2020-01- Postdoctoral position in Bioinformatics and/or Computational Biology

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E2S: Energy and Environment Solutions
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Postdoctoral position: Mining metagenomes and metatranscriptomes 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 at the Universite de Pau et des Pays de l’Adour.

We are seeking a highly motivated postdoctoral research scientist with experience in analysis of (meta‑)genomics/(meta‑)transcriptomics data to work at IPREM, in the context of the MesMic project.
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.
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 (Metals in Environmental Systems Microbiology) project funded by E2S UPPA from 2018 to 2022. The MeSMic 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 (https://uppatech.univ-pau.fr/fr/plateaux.html). 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.

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.

 

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.

 

Keywords: Omics approaches - bioinformatics - biostatistics - data mining - microbial communities – microbial ecology - environment - metallophores - biotic interactions - metals acquisition/chelation

 

Working conditions

Hosting laboratory: IPREM
Institute of analytical and physicochemical sciences for the environment and materials, UMR 5254 CNRS-UPPA

Post-doc Supervisors:
Béatrice Lauga and Robert Duran

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

The successful applicant will be fully integrated in the team working in environmental microbiology, actively participating in lab meetings, seminars and training. S/he will also interact closely with members of the MesMic consortium. To fulfil this role, s/he will be given a high degree of responsibility and freedom.

Localisation address: IBEAS – Campus universitaire, Allée Jean Loiseau, Université de Pau et des Pays de l’Adour, -  BP 1155 - F64013 Pau, Nouvelle-Aquitaine, France

Starting period: 1st semester 2020

Duration: 1 to 3 years (full-time)

Gross salary: 2960 euros/month (inclugind 64h of teaching)

Funding: This postdoc position is funded by the project E2S UPPA (Energy Environment Solutions) which has a core scientific domain focused 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.
https://e2s-uppa.eu/en/index.html

 

Requirements

Bioinformatics, computational biology, and NGS data analysis in the context of microbial ecology, evolutionary biology and biostatistics

 

Application procedure

Applications must be sent as a single pdf file and must include:

  • a CV (max 2 pages)
  • a cover letter describing thecandidate's motivations, previous research experience and how it is related to the present position (one, or maximum two pages)
  • a copy of the candidate's PhD thesis diploma
  • candidate's PhD abstract and publications
  • two reference letters
  • contact details (3 referees, including at least the PhD supervisor and the post-doc supervisor (if applicable))

 

Selecion criteria and Evaluation

Two steps selection process:

1st step:

Potential candidates will be pre-selected on the basis of CV and motivation letter. The selected candidates will be called for interview.

2nd step:

  • Interview of the selected candidates (either at the IPREM or by videoconference)
  • Candidates will have 5 min to present their CV, 5 min to present their PhD and 5min to present their views on the post-doc subject
  • Discussion with the candidates for at least 20min


Criteria used during the selection of the candidates:

  • The candidate's motivation, scientific maturity and curiosity.
  • Candidate's expertise in Bioinformatics/Computational Biology
  • Interest in microbial ecology, evolutionary biology and skills in biostatistics
  • Oral and written communication skills as well as the candidate's ability to present his work
  • Candidate's proven ability to work in a multidisciplinary research group
  • Candidate's publications
  • English proficiency
  • Experimental proficiency

 

Application deadline

The position is opened until filled.

Please submit your application to Béatrice Lauga : Beatrice.Lauga @ univ-pau.fr / Robert Duran : Robert.Duran@univ-pau.fr  (Robert.Duran @ univ-pau.fr)before February 20th , 2020, mentioning [Postdoc] in the subject of your email.