Molecular Plant-Microbe Interactions

Course content

This course provides an overview of the biology of host-microbe interactions at the molecular level, with a specific focus on pathogenic microorganisms. In addition to lectures and research article-driven learning, the course includes a series of simple experiments to provide hands-on experience, illustrates how the plant immune system works, and lays the foundation for understanding how plants stay free of disease.

Plant diseases caused by pathogenic microorganisms are among the most important factors affecting quality and yield of crop plants – causing typically up to 20% losses.

An understanding the biology of plant microbe and microbe-microbe interactions gives an insight and inspiration for sustainable approaches for plant protection (UN development goal (UNDG) 2 and 17).

The rapid development of biotechnology in plant and microbial science is leading to enhanced knowledge of the physiology and molecular biology of plants, and of the crosstalk between microorganisms and plants both as individual organisms and as microbiomes – in combination: the holobiome. Disease resistance is the consequence of successful activation of plant’s immune system. Biological control of plant diseases is based on the exploitation of microbe-microbe-plant interactions to suppress disease.

The study of these fundamental biological processes leads not only to the improvement of these environmentally-friendly strategies for disease control in plant production, but also to the discovery of molecules and genes with novel applications for industry.

This course addresses several UN development goals by providing knowledge which can be used to improve agricultural efficiency (UNDG 2 and 13 by using microbiomes to improved resilience to abiotic stress) and product quality (UNDG 3 by, e.g., reducing mycotoxin contamination).

Topics covered include:

  • Diseases caused by viruses, bacteria, fungi and oomycetes and their infection strategies including, symbiotic, biotrophic, hemibiotrophic and and necrotrophic lifestyles.
  • Pattern-Triggered Immunity (PTI) and Effector-Triggered Immunity (ETI), pathogen effectors and their interplay with PTI and ETI. Plant immune signalling pathways (MAP kinases, salicylic acid, pipecolic acid, jasmonic acid, etc).
  • Execution of immunity (antimicrobial specialised metabolites, cell wall, antimicrobial proteins, membrane trafficking, hypersensitive response)
  • Application of biotechnological tools, including genomics (NGS), transcriptomics, molecular genetics, gene editing (e.g. CRISPR-Cas9) and gene silencing (PTGS, HIGS etc)
  • Disease resistance through transgenic plants, new strategies for resistance breeding
  • Biological control of disease by understanding the biological basis of microbial interactions. Microbiome interactions with pathogens and plants.



MSc Programme in Agriculture
MSc Programme in Biotechnology


Learning outcome

The course gives an understanding of the biology of plant-microbe interactions at the molecular level.

After completing the course the student should be able to:


  • Give an overview of the mechanisms by which plants respond and protect themselves against pathogens.
  • List major cellular signal transduction mechanisms in plants and microorganisms.
  • Describe the molecular mechanisms used by pathogens for overcoming host defences.
  • Have an understanding of the continuum from mutualistic symbiosis to necrotrophy.
  • Understand how these processes can be applied to crop protection.


  • Explain how the above topics are studied experimentally including the use of ’omics technologies and molecular genetics.
  • Interpret primary data from research articles relating to these molecular interactions and apply the knowledge to new situations in biology.
  • Obtain basic experimental skills in studying plant immunity.


  • Discuss the potential of biotechnological and plant breeding technologies for developing disease resistant plants
  • Consider the ethical aspects of the use of different approaches (e.g. transgenic, new genomic technologies, biological control) for disease problems associated with plant protection and to put these into perspective.
  • See the potential for industrial processes using novel molecules derived from plant-microbe interactions.
  • Critical approach to digital scientific information searches incl. reference management.

Lectures, journal clubs, colloquia, miniproject with oral presentation

Tronsmo AM, Collinge DB, Djurle A, Munk L, Yuen J, Tronsmo A (2020) Plant Pathology and Plant Diseases 440 pp CABI International, Wallingford. ISBN 9781789243178

Review articles and primary literature.

Further information will be available on Absalon.

Knowledge of Molecular Biology, Genetics and Microbiology

Academic qualifications equivalent to a BSc degree is recommended.

Continuous feedback during the course of the semester
Peer feedback (Students give each other feedback)

The feedback to the students will be given in different forms: For the journal club where each student will prepare a PowerPoint presentation, it will be given individually.

In journal clubs held in plenum, it will be oral given to each group.

Use of quizzes in Absalon.

7,5 ECTS
Type of assessment
Oral examination, 20 min under invigilation
Type of assessment details
Oral examination with preparation time. Weight: 100%
Exam registration requirements

Active participation in Journal Clubs (80% of assignments completed) 

Approved project Work (group assignnment)

All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
Two internal examiners

Oral exam 20 min with 20 min preparation.

If the requirements for the exam is not met, - the students need to give a project presentation

Criteria for exam assessment

See learning outcome.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 40
  • Class Instruction
  • 20
  • Preparation
  • 104
  • Theory exercises
  • 18
  • Laboratory
  • 20
  • Exam
  • 4
  • English
  • 206


Course number
7,5 ECTS
Programme level
Full Degree Master

1 block

Block 3
No limitation
The number of seats may be reduced in the late registration period
Study Board of Natural Resources, Environment and Animal Science
Contracting department
  • Department of Plant and Environmental Sciences
Contracting faculty
  • Faculty of Science
Course Coordinator
  • David B. Collinge   (3-6967684575716a7333707a336970)

Hans Thordal-Christensen, Mads Eggert Nielsen, Elizabeth Heather Jakobsen Neilson, Nanna Bjarnholt

Saved on the 28-02-2023

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