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-PhD thesis (M/F) Genomics of snow algae: life in the snow, from the genome to the cell and populations

This offer is available in the following languages:
Français - Anglais

Date Limite Candidature : lundi 11 juillet 2022

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General information

Reference : UMR5168-ERIMAR-004
Workplace : GRENOBLE
Date of publication : Monday, June 20, 2022
Scientific Responsible name : Eric Maréchal
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

We are looking for a candidate for a PhD thesis project entitled "Genomics of snow algae: life in the snow, from the genome to the cell and to populations". This thesis is part of the CNRS "80 Prime" program of excellence. The candidate should have a strong background in bioinformatics, with a high degree of autonomy, to manipulate genomic data (assembly, annotation, genome comparisons, etc.) and metagenomic databases. The candidate should have an interest in the study of microorganisms in their ecosystems and adaptive processes, in a context of environmental change related to global warming. He/she will develop his/her work mainly through in silico approaches, in contact with colleagues developing experimental aspects. He/she should therefore be both autonomous and comfortable in a multidisciplinary team context. Subject description: Snow is populated by unicellular organisms of which very few species have been described, and no genome characterized. Above the tree line, the pioneer forms are photosynthetic microalgae, some of which can become dominant, accumulating carotenoids and coloring the snow red. In the framework of the Alpalga program (https://alpalga.fr/), collections made by the laboratories proposing this project, in the Alpine Workshop Zone carried out from 2017 to 2022 have allowed the isolation of different species: 4 cultivable algal genomes have been sequenced, 1 non-cultivable algal genome is being sequenced from metagenomic data and 1 unicellular snow fungus is also being sequenced. The thesis project therefore aims at the first genomic characterization of eukaryotic microorganisms inhabiting snow, at the molecular, cellular (functional genomics), and population levels, in order to decipher the genomic and eco-physiological mechanisms that allow them to "live in the snow".
The project will rely on significant student expertise in bioinformatics/genome analysis (annotation, genome comparison, metagenomics), requiring access to original genomic data that are largely already available. The project therefore combines a low-risk or even no-risk parts of annotation and comparative genomics, For the second part, the risk will be controlled by focusing on a reasonable number of species, characteristic of the environments explored.

Work Context

The thesis will take place in two insitutes in Grenoble. First, at the LPCV (Laboratory of Cell and Plant Physiology), a laboratory expert in the culture and manipulation of microalgae, studying these organisms from the molecular level (genes) to the cellular level. The LPCV is composed of about 100 people. It has microalgae culture facilities, and all the technical means to extract and sequence their genomes, characterize their physiological state and transcriptomic and lipidomic profiles. See https://www.lpcv.fr/Pages/Lipid/Presentation.aspx for more information on the LIPID team. In a second phase, the thesis will be pursued at the LECA (Alpine Ecology Laboratory), a reference laboratory for the study of ecosystem functioning and environmental DNA. The thesis will be based on original genomic data already produced or being produced in the framework of the Alpalga program (https://alpalga.fr/). It will explore these data using bioinformatics approaches mastered by the two units, to contribute to the identification of potential adaptation mechanisms to life in the snow, and to explore the structuring of the corresponding populations in the natural environment and their dynamics.

Constraints and risks

The project does not present any particular risk exposure

Additional Information

We are looking for a candidate for a PhD thesis project entitled "Genomics of snow algae: life in the snow, from the genome to the cell and to populations". This thesis is part of the CNRS "80 Prime" program of excellence. The candidate should have a strong background in bioinformatics, with a high degree of autonomy, to manipulate genomic data (assembly, annotation, genome comparisons, etc.) and metagenomic databases. The candidate should have an interest in the study of microorganisms in their ecosystems and adaptive processes, in a context of environmental change related to global warming. He/she will develop his/her work mainly through in silico approaches, in contact with colleagues developing experimental aspects. He/she should therefore be both autonomous and comfortable in a multidisciplinary team context. Subject description: Snow is populated by unicellular organisms of which very few species have been described, and no genome characterized. Above the tree line, the pioneer forms are photosynthetic microalgae, some of which can become dominant, accumulating carotenoids and coloring the snow red. In the framework of the Alpalga program (https://alpalga.fr/), collections made by the laboratories proposing this project, in the Alpine Workshop Zone carried out from 2017 to 2022 have allowed the isolation of different species: 4 cultivable algal genomes have been sequenced, 1 non-cultivable algal genome is being sequenced from metagenomic data and 1 unicellular snow fungus is also being sequenced. The thesis project therefore aims at the first genomic characterization of eukaryotic microorganisms inhabiting snow, at the molecular, cellular (functional genomics), and population levels, in order to decipher the genomic and eco-physiological mechanisms that allow them to "live in the snow".

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