MIB-31306 Microbial Ecology


Credits 6.00

Teaching methodContact hours
One day excursion4
Literature study
Practical intensively supervised25
Problem-based learning4
Course coordinator(s)prof. dr. H Smidt
Lecturer(s)prof. dr. H Smidt
dr. ir. D Sipkema
Examiner(s)prof. dr. H Smidt

Language of instruction:


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, lower eucaryotic protozoa, yeasts and fungi) in man-made and natural ecosystems. The lectures deal with: 1. microorganism interactions with their biological and physico-chemical environment;
2. biotransformations of organic pollutants and specific elements, like S, Fe and Hg in natural and man-made ecosystems;
3. detection, identification and functional characterization of microorganisms at the DNA- and rRNA-level by using molecular fingerprint techniques, cloning and 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.
In addition to the lectures, students will perform a literature study. In small groups 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:

At the end of the course the student is expected to be able to:
- demonstrate more insight in and have more knowledge of modern microbial ecology as an integration of an holistic and a reductionistic approach;
- analyze complex ecosystems with modern molecular techniques;
- predict ecological functions from genomic studies.


Attend the lectures that are supported by a reader and the textbook. Study literature (problem-based-learning followed by a short presentation. Perform several practical experiments and write a report for each experiment.


The final mark is based on a written exam that covers the lectures, the practical course and the literature study (70%), a written report of the literature study (15%) and written reports of the experiments in the practical course (15%). To pass the course, the mark for the exam should be at least 6.0.


Reader 'Microbial Ecology' and practical course handbook (both are available at the laboratory of Microbiology). Textbook 'Microbiology' (Prescott et al. 7th ed.).

Restricted Optional for: MBIBiologyMScB: Plant Biology1AF
MBIBiologyMScC: Animal Biology1AF
MBIBiologyMScD: Ecology1AF
MBTBiotechnologyMScE: Environmental Biotechnology1AF
MMLMolecular Life SciencesMScE: Environmental Chemistry1AF