Course manual 2024/2025

Course content

1. Global content

Theory

Although microorganisms are invisible to the naked eye, their role in nature and the economic world is immense. Not only are they important because their total mass on Earth far exceeds that of all higher eukaryotes combined, but they also display many unique physiological traits that have not been detected in eukaryotes and have an enormous impact on the physical state of our planet. Additionally, microorganisms significantly impact the health and disease of plants and animals, including humans. Finally, they are crucial for processing many different types of food and production in biotech and biopharmaceutical industries. The vast diversity in structure, physiology, cellular differentiation, underlying molecular regulatory mechanisms, and their capacity to grow fast and adapt to the most extreme environmental conditions will be addressed in the lectures.

Due to their many unique capabilities, such as extracting energy for growth from organic resources, minerals, and light, microorganisms play an important role globally, from the deep oceans to freshwater environments, from snow on mountains to tropical forest soils, and from growth-supporting plant and intestinal microbiomes to the production of foods like beer, bread, and yoghurt, life-saving antibiotics, and many biopharmaceuticals. They also play crucial roles in many diseases and are responsible for the global antimicrobial resistance problem. In this course, the diversity of molecular mechanisms that underlie the enormous capacity and impact of bacteria will be illustrated by discussing (i) the role of different heterotrophic microorganisms in soil essential for carbon cycling, (ii) the role of nitrogen-fixing cyanobacteria in the oceans, (iii) examples of food processing in industrial biotechnology and mineral extraction in mining, (iv) the conserved regulatory mechanisms that support the cellular differentiations underlying many of these and other processes, such as disease, and (v) the modern molecular biology and next-generation sequencing tools used to investigate these mechanisms.

Practical

Working with microorganisms requires specific abilities to work safely while preventing unwanted contamination. Acquiring these abilities is incorporated into the practical work of two small research projects each student will carry out, one in an IBED laboratory and one in a SILS laboratory. Various projects will be offered, from aquatic microbiology, microbial ecology, molecular microbiology, and microbial physiology. The projects will be carried out by 2 to 4 students and will be supervised by PhD students, postdocs, and technicians of the two institutes. Participants will learn how contemporary knowledge about microorganisms is translated into fundamental research questions and gather hands-on experience. The students will present the results of these practicals to peers and instructors in a mini-symposium.

2. Intended learning outcomes.

After finishing the course, students will be able to:

Explain the functional structure of Prokaryotes (i.e., the structure of cell wall, cell envelope, nucleoid, storage granules, pili and flagella, etc.).
Explain the growth kinetics of microorganisms and their physiology and mechanisms of physiological adaptation.
Describe the metabolic diversity within the microbial world.
Explain the unique properties of prokaryotic genomes and the molecular genetics and regulation of gene expression in this class of organisms.
Describe the key structural differences between Bacteria, Archaea and Eukarya.
Explain the role of microorganisms in the global cycles of elements (like the carbon cycle), the food web and selected ecosystems.
Formulate fundamental questions for microbial research about the translation of microorganisms' (molecular) properties and their biotic and abiotic environment.
To provide examples that illustrate microbiology's societal and economic role and current interests in microbial research.
Understand modern molecular biology and next-generation sequence tools.

3. Teaching methods.

Staff members of SILS-MMP (Molecular Microbial Physiology) and IBED-FAME (Freshwater and Marine Ecology) will give the lectures and the seminars ('werkcolleges'). Teaching is based on the book Brock Biology of Microorganisms (15th edition), Madigan, Martinko, Bender, Buckley and Stahl eds. Global Edition, Pearson.

The course contains three parts.

Part 1 contains daily lectures followed by a written exam.
Part 2 is a seminar given by PhD students, postdocs, or staff members of SILS and IBED.
Part 3 contains two short practical projects, which are finished with presentations.

4. Attendance

Attendance to the lectures is highly recommended as absence frequently coincides with failure in the written exam. Attendance to the seminars and the practical projects is mandatory as written in the general Teaching and Examination Regulations. (OER Deel B, Artikel 4.8).

5. Assignments

In the practical, assistants will assign a research question to a team of two to four students and discuss how to deal with it in laboratory practice. The students will plan, organize the materials, do the experiments (usually based on written protocols), collect results, and analyse and visualise the data. The students must take the so-called empirical cycle into account. The results of each project will be presented in a short PowerPoint presentation to peers and lecturers.

6. Course materials

PowerPoint slides of the lecturers. Canvas serves for the exchange of details about these materials and other aspects of the course.

7. Timetable and course structure.

The up-to-date timetable can be found in DataNose. A more detailed schedule will be provided via Canvas.

In the schedule below, you will find the relation between the amount of ECTS and the study load.

Lectures	20 hours
Seminar	8 hours
Practical projects	80 hours
Exam	4 hours
Presentations	8 hours
Self-study	48 hours
Total ECS 6 x 28	168 hours

8. Assessment and inspection of assessed work.

A student has passed the course when the weighted final grade is 5.5 or above, both for the exam and the practical.

Knowledge about the contents of the lectures will be tested in a written exam, which consists of 40 multiple-choice questions and four open questions. Marking of the practical will be based on practical skills, overview, and data handling (grading by the assistant), and half on the oral presentation (grading by all assistants and lecturers that come to listen).

