PhD position in the ecology & evolution of microbial communities

UNIL is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility.

The Department of Fundamental Microbiology offers a doctoral position in the ecology & evolution of microbial communities.

The Mitri lab (https://unil.ch/mitrilab/) is interested in understanding, controlling and designing small microbial communities under controlled laboratory conditions. Within these communities, we focus on how microbial species interact and how these interactions shape their ecological and evolutionary dynamics, and their community function. We strongly believe in combining different research methodologies, including mathematical modeling, computer simulations and laboratory experiments.  

We are seeking to recruit an experimentalist PhD student interested in one of two projects: (1) controlling species coexistence in microbial communities, and (2) studying division of labour in denitrifying communities. Applicants are also welcome to suggest other topics that are in line with the interests of the lab.

Project 1: Natural microbial communities are often composed of many different species that stably coexist together over long timescales, exhibiting impressive emergent properties, such as the production of valuable nutrients in the gut or the regulation of the global carbon cycle. Taking inspiration from these and building similar, simpler communities from scratch, would enable and enhance many key technologies, including the degradation of pollutants, the sequestration of greenhouse gases or the production of valuable chemicals. Yet artificially combining environmental isolates to stably coexist in the long term is far from being a predictive science. This project aims to address this challenge: given a set of species, which ones should one combine in what chemical and physical environment to guarantee their long-term coexistence? The student will build a collection of species and characterize their growth and interactions in different chemical environments. Based on these measurements, a mathematical model will predict which species to combine in which environment to achieve stable coexistence. The student will then test these predictions through growth-and-dilution experiments. To deepen our understanding and ability to control these communities, these experiments will be repeated in altered chemical environments to break coexisting communities and fix ones that do not.

Project 2: Nitrous oxide is a potent greenhouse gas that is emitted in high concentrations from wastewater treatment plants and agricultural soil. Nitrous oxide is produced as the last step part of the denitrification pathway, which involves the conversion of oxidized nitrogen compounds to nitrogen gas. Individual steps of this pathway can be performed by many different bacteria in the environment. Such division of labour requires a delicate balance between all involved species, without which the populations of species that perform the last step in the pathway – the removal of nitrous oxide – may collapse, leading to a burst of nitrous oxide production. The goal of this project then is to understand and control this balance, such that the different denitrifying species can coexist together in a way that minimizes nitrous oxide production. The student will begin by constructing a collection of natural isolates that can perform different steps of the pathway. Each will be characterized according to its growth preferences. Using this information coupled with mathematical models developed in the lab, we will predict the conditions that balance the abundances of the different species to minimize nitrous oxide production. These predictions will then be tested in the lab.

Expected start date : 01.01.2025 (earliest)

Contract length : 1 year, renewable twice

Activity rate : 100%

Workplace : University of Lausanne

The candidate will be responsible to carry out in-depth research on one of the projects described above. The focus of the project can be adapted to the interests of the applicant. After a period of reading, project design and training in the laboratory, the candidate is expected to execute their work independently.

Your responsibilities will include:

•    Plan and execute experiments as needed and discussed with the group leader

•    Analyse and interpret collected data

•    Contribute to teaching duties (organization and supervision of student practical exercises) and general life at the Department of Fundamental Microbiology

•    Write publications

•    Present work in lab meetings, departmental seminars and at national and international conferences

•    An excellent MSc in science, preferentially in microbiology, molecular microbiology, microbial ecology, biotechnology or a related field

•    Experience in microbial ecology, microbiology, metabolomics, or molecular microbiology

•    A theoretical background is highly valued, although this project will mainly be experimental

•    Excellent organizational skills and detail-oriented working style

•    Personal motivation and the ability to work independently and as a member of a team

•    Excellent oral and written communication skills in English

•    Strong personal motivation to excel and curiosity in addressing highly relevant questions in microbial ecology

Our group consists of theoreticians and experimentalists from all over the world, generously funded through the University of Lausanne and the Swiss National Science Foundation. We are part of the Department of Fundamental Microbiology, a highly collaborative, multidisciplinary, and team-oriented scientific environment with expertise in microbial ecology, evolution, molecular biology, cellular microbiology and biochemistry. We are equipped with state-of-the art infrastructure enabling cutting-edge research with access to many core facilities located on campus (microscopy, proteomics, sequencing facilities). Our group has strong ties to other departments within the University. We are also part of the NCCR Microbiomes, which provides a collaborative research network including 23 groups in 6 institutions across Switzerland working on translational aspects of microbiome research. Please visit our website for more information on our group, research interests and publications: https://wp.unil.ch/mitrilab/

The city of Lausanne and its surroundings enable an excellent quality of life during your studies. Our department is situated on a beautiful campus on the shore of Lac Léman with a spectacular view of the Alps. Extensive and reliable public transport give you plenty of opportunities for outdoor activities by the lake and in the mountains. Lausanne is also centrally located within Europe, offering excellent train connections in all directions (Geneva airport: 1 hr; Zurich: 2 hr; Milan: 3.5 hr; Paris: 4 hr). 

Prof. Sara Mitri: Write an email

Application deadline: 31.08.2024

Please include your full application in a single PDF (motivation letter, CV, list of publications and the contact details of two referees) in English.

Only applications through the university website will be taken into account. We thank you for your understanding.

UNIL is committed to equal opportunities and diversity.
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UNIL supports early career researchers.
www.unil.ch/graduatecampus