Project #2 PROTEUS: Leveraging large-scale protist genomics to predict and enhance theculturability of protist lineages

PhD Supervisor: Fabrice NOT

PhD Co-supervisor: Ian PROBERT

PhD Co-supervisor: Samuel CHAFFRON 

Host Laboratory: Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff

Other Host Laboratory: Laboratoire des Sciences du Numérique de Nantes (LS2N), UMR 6004, 2, chemin de la Houssinière, 44322 Nantes

Doctoral School: ED 227 – DIVersités, Origines, Natures, MNHN-SU

ATLASea Targeted Project involved in the project: DIVE-Sea, SEQ-Sea

Available resources in the host laboratories: The PhD student will be hosted at the Roscoff Biological Station, that offers a leading research environment in marine biology especially for the studies and the culture of marine protists. He.She will benefit from a direct access to specialized infrastructure for the culture of marine protists, especially to the Roscoff Culture Collection, dedicated to the culture of marine micro-organisms,and also through the platform ABIMS, co-coordinator of SEQ-Sea, for the analysis of genomic data.

In addition the PhD student, will be affiliated to LS2N (UMR 6004, CNRS / Université de Nantes), that brings a recognized expertise in bioinformatics, modeling, and machine learning. He/She will have a dedicated workstation, a high-performance computer, and access to the computing infrastructure necessary for large-scale data processing and analysis.

Time estimated in each laboratory: 50% SBR / 50% LS2N

Skills requirements: Bioinformatics and microbiology

Summary

Protists represent the majority of eukaryotic diversity and play key roles in marine biogeochemical cycles. However, a large fraction of this diversity remains experimentally inaccessible, as most lineages are not cultivated. Even for cultured species, conditions are often suboptimal and poorly standardized, limiting our understanding of their physiology, ecological interactions, and functional roles. In this context, the project aims to leverage genomic data generated within the PEPR ATLASea to better understand and optimize protist physiology in culture, while facilitating access to new lineages. It proposes to transform genomic data and functional annotations into predictive tools to guide cultivation, thereby addressing a major methodological bottleneck identified by ATLASea.

Scientific questions:

  • What genomic and metabolic determinants govern growth in culture?
  • Can limiting factors in current media be identified for already cultured species?
  • To what extent can genomes and their associated functional/metabolic potentials predict optimal culture conditions (nutrients, cofactors, interactions)?
  • Can these signatures be transferred to uncultured lineages?

Objectives:

  1. Characterize the genomic bases of growth in culture for marine protists using ATLASEA data;
  2. Enable exploration of metabolic pathways of interest via the Marine Genome Portal;
  3. Compare functional potentials and metabolic networks to identify auxotrophies and dependencies;
  4. Develop predictive models (machine learning-based) linking genome, environment, microbiome, and culturability;
  5. Experimentally validate genome-guided cultivation strategies.

Methodology:

The project will adopt an integrated approach based on ATLASEA resources:

  • Comparative genomics to identify determinants of culture performance;
  • Reconstruction of metabolic networks to detect specific requirements and auxotrophies;
  • Analysis of existing culture conditions and their relationship to genomic capacities;
  • Statistical modeling and machine learning to predict growth (e.g., codon usage bias);
  • Experimental validation: axenization, optimization of media (nutrients, vitamins, cofactors), adjustment of culture parameters, and co-culture experiments.

Environmental genomics data (e.g., from Tara expeditions) will be used selectively to contextualize specific results.

Expected results and impact:

The project is expected to:

  • Identify genomic determinants of culture performance;
  • Develop optimized and rationalized culture media;
  • Develop predictive tools transferable to other lineages.

In the longer term, it will contribute to:

  • Improving the efficiency and reproducibility of ex situ protist cultivation;
  • Bridging the gap between genomic data and experimentation;
  • Facilitating functional studies of marine biodiversity;
  • Expanding access to lineages of interest for sequencing within ATLASea;
  • Stimulating new biotechnological applications.

By framing culture as a quantifiable and predictable trait, this project paves the way for a more systematic and integrated approach to protist biology.

Keywords: Marine protists; comparative genomics; metabolic networks; predictive modelling; microbial culturability.

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