Doctoral contract on temporal biodiversity monitoring in French Guiana (M/F)

Job Description

Thesis Subject

Context :
The GENE-AMA project, funded by the CNRS MITI, aims to strengthen capacities for monitoring Amazonian biodiversity through environmental genomics in French Guiana, Brazil, and Guyana. It builds on advances in high-throughput sequencing, particularly Oxford Nanopore sequencing, to develop local, rapid, and standardized approaches for environmental DNA analysis. The PhD project will contribute to structuring a network of genomic observatories for the temporal monitoring of Amazonian ecosystems.

Mission :
Develop, test, and compare environmental genomics approaches for multi-taxonomic and temporal monitoring of Amazonian biodiversity. Produce reproducible data, tools, and protocols to link variations in eDNA detection with environmental parameters and conservation issues.

Activities
Activity 1: Develop genomic approaches for environmental DNA
• Contribute to the design and evaluation of a multi-marker, multi-taxon capture kit adapted to Amazonian biodiversity.
• Prepare sequencing libraries and compare metabarcoding, hybridization capture, and/or digital capture approaches.

Activity 2: Produce and analyze temporal biodiversity data
• Contribute to the bioinformatic processing of sequencing data.
• Analyze temporal variations in communities detected through eDNA and relate them to physicochemical and seasonal parameters.

Activity 3: Contribute to ecological monitoring and validation of the approaches
• Support the standardization of monthly sampling protocols across monitoring sites in French Guiana, Brazil, and Guyana.
• Compare, where data are available, eDNA results with independent biodiversity monitoring data.

Activity 4: Dissemination and knowledge transfer :
• Write scientific articles and communicate results at conferences and consortium workshops.
• Participate in training and capacity-building activities with regional partners, particularly on eDNA protocols, sequencing, and bioinformatic analysis.

Team supervision and coordination :
This position does not involve hierarchical supervision. However, the successful candidate may contribute to the functional scientific coordination of the consortium and to the occasional supervision of interns, under the responsibility of the thesis supervisors.

Specific or cross-cutting activity :
Participation in an international and interdisciplinary project combining ecology, genomics, bioinformatics, taxonomy, environmental hydrology, and conservation. Contribution to the harmonization of practices and to the networking of biodiversity observatories in Amazonia.

Expected skills :
Knowledge
• Molecular ecology, environmental genomics, and environmental DNA.
• Tropical biodiversity, community ecology, and conservation issues in Amazonia.
• Principles of second- and third-generation high-throughput sequencing, particularly Illumina and Oxford Nanopore.
• Basic knowledge of bioinformatics, metagenomics/metabarcoding, reference databases, and taxonomic assignment.

Technical skills
• Implement, or rapidly learn, laboratory protocols: DNA extraction, library preparation, and quality control.
• Use a Linux environment and tools for processing sequencing data.
• Conduct statistical and graphical analyses in R; organize reproducible datasets.
• Write manuscripts, reports, and presentation materials in French and English.
• Participate in field missions in tropical environments and comply with safety and traceability protocols.

Interpersonal skills
• Scientific rigor, progressive autonomy, organizational skills, and ability to meet deadlines.
• Ability to work as part of a team in an international and intercultural context.
• Scientific curiosity, critical thinking, and adaptability to field, laboratory, and computational work environments.
• Motivation to work in French Guiana and contribute to research conducted in and for Amazonia.

Your Work Environment

Working conditions :
Full-time doctoral contract based primarily in Cayenne. The work will be divided between laboratory activities, bioinformatic analyses, and occasional field missions in French Guiana and, depending on project needs, with partners in Brazil and Guyana. Travel for workshops, training sessions, and conferences should be expected. Compliance with safety rules in molecular biology laboratories and in the field will be required; personal protective equipment will be provided according to the activities.

Work environment :
The position is part of the GENE-AMA project and will be conducted in interaction with the GUYOMIQUE platform, the Nouragues Research Station, the HYBAM observatories, and academic and institutional partners in Amazonia. The successful candidate will work in an interdisciplinary and international environment aimed at developing transferable and sustainable biodiversity monitoring methods.

Resources provided :
Access to the facilities of the GUYOMIQUE platform in Cayenne, molecular biology equipment, Oxford Nanopore sequencing platforms, computing resources, and the genomic datasets and reference databases developed by the consortium. Operating and travel budgets will be available according to the project resources.

Main contacts :
CNRS supervisors and partners from UAR LEEISA, UMR AMAP, the GUYOMIQUE platform, the Nouragues Research Station, UFPA partners in Brazil, the University of Guyana/Sophia Point Rainforest Research Centre, HYBAM observatories, and collaborators in taxonomy, bioinformatics, ecology, and conservation.

International scope :
This project will benefit from strong local roots in French Guiana and will contribute to strengthening international research cooperation across the Amazonian region. The work carried out will contribute to the methodological innovation and harmonization objectives promoted by the International Research Network (IRN) “Amazon Bio-Track”, which brings together four Amazonian countries: Peru, Guyana, Brazil, and Colombia.

Compensation and benefits

Compensation

2,300 € basic salary+ DROM-COM complementary allowance of 920 € 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

The research professions