Applied Microbiology

Course content

Microorganisms in natural environments represent a largely untapped resource for novel enzymes and bioactive metabolites that can be used in industrial biotechnology. Furthermore, the use of beneficial microorganisms to promote the growth of crop plants is a rapidly expanding area of environmental biotechnology. The course covers methods used and approaches taken from the stage where you screen for microorganisms with a desired function, identify and characterize selected microorganisms, and until you assess the performance of selected microorganisms in a complex environment.

The aim of the course is to give the students theoretical and practical 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 interactions between microorganisms. The techniques include: PCR genotyping, bacterial genomics, single cell detection techniques, reporter gene technology, quantitative PCR and targeted environmental transcriptomics. Furthermore, the students will achieve theoretical knowledge on the use of microorganisms for environmental and biotechnological applications.

 The following experimental areas of applied microbiology will be covered:

 - Microbial bioprospecting and population analysis: Screening for enzyme or metabolite producers; genotyping of microorganisms and assessment of biodiversity of cultivated populations.

 - Detection of specific microorganisms: Molecular methods to determine abundance and fate of specific microorganisms in complex environments.

 -  Activity and function of specific microorganisms: Methods to demonstrate metabolic activity or specific gene expression by microorganisms in complex environments.

- Bacterial genome assembly and annotation.

The following theoretical areas of applied microbiology will be covered:

 - Extremophilic organisms: Benefits of using extremophiles as sources for novel enzymes or bioactive metabolites. Applications of extremophilic microorganisms and their products.

 -  Microbial interactions in agriculture: Interactions involved in biological control of plant pathogens through production of antifungal metabolites, as well as in microbial biofertilization.

 - Aquaculture microbiology: Biology of taste-and-odour producing bacteria in fish ponds and their impact on fish quality.


MSc Programme in Agriculture
MSc Programme in Biology-Biotechnology
MSc programme in Biology
MSc Programme in Biochemistry
MSc Programme in Environmental Science

Learning outcome

After completing the course the students should be able to:

Classify microorganisms phylogenetically.
Display an overview of extremophilic bacteria and their enzymes as well as the application potential of organisms and enzymes.
Describe methods for investigating interactions between bacteria and fungi.
Display an overview of methods used for detection of microorganisms and their activity in complex environments.
Display an overview of the influence of microorganisms on the quality of drinking water and aquaculture products.
Reflect over the properties of qualitative and quantitative methods for detection of microorganisms in complex environments.

Evaluate the potential of microorganisms for production of enzymes or bioactive molecules.

Evaluate approaches for analysis of bacterial genome DNA sequences
Evaluate methods for investigation of microorganisms in complex environments and communicate knowledge in this area.

Select and discuss basic and advanced methods for investigation of microorganisms in complex environments.
Evaluate the interactions between selected microorganisms and their potential influence on the environment.
Evaluate the application potential of microorganisms within biotechnology in relation to environmental sciences.

Teaching at 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 microbial performance in complex environments. Furthermore the course participants will work in project groups with assembly and annotation of bacterial genomes.

Brock: Biology of Microorganisms, 14th edition. Pearson Education Inc. 2015.
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.

7,5 ECTS
Type of assessment
Oral examination, 30 min
A time period of 30 min is used for preparation for the exam.
Weight: Examination in reports from exercises: 20%. Examination in reports from project work: 20%. Examination in textbook, reviews and original papers: 60%
All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
One internal examiner
Criteria for exam assessment

Please refer to the learning outcome.

Single subject courses (day)

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