The main goals of the course are to develop an appreciation and understanding of the functional diversity and ecology of microorganisms and to learn the approaches used to unlock the secrets of the microbial world.
The main goals of the course are as follows:
Skills to be developed
- Gain knowledge of the microbial processes driving the major biogeochemical cycles
- Develop an understanding of the evolutionary forces that have driven microbial innovation
- Learn the principles of both classical as well as modern molecular and genomics approaches used in studying the diversity and functioning of microbial communities
- Critical analysis of manuscripts in microbial ecology
- Combining ecological theory and practice in microbial ecology
- Basic understanding of how to deal with large phylogenetic and metagenomic datasets
- Ability to design experiments in microbial ecology
- Data/statistical analysis capabilities
- Scientific writing and presentation skills
The course is part of two study paths: Ecologie en Natuurbeheer en Microbiologie.
We live on a microbial planet!
The fate of the planet has been interlinked with microbial diversity and evolution. Microbial activities are responsible for many of Earth’s ecosystem processes and drive the planet’s biogeochemical cycles. Whether in the ocean or soil, or in and on our own bodies, microbes are vast in their numbers and amazing in their diversity.
This course seeks to introduce you to our fascinating microbial world. We will explore the evolution and ecology of microbial organisms across a wide range of habitats and niches. We examine numerous forms of microbial interactions, including both interactions between microbes as well as between microbes and larger organisms. We will examine both highly fundamental principles in microbial ecology and biogeography as well as more applied and biotechnological issues that seek to harness the power of the small.
Microbial ecology is a young and dynamic field, with an extremely rapid pace of discovery over the past decades. We will also focus on the rapidly evolving microbial toolbox, which is providing unprecedented windows of observation into the diversity and functioning for microbial organisms across diverse habitats. With a number of laboratory activities and a microbial bioinformatics block, we seek to combine theoretical and practical aspects in the rapidly emerging field of microbial ecology.
Due to the heavy reliance on primary literature, the course will be given in English.
The course is designed to cover the full spectrum of microbial ecology. Lectures and associated lab practical session will therefore focus on general issues in microbial ecology as well as specific microbial groups and microbe-driven processes. Specific topics that will be covered include:
- The history of microbial ecology
- Patterns of microbial diversity and diversity/function relationships
- Linking microbial identity with function
- Microbiology of the soil and the rhizosphere
- Plant disease and plant disease protection
- Microbial ecology of the C-cycle
- Decomposition of recalcitrant organic matter
- Microbial ecology of the N-cycle
- Microbial ecology of the S-cycle
- Microbial diversity of aquatic habitats
- Microbial diversity of extreme habitats
- Human microbiology and the human microbiome
- Microbial genomics
- Fungal ecology and bacteria-fungal interactions
- Ecology and Evolution of microbial symbioses
- Microbial biotechnology
- Microbes in trophic interactions and food webs
The course is comprised of a combination of lectures and laboratory activities. Most course days are half theoretical and half practical. A number of experiments will be conducted during the course, which will be analyzed at different times throughout the course. One week will also be devoted to a computer practical designed to teach about handling and analyzing high throughput DNA sequencing data. The course will also contain a number of guest lectures from experts in specific hot topics in microbial ecology.
The theoretical components of the course will be tested in a final exam.
The experimental portions of the course will be judged based upon participation and laboratory write-ups and presentations. There will also be a critical manuscript review assignment.
The computer practical section of the course will have a separate project.
The final grade will be built up as follows:
There will be one opportunity for a retake of the final exam if necessary (to be held one week after the final exam).
- final exam (35%)
- laboratory participation, reports and presentations (45%)
- manuscript review assignment (10%).
- Computer practical (10%, groepscijfer).