PhD offer on the environmental determinants of microbial community metagenomes across physicochemical gradients (M/F)

Job Description

Thesis Subject

Comparative genomics of prokaryotes pioneered early studies revealing patterns of gene repertoires (e.g. core, shell and cloud genes) and leading to the concept of pangenome. The study of gene distribution in microbes sampled along environmental gradients, such as marine cyanobacteria in the ocean water column across latitudes, further revealed molecular mechanisms of adaptation. With the development of high-throughput metagenomics, it is now possible to extend these analyses to complex microbial ecosystems and move from organismal-centred to community-level eco-evolutionary questions. Integrating environmental metadata with metagenome-inferred phylogenetic diversity, functional predictions and other genetic components (e.g. selfish genetic elements facilitating horizontal gene transfer composing the mobilome) can reveal higher-order patterns and help building predictive models.
Based on the possibility to infer functions and traits from metagenomes, early comparative analyses suggested that taxonomic diversity can be highly variable despite a stable functional core. These principles can be powerful to predict future trends but also historical events. However, these comparative studies are still in their infancy and it is not yet possible to address broader eco-evolutionary questions, not only about how functions and microbial diversity are shaped by environmental parameters and evolve across time and space, but also about how microorganisms interact and potentially generate community-level traits.
In this PhD project, we propose to explore these questions using as models microbial ecosystems from a ~1,100 km transect along the Chilean Altiplano. Located at high altitude (~4,000 m) in the Andes dry Puna, bordering the Atacama Desert, the area is hyperarid. Yet, it harbors unique aquatic ecosystems, including saline-to-hypersaline lakes and ponds and thermal springs associated with active volcanism. Accordingly, environmental conditions span broad gradients of hydrochemistry, temperature, pH, salinity, uv-radiation and redox potential. This physicochemical heterogeneity, combined with the geographic isolation of individual sites, makes these systems particularly well-suited to investigate to what extent environmental conditions shape the functional organization of microbial communities, from the genes they carry to how metabolic roles are distributed among organisms. We will analyze an available dataset of metagenomes and metagenome-assembled genomes (MAGs) generated by the DEEM team together alongside physicochemical metadata. This project will address three major interconnected questions:
1. What is the genetic/functional repertoire of these communities and how is it structured along environmental gradients?
2. How is the metabolic work distributed among co-occurring organisms?
3. What is the extent and pattern of horizontal gene transfer within these communities?
The proposed work will involve an in-depth analysis of metagenomes and the use of diverse biostatistical approaches. The expected results will provide an overview of how broad environmental gradients structure microbial community genomes at multiple levels, from gene content and metabolic interactions to (meta)genome dynamics, and set the basis for further theoretical models.

Your Work Environment

This PhD is funded by the grant ERC AdG SYMBEK. The student will join the DEEM team - Diversity, Ecology and Evolution of Microbes (http://www.deemteam.fr/en/). Our lab is situated in the new campus of the University Paris-Saclay, ca. 30 km south of Paris. A suburban trains connects with Paris.

Constraints and risks

The PhD work requires bioinformatic work and does not involve any major risk. Work will be done under normative security rules.

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

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