Missions

Impacts of current global changes on soil microbial diversity are unknown in the absence of historical records. The project makes use of soils associated to herbarium plants, collected over the last 100-200 years, as sources of ancient DNA representative of the past soil microbial diversity. Following a paleogenomics approach, DNA extracted from these soils are sequenced. After validation of the ancient origin of the DNA samples, sequences are annotated to highlight both the taxonomic and functional diversity of the historic communities. These communities will then be compared to extant ones analyzed using a similar approach.
For this project, we already generated 60 sequence datasets from 60 historic soil samples collected since 1820 all over the French territory. A similar number of sequence datasets is currently being secured for modern agricultural soils from fields located in the vicinity of historic soil sampling places.

Activities

- Bioinformatics treatment of high-throughput sequence datasets, Merging, assembly and extraction of sequences of microbial origin. Validation, authentication, and bioinformatic processing of ancient DNA sequences. (main)
- Taxonomic and functional annotation of modern and ancient DNA sequences (main)
- Data management, submission to public databases (main)
- Analysis of quantitative data and statistics in R environment (main)
- Presentation of the results to the scientific community (posters or oral presentations in English) (main)
- Publication in scientific journals (main)

Skills

- Background training and knowledge in microbial ecology and plant-microbe interactions
- Knowledge and expertise in paleogenomics/paleogenetics
- Skills in bioinformatics in the context of metagenomics
- Skills in analysis of quantitative date and statistics in the R environment
- English (read and spoken)
- Communication skills to interact with other reasearch team members
- Presentation of scientific results (poster and congress in English), bibliographic synthesis and participation in writing publications.

Work Context

The recruited researcher will join the ISYEB UMR7205 at the Muséum National d'Histoire Naturelle (Jardin des Plantes, Paris), in interaction with UMR7209 AASPE of the MNHN for the manipulation of ancient DNA, the LCQB UMR7238 of Sorbonne University for the functional annotation of sequences and bioinformatics platform Migale (INRAE). The position corresponds to a project supported by the Emergence program of Sorbonne University. Within the ISYEB, the projet co-involves two teams, the "Interactions et Evolution Végétale et Fongique" and the "Atelier de Bioinformatique" ones.