Microbial ecology

Course goals

Learning goals
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:

• 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

Skills

• 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.

 

Skills	Part of the course?	Explicitely examined?
Writing	X	X
Presenting	X	X
Data handling	X
Practical research skills	X
General research skills	X	X
Co-operation	X	X
Critical thinking	X	X
Career orientation	X
Interdisciplinarity	X	X

 

Content

Entry requirements
The course Microbial Ecology does not have any standardized prerequisite courses. However, it is suggested that students should have understanding of statistics (Voortgezette statistiek en R) have taken several previous ecology and/or microbiology level 1 and 2 courses. 

Study Path
The course is part of two study interest paths: Ecologie en Natuurbeheer en Microbiologie.

Introduction
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. Although this year’s course will necessary not involve experimental laboratory activities, we still seek to provide you insights into practical aspects of microbial ecological research. As such, you will carry out an experiment at home, design and analyze a virtual experiment and carry out bioinformatics analyses involving large datasets of microbial diversity and function as related to modern high-throughput DNA sequencing approaches. We thus seek to combine theoretical and practical aspects in the rapidly emerging field of microbial ecology. 
Due to the heavy reliance on primary literature and input from guest lecturers, the course will be given in English.

Content
The course is designed to cover the full spectrum of microbial ecology. Lectures and associated (virtual) lab practical sessions 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,
• Bioremediation,
• Microbial ecology of the N-cycle,
• Microbial ecology of the S-cycle,
• Human microbiology and the human microbiome,
• Microbial genomics,
• Metagenomics,
• Fungal ecology and bacteria-fungal interactions,
• Ecology and Evolution of microbial symbioses,
• Microbial biotechnology,
• The ecology of protists,
• Viral ecology.

Work formats
The course is comprised of a combination of lectures, laboratory activities, interactive group work, data analysis tutorials and assignments. Lectures also include guest lectures from experts in specific hot topics in microbial ecology. One dedicated session is devoted to computer practical work to familiarize students with the handling and analysis of high throughput DNA sequencing data. Students are responsible for a number of individual as well as group assignments. Group assignments include literature presentations and a poster presentation based upon experimental data and group experimental report. The course has a strong focus on the scientific method and several forms of scientific communication, and students also learn about the peer review process during a manuscript review workshop.


Grading
To pass this course, a minimum of 5,5 is mandatory. In order to pass the course, you must have a minimum grade of a 5,0 on the final exam. Your grade is calculated by the following components:

• Mini-Test on biogeochemical cycles:                                      10%
• Final exam:                                                                      35%
• Show-and-tell on at-home Winogradsky column experiment:       10%
• Group Poster:                                                                   10%
• Personal poster presentation:                                               10%
• Phyllosphere experiment report:                                           15%
• Course workbook and participation:                                       10%

The theoretical components of the course will be tested in one small test after the first two weeks of the course, as well as a final exam at the end of the course. Students will conduct two simple laboratory experiments, one related to patterns of microbial diversity and one community self-assembly as driven by biogeochemical cycles. The first experiment is combined with the bioinformatic analyses, with results being presented as a group report. The second experiment is discussed at the end of the course and graded based upon the quality of the related discussion. All students must participate in a peer review workshop, and the resulting group review report is graded on a pass/fail basis. Student groups also have the opportunity to design their own microbial interactions experiment for which data is generated based upon the experimental design presented. These data are used to generate scientific posters for a course poster session. Posters are judged at the group level, while each student is graded individually on their presentation of the poster. Students will also be responsible to submitting workbook exercises including peer review of other student presentations. In order to pass the course, students must participate in all mandatory events and submit all assignments. There will be one opportunity for a retake of the final exam if necessary.

Materials 
Mandatory:

• Reader with overview of course, lab protocols, instructions for assignments, syllabus.
• Primary and review articles will be provided as background materials to the lectures
• Lab coat.