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Cursus: NWI-BB027B
Ecologische Microbiologie
Cursus informatieRooster
Studiepunten (ECTS)6
CategorieBA (Bachelor)
Aangeboden doorRadboud Universiteit; Faculteit der Natuurwetenschappen, Wiskunde en Informatica; BioWetenschappen;
VorigeVolgende 3
dr. A. Arshad
Overige cursussen docent
prof. dr. H.J.M. op den Camp
Overige cursussen docent
prof. dr. H.J.M. op den Camp
Overige cursussen docent
Contactpersoon van de cursus
prof. dr. H.J.M. op den Camp
Overige cursussen docent
dr. L. Gambelli
Overige cursussen docent
KW3  (30-01-2017 t/m 09-04-2017)
Inschrijven via OSIRISNee
Inschrijven voor bijvakkersNee
  • You will have learned about the microorganisms responsible for the conversion of elements at different redox states (e.g. NO3- reduction to N2 or CH4 oxidation to CO2) and key types of energy metabolisms of microorganisms (e.g. denitrification, photosynthesis, methanogenesis, fermentation, ammonium and methane oxidation).
  • You will have understood the biogeochemical processes within carbon, nitrogen, sulphur and iron cycles and the impact of humans on these cycles.
  • You will have learned an overview of the biodiversity of prokaryotes and the evolutionary relations between ecologically relevant species including current theories and concepts concerning microbial evolution.
  • You will have a detailed understanding of molecular ecology in theory and practice.
  • You will have designed and planned your own experiments in a team of two.
  • You will have learned and applied state-of-the art techniques and tools such as PCR, fluorescence in situ hybridization, metagenomics and gas chromatography complemented by bioinformatics analyses.
  • You will have written a scientific report of the synthesis of your own results in the format of a scientific article, discussed your article with the lecturer and your peers (performed in a team of two).
  • You will have learned how to critically read and discuss scientific literature, and present your analyses (performed in a team of two).
This course is a must for all biology and MLW students interested in biogeochemical cycles and the role of microorganisms in natural and manmade ecosystems. The lectures and practicals show the importance of unicellular organisms for the biogeosphere and how humans are dependent on their activities: the air we breathe, the water we drink, the temperature of the earth and the occurrence of epidemics. The lectures present many key themes in microbial ecology and focus on the multidisciplinary approach of this field of research. Recent articles from the scientific literature will be discussed during a mini-symposium at the end. The influence of human activity on the environment and human health (medical microbiology from an ecological point of view) will also receive attention.
Practicals: Laboratory classes, in which you work together with a partner, generally take place in the morning followed by lectures or "werkcolleges" in the afternoon. The experimental part will provide you with hands-on experience in several complementary approaches to answer questions in microbial ecology and to study the biogeochemical element cycles: DNA-based microbial community analysis (including in silico phylogenetic analysis), measuring microbial activities, enrichment of microorganisms and visualization of these by fluorescence in situ hybridization and microscopy.
The overall approach of this practicum is to keep things as close to "real life" scientific situations as possible. Therefore, you will have a certain degree of freedom and responsibility to plan your own experiments and monitor them with the methods you will learn. Before you can start your experiments, we want to make sure that you understand both the method you use and the general idea behind the experiments.
For this reason, an assignment for each of the experimental approaches has to be answered and discussed with the assistants before you start. Keep in mind that there are often several ways to achieve the same goal, different answers may be correct, things may go wrong and results may not be what you expected. Consider this course as a first taste of these methods. To become really proficient you have to practice much longer, for example by conducting an internship at our department.

As a case study, we have selected a wastewater treatment plant (wwtp). In this wwtp, different clades of microorganisms are used to degrade pollutants to relatively less harmful compounds such as CO2 and N2, or CH4 (biogas) that may be re-used, making it a perfect site to study the elemental cycles. We will measure the rates of several processes in the C and N cycles and will try to detect and identify the responsible microbes. Sludge (biomass) from two different steps - anaerobic digestion (granular sludge) and nitrogen removal (flocculent) - will be used. In this course we will perform four lines of experiments. (1) In week one and two we will start by constructing an inventory of the microbial biodiversity of two different types sludge. (2) Afterwards, we will measure the rates of several biogeochemical processes and try to cultivate the responsible microorganisms. (3) We will detect (or identify) these microorganisms with fluorescent in situ hybridization (FISH) microscopy. (4) We will investigate the potential for electricity production with the wwtp sludge with microbial fuel cells. Ultimately we aim to reach an understanding how these three different approaches may be used to understand a complex environment, with the wastewater treatment plant as an example.
Communicating your results to the scientific community is an essential part of scientific practice. Therefore, we will discuss your report drafts in small groups, where you receive feedback from each other and the lecturers to improve your writing skills.
The course will be taught in English. In order to pass, all components of the course have to be graded a minimum of 5.5.
The course will be given on Thursday and Friday during the period indicated. You will need to use a lab coat and safety glasses.
In order to receive a passing grade, all parts of the course need to be evaluated with at least five and a half (5.5). The final grade is composed of: exam (60%), performance and attitude during the practicum, presentation and report (40%).
Geomicrobiology (propedeuse) and Biology of Microorganisms (2nd year). Please contact one of the lecturers in advance if you do not meet these criteria.
Brock, Biology of microorganisms, 13th edition or higher, Prentice Hall, (price ca. € 90,-)

• Powerpoint slides (will be available on BlackBoard after the lectures)
• Reader (will be on sale before the course)

• 4 hours computer course
• 20 hours lecture
• 67 hours laboratory course
• 4 hours student presentation
• 10 hours problem session
• 63 hours individual study period
Verplicht materiaal
Brock, Biology of microorganisms, 13th edition or higher, Prentice Hall
Reader (will be on sale before the course)







GelegenhedenBlok KW3, Blok KW4

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