Component	Deadline	Weight %	Minimum grade	Compensation	Resit (grade doesn’t expire, expires, resit is possible) *
Written Exam	09/11/23	50%	5.5	No
Practical 1	17/11/23	25%	5.5	No
Practical 2	24/11/23	25%	5.5	No

* Grades for interim components are valid until the end of the academic year.

For at least twenty working days after the announcement of the results of a written examination, the student can, on request, inspect his/her assessed work, the questions and assignments set, as well as the standards applied for marking. The place and time will be announced via Blackboard (from the Teaching and Examination Regulations).

9. Fraud and plagiarism

This course uses the rules and regulations on fraud and plagiarism control of the University of Amsterdam. Plagiarism or fraud means copying another student's work or scientific sources (for example, from books, magazines, and the Internet) without mentioning the source. Obviously, plagiarism is prohibited. It is carefully monitored and strictly acted upon. Upon suspicion of plagiarism, it will be mentioned at the Examinations Board. When the Examinations Board is confident that there has been plagiarism, then this can lead to a maximum exclusion of all education for an entire calendar year. For more information on fraud and plagiarism rules of the University of Amsterdam, see www.uva.nl/plagiarism.

10. Application and further information

Course registration is via the web form. Information on the registration procedure will be emailed to the students concerned.

Number of participants

A maximum of 24 students

11. Contact

Coordinator/Lecturer	Bacterial Cell Biology / SILS
Name	Prof. dr. Leendert Hamoen
Address: Science Park 904	Room C3.111
E-mail	L.W.Hamoen@uva.nl

Lecturer	Freshwater and Marine Ecology / IBED
Name	Prof. Dr. Gerard Muijzer
E-mail	g.muijzer@uva.nl

Lecturer	Bacterial Cell Biology / SILS
Name	dr. Gaurav Dugar
E-mail	G.Dugar@uva.nl

Lecturer	Freshwater and Marine Ecology / IBED
Name	dr. Merijn Schuurmans (Merijn)
Email	j.m.schuurmans@uva.nl

Lecturer	Microbiome Engineering / SILS
Name	Prof. Dr. Sahar El Aidy
E-mail	s.elaidy@uva.nl

Study materials

Practical training material

Will be handed out

Other

Powerpoints, key concepts and terms, videos

Objectives

Gaining knowledge about the functional structure of Prokaryotes (i.e., structure of cell wall, cell envelope, nucleoid, storage granules, structure of pili and flagella, etc,).
Becoming acquainted with the growth kinetics of bacteria and their physiology and mechanisms of physiological adaptation.
Gaining insight into the metabolic diversity within the microbial world.
Gaining knowledge about the unique properties of prokaryotic genomes and the molecular genetics and regulation of gene expression in this class of organisms.
Gaining knowledge about the key structural differences between Bacteria, Archaea and Eukarya.
Acquiring insight into the role of microorganisms in the global cycles of elements (like the carbon cycle), the food web and selected ecosystems.
To become acquainted with the translation of the (molecular) properties of microorganisms and their biotic and a-biotic environment can be translated in fundamental questions for microbial research.
To become informed about the societal and economic role of microbiology and current interests in microbial research.
Gaining knowledge on various techniques that are commonly used to study bacteria

Teaching methods

Lecture
Computer lab session/practical training
Presentation/symposium
Self-study
Seminar

Learning activities

Activity	Hours
Practicum	80
Presentatie	8
Tentamen	4
Lectures and seminar	28
Self-study	48
Total	168	(6 EC x 28 uur)

Attendance

Programme's requirements concerning attendance (OER-B):

Participation in all practical (computer) sessions, field work and seminars in the curriculum is in principle obligatory. Any additional requirements are described per section in the course manual. Also the possible consequences of not fulfilling this obligation are described.

Additional requirements for this course:

If you cannot attend a tutorial or practicum, please inform the coordinator T.denBlaauwen@uva.nl or the practicum coordinator J.M.Schuurmans@uva.nl, respectively. If the lecture is live, please do a Corona self test every morning before you leave and if in doubt, do not attend. All lectures are recorded and will be made available on canvas.

Assessment

Item and weight	Details
Final grade
1 (100%) Tentamen

Knowledge about the contents of the lectures will be tested in a written exam and a minimum score of 5.5 should be acquired. The two practicals are obligatory and contribute each 25 % to the final grade, and each of them should be passed. Marking of the practical will be based on practical skills, overview and data handling (grading by the assistant), and half on the oral presentation (grading by all assistants and lecturers that come to listen).

Inspection of assessed work

A model for the content of the exam answers that are required will be available after the exam.

Assignments

The practical course will be in a small group depending on the total number of students and each member of the group will participate in the presentation of the practical work.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

College rooster power of microbes 2024
datum	tijd	docent	topic

Owner	Bachelor Biologie
Coordinator	prof. dr. L.W. Hamoen
Part of	Exchange Programme Faculty of Science, specialisation BSc Biology, year 1 Bachelor Biology, year 3 Bachelor Bèta-gamma, major Biologie, year 3
Links	Visible Learning Trajectories

The Power of Microbes