PhD student in systematic biology

The Department of Organismal Biology teaches and explores the evolution, development and function on the organismal level. For more information see Department of Organismal Biology – Uppsala University

Project description

VR-funded project: Meringosphaera as a new model to study the origin of plastids by endosymbiosis.

The position is associated with an ongoing project in the Burki lab on characterizing a marine endosymbiosis in a group of microbial eukaryote called Meringosphaera. These are very interesting single-celled eukaryotes that are globally distributed in the oceans and likely represent a multi-species complex that may include species with permanent photosynthetic organelles (plastids), others only stealing plastids from preys, and still others being non-photosynthetic. The overarching goal of this fully-funded four-year PhD project is to study the modifications that have occurred early during the plastid endosymbiosis in Meringosphaera at different biological levels, using advanced subcellular imaging techniques (such as Expansion Microscopy U-ExM, FIB-SEM, and HISH-SIMS), molecular methods (such as single-cell transcriptomics), and flow cytometry cell sorting. The position is based in the laboratory of Dr. Fabien Burki in the Department of Organismal Biology at Uppsala University, but includes a strong collaborative component with the laboratories of Dr. Omaya Dudin at Geneva University (Switzerland) and Dr. Filip Husnik at OIST (Okinawa, Japan).

Duties

The project involves both lab work and bioinformatics, and the student is expected to be involved in both aspects. Lab work includes: field trips and sampling, cell isolation, imaging with advanced microscopy methods, attempts for cultivation of interesting cells in enrichment cultures, flow cytometry, and single-cell sequencing. Bioinformatics includes analysis of diversity datasets, phylogenetics, analysis of transcriptomic datasets, comparative and functional genomics. Disseminate results in appropriate formats, including leading peer-reviewed publications and conferences. Training will be provided when necessary.

Requirements

Completed university education of 240 university points (högskolepoäng, hp) out of which 60 hp on advanced level corresponding to master degree in relevant field to the project. The selected candidate must possess expertise and knowledge in microbial sampling as well as identifying and handling protist cells. Experience in culturing of microbial eukaryotes, and a background in eukaryotic diversity and photosymbiosis will be seen as highly valuable. A suite of methodologies will be used as described in the project description and are all desirable attributes of the candidate. In particular, previous experience with cell sorting, volume and Expansion microscopy, as well as in general principles of fluorescence microscopy, will be looked for in candidates. Proven expertise in bioinformatics (e.g. phylogeny, genomics) and use of a scripting language (Python, R) are essential. Great emphasis is placed on personal qualities such as planning and organizational skills, problem solving and good collaborations and communication skills with other researchers. Above all, we are looking for highly-motivated candidates who are passionate about academic research. The applicant must have documented experience and proficiency in oral and written presentation in English.

Additional qualifications

In filling this position, the university aims to recruit the person who, in the combined evaluation of competence, skills and documented qualifications, is judged most suitable to carry out and develop the work-in-hand and to contribute to a positive development of the department.

Position

The PhD-student position is a 4-year appointment, and the candidate will primarily devote the time to his/her own research studies. Other departmental work, such as teaching or administration are typically part of the position (maximum 20 %). Salary placement is in accordance with local guidelines at Uppsala University. The applicant must be eligible for PhD studies at Uppsala University.

Information about research education can be found at the web site of the Faculty of Science and Technology, Doctoral Student – Uppsala University.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University’s rules and guidelines Policies and regulations – Uppsala University.

About the employment

The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date 2026-02-01 or as agreed. Placement: Uppsala

The application should include

1) a letter of intent describing:

• Yourself
• Your research interests
• Why you are interested in the position
• Which of your experiences and skills you consider most relevant for this role
• Which of your personal qualities (behaviors, abilities) you would like to highlight as suitable

2) a CV

3) a copy of your master degree and course grades

4) the names and contact information (address, email address, and phone number) of at least two reference persons

5) relevant publications (including master thesis). The application should be written in English.

For further information about the position, please contact: Dr. Fabien Burki; fabien.burki@ebc.uu.se.

Please submit your application by 10 December 2025 UFV-PA 2025/3493.