2018-07-Offer for a Thesis Allowance Subject: Influence of the environmental conditions on the methylation rates and source of Hg species in microorganisms

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E2S: Energy and Environment Solutions

What is E2S UPPA?

What is E2S UPPA?

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 Allowance Subject: Influence of the environmental conditions on the methylation rates and source of Hg species in microorganisms

Offer for a Thesis AllowanceSubject: Influence of the environmental conditions on the methylation rates and source of Hg species in microorganisms

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, the methylation process cannot be fully explained. Environmental parameters, particularly the sulfur containing ligands, have been shown to play a role in the Hg uptake and methylation process. However, to date, little is known about the cellular and environmental mechanisms favouring MeHg production, and Hg methylation processes are far from being deciphered. In this work, the PhD student will focus on the environmental parameters (thiol containing ligands, Se, Cl…) involved in Hg uptake, methylation and demethylation.

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 intend to decipher 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 investigate the molecular aspects of mercury biotransformations, including studies on the biomolecular speciation and the localization of Hg transformations at the subcellular level by combining chemical and physical analytical methods.

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 the 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 chemistry and imaging (the present proposition), PhD2 on genetic microbiology and physiological studies, 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, Hg speciation, mass spectrometry, electron microscopy


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: Mathilde Monperrus
Thesis co-director: Marie-Pierre Isaure

In collaboration with Marisol Goñi-Urriza

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

Starting date: November/December 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 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). For instance, mercury speciation in the extracellular medium affects the methylation (Ndu et al. 2012, Liu et al. 2016), and Hg uptake is also enhanced by some thiols such as cysteine (Ndu et al. 2012; Schaefer et al. 2014). Our preliminary studies also showed that Hg and MeHg were both associated to thiol ligands pointing out the crucial role of sulfur in Hg trafficking and methylation.

 II. Objectives
The objective of this pHD thesis is to contribute to the  understanding of the environmental parameters involved in Hg methylation/demethylation and on the identification of Hg biomolecules produced by sulfato reducing bacteria. For that, the identification of the Hg species, particularly thiols-complexes suspected to play an important role, is thus crucial, and the PhD student will carry out a combination of hyphenated mass spectrometry (Gaz Chromatography – Inductively Coupled Plasma Mass Spectrometry GC-ICPMS, and High Performance Liquid Chromatography- Electrospray Ionization –Mass Spectrometry HPLC-ESI-MS/MS). Results will be compared to speciation using modelling approach. An objective is also to track the origin of sulfur groups binding Hg and MeHg and for that, the PhD student will design experiments with NanoSIMS to follow sulfur. The impact of Hg and MeHg on the bacterial cell will finally be followed using transmission electron microscopy.

III. Work plan
The pHD student will focuss her/his work on the understanding of the environmental parameters involved in Hg methylation/demethylation and on the identification of Hg biomolecules.

  • He/she will be in charge of the bacterial cultures in various conditions and various ligands.
  • He/she will have to model Hg speciation using (bio)geochemical software (VMinteq).
  • He/she will perform incubations using isotopically enriched mercury species followed by GC-ICPMS analysis to establish simultaneously methylation and demethylation rates and quantities of net methyl mercury production rates.
  • He/she will be strongly involved in the identification of thiols ligands by HPLS-ESI-MS/MS.
  • He/she will also set experiments with labeled stable S isotopes to track source of S in Hg-S containing compounds, particularly using nanoSIMS imaging.
  • He/she will also implement transmission electron microscopy combined to energy dispersive spectroscopy (TEM-EDS, HRSTEM-EDS) to examine cell structures (membranes, periplasm, cytoplasm). Correlative imaging with NanoSIMS will be also performed. This will be done in collaboration with the Bordeaux Imaging Center.
  • He/she will work with another PhD student involved in microbial genetics and physiology and a post-doc, involved in X-ray imaging and X-ray Absorption Spectroscopies techniques. The role of candidate genes in Hg methylation will be assessed through gene deletion and complementation in D. hydrargyri BerOc1. Applying 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.

The PhD student will also participate to teaching activities at the undergraduate level (96h/3 years)


Required skills and competences

We are looking for a candidate with skillsin speciation, mass spectrometry, separative techniques, (GC, HPLC), electron microscopy. The candidate should have a strong predilection for laboratory work, analytical chemistry and modeling for speciation using speciation software (VMinteq…).

The ideal candidate has a master degree in in analytical chemistry.


  • 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.
Those selected after this first step, will then be interviewed.

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”: 
Mathilde Monperrus mathilde.monperrus @ univ-pau.fr
Marie Pierre Isaure marie-pierre.isaure @ univ-pau.fr
Marisol Goñi marisol.goni @ univ-pau.fr

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

Submission deadline : October 10th, 2018