Applied Microbiology

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.