2018-07-Offer for a Thesis Allowance Subject: Genetic determinisms involved in mercury methylation by sulfate reducing bacteria

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E2S: Energy and Environment Solutions

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What is E2S?

The consortium at the heart of the Energy Environment Solutions (E2S) project is a composed of the University of Pau and the Pays de l’Adour (UPPA) and two national research organisations, National Institute...

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Offer for a Thesis AllowanceSubject: Genetic determinisms involved in mercury methylation by sulfate reducing bacteria.

Thesis subject

Mercury (Hg) is a persistent pollutant in the environment, highly volatile and able to be converted into highly toxic methylmercury (MeHg). MeHg is a serious threat as it is a neurotoxic compound, which is bioaccumulated and bioamplified in food webs. Microorganisms play a central role in MeHg conversion, either directly by controlling Hg methylation and MeHg degradation. Although hgcA and hgcA genes have been identified as necessary for Hg methylation, today, the methylation process cannot be fully explained. Together with environmental factors, other genetic determinisms are suspected to be involved in mercury methylation. To date, little is known about the cellular and environmental mechanisms favouring MeHg production, and Hg methylation processes are far from being deciphered.

Our team at IPREM lab aims to characterize Hg methylation at cellular level, from Hg recognition by the cell to Hg export, including methylation steps. We have started to study the role of Hg cell trafficking in the Hg methylation process in two Sulfate Reducing Bacteria (SRB) model strains, Desulfovibrio hydrargyri BerOc1, able to methylate Hg and demethylate MeHg and Desulfovibrio alaskensis G20, able to exclusively demethylate MeHg. The objective of the thesis is to generate D. hydrargyri BercOc1 mutants deleted in genes involved in either methylation, sensing, and export, and their heterologous expression in G20. The effect in methylation and demethylation will be then evaluated on mutants and compared to wild strains.

The proposed PhD is part of the project ‘GO-BEAM’ (Go inside a bacterial cell methylating Mercury) funded by E2S UPPA from 2018 to 2021.

GO-BEAM, selected as a ‘Key Scientific Challenges E2S UPPA’ (http://e2s-uppa.eu/en/index.html) is a collaborative and transdisciplinary project involving genetic microbiology, analytical chemistry, imaging and spectroscopy. The objective of this project is to improve the understanding of the Hg methylation/demethylayion processes at the cell level.

2 PhD and 1 Post-Doctorate are funded for the GO-BEAM project:
PhD1 on analytical and imaging, PhD2 on genetic microbiology and physiological studies (the present proposition) and the Post-Doc on both imaging and spectroscopy. PhD1, PhD2 and Post-Doc will all start in 2018

Key words: mercury methylation, sulfate-reducing bacteria, genetics of SRB


Working conditions

Hosting laboratory: Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM) - Joint Research Unit CNRS / UPPA (UMR 5254)                                                                                                                                     

Thesis Director: Marisol Goñi-Urriza
Thesis co-director: Mathilde Monperrus

In collaboration with Marie-Pierre Isaure, Bahia  Khalfaoui-Hassani

Localisation address: Université de Pau et des Pays de l’Adour, campus of Pau, Pyrénées-Atlantiques, France

Starting date: October 2018

Length: 3 years

Employer: Université de Pau et des Pays de l’Adour (UPPA)
Funding: E2S UPPA

Gross monthly salary: 1868 €
(UPPA doctoral contract, according to E2S Key scientific challenges project, including 96h of teaching during the three years)


Missions - principal activities

I. Scientific Context
Mercury (Hg) is one of the major contaminants at the global scale. It is persistent, highly volatile and is able to convert into highly toxic methylmercury (CH3Hg or MeHg), a strong neurotoxic. The production of highly toxic methylmercury (MeHg) is mediated by microorganisms but little is known about the cellular and environmental mechanisms favoring MeHg production. Understanding the biotransformation processes of Hg by microorganisms is thus a key for Hg risk assessment in ecosystems and human health. A few years ago, Parks et al. (2013) identified two genes, hgcA and hgcB required for Hg methylation. However, strains carrying hgcAB genes produce methylmercury at different rates, partly depending on their physiological state and environmental parameters (Goñi-Urriza et al. 2015). Furthermore, our results coupled with other studies with different mercury concentrations suggest that mercury methylation can be regulated by the export and/or by the intracellular contents of mercury.

