Mots-Clés

Metagenomics – Microbial ecology – Population genomics – Coastal ecosystem

Description

Patterns of gene selection in coastal bacteria along an 8-year time seriesPatterns of gene selection in coastal bacteria along an 8-year time series

Coastal ecosystems face a strong short-term variability of environmental conditions as well as long-term changes that affect the oceans globally. How do bacteria adapt to these short and long-term changes? Little is known about the timescales and drivers of bacterial evolution in the oceans, but their short generation time allows to observe evolutionary processes in real time. To do so, one needs to explore the genetic diversity of intraspecific populations and follow it through time. Metagenomics, the sequencing of DNA from the whole community in natural samples, allows to do so directly in the bacteria natural environment.

In the Ecogenomics group, we use metagenomics on various oceanic ecosystems as a method to study bacterial communities. We recently sequenced metagenomes from an 8-year monthly time series sampled at a coastal location in the Bay of Brest, for a total of 100 metagenomes. The analysis of the first years of this time series revealed the presence of ‘generalist’ bacteria, which are abundant during the whole year, and ‘specialists’, which peak in abundance at a specific month or season. Among other specificities, preliminary results indicate that generalist and specialist bacteria use different set of genes. We expect some of these genes to be under a strong selective pressure.

In this project, we propose to study in more details the evolution of the genes that differentiate generalists and specialists. During your internship, you will use bioinformatics methods in a population genetics framework to leverage the 8-year metagenomics data. With a fine analysis of the Single Nucleotide Variants and Single Amino-Acid Variants of the target genes from representative genomes, you will determine i) if these genes are under selection ii) if selection induces the sweep of specific alleles through time and iii) if generalists and specialist genes show different evolutionary patterns. The internship will take place in the Ecogenomics group at the European Institute for Marine Studies, with full access to cutting-edge bioinformatics resources including the High Performance Cluster DATARMOR.

Reference: Lemonnier C, Perennou M, Eveillard D, Fernandez-Guerra A, Leynaert A, Marié L, Morrison HG, Memery L, Paillard C and Maignien L (2020) Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. Front. Mar. Sci. 7:376. doi: 10.3389/fmars.2020.00376

Pre-requisites:

- Background in bioinformatics and in evolution and/or microbiology

- Ability to work autonomously in a Unix environment, and with R or Python

- Previous experience with metagenomics data would be a plus

- Interest in marine microbial ecology and/or microbial evolution