[Expired] PhD: Use of a combined Microbiology-Geochemistry approach to identify the determinants of copper toxicity

PhD Title

Use of a combined Microbiology-Geochemistry approach to identify the determinants of copper toxicity


The work will be carried out in two laboratories alternating (depending on the experimental periods):

– BIP (Chemin Joseph Aiguier, Marseille)

– CEREGE (Europole de l’Arbois, Aix en Provence)


Marianne Ilbert (CNRS, BIP) and Emmanuel Doelsch (CIRAD, CEREGE)


Copper is an essential nutrient for life, but at high concentrations it becomes toxic for living beings. This property is used in many economic sectors. In agriculture, copper, as an antimicrobial agent, is used for the treatment of fruit and vegetable crops. This property is also used in the biomedical, biotechnological and industrial fields.

These uses of copper are at the origin of its dissemination and accumulation in the various environmental reservoirs (soil, surface water). The toxicity of copper therefore poses a threat to the organisms present. Many studies emphasize that knowledge of copper concentration alone is insufficient to understand its toxicity. Indeed, the definition of a threshold of copper toxicity faces an experimental difficulty, to determine the concentration of “toxic” copper for the organisms. The latter will mainly depend on the chemical forms of copper present in the environment, i.e. its speciation. Indeed, bacterial culture media are rich in elements likely to modify the speciation of copper and are not very representative of environmental media. A better appreciation of the reactivity of copper according to the culture media used and the species formed is therefore necessary.


This thesis is articulated in two parts, divided into four steps:

Part 1: Establish a link between speciation and toxicity of copper on bacteria in different culture media

  • Characterisation of copper speciation in different culture media

Copper is present in culture media commonly used in microbiology. Surprisingly, the copper speciation present in these media is unknown. In order to relate speciation to toxicity, the first step of this project will be to determine the speciation of copper in different bacterial culture media. Several approaches will be used to determine the speciation of copper in these media (selective electrode; geochemical modelling; X-ray absorption spectroscopy).

  • Evaluation of copper toxicity on bacteria cultivated in these environments

The impact of copper in these media on model bacteria (Escherichia coli and Shewanella oneidensis) will be evaluated using different approaches (bacterial survival, cell growth, microscopy, inhibition halot, mobility etc.). The toxicity results will be compared with the speciation results from the previous stage in order to confirm or refute the toxic role of copper according to its speciation.

Part 2: testing innovative methods for assessing the toxicity of a contaminated environment and for substituting copper salts traditionally used as antimicrobial agents

  • Towards a better definition of the copper toxicity threshold

The toxic effect is currently measured on the basis of a life/death assessment of cells. However, a compound can be toxic in the long term, and at certain concentrations it can also create selection pressure allowing the development of resistance mechanisms. The toxicity threshold is therefore difficult to define and determine. We propose to use new biosensors to define the “stress state” of the E. coli bacterium.

  • The use of copper complexes as an alternative to copper salts

Recent advances in chemistry have allowed the synthesis of copper complexes as new antimicrobial agents. We will evaluate the stability of these copper complexes in culture media over time. Then, we will study the speciation of copper in bacteria exposed to each of the complexes in order to understand their in situ stability. Their mechanisms of action on model bacteria will be described.


The candidate should have a background as an environmental microbiologist/chemist.  The candidate must be willing to explore new areas of expertise to integrate an interdisciplinary research project which will require the candidate to have the ability to train in different fields ranging from microbiology, biochemistry, biophysics, geochemistry. The student recruited will have obtained a degree in Biology at Master 2 level or equivalent. A good level of English is expected. A motivated and dynamic student profile, capable of rapidly acquiring autonomy, will be sought.


A letter of motivation, a CV, the available grades of M1 and M2 (with mention and ranking in the group of students), a letter of recommendation (e.g. from the internship supervisor or the master’s thesis director) and a previous internship report in pdf (for example the one of the last master degree) should be sent to M. Ilbert () and E. Doelsch ()

DEADLINE application

Applications must be sent before 30 April 2023. For selected candidates, interviews will take place between 9 and 11 May 2023.