 II. Objectives
The main objective of this PhD thesis is to evaluate the role of various genes (involved in Hg recognition, methylation and export) in Hg methylation/demethylation.

III. Work plan
The thesis work will be devoted at characterizing the role of candidate genes in Hg methylation. It will be assessed through gene deletion and complementation in D. hydrargyri BerOc1 and through heterologous expression in the non methylating strain G20 as follows:

- Gene deletion: Specific gene knockout in D. hydrargyri BerOc1 will be performed using one-step homologous double-crossover procedure. Genetic tools have been already optimized for D. hydrargyri BerOc1.

- Over-expression of genes of interest: The genes encoding hgcAB or the export systems will be overexpressed in wild type D. hydrargyri BerOc1 in order to evaluate the limits of mercury methylation and the effects on MeHg demethylation.

- Heterologous expression of genes of interest in G20: The genes encoding hgcAB or the export systems will be co-expressed in the non-methylating strain D. alakansis G20.

The Ph.D laureate will also perform physiological studies to understand the changes in growing, gene expression and mercury methylation and speciation. The gene deletion and over-expression in BerOc1 as well as the heterologous expression in G20 will be done in close collaboration with Alain Dolla and Nathalie Pradel from MIO laboratory in Marseille.

He/She will work with another PhD student involved in analytical chemistry and a post-doc, involved in X-ray imaging and X-ray Absorption Spectroscopies techniques. By applying isotopic tracer approaches and X-ray imaging on the wild type and mutants, the Hg methylation potentials and localization will be characterized in order to decipher the role of the genes on Hg pathways.

He/She will also participate to teaching activities at the undergraduate level (96h/3 years).


Required skills and competences

We are looking for a candidate with skills in microbial genetic, molecular biology and microbial physiology.The candidate should have a strong predilection for laboratory work.

The ideal candidate has a master degree in molecular biology, genetics or microbiology.


  • is rigorous and highly motivated,
  • must be able to take initiatives
  • must have the capacity to work autonomously
  • must be organised and thorough, with good relational qualities
  • and must have a good English level

Spoken French will be a plus (teaching activities).


Application - Evaluation criteria

Application file assessment: Selection committee

Candidates will first be selected based on their application file.
Selected candidates will be contacted by mail before August 24th.
Those selected after this first step, will then be interviewed.

Auditions will take place on August 28th and August 29th.
Candidates selected after the 1st step of selection will have 5 min to present their CV, 5 min to present their Master2 thesis and 5 min to present the phD subject. This presentation will be followed by questions and discussion.

Application files will be evaluated based on the following criteria:

  • Candidate's motivation, scientific maturity and curiosity
  • Candidate's knowledge
  • Grades and ranking during both your undergratuate studies and your Master degree, steadiness in your academic background
  • English language proficiency
  • Candidate’s ability to present her/his work and results

Work experience similar to an internship in a laboratory – or likewise; previously achieved research work (reports, publications).


Application file composition and submission deadline

Application will include: (in a single pdf file)

  • CV
  • Cover letter detailing the candidate's motivations
  • Candidate's undergraduate and Master grade transcripts and ranking
  • Reference letter
  • Contact details of at least two people, from you work environment, who can be contacted for further reference

Applications must be sent to the following email addresses with the title “Doctoral application”: 
Marisol Goñi marisol.goni @ univ-pau.fr
Marie Pierre Isaure marie-pierre.isaure @ univ-pau.fr
Mathilde Monperrus mathilde.monperrus @ univ-pau.fr

For more details, please visit our websites: http://e2s-uppa.eu/en/index.html

Submission deadline : August 15th, 2018