PhD fellowship in plant-microbiome assembly

The Department of Biology, Section of Microbiology invites applicants for a PhD fellowship to study social interactions in the plant root microbiome.

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

The project

Novel strategies for eco-friendly and sustainable food production seek to explore and exploit the potential of the plant microbiome to promote growth, acquire nutrients, and induce resistance against pests and pathogens.  Yet, we lack a fundamental understanding of the ecological factors controlling the establishment of a beneficial plant microbiome. Hence, we seek to test the ecological and evolutionary role of microbe-microbe interaction in the assembly and maturation of complex plant root microbiomes.

This project investigates the role of microbial interactions as key drivers for microbiome composition and activity, specifically focussing on interspecies cooperation/competition and the resulting priority effects. We work with the overarching hypothesis that microbial communities are composed of collaboromes, rather than independent species, that are characterized by being microscale focal points of interdependent bacteria showing essential microbe-microbe interactions. The emergent properties of these collaboromes present many beneficial consequences for plant growth and health.

The experimental design of this project goes beyond simple co-occurrence in bulk microbiome samples. Instead, it focuses on co-occurrence network analysis on microscale samples, which is complemented with detailed co-localization analyses to identify putative interactions. Finally, selected identified putative interactions are experimentally validated in simple microcosm experiments

Who are we looking for?

We are seeking a highly motivated and ambitious individual with good interpersonal and communication skills. Highly desired candidates will have a solid theoretical background in plant-microbiome interactions. As well as practical experience with techniques in microbiology and molecular biology. A strong interest in bioinformatics and/or bioimaging is also considered advantageous. 

Applicants should hold an MSc degree in Plant Biology, Microbiology, Bioinformatics, Biochemistry, Biotechnology, or similar with good results and good English skills. As criteria for the assessment of your qualification emphasis will also be laid on previous publications (if any) and relevant work experience. The MSc degree must be awarded prior to the employment date.

Our group and research- and what do we offer?

The PhD fellow will be part of the Section of Microbiology, headed by Prof. Søren Sørensen. His research group focuses on social interactions in microbial populations in in-vivo systems such as soils, plants, animals, and humans. The section houses state-of-the-art both culture-dependent and culture-independent experimental infrastructure that enables us to examine how microbes interact at a scale that is relevant for such small organisms and study the roles of the individual species in these interactions. To do so we use techniques such as high throughput sequencing, flow cytometry, ultra-high resolution bioimaging, confocal microscopy, and microbial reporter systems, combined with the reductionist synthetic community approaches, allowing in-depth investigation of the microbe-microbe or host-microbe interactions mechanism.

The Section offers a highly diverse and inclusive environment consisting of ≈35 researchers who specialize in microbial community interactions, mobile genetic elements, horizontal gene transfer, and the early life human microbiome. The group has gained an international reputation for 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.

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

The PhD programme

Qualifications needed for the PhD 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. Plant Biology, Microbiology, Bioinformatics, Biochemistry, Biotechnology, or similar. 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 plant-microbiome interactions
  • Good language skills


Nice-to-have qualifications:

  • Experience with plant experimental work, including cultivation, maintenance, and site-specific sampling of microbial communities in the rhizosphere; rhizoplane, and endosphere.
  • Experience with any or all of the following methodologies: FISH detection in combination with CLSM microscope imaging and FACS analyses, molecular cloning, preparation of sequencing libraries (Illumina, PacBio, ONT), and analysis of sequencing data.




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 2024.

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


Ke Tao


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

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