Mots-Clés
metagenomic
marine biology
transcriptomic
microalgue
Description
SCIENTIFIC CONTEXT: Marine phytoplankton account for more than 45% of net primary production on Earth and play an essential role in supplying organic matter to marine food webs. A global decline of phytoplankton biomass has been reported over the past century (1% of chlorophyll-a concentration per year) leading to a decrease of net primary production in many oceanic regions (Boyce, Lewis, et Worm 2010). It is challenging to predict the potential capacity of phytoplanktonic organisms to acclimate (i.e. short-term phenotypic plasticity) or adapt (longer-term genomic compensation) to rising temperatures and variations in nutrient availability. In this project, we propose to use Pelagomonas calceolata, which is a cosmopolitan and abundant pico-phytoplanktonic (<3μm cell size) member of the ecologically important Pelagophyceae class, as a model organism to study the adaptation of open-ocean phytoplankton to various environmental conditions. In a recent study, we assembled the genome of P. calceolata and used it to evaluate the relative abundance of P. calceolata in environmental datasets (Tara Oceans). We observed that this species is one of the most abundant eukaryote in the open oceans with an abundance driven by high temperature and low-iron conditions (Guérin et al. 2022). In addition, we observed important variations of gene expression for many genes suggesting that this species has developed specific molecular mechanisms to rapidly modulate gene expression in response to physico-chemical variations. However, acclimation alone do not explain the presence of this species in very different environmental contexts across all oceans. Our preliminary results on the density and distribution of genomic variants in P. calceolata genome suggests that P. calceolata is a fast-evolving species with several ecotypes carrying many variants in key genes facilitating their adaptation to the environment.
PROJECT: This 2-years PostDoctoral project aims to resolve the population structure of P. calceolata in the oceans, discover the key genes involved in P. calceolata adaptation and compare the physiology of different cultivated P. calceolata strains. Using bioinformatics approaches, the population structure can be obtained by the analysis of genomic variants across a large number environmental datasets including Tara Oceans and Tara Pacific resources (Pesant et al. 2015). The candidate will have to choose and adapt bioinformatics tools for variant discovery (such as GATK, BCFtools) to work on complex metagenomic data. The identification of structural variations (insertion/deletions, gene duplications …) and SNPs from in situ data will bring several hypotheses on the importance of specific genes on P. calceolata adaptation. In this project, we suggest to complement in situ results with the large collection of strains collected in several oceans and maintained in the Roscoff Culture Collection. Different strains of P. calceolata could be cultivated in the lab to observe the gain or loss of fitness under different culture conditions and study the adaptation at the transcriptomic, protein and/or metabolomic levels. Overall, this project should provide new insights into the acclimation and adaptation capacities of PPEs in a context of global environmental changes.
TEAM: The candidate will work in the Laboratory of Genomic Analysis of Eukaryotes (LAGE), part of the Genoscope at Evry (91000) in France, in a team of 20 researchers and students currently working on several Tara projects (https://lage.genoscope.cns.fr/). The project will lead to collaborations with several scientific teams of the Tara Oceans consortium.
CONTRACT: The position is funded by the ANR (PelagoAdapt project https://anr.fr/Projet-ANR-22-CE20-0012). The contract will start before october 2023 for 24 months. The salary is based on the CEA salary grid and depends of qualifications and experience.
PROFIL:
- PhD in biology (genomic or bioinformatics).
- A strong background in bioinformatics (Metagenomics, Variant analysis, large datasets studies).
- A sound knowledge of cellular biology, genomic and evolution as well as biostatistics.
- Experience in marine genomics/biology is a plus.
REFERENCES:
Boyce, Daniel G., Marlon R. Lewis, et Boris Worm. 2010. « Global Phytoplankton Decline over the Past Century ». Nature 466(7306):591‑96. doi: 10.1038/nature09268.
Guérin, Nina, et al. 2022. « Genomic Adaptation of the Picoeukaryote Pelagomonas Calceolata to Iron-Poor Oceans Revealed by a Chromosome-Scale Genome Sequence ». Communications Biology 5(1):983. doi: 10.1038/s42003-022-03939-z.
Pesant, Stéphane, et al. 2015. « Open Science Resources for the Discovery and Analysis of Tara Oceans Data ». Scientific Data 2(1):150023. doi: 10.1038/sdata.2015.23.