) and antibiotic resistance genes (ARGs). These resistance mechanisms, often linked on mobile genetic elements, threaten ecosystems and human health, with antimicrobial resistance projected to cause 10 million annual deaths by 2050 if unaddressed. This project leverages paleoecological archives (sediment DNA) to study the long-term relationship between metal pollution and antibiotic resistance and is funded by the Paleo-MARE ERC project. By reconstructing microbial responses to historical geochemical changes, we aim to uncover the mechanisms driving ARG spread and inform policy on environmental risk mitigation.

The experimental work for this PhD will be carried out in the dedicated paleogenetic laboratory at Chrono-Environnement, which provides state-of-the-art facilities for ancient DNA research. Chrono-Environnement is a multidisciplinary research institute bringing together experts in ecology, paleo-environments, biodiversity, Earth sciences and archeology. Its teams investigate the interactions between environment, climate, and societies through experimental, observational, and modeling approaches.