We are searching for a highly motivated PhD student to join an IRD-funded research project studying the role of the microbiome in facilitating the successful spread of invasive Drosophila species in natural populations of the Amazonian rainforest.
The PhD research project will be tightly embedded and supervised in joint guardianship between the University of Guyana and University of Paris-Saclay by Mathieu Chouteau (LEEISA) and Aurélie Hua-Van (EGCE), and will benefit from the co-supervision of Wolfgang Miller of the Medical University of Vienna.
The PhD student will be mainly based in French Guiana in the LEEISA laboratory, in the EEBA team of Mathieu Chouteau, but may be required to spend time in the European laboratories in Paris and Vienna which are tightly associated with the project. He/she will have access to the CNRS campus of Montabo, Cayenne (DNA laboratory, equipment, server), and will be able to use the vehicles of the site for his/her collection missions.
The successful candidate will be embedded in a collaborative research team mainly at the University Guyana, South America, but also at the University Paris Saclay, France, and the Medical University of Vienna, Austria. She/he will need to apply a multilevel experimental approach to address the project’s research goals.
Project Background and Significance: The Amazon rainforest is one of the richest areas of the planet in terms of biodiversity, but in great danger due to human activities, global warming, or the expansion of invasive species. These invasive species compete with native species and their success can be accompanied by the transmission of the microbiome (bacteria, viruses) that they harbor. This microbiome, which may have a beneficial role (protection, speciation) in their usual hosts, may affect the fitness of new hosts at various scales (reproduction, physiology, nutrition), thus massively weakening local biodiversity and increasing the risk of extinction. While the microbiome is well studied mainly in model species in the laboratory, we have little information on its complexity and dynamics in nature. Drosophila represent a model of choice for the study of microbiome dynamics, due to the promiscuity of species that share their feeding and oviposition sites. In French Guiana, which is mainly covered by primary rainforest, the high diversity of endemic Drosophila species is endangered severely by the regular arrival of potentially invasive challengers from metropolitan France via human activity.
Thesis topic: This thesis is aimed to uncover the diversity and dynamics of the microbiome in endemic and invasive Drosophila species, and the risks of their reciprocal transfer and trans-infection in (i) their natural conditions (field), (ii) semi-natural (field cages), and (iii) controlled laboratory conditions.
In a first step, the PhD student will collect systematically Drosophila specimens at different seasonal times and locations (reflecting an anthropic gradient). The collected species will be identified via COI barcoding, which will allow to describe the diversity of this group of species. The microbiome will be identified by DNA or RNA sequencing of specimens grouped by species. This will allow to evaluate the introgression rate of the microbiome from invasive species. In a second step, the PhD student will set up experimental evolution experiments in semi-natural conditions (population cages) in order to measure the relative fitness of native and invasive species under different conditions and to specify the transfer rates of the microbiome under controlled conditions. Finally, the effect of microbiome deletion or exchange will be tested in the laboratory on wild-derived isofemale lines stripped of their natural microbiome and brought into contact with the feces of other species.
Your qualifications: Applying candidates should have a keen interest in field as well as laboratory work using the model system Drosophila, microbiology, genomics, population genetics, plus a high degree of scientific curiosity. An excellent background in molecular biology, very good experimental skills and an MSc degree in molecular life sciences, or a related field are required as well. Earlier experience in any of the mentioned field will be an added advantage. Good communication skills, fluently speaking French and English, independence, and a high sense of responsibility are required.
The successful PhD candidate will be enrolled in the Doctoral school program: ED 577 Structure and Dynamics of Living Systems from the Université Paris-Saclay, and ED of the University of Guyana in joint guardianship. The salary will be de 2.765 € monthly for 3 years.
The starting date is December 1 st , 2022.
Please send your full application not later than October 15, including your CV, the Letter of Motivation and a list of publications, if any, to: Mathieu Chouteau (mathieu.chouteau 'at' cnrs.fr), Aurélie Hua-Van (aurelie.hua-van 'at' universite-paris-saclay.fr), and Wolfgang Miller (wolfgang.miller 'at' meduniwien.ac.at).