2021-02- Postdoctoral positions - Mining genomes

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E2S: Energy and Environment Solutions

E2S UPPA, an I-Site since 2017

E2S UPPA, an I-Site since 2017

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"I-site" stands for “Initiatives Science-Innovation-Territoires-Economie".
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Two Postdoctoral positionsMining (meta-)genomes and (meta-)transcriptomes for metallophore biosynthetic genes or gene clusters

Context

The MeSMic consortium (Metals in Environmental Systems Microbiology consortium) is recruiting two collaborators in Bioinformatics and/or Computational Biology in the domain of microbial ecology at the Université de Pau et des Pays de l’Adour. The fellowships will have the duration of 12 months with possibility of extension at the end of this period.

The post-doctoral positions are part of the MeSMic (Metals in Environmental Systems Microbiology) project funded by E2S UPPA. The project brings together an interdisciplinary research team (genetics, molecular biology, physiology and microbial ecology, biogeochemistry, environmental and analytical chemistry), 6 PhD students and 7 post-doctorates and relies on a set of advanced instruments in analytical chemistry and environmental microbiology. More than 20 permanent researchers are collaborating on this project. Scientific team particularly involved around the post-doctoral theme: B. Lauga, R. Duran, F. Rigal, C. Cagnon, C. Cravo-Laureau, A. Carbon.

 

Scientifc context

In a natural environment, at pH where most life exists, microbial growth can be limited by the availability of metals. This limitation in the environment can have significant consequences on ecosystem functioning. To ensure their survival and their development, microorganisms have developed strategies for the recovery and absorption of metals from the surrounding environment (Hider and Kong 2010). The capture of metal is ensured by the synthesis of siderophores (iron) or more generically metallophores. The biosynthetic potential of metallophores does not appear to be equally distributed among organisms, environments or microbial life cycles, but rather is enriched within a number of prolific clades (Cimermancic et al. 2014, Smanski et al. 2016). One field of investigation aims at seeking for new metallophore biosynthetic genes to enlarge our view of their diversity in the microbial world and investigate these data in an eco-evolutionary perspective.


References

  • Cimermancic, P, Marnix H Medema, J Claesen, K Kurita, Laura C Wieland Brown, K Mavrommatis, A Pati, Paul A Godfrey, M Koehrsen, J Clardy, Bruce W Birren, E Takano, A Sali, Roger G Linington, and Michael A Fischbach. (2014) Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters. Cell 158: 412-421.
  • Hider, R. C., & Kong, X. (2010). Chemistry and biology of siderophores. Natural Product Reports, 27(5), 637-657.
  • Hopwood, M, P Statham, SA Skrabal, and JD Willey. 2015. Dissolved iron (II) ligands in river and estuarine water. Marine Chemistry 173: 173-182.
  • Smanski, MJ, DC Schlatter, and LL Kinkel. 2016. Leveraging ecological theory to guide natural product discovery. Journal of Industrial Microbiology and Biotechnology 43: 115-115-128.

 

Position and assignments

The post-doctoral fellows will work at the IPREM Institute under the supervision of Pr. B. Lauga and Pr R. Duran, and in collaboration with international partners (e.g. U. Wageningen, bioinformatics groups).

The two post-doctoral fellows will form a team bringing all the bioinformatics expertise required for a fine investigation of metagenomic and metatranscriptomic data generated on field collected, microcosm generated samples and worldwide databases in order to

  1. establish an inventory of metallophore biosynthetic gene clusters (BGC), in microbial genomes and metagenomes from diverse environments,
  2. infer their role in microbial assemblages by linking them to known metallophores and natural products,
  3. conduct meta-analysis on the distribution of BGC across worldwide habitats in order to highlight any specific distribution and reveal if hot spots of genetic diversity exist for metallophore BGC.

Our ultimate goals are

  1. to better understand the metabolic interactions occurring within complex multi-species microbial assemblages,
  2. to evaluate, at the ecosystem level, how metallophores contribute to community assembly, functioning, and beyond, to ecosystems functioning.

 

Work conditions

Hosting laboratory: IPREM, UMR CNRS 5254, Université de Pau et des Pays de l’Adour
IPREM is a joint Research Unit CNRS/UPPA (UMR 5254) in France. IPREM has an extensive and highly competitive research program that comprises the development of fundamental knowledge in physical-chemistry, analytical chemistry and synthesis of functional/bio-inspired materials, in relation to conversion and electrochemical/chemical storage of renewable energies.

Location: Pau, France 

Starting period: March 2021

Duration: 12 months

Employer: Université de Pau et des Pays de l'Adour

Monthly gross salary: 2960 €, including 64 hours of teaching/year (compulsory)
The salary of  the successful candidate will be based on  level chart  for  teaching and  research personnel  in  the  salary  system of  French universities.

Funding: This post doc position is funded by the project E2S UPPA (Energy Environment Solutions) whom core scientific domain focuses on Environment and Energy to meet challenges related to the energy transition, geo-resources, aquatic habitats and the environmental effects of natural and anthropogenic changes


Requirements

Recruitment grade: young researcher (i.e. with PhD)

We are seeking highly motivated postdoctoral research scientists with expertise in the analysis of (meta‑)genomics/(meta‑)transcriptomics data to work at IPREM. The ideal candidates should have a PhD in the fields of Bioinformatics or Computational Biology and microbial ecology, with research experience in NGS data analysis. A good background in microbial evolution and biostatistics would be appreciated.

English proficiency is mandatory.


Application

Applications must be written in English and sumitted as a single .pdf file.

Required documents:

  • CV
  • Cover letter
  • Candidate's PhD abstract and publications
  • Copy of the doctoral diploma.
  • 2 letters of recommendation
  • Contact details of at least 3 referees, including at least the PhD supervisor and the post-doc supervisor (if applciable)

 


Please submit your application by email to both of the followiing addresses: beatrice.lauga @ univ-pau.fr and Robert.duran @ univ-pau.fr

The deadline for submitting the application is February 28th, 2021