PhD in Environmental Microbiology & Ecology: France/UK

Ecole Centrale de Lyon, University of Lyon, France and NCIMB Ltd., Scotland UK are offering a PhD scholarship in environmental microbiology with expected commencement March 2021 or as soon as possible thereafter. The PhD will be awarded by the Ecole Centrale de Lyon, France. The position is offered in the frame of the ARISTO (The European Industry – Academia Network for Revising and Advancing the Assessment of the Soil Microbial Toxicity of Pesticides) project. ARISTO is an International Training Network (ITN) funded by the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement.

Project title: In vitro assessment of the toxicity of pesticides on ammonia oxidizing microorganisms

Project description: Nitrification is the microbial conversion of ammonium to nitrate and a key process in the global nitrogen cycle. In soil these reactions are mediated by two autotrophic functional groups of nitrifying microorganisms (ammonia oxidizers microorganisms (AOM) and nitrite-oxidizing bacteria (NOB)) or in one cell by complete ammonia oxidizers (comammox). As the activity of these organisms is essential for soil health, they are ideal candidates for testing the impact of pesticides on microbial communities and soil ecosystem functioning. The PhD program will determine the ecotoxicological response of AOM as microbial indicators of pesticides toxicity. The objectives of the program are to (i) to establish, optimize and standardize in vitro assays for assessing the toxicity of pesticides on AOM, (ii) to identify toxicity on other microorganisms participating in the nitrification process, (iii) to explore the toxicity mechanisms of pesticides on AOM. The work will utilize both cultivated nitrifier populations and soil microcosm incubations requiring the use of molecular ecology approaches (quantitative PCR, amplicon sequencing). The program will also develop a novel screening platform for the analysis and determination of the functional health of soils and other environmental samples in response to pesticide amendment.

Principal supervisors: Prof. Graeme Nicol (, +33 472 18 60 88) and Dr Carol Phillips (, +44 1224 009333).

Planned secondments: Three months at the DSMZ (German Collection of Microorganisms and Cell Cultures), Supervisor: Dr. Michael Pester. Purpose: to receive training on the cultivation and testing of pesticides toxicity on NOB and other AOM to expand the range of microorganisms tested.

Key criteria for the assessment of candidates

  • A master’s degree related to the subject area of the project
  • The grade point average achieved should be more than 75 % of the maximum
  • Professional qualifications relevant to the PhD programme (Relevant skills: microbial cultivation, molecular biology, soil microbial ecology)
  • Previous research publications
  • Other professional activities
  • Language skills: fluency in English

Place of Employment

  1. Ecole Centrale de Lyon, Laboratoire Ampère, Univerity of Lyon, France (Month 1 to 18)
  2. NCIMB Ltd, Aberdeen, Scotland UK (Month 19 to Month 36)

Formal requirements and eligibility for all available positions
At the time of commencement, it is required that the candidate shall at the date of recruitment, be in the first four years (full time equivalent research experience) of their research careers and have not been awarded a doctoral degree. Furthermore, the candidate must not have resided or carried out their main activity (work, studies, etc.) in the countries where the hosting organizations are located for more than 12 months in the 3 years immediately prior to their recruitment. Short stays, such as holidays, are not taken into account.

Terms of employment
Recruitment and Terms of appointment will be done according to the rules and regulations of the hosting institutions and according to the rules and regulations laid down by European Union’s Horizon 2020 Marie Curie Initial Training Networks. The stipend includes a living allowance (3270 €, adjusted by a country correction factor), mobility allowance (600 €) and family allowance (500 €), the latter allowance depending on the family status of the fellow. All PhD fellowships available involves a split PhD studentship between an academic and an industrial partner, while the fellow will also spend time to other partners through short secondments.

Application Procedure
The application, in English, must be submitted by email to the supervisors of each advertised position and the coordinator of the project You are encouraged to apply for more than one of the available positions. In this case please indicate the position for which you are applying.

For your application please include

  • Motivation Letter, stating which PhD project you are applying, why you want to pursue a PhD career in academic and industrial sectors, and to what extent does the given project complies with your skills and ambition.
  • A statement if (and which) you have applied for other ARISTO PhD fellowships
  • Full CV including studies, research experience, work experience and publications if any
  • Diploma and transcripts of records (BSc and MSc)
  • 3 professional referees (Name, address, telephone & email)
  • Documentation of English language qualifications
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