About the project

This PhD project will develop controlled experimental systems to investigate top-down and bottom-up ecological strategies that directly shape the biosignatures of sulfur-cycling bacteria in low-oxygen environments. The main focus will be on virus–host interactions in purple (PSB) and green (GSB) sulfur bacteria related to the microbial anoxic communities of meromictic Lake Cadagno. The work will combine laboratory-based experiments at the University of Lausanne (UNIL) and at Scuola universitaria professionale della Svizzera italiana (SUPSI, Mendrisio) with field observations in stratified aquatic environments (e.g., meromictic lakes), particularly during June-October.

The candidate will generate the empirical foundation needed to quantify how viral perturbations affect microbial metabolism and biogeochemical outputs.

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Job information

Expected start date in position : fall 2026 or upon agreement

Contract length : 4 years (1+2+1)

Activity rate : 100%                     

Workplace : Géopolis building, Institute of Earth Sciences, Faculty of Geosciences and Environment, University of Lausanne

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Responsibilities and qualifications

The successful candidate will investigate virus–host interactions in anoxygenic phototrophic sulfur bacteria through a combination of field, laboratory, and molecular approaches. The project will involve monitoring and isolating viruses from natural environments, performing infection experiments with different anoxygenic phototrophic sulfur bacteria, and conducting anaerobic microbiology experiments under controlled redox conditions using systems such as microfluidics and mesocosms. The candidate will characterize microbial responses using flow cytometry, viability assays (e.g., live/dead staining), microscopy, and spatial analyses, while developing molecular workflows including qPCR quantification, RNA extraction, and transcriptomic sample preparation. The position also includes organizing and participating in field monitoring campaigns at Lake Cadagno (Ticino, Switzerland) and working closely with computational collaborators to integrate experimental and multi-omics data into a comprehensive understanding of virus-driven microbial processes.

We are looking for a motivated candidate with a strong interest in environmental microbiology and geomicrobiology. A master’s (or equivalent) degree in microbiology, environmental sciences, biology, or a related field is preferred. We encourage candidates with an interest in microbial ecology and biogeochemistry and a motivation for fieldwork in lake environments to apply.

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Application

The application can only be officially sent through here, and should include:

• Your CV including academic background, previous research/publications and/or industrial experiences as well as the names and contact details of 2-3 referees
• A cover letter outlining your research motivation and interests (max. 1 page)
• Copy of your diplomas

The application deadline is August 20th, 2026.

Contact information: alice.boscosantos@unil.ch

About the project
The Institute of Earth Sciences (ISTE) at the University of Lausanne (UNIL) invites applications for a PhD position in computational biosignatures and quantitative modeling within the framework of the National Centre of Competence in Research (NCCR) Genesis. The successful candidate will work under the joint supervision of Alice Bosco Santos (UNIL) and Paolo De Los Rios at École Polytechnique Fédérale de Lausanne (EPFL).

This PhD project aims to quantify how viral perturbations of microbial metabolism translate into measurable biosignatures in low-oxygen environments. Focusing on sulfur-cycling microbial communities (e.g., purple sulfur bacteria and associated viruses), the project will combine bioinformatics, quantitative modeling, and experimental data integration to identify key metabolic control points targeted by viruses and evaluate how their perturbation propagates through microbial and biogeochemical systems, producing detectable shifts in biosignatures (e.g., isotopic fractionation, pigment production).

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Job information

Expected start date in position : fall 2026 or upon agreement

Contract length : 4 years (1+2+1)

Activity rate : 100%                     

Workplace : Institute of Earth Sciences, Faculty of Geosciences and Environment, University of Lausanne

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Responsibilities and qualifications

The successful candidate will analyse multi-omics datasets, including metagenomes, metatranscriptomes, viromes, and viral auxiliary metabolic genes (AMGs), to investigate how viral infections reshape microbial metabolism. The project will involve identifying metabolic pathways (KEGG pathways) and rate-limiting reactions targeted by viruses, integrating these data into quantitative models that simulate microbial metabolic networks, quantify the impact of viral perturbations, and estimate the thresholds at which viral activity produces detectable biosignature shifts. The candidate will contribute to the interpretation of carbon and sulfur cycling in natural environments, participate in field campaigns to gain familiarity with the studied ecosystems, and have the opportunity to take part in laboratory experiments, such as gene expression analyses, to validate and parameterize the quantitative models.

We are looking for a motivated candidate interested in the intersection of biology, physics, and Earth sciences, with a strong inclination toward computational approaches. You must have a MSc (or equivalent) in bioinformatics, computational biology, physics, environmental sciences, or a related field. Have a strong interest in quantitative analysis and modeling, programming skills, and the ability to work at the interface of disciplines. We are looking for a candidate that has interest in linking models to experimental data.

We are committed to fostering an equitable, diverse, and inclusive research environment. We particularly encourage applications from individuals who are underrepresented in science, including those from diverse cultural and ethnic backgrounds and those who have followed non-traditional academic paths. We believe that diversity strengthens our science and actively seek to build an inclusive and supportive team.

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Application

The application can only be officially sent through here, and should include:

• Your CV including academic background, previous research/publications and/or industrial experiences as well as the names and contact details of 2-3 referees
• A cover letter outlining your research motivation and interests (max. 1 page)
• Copy of your diplomas

The application deadline is August 20th, 2026.

Contact information: alice.boscosantos@unil.ch