BIO-3038 Molecular methods in environmental microbiology - 10 stp

Master level course for biology students. It is mandatory for students admitted to the Molecular environmental biology discipline (prioritized).

The course has a maximum capacity of 12 students.

The course is not available as a singular course.

The aim of this course is to give a thorough introduction to molecular methods and basic bioinformatics used in modern environmental microbiological research. The course will give a basis for advanced studies in microbial ecology and include practical exercises followed by data analyses including computer analyses of own data sets.

The students will perform fieldwork, isolate DNA and RNA from different types of samples, perform an incubation experiment including gas analyses, perform fluorescent labeling of microorganisms and prepare DNA and RNA samples for qPCR, sequencing and bioinformatics. The laboratory and computer work is running for two weeks and the results are discussed and presented by the students in plenum. In addition comes lectures, colloquiums and seminars.

The students have to write individual laboratory reports shaped as scientific articles. The use of AI will be discussed, but encouraged only for text polishing and minor adjustments, and large errors originating from hallucination and bad commands will count highly negatively in the evaluation. The lectures will be closely connected to the practical problems to be solved in the laboratory and relevant background theory. Selected articles from the scientific curriculum are topics for seminar presented by the students. Curriculum consists of lectures, lab materials and scientific articles.

Knowledge

The student:

• has a basic understanding of modern molecular methods used in environmental microbiology, including DNA and RNA extraction, qPCR, nanopore sequencing, and fluorescence microscopy
• has knowledge of methods for analyzing gas samples, including the use of gas chromatography and laser spectrometry
• has some basic insight into sequence data analysis
• has knowledge of the microbial methane cycle and relevant microbiological and climate‑related processes
• understands key principles of experimental design, replicates, error sources, and simple statistical evaluation of results
• is familiar with the structure of scientific articles and the basic requirements for scientific writing at the master’s level

Skills

The student can:

• perform basic laboratory techniques such as pipetting, sterile work, handling gases, molecular biology procedures, and working with syringes and gloves
• isolate DNA and RNA from various sample types and prepare samples for qPCR and sequencing
• carry out fieldwork, laboratory incubations, and fluorescence labeling of microorganisms
• produce, process, and analyze data from gas chromatography, laser spectrometry, qPCR, and nanopore sequencing
• use basic bioinformatic tools to analyze their own datasets
• interpret scientific results and evaluate methods, replicates, uncertainty, and data quality
• write a scientific report in article format based on their own results

General competence

The student:

• can plan, carry out, and document practical and analytical work in environmental microbiology
• can communicate subject matter and their own research results orally and in writing, including presenting scientific articles
• can reflect on and discuss methodological choices, data quality, and limitations of different molecular methods
• can work independently and in groups in field, laboratory, and analytical work
• understands the responsible use of AI tools in scientific writing and can identify and avoid typical errors related to misuse or hallucinations