Applied Microbiology

Course content

Microorganisms play vital roles in the environment including cycling of nutrients, causing and preventing diseases in other organisms, and a host of other essential functions. We can therefore use microorganisms as a resource to solve problems or improve on critical aspects in our society. Examples of cases where we can apply microorganisms include growth promotion of crops, prevention of plant diseases, microbially-produced enzymes that can improve food production and many other possible applications. The Applied Microbiology course is focused on the implementation of both common and highly advanced methods in microbiology for studying real world problems. Cases will vary from year to year but may for example be:

  • Identification of plant pathogenic bacteria as well as bacteriophages that combat the pathogen.
  • Isolation of bacteria that degrade an important environmental pollutant.
  • Microbial interactions involved in biological control of plant pathogens through production of antifungal metabolites, as well as in microbial biofertilization.


Initially, the course introduces screening for microorganisms with a desired function, then presents approaches to identify and characterize selected microorganisms, and finally addresses how you assess the applicability of the studied microorganisms as a resource for a real-world problem.

The aim of the course is to give the students practical and theoretical skills in applied microbiology at an advanced level. During the course, the students will obtain hands-on experience with a range of techniques for characterization of microorganisms and for studying microbial interactions, as well as genome mining for specific traits, and expression of functional genes. The techniques include: DNA sequencing with Illumina and Nanopore, bacterial and phage genomics, reporter gene and tagging technology, quantitative PCR, and screening for production of secondary metabolites. Furthermore, the students will achieve theoretical knowledge on the principles of the above methods and their application in studies of environmental biotechnology.


The following experimental areas of applied microbiology will be covered:

  • Isolation of bacteria with desired traits, such as plant pathogenicity, production of a specific metabolite, antagonism against a bacterium or fungi, production of a specific secondary metabolite, or degradation of a pollutant.
  • Isolation of bacteriophages that infect specific bacteria.
  • Phenotypic tests and bioassays on isolated bacteria, including confrontation assays, antibiotic resistance tests, motility assays, and other relevant assays.
  • Isolation of DNA, sequencing library construction and subsequent sequencing on Illumina and Nanopore platforms, of both bacteria and bacteriophages.
  • Bioinformatic analyses of genome sequences, including assembly, gene annotation, genome mining for desired traits such as secondary metabolite gene clusters, phylogenetic analyses, and more.
  • Application of qPCR to study bacterial growth dynamics in a given environment or culture condition.
  • Application of reporter gene technology and labelling with fluorescent tags to track microorganisms.


During the course, the students take on the role of researchers. In this course, we strive to work on real world problems and challenges for students to tackle. Thus, the specific scope of research may vary from year to year. Hence, it is important to note that not all students will make the same discoveries. Students are in groups expected to identify and analyse the most interesting aspect(s) of their individual findings by themselves.


MSc Programme in Biology
MSc programme in Biotechnology
MSc Programme in Biotechnology with a minor subject
MSc Programme in Environmental Science

Learning outcome

It is expected that the overall outcome from this course is to provide an understanding of the biological principles that can be manipulated using microorganisms and microbial consortia and the means by which this can be achieved.


Upon completion of the course, students will have acquired the following:


The ability to display an overview and detailed knowledge of methods used for isolation, detection, and phenotypic characterization of microorganisms and bacteriophages that perform a specific function.

Account for advanced molecular methods in microbiology, including 2nd and 3rd generation sequencing, qPCR, and reporter gene technology.

Classify microorganisms phylogenetically and understand the principles behind the applied microbial bioinformatics.


Reflect on the properties of qualitative and quantitative methods for detection and isolation of microorganisms from complex environments.

Suggest phenotypic tests and bioassays that are relevant for the scope of the study.

Evaluate approaches for analysis of bacterial genome DNA sequences.

Evaluate advantages and disadvantages of methods for investigation of microorganisms in complex environments.

Communicate knowledge in the applied area covered by the course.


Select and discuss basic and advanced methods for investigation of microorganisms in complex environments.

Formulate a strategy for how individual methods covered by the course can be integrated into a research strategy to study a real-world problem.

Evaluate the application potential of microorganisms within biotechnology in relation to environmental sciences.

Teaching on the course will include practical exercises, lectures, and group work. Group work will focus on cases employing methods presented at the course to obtain insight into applied microbiology. Furthermore, the course participants will work in project groups with bioinformatic analyses of bacterial and bacteriophage genomes. Student groups will write a report at the end of the course that is focused on the students’ own findings and analyses. The report should contain results and discussion from relevant topics of the course, including isolation methods, bioassays and phenotypic tests, bioinformatics, qPCR, etc.

Review papers and original research papers as specified in the course curriculum.
Manual of practical exercises.

The students are expected to have passed a basic course in microbiology.

Academic qualifications equivalent to a BSc degree is recommended.


Feedback will be given as written comments to reports and group work, and as in dialoque during colloquium and exercises.

7,5 ECTS
Type of assessment
Oral examination, 30 min with 30 min preparation
Type of assessment details
The assessment will be made based on examination in reports and preparations from the group work (30%) and examination in textbook, reviews and original papers (70%)
All aids allowed

However, no internet access is allowed at the exam.

Marking scale
7-point grading scale
Censorship form
No external censorship
Two internal examiners
Criteria for exam assessment

Please refer to the learning outcome.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 20
  • Preparation
  • 65
  • Theory exercises
  • 20
  • Practical exercises
  • 40
  • Project work
  • 60
  • Exam
  • 1
  • English
  • 206


Course number
7,5 ECTS
Programme level
Full Degree Master

1 block

Block 2
34 students
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
  • Lars Hestbjerg Hansen   (4-736f6f684777736c7535727c356b72)

Lars Hestbjerg Hansen, Witold Kot, Mette H. Nicolaisen, Rosanna Hennessy, Tue Kjærgaard Nielsen

Saved on the 28-02-2023

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