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H/F Analysis of the dynamics of microbial diversity

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General information

Reference : UMR5557-BEABIG-007
Workplace : VILLEURBANNE
Date of publication : Monday, December 02, 2019
Scientific Responsible name : Yvan Moënne-Loccoz
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 2 January 2020
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

The Lascaux cave is the subject of microbial ecology analyzes to characterize the community of microorganisms colonizing the cave walls and to document their population dynamics, with a practical goal of cave management to optimize the conservation conditions. paintings and engraving.
The general objective is (i) to evaluate the spatio-temporal dynamics of microbial communities in the cave, (ii) to characterize the metabolic genes and potentialities of the microbial community, and (iii) to analyze the interactions between microorganisms and Collembola present in the cave.
The different parts concern:
A. Characterization of microbial successions on the walls.
Microbial diversity will be analyzed over time in particular areas, by targeted sequencing of bacteria (16S rRNA gene), archaea (16S rRNA gene) and micro-eukaryotes (18S rRNA gene), with a focus on mushrooms (ITS). These communities will be characterized by metabarcoding (high throughput sequencing). Sequencing results will be processed by bioinformatics, followed by multivariate statistical analyzes.
B. Characterization of the genetic potential of microbial communities.
A global metagenomic approach will be put in place on different surfaces of the cave. All DNA will be extracted and sequenced with high-speed technology. Sequencing results will be processed by bioinformatics. Quantitative PCRs are also planned.
C. Analysis of relations between Collembola and microorganisms.
Collembola present in the cave will be farmed, and their interactions with Lascaux microorganisms will be characterized by Pasteurian techniques and sequencing.

Work Context

Thesis directed by Mr MOËNNE-LOCCOZ Yvan and Mrs HUGONI Mylène. The work will be done in the field (sampling in caves) and in the Microbial Ecology Laboratory (UMR 5557) on the Doua campus.

Constraints and risks

Need to be able to work in caves, and to combine approaches of microbiology and bioinformatics.
Risks related to CO2 levels in caves, and the use of conventional chemicals in the laboratory.

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