2020-07- Postdoctoral position: Mining (meta-)genomes and (meta-)transcriptomes for metallophore biosynthetic genes or gene clusters

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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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Postdoctoral position: Mining (meta-)genomes and (meta-)transcriptomes for metallophore biosynthetic genes or gene clusters

Context

The MesMic consortium (Metals in Environmental Systems Microbiology consortium) is recruiting a collaborator in Bioinformatics and/or Computational Biology in the domain of microbial ecology at the Université de Pau et des Pays de l’Adour. The fellowship will have the duration of 12 months with possibility of extension at the end of this period, for a maximum of 3 years.

The post-doctoral position is part of the MeSMic project (Metals in Environmental Systems Microbiology)  funded by E2S UPPA from 2018 to 2022. The project brings together an interdisciplinary research team (genetics, molecular biology, physiology and microbial ecology, biogeochemistry, environmental and analytical chemistry), 6 PhD students and 6 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 context

In a natural environment, at pH value 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.

Literature 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 fellow will bring 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 i) establish an inventory of metallophore biosynthetic gene clusters (BGC), in microbial genomes and metagenomes from diverse environments, ii) infer their role in microbial assemblages by linking them to known metallophores and natural products, iii) 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 i) to better understand the metabolic interactions occurring within complex multi-species microbial assemblages, ii) to evaluate, at the ecosystem level, how metallophores contribute to community assembly, functioning, and beyond, to ecosystems functioning.

 

Working conditions

Host laboratory : IPREM Institute

Localisation : Université de Pau et des Pays de l’Adour (UPPA), Pau, France

Supervision : The post-doctoral fellow will work under the supervision of Pr. B. Lauga and Pr R. Duran.

Scientific team particularly involved around the post-doctoral theme: B. Lauga, R. Duran, F. Rigal, C. Cagnon, C. Cravo-Laureau, A. Carbon.

Duration: one year, with possibility of extension

Starting period: November 2020

Monthly gross salary: 2960 €, including 64 hours of teaching/year

 

Requirements

We are seeking a highly motivated postdoctoral research scientist with expertise in the analysis of (meta‑)genomics/(meta‑)transcriptomics data to work at IPREM.

The ideal candidate 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 compulsory.

 

Application

Applications must be written in English and submitted as a single pdf file.
They must be sent by e-mail to both of the following addresses:
beatrice.lauga @ univ-pau.fr and robert.duran@univ-pau.fr (Robert.duran @ univ-pau.fr)

Applications must include:

  • a CV (max 2 pages)
  • a cover letter
  • the candidate's PhD abstract and publications
  • 2 letters of recommendation
  • contact details of at least 3 referees (including, at least, the PhD supervisor and the post-doc supervisor (if applicable))

 

 

Application deadline : September 25th, 2020