Context of intervention
LIST’s Environmental Research and Innovation (ERIN) research department comprises more than 180 life, environmental and IT scientists and engineers across four research units. These units bring together the necessary interdisciplinary knowledge and skills to tackle the major environmental challenges our society is facing today, including climate change mitigation, efficient use of renewable resources and environmental pollution prevention and control. As part of their activities in the Environmental microbiology and biotechnology group, researchers develop knowledge, know-how and innovative solutions in relation to the contamination of water, food and the environment by pathogenic microorganisms. The research group is engaged in understanding the way these microorganisms interact with the matrices they encountered (water, air, food, soil, sediment, etc.) in order to precisely characterize the risk associated with food or water production and consumption, water-based recreational activities, water reuse in agriculture or cities.
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for microorganisms in human, animal as well as clinical samples. However, implementation of high-quality NGS and bioinformatics for complex environmental matrices such as water or soil samples is still challenging. Currently, technical challenges with separating, isolating, and extracting DNA/RNA from viruses in soils and water remain. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of environment viruses and their genomes.
Here, the objective of this internship project is the characterization of the genetic and phylogenetic diversity of viruses occurring in water and soil samples, by a shotgun metagenomics approach. The needed sequencing tools (library preparation, Illumina sequencing) will be developed and optimized during this internship, and the candidate will specifically work on molecular data generation and bioinformatics analysis for studying the diversity of the viruses collected from environmental samples.
This work will be part of the HYDROPHAGE project. The candidate will work in close relationship with the PhD student who conducts this project.
- Master 2 bioinformatics
- Knowledge in microbiology and virology
- English and French (spoken and written) is required