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PhD student in Environnemental Microbiology

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

Date Limite Candidature : jeudi 7 juillet 2022

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General information

Reference : UMR5240-AUDMAR-001
Date of publication : Thursday, June 16, 2022
Scientific Responsible name : HUGONI Mylène
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 15 September 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

Woesearchaeota are a phylum of Archaea described recently (2015), for which we lack knowledge about their ecology, metabolism, and interactions. In Lake Dziani Dzaha (Mayotte), an hypersaline alkaline tropical ecosystem characterized as a microbial network, the archaeal assemblage is dominated by Woesearchaeota sequences representing up to 70% of archaeal sequences, but sharing less than 80% sequence similarity with known Woesearchaeota. Based on the reconstruction of cooccurrence networks in this ecosystem, we have proposed that Woesearchaeota could be preferentially associated to the dominant photosynthetic microorganisms populating Lake Dziani Dzaha, i.e. the cyanobacterium Arthrospira fusiformis and the picoeukaryotic green algae Picocystis salinarum. Studying the microbial cortege (i.e. phycosphere) associated with A. fusiformis and P. salinarum sorted by flow cytometry, we showed that the Woesearchaeota OTUs were specific to either the water column (i.e. free-living fraction) or to the phycosphere of A. fusiformis and/or P. salinarum (i.e. associated fraction). In this context, we hypothesize that the niche partitioning observed at the 16S rRNA gene level reflects an ancient dichotomy in the ancestral Woesearchaeota population.

The PhD work will be conducted under the supervision of Associate Professor Mylène HUGONI, from the team “Microbiology of Extreme Environments (M2E)” in the lab “Microbiology, Adaptation, Pathogenicity MAP, UMR 5240” at the University of Lyon. The main objectives of this project are to decipher (1) the genomic specificities of Woesearchaeota related to the associated or free-living lifestyles and (2) the core metabolism of both fractions with a focus on the metabolism specific to the attached lifestyle to comprehend the microbial interactions taking place (i.e. nutrient and/or energy exchanges). We will take advantage of flow cytometry cell-sorting to access the attached fractions and NovaSeq very high-throughput sequencing to access Woesearchaeal sequences to reconstruct their genomes.

This PhD work will involve ambitious multidisciplinary and collaborative research, with the application and optimisation of different experimental approaches in microbiology, molecular biology, metagenomics and metatranscriptomics, and also innovative approaches such as flow cytometry cell-sorting done in collaboration with Marc Troussellier and Cécile Roques from the MARBEC lab (Montpellier). It will rely on the complementary expertises of Pr. Cécile Bernard (MNHN Paris) and Pr. Céline Brochier (LBBE Lyon). The PhD work include the preparation of reports, seminar and conference presentations, and scientific publications.

We are looking for an inquisitive, creative, and motivated young scientist for this PhD project in environmental microbiology. The PhD project is funded by the French National Research Agency ANR Young Researcher project MARWEL led by Ass. Pr. Mylène HUGONI.

Experimental work to be performed will include:

- Several field campaigns in Lake Dziani Dzaha (Mayotte). This part, conducted in a tropical environment, on a site where infrastructures are absent, requires good physical condition and aptitudes for rigor and meticulous organization underpinned by the implementation of field missions.
- Stays in Montpellier in the lab MARBEC to perform flow-cytometry cell-sorting allowing the collection of attached-Woesearchaeota to Arthrospira fusiformis and Picocystis salinarum.
- Sequencing libraries preparation and subsequent bioinformatic/biostatistics analyses.

Eligible applicants will have:
- A Master degree in microbiology, molecular biology or equivalent (delivered before September 2022
- Practical experience of several experimental techniques in microbiology and molecular biosciences
- Good command of oral and written communication, in French and/or in English
- An interest in data analyses and/or bioinformatics, will represent additional assets.

Work Context

Work context and complementary information :
The main objective of the M2E team is to understand microbial adaptative processes in prokaryotes thriving in extreme ecosystems, through a multidisciplinary approach ranging from physics to up-to-date environmental omics tools. The team focuses on Archaea, for which many novel phyla emerge daily and for which the ecology remains unclear, while our acknowledgement of their contribution to ecosystem functioning is increasing, and from which the team is developping novel, innovative biotechnological solutions.

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