PhD fellowship in Molecular Microbiology and Prophage Dynamics in Bacteria

The Department of Plant and Environmental Sciences invites applicants for a PhD fellowship in Prophage dynamics and influence on cell fitness, and intraspecies competition. The project is part of the research project The Helpful Yet Dangerous Tenants, which is financed by the Danish Research Council for Nature and Universe (DFF-FNU).

Start date is (expected to be) 1 October 2025 or as soon as possible thereafter.

The project

Microorganisms are capable of significantly shaping host phenotypes, whether it be human behavioural modification by the gut microbiome or plant growth promotion in the rhizosphere. Inside the microbial world however, is an even smaller world consisting of mobile genetic elements (MGEs), such as transposons and prophages. These MGEs are nearly ubiquitous in natural bacteria, with prophages playing a crucial role in regulating bacterial populations. Prophages are formed when bacterial viruses known as temperate phages integrate their genome into that of their bacterial hosts. Subsequently, some prophages can undergo induction, bursting out of their host cell to infect and kill neighbouring bacteria. Despite their importance, the study of prophages is complicated by the complex intracellular interactions between rival prophages and other MGEs. The research in the project will investigate increasingly complex combinations of prophages and characterise the constructed bacterial clones (lysogens) using growth, metabolic, and transcriptional assays. In addition, we will investigate competition between individual prophages intracellularly, and between the different bacterial clones to study how prophages spread and impact host fitness without interference from background MGEs. All this will be modelled and simulated in silico, and model outcomes will be further validated in the laboratory.

Who are we looking for?

We are looking for candidates that hold a MSc within microbiology, molecular biology, biotechnology, or other relevant research fields. The applicant should be confident with conducting microbiological work and should preferreably have practial experience within molecular biology laboratory techniques as well as practial experience with omics data analysis (e.g. NGS workflows and metabolomics data processing). Also, experience within the fields of phage biology and bacterial interactions is strongly desirable.

The candidate will be expected to conduct independent research on prophage-host interactions, developing assays and experimental workflows to study the phenotypic effects and intracellular dynamics of integrated prophages. Integrating data from various approaches such as bacterial growth and competition assays, phenotypic screening, and transcriptomics, the candidate will work to advance the understanding of prophages and disseminate findings through scientific papers.  Finally, the candidate is expected to some degree to engage in teaching and supervision and the post may also include performance of other duties.   

The candidate is expected to be enthusiastic about working in an interdisciplinary academic environment conduction research and teaching at the highest international level. The position, therefore, requires a highly motivated scientist who is comfortable working in teams, have good interpersonal skills, as well as a collaborative and open mind-set.

Our group and research- and what do we offer?

The Environmental Microbial Genomics group uses sequence-based analyses to describe genomic traits of keystone species and their prevalence and impact in natural and artificial microbial communities and metagenomes, including information on bacteriophages and how other mobile genetic elements shape microbial evolution and traits. Group activities span microbes in both natural, agricultural and health related systems. The EMG group harbours several funded projects that investigate bacteriophage dynamics, bacteriophage therapy / biocontrol and phage-host interactions. More information on the research group can be found on https://plen.ku.dk/english/research/microbial-ecology-and-biotechnology/environmental-microbial-genomics/. The group is a part of The Department of Plant and Environmental Sciences, Faculty of SCIENCE, University of Copenhagen. We are located in Copenhagen.

We offer an approximated 20 person group of creative researchers and stimulating working conditions in a dynamic and international research environment. Our research facilities include modern laboratories and In-house sequencers and bioinformatics servers.

1. Principal supervisor is Prof. Lars Hestbjerg Hansen, Department of Plant and Environmental Science. E-mail: lhha@plen.ku.dk. Phone: +45 28752053

The PhD programme is a three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. Microbiology, Molecular Biology, or Biotechnology. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programme

• Carry through an independent research project under supervision 
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

We are looking for the following qualifications:

• Professional qualifications relevant to the PhD project
• Relevant publications
• Relevant work experience
• Other relevant professional activities
• Curious mind-set with a strong interest in phage biology
• Good language skills

Application and Assessment Procedure

 Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include: 

1. Motivated letter of application (max. one page).Your motivation for applying for the specific PhD project.
2. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
3. Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
4. Publication list (if possible)
5. Reference letters (if available)

Application deadline:

The deadline for applications 25 July 2025 23:59 GMT +1, 2025

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.