MIB-31306 Microbial Ecology


Credits 6.00

Teaching methodContact hours
Individual Paper1
Excursion (one day)5
Course coordinator(s)prof. dr. H Smidt
Lecturer(s)PWJJ van der Wielen
prof. dr. H Smidt
Examiner(s)prof. dr. H Smidt

Language of instruction:


Mandatory knowledge:

ZSS06100 Laboratory Safety

Assumed knowledge on:

Microbiology & Biochemistry or General and Environmental Microbiology.


The Microbial Ecology course is an advanced course on the occurrence, diversity and activity of microorganisms (archaea and bacteria, protozoa, yeasts and fungi, and viruses) in man-made and natural ecosystems. The lectures deal with:
1. interactions of microorganisms with their biological and physico-chemical environment;
2. biotransformations of organic pollutants and specific elements, like S, N, Fe and Mn in natural and man-made ecosystems;
3. detection, identification and functional characterization of microorganisms and whole microbial communities at the DNA- and RNA-level by using molecular fingerprinting techniques, next generation technology sequencing and the use of fluorescently labelled probes towards 16S rRNA; application of additional cellular components as biomarkers for identity and function (e.g. phospholipids, proteome);
4. theories on genome stability, gene flux and adaptation;
5. phenomena of quorum sensing cell-cell communication and cross talk between microorganisms and their hosts in symbiotic and associative interactions such as in the mammalian intestine, plant-microbe interactions, and the soil biosphere.
6. novel strategies for the cultivation of the yet uncultured majority of microorganisms;
In addition to the lectures, students will perform a literature study. Specific cases related to microbial ecology will be studied. Examples are 'degradation of (organo) pollutants in soil', 'host-microbe interactions in the mammalian intestine' and 'structure-function analysis of complex ecosystems'.
The experimental part consists of an experiment in which the students become familiar with major laboratory techniques and computer analyses to be able to study microbial ecology. The experiment comprises:
- molecular detection and quantification of microorganisms;
- specific microbial transformations;
- microbial genomics;
- a fieldtrip of 1/2 day is part of the course.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- compare different types of interactions between microorganisms and their biological and physico-chemical environment;
- compare the role of microorganisms in the cycling of elements such as carbon, nitrogen and sulphur;
- explain how microorganisms can transform environmental pollutants;
- interpret experimental observations as indicators of specific microbial processes;
- apply modern molecular techniques for the analysis of complex microbial ecosystems;
- predict ecological functions from genomic and metagenomic data;
- design experimental strategies for the detection of microbes and their activities in the environment.


- attend the lectures that are supported by a reader and the textbook;
- study literature (problem-based-learning followed by a written report;
- perform several practical experiments and write a report for each experiment.


- written test with 10 open questions (70%);
- individual paper based on literature study (15%);
- written group report on experiments in the practical course & observations of practical performance (15%).
The written test needs a minimum mark of 5.5 to pass.


Microbial Ecology and practical course handbook (both are available at the Laboratory of Microbiology).
Michael T. Madigan; Kelly S. Bender; [et.al]. (2018). Brock Biology of Microorganisms. 15th ed. ISBN 13: 9781292235103


Restricted Optional for: MBIBiologyMScD: Spec. D - Ecology1AF
MBTBiotechnologyMScA: Spec. A - Cellular/Molecular Biotechnology1AF