Description du sujet de thèse

Project Summary
Phytoplankton are the foundation of marine ecosystems, and the zooplankton that graze them are the link to higher trophic levels. Our understanding of marine ecosystems was revolutionised by the discovery that, on average, there are more than 10 million viruses per mL of coastal seawater, which each day are estimated to kill, by weight, ~20% of life in the oceans. Thus, viruses have an enormous impact on community composition, marine food webs and nutrient cycling (Suttle 2005, 2007).
This project represents a unique opportunity to bring together two groups with different, but complementary expertise to study the interaction of two key components of marine ecosystems with the viruses that infect them: phytoplankton and zooplankton. The overall project aims are to (i) identify viruses linked to key plankton groups, members of the genus Micromonas, one of the most widespread and important primary producers in the world's oceans, and crustacean zooplankton; and (ii) measure the spatial/temporal dynamics of viral infection of these keystone plankton.

This PhD, hosted in the Banyuls-sur-Mer Oceanological Observatory, France, will focus on phytoplankton–virus co-evolutionary and ecological dynamics. Specific objectives are to:
1) Elucidate the co-evolutionary dynamics of Micromonas during infection by prasinoviruses and discover the genomic and phenotypic variations associated with host-virus co-evolution.
2) Implement an exhaustive discovery effort of viruses infecting Micromonas and tracking of ecological dynamics in field time-courses from meta'omics datasets.
3) Develop mathematical models describing the eco-evolutionary dynamics of virus infection of plankton and integration of experimental measurements of virus traits to infer in situ host–virus dynamics.

Candidate profile
We seek a highly motivated student open to engaging in a multidisciplinary project, combining high-level computing skills in bioinformatics (variant detection, genome assembly, comparative genomics, meta'omics) and modelling (dynamical system, mechanistic and hybrid-modelling, Bayesian inference), as well as laboratory approaches (flow cytometry, molecular biology, field sampling, microbial culturing, virus phenotyping). We also desire a candidate that can work independently and who has excellent communication and writing skills to work effectively in this international collaboration.

Contexte de travail

This PhD scholarship and mobility costs are funded by the French National Center of Scientific Research University of British Columbia (CNRS-UBC), France–Canada Collaboration Program 2025. The Partner labs are: LBBM (CNRS: Laboratory of Microbial Biotechnology and Biodiversity) and Curtis Suttle (UBC) teams. The student will be enrolled at the doctoral school 277 "Natural and Human Sciences: Evolution and Ecology" of Sorbonne University and the National Museum of Natural History.
Supervision and mentorship :
The CNRS PhD will be supervised by Marcelino Suzuki (microbial ecology-bioinformatics), co-supervised by Sheree Yau and David Demory (expertise in phytoplankton virus genomics and modelling, respectively). The PhD will benefit from collaborative mentorship from the Suttle lab. They will also be trained in new techniques (i.e. HCR-FISH, MoRS, modelling– Choi et al. 2018; Zhong et al. 2023; Demory et al. 2024).