PhD fellowship in plasmid microbial ecology

The Department of Biology, Section of Microbiology invites applicants for a PhD fellowship in plasmid microbial ecology. The proposed position is affiliated with the project pTracker - Machine learning methods for data-driven discovery of antibiotic resistance plasmid dissemination and evolution, the project ROOT-MOBIL: Exploring the ROOT-MOBILOME: Horizontal Gene Transfer and Plasmid Dynamics in the Rhizosphere and the long-read sequencing research platform CoDoN - Copenhagen DNA Analysis Center, all granted by the Novo Nordisk Foundation. All these projects are unified under the objective of integrating various sequencing methodologies to get the maximum of (meta)-genomic information from complex communities and samples.

Start date is (expected to be) 1 August 2024 or as soon as possible thereafter.

The project

We are looking for a PhD student to join this project and participate notably with the isolation of high quality DNA from a variety of samples, preparation of various sequencing libraries type (WGS, metagenomic, HiC) for diverse sequencing platform: Illumina, PacBio, Oxford Nanopore. Metagenomic sequence assembly and annotation, linkage of mobile genetic with Metagenome Assembled Genomes (MAGs) in order to decipher plasmid-host networks in the rhizosphere

Effort will be made to implement DNA crosslinking protocols (HiC, meta3C) and single-cell encaspulation (microfluidic semi-permeable capsules; single-cell FACS) to soil samples. These methods combination will improve plasmid sequence assembly and link mobile genetic elements to their cellular host in complex environmental samples which is currently not achieved at a high-throuput.

The qualified candidate will primarily have hands-on experience in molecular biology, handling of high-molecular weight DNA and sequencing library preparation with different sequencing platforms. Previous experience with handling of (meta)-genomic data and associated bioinformatics tools is highly appreciated.

Who are we looking for?

We are looking for candidates within the field(s) of microbiology, microbial biotechnology, molecular biology or equivalent with research experience and a background in Microbiology. Applicants with the following proficiencies will be regarded highly qualified and will be prioritized: 

  • Experience with genome and plasmid sequencing, assembly and annotation from microbial isolates and shotgun metagenomics.
  • Experience on PacBio and/or Oxford Nanopore sequencing library preparation highly appreciated.
  • Knowledge on plasmid biology and research experience with long-reads sequencing technologies (PacBio, Oxford Nanopore) is highly desired.
  • Basic knowledge of command-line tools & UNIX environment highly appreciated.
  • Motivated to work in a multidisciplinary research team, as well as independently, with an open communication style and a problem-solving attitude.


Our group and research- and what do we offer?

The position is available at the Section of Microbiology, headed by Professor Søren Johannes Sørensen. The Section offers a highly diverse and inclusive environment consisting of ≈35 researchers that specialize in microbial community interactions, mobile genetic elements, horizontal gene transfer, and the early life human microbiome. The group has gained international reputation in applying a combination of bioinformatics and molecular biology approaches to address research questions of ecological, clinical, and biotechnological interest, which lie at the intersection of computational biology, genomics, and bacterial evolution.

The group is a part of the Department of Biology, Faculty of SCIENCE, University of Copenhagen. We are located in Copenhagen.

We offer creative and stimulating working conditions in dynamic and international research environment.

Principal supervisor is Professor Søren Sørensen (, Section of Microbiology, Department of Biology. The student will be co-supervised by Dr. Joseph Nesme (

The PhD programme

Qualifications needed for 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. microbiology, microbial biotechnology, molecular biology or a closely related subject. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the PhD 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 plasmid microbial ecology
  • 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)
  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 is Tuesday 27 February 2024, 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


Interviews with selected candidates are expected to be held in week early to mid May

For specific information about the PhD fellowship, please contact the principal supervisor or co-supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website:

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


Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.


Søren Johannes Sørensen


Joseph Nesme


Application deadline: 27-02-2024
Employment start: 01-08-2024
Working hours: Full time
Department/Location: Department of Biology

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