The Power of Microbes

Course manual 2021/2022

Course content

Although microorganisms are invisible to the naked eye, their role in nature and in economic life should not be underestimated. Not only are they important because their total mass on Earth by far exceeds that of all higher eukaryotes combined, they also display many unique physiological traits that have not been detected in eukaryotes and that have an enormous impact on the physical state of our planet. The huge diversity in structure, physiology and molecular regulatory mechanisms among them, and their capacity to grow very fast and to adapt to the most extreme environmental conditions, are topics that will be addressed in the lectures.   

Because of their many unique capabilities, such as extracting energy for growth not only from organic resources, but also from minerals and light, combined with a very high specific growth rate, micro-organisms play an important role around the globe, from the deep oceans to freshwater environments, up to the snow on mountains, from tropical forest soils, and intestinal rumen, to the production of daily foods, like beer, bread, yoghurt etc., not to forget about the role of bacteria in many diseases. This will be illustrated with the role of heterotrophic microorganisms in the soil that are essential for carbon cycling, and with the essential role of nitrogen-fixing cyanobacteria in the oceans, and examples of the processing of various food products in industrial biotechnology, and mineral extraction in mining. Although not in particular lectured in this course, pathogenic microorganisms cause a large range of diseases that ultimately can be fatal for plants, animals and/or mankind.

The lecturers will detail on: (i) the diversity of micro-organisms, (ii) their structural and functional properties, (iii) the mechanism of storage and regulated expression of genetic information typical for prokaryotes, and (iv) the role of microorganisms in global ecology and in society.

Practical

Working with micro-organisms requires specific abilities to work safely while preventing unwanted contamination. Acquiring these abilities is incorporated in the practical work of two small research projects that each student will carry out, one in an IBED laboratory and one in a SILS laboratory. A range of projects will be offered from the fields of 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 in the broad field of microbiology and will gather hands-on experience. The results of these practicals will be presented by the students to peers and instructors in a mini-symposium.

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 trhat are commonly used to study bacteria

Teaching methods

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

Learning activities

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

Knowledge about the contents of the lectures will be tested in a written exam and  a minimal score of 5.6 should be acquired. The two practicals are obligatory and contribute each 15 % to the final grade, and each of them should be passed. Marking of the practical will be based half on practical skills, overview and data handling (grading by assistant), and half on the oral presentation (grading by all assistants and lecturers that come to listen).

Due to Corona rules that are not yet clear at the time of publication, the exam can have a different format that fits a live version or a online version.

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 presentatyion 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

Timetable

The schedule for this course is published on DataNose.

Contact information

Coordinator

• dr. T. den Blaauwen

Staff

• dr. G. Dugar
• prof. dr. L.W. Hamoen
• prof. dr. Gerard Muijzer
• dr. J.M. Schuurmans