Plant beneficial and plant pathogenic microorganisms
PhD School at the Faculty of SCIENCE at University of Copenhagen
This is a specialised course where 50% of the seats are reserved for PhD students enrolled at the Faculty of SCIENCE at UCPH and 50% of the seats are reserved for PhD students at other faculties and universities. Seats will be allocated on a first-come, first-served basis and according to the applicable rules.
Anyone can apply for the course, but if you are not a PhD student, you will be placed on the waiting list until enrollment deadline. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.
Applicants must apply for the course and also send submit half page motivation letter and support letter from their supervisor. The letter must be sent to Flemming Ekelund by the latest on 10 May 2026 (fekelund@bio.ku.dk)
Aim and Content
The course aims to introduce the students to plant-associated microorganisms through theoretical and practical engagement with experts in the field of microbiome research in plants and other hosts in terrestrial ecosystems. We aim to unravel the role of microorganisms in the One Health concept, i.e. to teach students about the role of microorganisms in sustainable and unified optimization of health of people, animals and plants. We will tackle the topics such as the role of microorganisms in plant and animal systems, comprising both symbiotic and antagonistic relationships. We will focus on belowground plant-microbe and microbe-microbe interactions. Major topics will be plant-pathogen interactions and beneficial plant-microbiome interactions. We will also comprise the drivers of plant- and animal-microbiome interactions such as global change factors and intrinsic host-microbiome associations. We will round up the course with knowledge on the management practices for a sustainable plant growth.
Our course aims to bridge the gap between the theoretical studies and research experience. Therefore, we aim to organize practical exercises for the students along with the lectures. We plan to start our course with a poster session where the students will introduce themselves and their own work. We aim to distribute the relevant literature to the students and ask them to do their own literature research for the course. The course will end with a presentation of the practical work and an engaging discussion on how the acquired knowledge from the course can be applied to the students’ own work.
The course is relevant if you work with plants and soil in the context of environmental, agricultural or natural science. E.g.: (1) studies on the plant and animal holobiont, (2) plant-microbe interactions (pathogenic and beneficial), (3) microbe-microbe interactions in the context of plant performance and nutrient cycling, (4) work on new methods to identify specific groups of organisms in situ, or (5) soil food web analysis in the context of plant performance. The lectures and discussions will stimulate the interaction between teachers and participants and are essential for a successful course
We cover the following topics: The holobiont: Concept of the holobiont; host-microbe interactions; plant holobiont. Plant-microbe interactions: pathogenic and beneficial plant-microbe interactions. Soil microorganisms and microbe-microbe interactions: The structure and function of microbial communities; diversity of soil bacteria; mycorrhiza; protozoa, nematodes and their relevance in plant performance. Molecular biology and bioinformatics: a linkage between plant-microbe interactions, microbial ecology, and organism-biology using bioinformatics.
A major theme in the course will be the bridge between the good hypothesis, the well-planned experiment and the firm discussion and conclusion. Student group work will focus on this and it will be the topic of group presentation and the final written assignment. Many scientific papers are unfocussed and difficult to follow and we hope to improve that.
Learning outcomes
Intended learning outcome for the students who complete the course:
Knowledge:
• Holobiont – relevance, methods and application
• Plant-microbe interactions in the rhizosphere and aboveground
• Nematode-protist-microbe interactions
• Sustainable management practices for plant growth
Skills:
• Literature review
• Scientific writing and presentation
• Structure of scientific review
• Ability to design an expriment/project
•
Competences:
• Individual and team work
• Project management
• Bridging and application of acquired knowledge to students’ own work
Target Group
PhD students working with microbiome related research
Recommended Academic Qualifications
Master of Science in biology, microbiology, nematology or similar qualifications
Research Area
Biology, plant pathology, microbiology, nematology
Teaching and Learning Methods
Lectures, exercises, individual and group work, excursions, data analyses, report writing
Type of Assessment
Attendance
Poster presentation
Presentation of group work
Report on and critical evaluation of the teaching
Literature
State of the art scientific papers
Course coordinator
Flemming Ekelund
Lecturers
- Flemming Ekelund (Department of Biology, University of Copenhagen)
- Rasmus Kjøller (Department of Biology, University of Copenhagen)
- Anders Priemé (Department of Biology, University of Copenhagen)
- Nikolaj Kindtler (Department of Biology, University of Copenhagen)
- Rute Andreia Rodrigues da Fonseca (GLOBE Institute, University of Copenhagen)
- Frederik Bak (Department of Plant and Environmental Sciences, University of Copenhagen)
- Alexandr Gavrin (Department of Molecular Biology and Genetics, Aarhus University)
- Enoch Narh Kudjordjie (Department of Agroecology – Plant Pathology and Microbiology, Aarhus University)
- Mette Vestergård (Department of Agroecology – Plant Pathology and Microbiology, Aarhus University)
- Ahmed Abdelfattah (Leibniz Institute of Agricultural Engineering and Bio-economy)
- Olivera Topalovic (INRAE, IGEPP - Institute for Genetics, Environment and Plant Protection)
Dates
23-27 June 2026:
23 - 27 June: Lectures, discussions, student poster presentations.
27 June: Student project presentations, evaluation, and departure
Course location
Campus North, Department of Biology, University of Copenhagen
Registration deadline
10 May 2026
Applicants must apply for the course and also send submit half page motivation letter and support letter from their supervisor. The letter must be sent to Flemming Ekelund by the latest on 10 May 2026 (fekelund@bio.ku.dk)
Course fee
• Participant fee: 0 DKK
• PhD student enrolled at SCIENCE: 0 DKK
• PhD student from Danish PhD school Open market: 0 DKK
• PhD student from Danish PhD school not Open market: 3000 DKK
• PhD student from foreign university: 3000 DKK
• Master's student from Danish university: 0 DKK
• Master's student from foreign university: 3000 DKK
• Non-PhD student employed at a university (e.g., postdocs): 3000 DKK
• Non-PhD student not employed at a university (e.g., from a private company): 8400 DKK
Cancellation policy
• Cancellations made up to two weeks before the course starts are free of charge.
• Cancellations made less than two weeks before the course starts will be charged a fee of DKK 3.000
• Participants with less than 80% attendance cannot pass the course and will be charged a fee of DKK 5.000
• No-show will result in a fee of DKK 5.000
• Participants who fail to hand in any mandatory exams or assignments cannot pass the course and will be charged a fee of DKK 5.000
Course fee and participant fee
PhD courses offered at the Faculty of SCIENCE have course fees corresponding to different participant types.
In addition to the course fee, there might also be a participant fee.
If the course has a participant fee, this will apply to all participants regardless of participant
type - and in addition to the course fee.