PhD position in evolutionary microbiology, paleomicrobiology and biogeochemistry M/F

CNRS; France; Sur place; EUR 30 000 - 40 000; Plein temps

Résumé du poste

A leading research organization in France is seeking a highly motivated PhD candidate to study the long-term relationship between metal pollution and antibiotic resistance. The role involves metagenomic analysis of environmental DNA and aims to uncover the mechanisms of antibiotic resistance spread. The ideal candidate holds a Master's degree in a relevant field and possesses strong skills in molecular biology, bioinformatics, and data analysis. This position offers a full-time, temporary contract with a start date in February 2026.

Qualifications

• Master's degree in molecular biology, bioinformatics, microbial ecology, or a related field.
• Strong taste for data analysis and ability to integrate into diverse teams.
• Autonomous and proactive.

Responsabilités

• Unravel the links between heavy metal use and antibiotic resistance through metagenomic analysis.
• Explore the evolutionary history of resistance genes through sequence analysis.
• Identify drivers of antibiotic resistance spread via time-series modeling.

Connaissances

DNA extraction

Metagenomic workflow

Data analysis

R programming

Python

Microbial ecology

Communication skills

Formation

Master's degree in molecular biology, bioinformatics, microbial ecology, or related field

Description du poste

Organisation/Company CNRS Department Laboratoire Chrono-Environnement Research Field Environmental science Biological sciences Geosciences Researcher Profile First Stage Researcher (R1) Country France Application Deadline 30 Dec 2025 - 23:59 (UTC) Type of Contract Temporary Job Status Full-time Hours Per Week 35 Offer Starting Date 2 Feb 2026 Is the job funded through the EU Research Framework Programme? Horizon Europe - ERC Is the Job related to staff position within a Research Infrastructure? No

Offer Description

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.

"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.