211-2102/25-2H PhD fellowship in deep-sea viral ecology

PhD fellowship in deep-sea viral ecology
Department of Biology
Faculty of SCIENCE
University of Copenhagen
PhD project: Prophage-encoded auxiliary metabolic genes: Key components of prokaryotic metabolism in deep-sea sediments?

 The Marine Biological Section, Department of Biology invites applicants for a PhD project on investigating the role of prophages and auxiliary metabolic genes for the cycling of organic matter in the deep-sea sediments. The project is funded by the Independent Research Fund Denmark and is associated with the HADAL Centre of Excellence, funded by the Danish National Research Foundation.

Start date is 1st of August 2025 or as soon as possible thereafter.

The project
Bacteriophages (phages) have a significant impact on marine prokaryotic mortality, diversity, and biogeochemical cycling. They do this by infecting and lysing cells, which release labile dissolved organic matter and stimulate the mineralization of inorganic nutrients. However, through the use of phage-encoded auxiliary metabolic genes (AMGs), phages can also affect host metabolism either during infection or upon integration as prophages into the host genomes. Such prophage-encoded AMGs can increase the metabolic capacity of the host and thus support host functional properties.

Our project aims to assess the role of phages in elemental cycling in deep-sea sediments with emphasis on prophages and their AMGs, using a combination of bioinformatic and experimental approaches. This will be done by three different approaches: 1) analyse AMGs from lytic and temperate phages and map their associations to environmental conditions using metagenomic data. 2) identifying phage-host systems from metagenomic data for in silico evaluation of the role of AMGs in phage-host interactions. 3) investigating trade-offs of lysogeny for the host by quantifying the metabolic contribution and regulation of prophage-encoded AMGs in benthic element cycling using experimental approaches with phage-host systems in cultivation.

The work will therefore entail a combination of bioinformatic approaches (analysis of large metagenomic and genomic dataset), microbiological analyses (phage and host Isolation, cultivations, and characterization) and molecular approaches (e.g. Real-Time PCR and genomic sequencing), in association with laboratory experiments. There will likely also be the opportunity to join sea going research expedition for collection of deep-sea samples.

Who are we looking for?
We are looking for an enthusiastic and ambitious candidate within the fields of microbial ecology/bioinformatics/molecular biology/marine biology and with a strong interest in bacteriophage biology and phage-host interactions. Documented knowledge and experience on bioinformatics and bacteriophage biology is an advantage. The position is open to both Danish and international applicants, and good English language skills will be required. The main criterion for selection will be the research potential of the applicant.

Our group and research - and what do we offer?
The successful candidate will become an integrated part of the research group of Professor Mathias Middelboe. We offer creative and stimulating working conditions in a dynamic and international research environment, with state-of-the-art research facilities and equipment for phage research. The group works with many aspects of marine microbial ecology, including deep sea microbiology, bacteriophage genomics, ecology and potential use of phages in disease control are key research areas in the group. We have long-term experience with phage-host research, primarily focusing on marine systems. The project is a continuation of previous and ongoing projects on the topic and is strongly associated with the HADAL Center, a DNRF-funded project based at the University of Southern Denmark, which focuses on the exploration of the deepest sites in the global ocean, the hadal trenches. The project will be carried out at the Middelboe Lab at Marine Biological Section, located in Helsingør, 45 km north of Copenhagen. However, research visits at the laboratory of our collaborator Melissa Duhaime at University of Michigan, USA, as well as participation in activities at the HADAL Center at SDU are expected.
The Marine Biological Section is part of the Department of Biology, Faculty of SCIENCE, University of Copenhagen.

Principal supervisor is Professor Mathias Middelboe, Marine Biological Section, Department of Biology. E-mail: mmiddelboe@bio.ku.dk. Phone: (+45 41178798), and co-supervisor is Dr. Sachia Jo Traving. E-mail: sjtraving@bio.ku.dk.

The PhD programme
The position is a three year full-time study within the framework of the regular PhD programme (5+3 scheme), which requires that 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. aquatic microbiology, phage biology. 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
• 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
• Proficient communication skills and ability to work in multi-disciplinary teams.
• Curious mind-set with a strong interest in microbiology and bacteriophages
• Excellent English communication skills, both written and spoken

The PhD programme
To be eligible for the 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. Biology, physiology or biochemistry. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment
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.

The terms of employment and salary are in accordance to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State (AC). The position is covered by the Protocol on Job Structure.

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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)
2. 2 page 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 is 1 April 2025, 23:59 GMT+1

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://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.