PhD Position: Evolution of the marine microbiome in response to climate and environmental changes in the South Pacific (M/F)

Job Description

Thesis Subject

Coral reefs and lagoons in the South Pacific, renowned for their biodiversity, are under severe threat from climate change, extreme events, pollution, and urbanization. Their resilience is partly dependent on their microbiomes, which are essential for their health. The MIRACLE project (Evolution of the Marine Microbiome in Response to Climate and Environmental Changes Observed in the Tropical Pacific) aims to understand how current and past global changes influence the evolution of these microbial communities. By studying the links between microbial biodiversity and past/present environmental variations, the goal is to better assess the resilience of these fragile ecosystems and anticipate their future evolution.
The PhD candidate will analyze both modern and ancient marine microbial biodiversity using environmental DNA from selected sites of New Caledonia (urbanized, mining-affected, pristine, etc.). They will also examine geochemical signatures from living marine carbonate (corals and foraminifera) from the same sites, calibrated with measured environmental data (temperature, pH, salinity, metal concentrations, etc.). In a second phase, the use of sediment cores will allow to correlate the microbial biodiversity dynamics (ancient DNA sequencing – SedaDNA) over the past decades/century, as an answer to reconstructed environmental parameters.
We anticipate strong links between microbial community evolution and environmental changes, whether gradual (climate warming) or abrupt (ENSO events, cyclones, intensification of human activities, and associated disturbances such as mining). Based on these findings, predictive models using artificial intelligence tools will be developed to forecast future microbial biodiversity trends from past and current environmental data, and therewith help predict coral reefs resilience to both global change and local pollutions.
This PhD offers interdisciplinary training, supported by supervision and collaborations involving microbiologists, geochemists, data scientists, local communities, and policymakers. The aim is to understand the past, monitor the present, and anticipate the future of New Caledonia's reefs. Addressing this issue is a major scientific challenge: it will enable a more robust assessment of the resilience of island coral ecosystems to global pressures and the design of conservation and sustainable management strategies based on quantitative and predictive data. This project is intended to be extended to other Pacific Island territories (Palau, Nauru, Fidji...).

PhD Missions
- Sampling of sediment cores, coral cores, and seawater from contrasting sites in New Caledonia and the South Pacific islands.
- Extraction and sequencing of ancient and modern eDNA to analyze microbial biodiversity.
- Bioinformatics and statistical analysis of sequencing data.
- Washing, picking and identification of foraminifera from sediment cores samples.
- Geochemical analyses of both foraminifera and coral carbonate to reconstruct past environmental conditions. (proxies: Mg/Ca, Sr/Ca, B/Ca, Ni/Ca, δ11B, δ18O, etc.).
- Integration of microbial and geochemical data to identify resilience biomarkers and model future trajectories of reef microbiomes.

Your Work Environment

The PhD will be co-supervised by Véronique ANTON-LE BERRE, CNRS Research Director (EMR SantEco/UMR ENTROPIE), a microbiologist, and Delphine DISSARD, IRD Researcher (UMR LOCEAN), a geochemist and paleoclimatologist. The PhD student will be affiliated with EMR 9001 SantEco and will benefit from close collaboration with data management and modeling experts at the University of New Caledonia (ISEA/UNC).
Scientific and Institutional Environment
EMR 9001 SantEco (Health of Tropical Ecosystems) is part of UMR 250 ENTROPIE (Tropical Marine Ecology of the Pacific and Indian Oceans), a research unit specializing in the study of marine and coastal biodiversity in the Indo-Pacific region. It is distinguished by its dual geographic presence: one site in Réunion (University of Réunion, Saint-Denis) and one in New Caledonia (IRD campus, Nouméa), where the PhD will be conducted. The scientific approach covers multiple scales, from genes to ecosystems, and focuses on natural and anthropogenic factors influencing these marine environments and their sustainable use.
Since 2014, research in New Caledonia has been structured around CRESICA (Consortium for Research, Higher Education, and Innovation in New Caledonia). This consortium brings together nine institutions (BRGM, CHT, Cirad, CNRS, IAC, Ifremer, IPNC, IRD, UNC) and aims to promote interdisciplinary research, coordinate stakeholders around strategic projects for the region, train young researchers in collaboration with the Pacific Doctoral School, disseminate results to society, and optimize resources by sharing equipment and facilities. Through its affiliation with CRESICA, EMR SantEco has privileged access to essential local infrastructure for the MIRACLE project, including the iSeq 100+ sequencer (Illumina) at IPNC, the Living Platform (microbiology and genomics), and the LAMA (Laboratory for Mineral and Environmental Analysis) equipped with (LA)ICP-MS and ICP-OES, dedicated to physicochemical analyses, on the IRD site.
The PhD student will benefit from multidisciplinary supervision and a rich scientific environment, with state-of-the-art infrastructure and a local, regional, and international network. This will enable the development of diverse skills in a tropical and island context, addressing major scientific and societal challenges.

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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