PhD student in molecular ecology (M/F)

Job Description

Thesis Subject

Title: Multi.Div – Complementarity of Standard and eDNA Approaches for Studying River Biodiversity

(i) Scientific Context
Detailed knowledge of biodiversity in aquatic environments and wetlands is essential for conservation, as these ecosystems are among the most vulnerable to climate change and suffer from a lack of standardized monitoring, particularly in transboundary areas. Environmental DNA (eDNA) metabarcoding has profoundly transformed inventory methods over the past decade. Non-invasive, it complements traditional methods (such as kick-sampling for macroinvertebrates) by detecting rare or cryptic taxa, without replacing them: eDNA broadens the detection spectrum but remains less precise locally and in terms of abundance. The reliability of metabarcoding depends critically on solid reference databases, built from specimens accurately identified by experts. Such work is underway in the Grand-Est region on regional flora (ITS2 marker), but invertebrates such as caddisflies (Trichoptera) remain under-documented. In EPT taxa, larvae are often identifiable only to genus, unlike adults (imagos); larva-adult association through sequencing therefore makes it possible to extend the coverage of reference databases and reveal cryptic diversity. Finally, intraspecific genetic diversity, a key dimension for populations' capacity to adapt to climate change, remains little explored through eDNA, despite a few promising pioneering studies, particularly for aquatic invertebrates and plants.

(ii) objectives:
Conduct field inventories of aquatic invertebrates and aquatic/riparian plants, using standardized traditional sampling methods (kick-sampling, transects), across roughly thirty sites in different contexts, ranging from human-impacted areas to core reserve zones.
Contribute to developing DNA barcode reference databases for aquatic invertebrate communities, prioritizing EPT taxa and, more specifically, caddisflies (Trichoptera) — a taxonomically complex group that is insufficiently represented in public databases (Weigand et al., 2019). Collection will prioritize adults (imagos), morphologically identified to species level and then sequenced for markers commonly used in metabarcoding, to ensure the reliability of deposited sequences. A larva–adult association component through sequencing will make it possible to assign a specific identity to morphologically unidentifiable larval stages, and an integrative taxonomy approach will be used to detect potential regional cryptic species (Zhou et al., 2007, 2010).
Deploy eDNA metabarcoding tools at the same thirty study sites, using water samples, in order to systematically compare the two approaches (traditional surveys and eDNA) in terms of detected richness, sensitivity, cost, and sampling effort, and to assess their complementarity for long-term monitoring of cross-border aquatic biodiversity.
For a model aquatic invertebrate species selected among EPT taxa, conduct a comparative study — using the same DNA markers — of population-level genetic diversity obtained on the one hand through individual sampling and genotyping, and on the other through eDNA analysis of river water, in order to test the relevance and limits of the eDNA approach for studying infraspecific genetic diversity at the watershed scale. The choice of species, to be finalized at the start of the thesis, will favor a taxon that already has documented markers and population-level framework, ensuring feasibility for this exploratory objective (Pauls et al., 2006).
In addition, and depending on available time, the construction of reference barcodes could be accompanied by the establishment of a regional reference entomological collection: sequenced imagos would be prepared, labeled, and preserved as voucher specimens, linking each sequence to a verifiable physical specimen. This specimen–sequence traceability is among the recommendations made for quality assurance of reference databases (Weigand et al., 2019) and would provide lasting value to the work beyond the thesis itself.

(iv) Required Skills
Applications will be evaluated particularly on naturalist skills in entomology, as well as skills in molecular biology for eDNA metabarcoding. Skills in botany, in the creation and management of naturalist collections, and knowledge of population genetics will also be valued.

Your Work Environment

This PhD topic is part of the Interreg MultiDiv project (2026–2029), which aims to address the lack of biodiversity data in the cross-border Vosges du Nord and Pfälzerwald forest massifs by bringing together researchers, natural area managers, natural history museums, and French and German institutions. Together, they will collect genetic data on insects, fish, and plants found in forests and rivers, establish joint monitoring of these environments, and create a cross-border network — the Upper Rhine Biodiversity Cluster — to share knowledge. This work will lead to analytical tools, action plans, training for professionals, and exhibitions for the general public. Ultimately, decision-makers will have solid information to adjust their policies, field practitioners will be better equipped, and the public will be more aware of the importance of biodiversity conservation.
The PhD student will be hosted at the Laboratoire Image Ville Environnement (LIVE, UMR 7362 Unistra CNRS ENGEES). They will work with a team of ecologists with varied expertise, ranging from population genetics and environmental DNA to the study of plant and animal communities and ecosystem restoration. More broadly, LIVE conducts multidisciplinary research on urban and human-impacted environments and hydrosystems, aiming to understand the impact of human activities on socio-ecosystems. The PhD student will enrolled at the doctoral school 413 from the University of Strasbourg.

On-site catering facilities
Social benefits
Possibility of remote working in accordance with the established protocol
Leave + RTT (additional days off): a maximum of 46 days per year to be taken during the contract period

Constraints and risks

The PhD student will need to work in the field in flowing aquatic environments, and must therefore know and follow the safety guidelines applicable to this type of setting. They will carry out multi-day field missions away from home. In the laboratory, they will handle CMR (carcinogenic, mutagenic, or reprotoxic) substances as part of molecular biology experiments, and must therefore know and follow the relevant safety guidelines.

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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