6 EC
Semester 1, period 1
5224MIEC6Y
1. Global content
The vast majority of life on this planet is microbial. Microorganisms are enormous in numbers, biomass and diversity, and Earth's evolution is tightly linked to microbial evolution and activities. We are also increasingly aware of the importance of microbial ecology in practical issues of society and the environment, from human health, nutrition and energy supply to understanding and predicting climate change.
However, our knowledge of microbial diversity and activities is still limited, mainly due to the difficulties of studying microbes (because of their small size and difficulty in isolating and cultivating them in the laboratory). Fortunately, recent breakthroughs in applying methods from molecular biology and genomics (including transcriptomics, proteomics and metabolomics) are now beginning to provide better ways to study the diversity and activities of microbes in their environment.
The course will first provide a brief history of microbial ecology and outline the general characteristics of microbes and microbial communities and their role in the cycling of chemical elements. It will then proceed to highlight the most important methodological approaches that have been essential to recent advances in microbial ecology. These highlights will pay special attention to the rapidly increasing influence of high-throughput sequencing technologies. Subsequently, several essential examples will be presented regarding the role of microbial ecology in key environmental issues, including the effects of global climate change, pollution and other anthropogenic pressures on ecosystems.
The course nicely complements other courses on macro-ecology and evolution in the Master Programme Biological Sciences, such as Current Trends in Evolution and Environmental Genomics and Adaptation. Furthermore, it gives a solid basis for performing research projects within the Department of Freshwater and Marine Ecology (FAME).
The prerequisite for participation in the course is a BSc. - degree in Biology or equivalent. Knowledge of microbiology and/or ecology is required. Basic knowledge of molecular biology and biochemistry is strongly recommended.
2. Intended learning outcomes
By the time the course is completed, the student should be able to:
3. Teaching methods
The course starts with a series of lectures on different topics in microbial ecology. Subsequently, groups of 3 students will choose a subject related to a topic in microbial ecology, look up relevant literature, summarize it, and present it as a short, 3-minute movie. Moreover, the students will visit Micropia - Science Museum Amsterdam and have a practical in which they create their own Winogradsky column and analyse existing columns by microscopy and 16S rRNA analysis. The latter will be done by sequence analysis on a Nanopore MinION device.
4. Attendance
Lecture attendance is highly recommended, mainly because the subject matter will be questioned during the exam. Attendance at the excursion and practical is mandatory (from the Teaching and Examination Regulations). The students will do the literature study during the seminars and as a self-study.
5. Assignments
The assignment is a literature study of a topic related to the course. For this purpose, relevant literature will be reviewed, summarized and presented as a 3-minute movie.
6. Course materials
Handouts of the lectures will be placed on Canvas. The course material for the literature study consists of articles that can be obtained from different scientific journals via the University Library. In addition, the textbook 'Brock-Biology of Microorganisms' (15th edition) is recommended as supplementary material. We will hand out protocols for the practical.
7. Timetable and course structure
[Copy the link to the timetable in DataNose. Mention the study load for the contact hours and self-study. 1 EC is 28 hours of study.]
|
Lectures (hoor-colleges) |
36 hours |
|
Seminars (werk-colleges) |
16 hours |
|
Practical training (excursion and practical) |
20 hours |
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Self-study, including the Literature study |
92 hours |
|
Exam |
4 hours |
8. Assessment and inspection of assessed work
The information taught in the lectures will be assessed in a written exam of open questions. The course instructors and students will evaluate the literature study, i.e., the movie. The movie will be evaluated on four criteria: (1) scientific content, (2) originality, (3) use of image and sound, and (4) overall impression. Scientific content is essential and will be weighted extra (see Rubric). The final mark for the course is the mean of the marks for the exam (70%) and the literature study (30%) (see table below). The excursion and practical will not be assessed but are mandatory.
|
Component |
Deadline |
Weight % |
Minimum grade |
Compensation |
Resit (grade doesn’t expire, expires, resit is possible) * |
|
Final exam |
18/10/2023 |
70 |
5 |
|
Yes |
|
Resit written exam |
08/01/2024 |
70 |
5 |
|
n.a. |
|
|
|
|
|
|
|
|
Literature study |
27/10/2023 |
30 |
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 copying 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. It will be mentioned at the Board of Examiners upon suspicion of plagiarism. When the Board of Examiners is confident that there has been plagiarism, 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
The maximum number of applicants is 40. Admission to the course will depend on the total number of applications and the individual student's background.
If the number of applications exceeds the capacity of the course, students may be selected, and priority will be given in the following order:
First-year students of the Master’s program Freshwater and Marine Biology and Ecology and Evolution will be allowed to register for this course in September. The procedure will be announced in August-September. All other students: Registration for this course via https://www.sis.uva.nl at least four weeks before the start of the semester is mandatory.
This course uses the Canvas website. Here, you’ll find all the necessary additional information, such as grouping for seminars, information on the assignments, and additional literature. Therefore, check out the site regularly!
Evaluation to improve the course
You will receive a form to evaluate the course at the end of the course. In addition, we will have a session to discuss what is good and, more importantly, what can be improved. We always carefully listen to your comments and try to incorporate your wishes into the course for next year. So, please don’t forget to fill out the form and give your frank opinion on the course, which will result in a better course for future students.
11. Contact
|
Coordinator and lecturer |
Prof. Dr. Gerard Muijzer |
|
Address: |
Science Park 904, room C4.227 |
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Tel. no: |
+31-6-8161-8136 |
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E-mail: |
g.muijzer@uva.nl |
|
|
|
|
Lecturer |
Prof. dr. Linda Amaral |
|
E-mail: |
linda.amaral-zettler@nioz.nl |
We will hand-out protocols for the practical.
Hand-outs of the lectures will be placed on Canvas
The course starts with a series of lectures (hoor-colleges) on different topics in microbial ecology. Subsequently, groups of ca. four students will choose a subject related to one of the topics in the lectures, look up relevant literature, summarize this and present it as a short movie. The students will be mentored in this by the teachers during the seminars (werk-colleges). Moreover, the students will have a one-day excursion and a one-day practical in microbiology/microbial ecology.
Activity | Number of hours |
Excursie | 8 |
Hoorcollege | 36 |
Practicum | 8 |
Presentatie | 4 |
Tentamen | 4 |
Werkcollege | 16 |
Zelfstudie | 92 |
Requirements of the programme concerning attendance (OER-B):
Additional requirements for this course:
Attendance at lectures and the literature discussion is highly recommended. Attendance at the excursion and practical is mandatory (from Teaching and Examination Regulations). The literature study will be done by the students as a self-study.
| Item and weight | Details |
|
Final grade | |
|
1 (100%) Tentamen |
The manner of inspection will be communicated via the digitial learning environment.
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 Teaching and Examination Regulations).
literature study of a topic related to the course. For this purpose relevant literature will be looked-up, summarized and presented as a short, 3-5 minutes movie.
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
| Weeknummer | Onderwerpen | Studiestof |
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| 2 | ||
| 3 | ||
| 4 | ||
| 5 | ||
| 6 | ||
| 7 | ||
| 8 |
The schedule for this course is published on DataNose.
This course uses the Canvas website. Here, you’ll find all the necessary additional information, such as grouping for seminars, information on the assignments, additional literature. Therefore, check out the site regularly!