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Cursus: NWI-BB027C
Applied and Environmental Microbiology
Cursus informatieRooster
Studiepunten (ECTS)6
Categorie03 (Verdiepend)
Aangeboden doorRadboud Universiteit; Faculteit der Natuurwetenschappen, Wiskunde en Informatica; BioWetenschappen;
VorigeVolgende 3
A.S. Boersma
Overige cursussen docent
dr. S. Lücker
Overige cursussen docent
Contactpersoon van de cursus
dr. S. Lücker
Overige cursussen docent
dr. S. Lücker
Overige cursussen docent
dr. S. Lücker
Overige cursussen docent
KW3  (29-01-2024 t/m 07-04-2024)
Inschrijven via OSIRISJa
Inschrijven voor bijvakkersJa
  • You will learn 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, ammonia and methane oxidation).
  • You will understand the biogeochemical processes within the carbon, nitrogen, and sulphur cycles and the impact of humans on these cycles.
  • You will obtain 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 gain a detailed understanding of molecular ecology in theory and practice.
  • You will design and plan your own experiments in teams of two.
  • You will apply state-of-the art techniques and tools such as fluorescence in situ hybridisation, PCR and sequencing, complemented by bioinformatic analyses.
  • You will write a scientific report of the synthesis of your own results in the format of a scientific article and learn how to critically read and discuss scientific literature (performed in teams of two).
  • You will present your results and analyses and discuss them with the lecturers and your peers (performed in teams 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, e.g., the air we breathe and the water we drink. The lectures present many key themes in microbial ecology and focus on the multidisciplinary approach of this field of research. You will prepare for these lectures in self-study and collaborative group work assignments.
Practicals: Laboratory classes, in which you work together with a partner, generally take place in the afternoon, with lectures and collaborative learning activities in the morning. 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 visualisation of these by fluorescence in situ hybridisation 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 methods 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. Activated sludge (biomass) from two different treatment steps - anaerobic digestion (granular sludge) and nitrogen removal (flocculent) - will be used.
In this course we will perform three 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 hybridisation (FISH) microscopy. 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. Additionally, you will present your results to your peers in a small research seminar at the end of the course.

Instructional modes
  • Lectures
  • Presentation
  • Tutorials
  • Self-study
  • Group assignments
To be best prepared for this course you should have followed the B1 and B2 Microbiology courses:

- Microbiology (NWI-BP033)
- Microbial Metabolism (NWI-BB090)
- Physiology of Microorganisms (NWI-BB024B)

and optimally also
- Genomics for Health and Environment (NWI-BB086)

Please contact the course coordinator in advance if you do not meet these criteria.
  • exam, counts for 60%, minimum grade 5.5
  • practical, counts for 40%, minimum grade 5.5
    • this practical grade is composed of the performance and attitude during the practicum (30%), presentation (10%) and report (60%)
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 final mark is composed of the exam (60%), performance during the practical, presentation and the report (40%). The course will be given on Mondays and Tuesdays in the third quarter. You will need to use a lab coat and safety glasses. The practical manual will be provided online on Brightspace only, thus bringing a laptop or tablet is advisable.
Verplicht materiaal
Titel:Brock Biology of Microorganisms
Auteur:Michael T. Madigan, Kelly S. Bender, Daniel H. Buckley, W. Matthew Sattley and David A. Stahl




Sustainability certificate

GelegenhedenBlok KW3, Blok KW4

Lab, Presentation, Report
GelegenhedenBlok KW3, Blok KW4

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