Société Française de Bioinformatique

Mots-Clés

Metagenomics Microbial ecology Cold adaptation Ice-nucleating proteins FAIR

Description

ABSTRACT:

Microbial communities in glacial habitats are adapted to endure extreme conditions such as low temperatures, freeze–thaw cycles, and limited water availability. Among the adaptations to these extremes, bacterial ice nucleation (IN), mediated by ice-nucleating proteins (INpro), may enhance survival during freeze–thaw cycles by inhibiting intracellular freezing. While direct evidence of INpros on glacier surfaces is lacking, snowfall enrichment of ice-nucleation-active (INA) bacteria, higher concentrations of ice-nucleating particles (INPs) toward the poles, and detection of INPs in Arctic glacier meltwaters and rivers during peak melt indicate regular exposure of glacier surfaces to ice-nucleating organisms.
AIM: The objective of this Master’s project is to investigate the prevalence of cold adaptation strategy genes (including the ice nucleation gene (ina) involved in across different cryospheric habitats, use metagenomics.

OBJECTIVES:

1. Literature survey
   * Identify and compile a reference list of genes known to be involved in microbial cold adaptation and freeze–thaw survival in cryospheric environments.
   * Establish a reference framework for comparing ina to other adaptation strategies.
   * Study the molecular specificity of these different protein candidates (protein domains, repeat or disorder loops etc.).

2. Profile creation and database building
   * Obtain sequence files from different public database to make gene and protein catalogs.
   * Curate protein alignments to build HMM profiles for a selected set of cold-adaptation related proteins.
   * Validate HMM profiles to ensure screening specificity and sensitivity.

3. Metagenomic screening
   * Carry out gene calling on contigs assembled from metagenomes from cryospheric habitats.
   * Search for cold-adaptation proteins using HMM profiles and threshold defined in step 2.
   * Use and adapt existing pipelines for efficient large-scale gene detection.

4. Comparative and downstream analysis
   * Carry out 3D structural analyses of obtained candidate proteins.
   * Assess the prevalence cold-adaptation genes across different habitats.
   * Perform ecological interpretation of the results to better understand microbial adaptation strategies in glacial and polar environments.

The results will contribute to understanding the role of cold adaptation in microbial survival in cold environments, and their implications for life in extreme environments.

Work context:
- You will work at the MEP CENTURI and benefit from interactions with the other bioinformatics engineers on the platform.
- You will join a large international multidisciplinary team of bioinformaticians, microbiologists, biogeochemists, and Earth system scientists.
- You will work on a cutting-edge topic related to the glacier ecosystem and to global climate change.
- You will receive a stipend in accordance with current regulations.

Required skills:
- Knowledge and experience in genomic sequence data analysis (such as NGS data processing) is mandatory.
- Experience with HMM-based methods.
- Experience in Linux bash scripting.
- Proficiency in programming in R and/or Python.
- Experience in containerization tools like Docker or Apptainer would be an advantage.
- Knowledge or experience of running analyses on computing clusters (job scheduling system such as SLURM).
- Experience in 3D model prediction is an advantage.
- Basic understanding of microbial ecology or cold adaptation mechanisms is an advantage.

The candidate should be proactive and capable of working independently, as well as working harmoniously as part of a team. The working language is English and thus fluency in English is required.