2020-03-Offer for a Thesis Allowance - Subject: Hg compounds specific transformation and isotopic fractionation by model bacteria and microbial consortia.

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E2S UPPA, an I-Site since 2017

E2S UPPA, an I-Site since 2017

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Offer for a Thesis AllowanceSubject: Hg compounds specific transformation and isotopic fractionation by model bacteria and microbial consortia.

Scientific context

Natural isotopic fractionation of Hg will be investigated to develop new proxy of parallel biotic and abiotic pathways that will be applied to decipher Hg biogeochemical pathways in the natural aquatic environment. Hg is recognized as a “non-traditional model element” for its isotopic system because it exhibits both significant mass-dependent (MDF) and mass-independent fractionations (MIF). The reaction mechanisms involving Hg (eg. methylation, demethylation and reduction) produce isotopic fractionation for biologically driven as well as dark- or light-induced processes.

In order to decipher biotic versus abiotic pathways taking place under various microbial cells culture a specific experimental strategy should be developed and conducted. Hg compounds isotopic fractionation during biotic transformations will be investigated under different conditions with pre-selected microorganisms. Selected strains and simple consortia (including both heterotrophs and phototrophs) will be studied in order to determine factors influencing the Hg isotopic fractionation during bacteria mediated Hg transformation.

The PhD work will be conducted in the framework of the MeSMic Hub (Metals in System Microbiology at E2S/UPPA). In this Hub, a dedicated Hg project will investigate how bacteria control Hg transformation through the interaction of the chemical species of this toxic metal (speciation).

Keywords: mercury stable isotopes, mercury speciation, methylation/demethylation, reduction/oxidation, microbial physiology, model strains, microbial consortia


PhD project: missions and activities

Most of the PhD work will consist in setting up biotic experiments and abiotic control that allows to evaluate the transformations kinetics and mechanisms of the Hg compounds via microbial pathways. In parallel, specific sampling and analytical techniques will be optimized in order to accurately determine the concentration and isotopic composition of the mercury compounds in the incubation system.

This PhD project includes intense team-work with other PhD candidates in chemistry and microbiology and one Postdoc in microbiology. Parallel and progressively complex experiments will be performed in the laboratory to investigate the metabolic and genetic drivers conducting to various Hg transformation in model heterotrophic and phototrophic bacteria. A similar approach will be then developed for consortia including two or more model bacteria that harbor metabolic complementarity or competition.

The candidate should have strong background in biogeochemistry and/or environmental and analytical chemistry. We also expect that the candidate must have strong skills in speciation and/or isotopic analysis and/or experimental work.


Working conditions

Hosting laboratories: Institute of Analytical Sciences and Physical Chemistry for Environment and Materials (IPREM), UMR CNRS 5254.

Laboratory expertise: The Institute of Analytical Sciences and Physical Chemistry for the Environment and Materials (IPREM) is a mixedresearch unit of the National Research Centrefor Science (CNRS) and of the UPPA (UMR 5254).Research activities focus onthe development of fundamental knowledge in physical chemistry, analytical chemistry and microbiology, in relation to applications concerning the structure of living matter, environmental monitoringand the functional properties of different classes of materials.Analytical strategies, modelling, physicochemical approaches, fine studies of structures and reactivity, development, characterization and implementation at different length scales are the major skills available in the institute, which enable an original positioningin severalfieldsof application andin variousindustrial sectors atbothnational and international levels.IPREM is locatedon 4 different sites: Pau (Helioparc and UPPACampus), Anglet and Mont de Marsan.

Localisation: Technopôle Helioparc, 2 avenue Pierre Angot, 64053 Pau Cedex 9, France

PhD supervisors: David Amouroux and Zoyne Pedrero (CNRS)

The proposed PhD is part of the project ‘MesMic’ (Metals in Environmental Systems Microbiology) funded by E2S-UPPA from 2018 to 2022. Selected as a ‘Hub E2S-UPPA’, MesMic is a collaborative and transdisciplinary project involving microbiology and analytical chemistry. The objective of the project is to unravel metal ion interactions with microbial ecosystems at the molecular, cellular and community levels. 6 PhD and 6 Post-Doctorates are funded for MesMic project.

Scientific team: D. Amouroux, Z. Pedrero, E. Tessier, M. Goni, B. Khalfaoui-Hassani, R. Guyoneaud, C. Gassie, L. Ronga, L. Ouerdane, R. Lobinski, 3 PhD students, and 2 post-docs.

Starting date: July-October  2020

Length: 3 years

Employer: UPPA, doctoral school ED 211 Doctoral School of Exact Sciences and their Applications

Gross monthly salary: 1878€ / month
(UPPA doctoral contract which includes extra gratification for teaching duties – 32h per year)


Required skills and competences - Who can apply ?

The ideal candidate has a Master degree in general Chemistry or inrelated disciplines (Biogeochemistry, Environmental Chemistry, Isotope Geochemistry, Analytical Chemistry).

He/She is passionate for identifying solutions to environment related concerns and for multidisciplinary research.

A previous experience would be a plus.

The candidate should have a strong predilection for laboratory work. Team working abilities are highly appreciated. 

He/She is rigorous and highly motivated, with the capacity to work autonomously.

Good knowledge in English and good writing skills are required.


Application - Evaluation criteria

Two steps selection process:

  • Evaluation of the applicants’ CV
  • Selected candidates will be contacted by e-mail before June 2nd 2020

2nd step (end of May):

Application file assessment: Selection committee

Candidates will first be selected based on their application file. Those selected after this first step, will then be interviewed:

  • Candidates will have 5 min to present their CV, 5 min to present their Master 2 thesis and 5 min to present the PhD subject
  • Discussion with the candidates for 20 min


Application files will be evaluated based on the following criteria:

  • Candidate's motivation, scientific maturity and curiosity
  • Candidate's basic knowledge and experimental skills
  • Academic results : grades and ranking in Licence/undergraduate, M1 and M2 ; steadiness in the academic background
  • English language proficiency
  • Oral and written communication skills
  • Candidate’s ability to present her/his work and results
  • Professional experience (e.g. Work experience similar to an internship in a laboratory – or likewise, any previously achieved research work, reports, publications ...)

Application file composition and submission deadline

Application must be sent to the following email addresses with the title “Doctoral application”: david.amouroux @ univ-pau.fr, zoyne.pedrerozayas @ univ-pau.fr and the following documents attached (altogether, in a single pdf file):

  • CV (max 2 pages) including the publication list when applicable
  • Cover letter detailing the candidate's motivations (max 2 pages)
  • Copy of your Bachelor and Master diplomas as well as academic records (marks and ranking)
  • Letter(s) of recommendation (if any)
  • Contact details ( Name and e-mail addresses) of 2 referees (including the Master thesis supervisor)


Submission deadline : May 20th, 2020


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