Advanced Microbiology

Objectives

Microbes play a central role in global environmental processes and earth biogeochemistry. The purpose of this course is to provide students with a deeper knowledge of microbes and their processes in either natural ecosystems or in laboratory-scale systems.

Learning objectives

• To explain the impact and the importance of microbial activity on Earth.
• To highlight the connection between metabolic processes of microorganisms and the benefits of biotechnology.
• To show an improvement in students skills when working in a microbiology laboratory using either traditional or modern molecular techniques.
• To demonstrate an improvement in team-working skills through lectures and studying cutting edge microbiology.

Learning outcomes

• Describe how microorganisms interact with the environment and specifically with other organisms.
• Determine the chemotherapeutical alternatives against different microorganisms.
• Apply different molecular techniques to identify microorganisms in mixed populations.
• Prepare an English oral presentation to revise content
• Write a synthetic review on a scientific issue in English.
• Use appropriate spoken language (verbal and non-verbal) to communicate in personal and professional situations in English.

Competencies

General skills

• Combine scientific knowledge with technical skills and technological resources to deal with problems in professional practice.

Specific skills

• Interpret results obtained in biotechnology laboratories on the basis of correct application of laboratory protocols and basic techniques, making appropriate use of suitable instruments, with due regard for established safety standards.
• Know about subcellular structure and the cell types of organisms, and understand the processes of functional integration in organisms.
• Understand the different levels of organisation of organisms and have overall knowledge of the different systematic groups.
• Use the molecular, cellular and physiological basis of organisms, including relationships with other organisms or agents, to design biotechnological products.

Basic skills

• Students have demonstrated knowledge and understanding in a field of study that builds on general secondary education with the support of advanced textbooks and knowledge of the latest advances in this field of study.
• Students have the ability to gather and interpret relevant data (usually within their field of study) in order to make judgements that include reflection on relevant social, scientific and ethical issues.

Core skills

• Interact in international and worldwide contexts to identify needs and and new contexts for knowledge transfer to current and emerging fields of professional development, with the ability to adapt to and independently manage professional and research processes.
• Use oral, written and audiovisual forms of communication, in one's own language and in foreign languages, with a high standard of use, form and content.

Content

Theoretical content

1. Methods in microbial ecology
2. Microbial diversity (soil, aquatic and biogeochemical cycles)
3. Biotechnology: History, microbes, definitions and core concepts
4. Microbial diversity in Biotechnology
5. Environmental Microbiology
6. Search for microbes with industrial interest
7. Antimicrobial products
8. Amino-acid biotechnological production
9. Enzyme biotechnological production
10. Environmental biotechnology and agriculture
11. Microbial biosensors
12. Clinical microbiology

Practical laboratory content

1. Microbes from soil with industrial interest
   • Isolation of Actinomyces and Bacillus species
   • Detection of enzymatic activitites of industrial interest from seleted microbial isolates
   • Detection of antimicrobial activities from selected microbial isolates
2. Ecological aspects of skin microbiome
   • Identification of Staphylococcus species
   • Study of the amensalistic effect of S. epidermidis on S. aureus biofilms
   • Detection of different genes of staphylococcus species

Evaluation

The subject will be assessed in a continuous form (theory exam 40% + quizzes 10% + seminars 20% + practical lessons [exam 20% + report 10%]) based on:

• Theoretical lectures (40% of final grade): 2 written tests (first test, units 1-5 and second test units 6-10) weighted score (50% each). If less than 4/10 is scored, you must retake this part. Tests will be based on short responses or multiple-choice questions. At the end of each unit, students will self-evaluate themselves by doing a short test, with a final weight of 10% (a minimum of 10 tests must be passed out of a total of 13).
• Quizzes (10% of final grade)
• Seminars (20% of final grade): oral presentations of hot scientific topics (one microbial ecology topic [units 1-5] and one microbial action and antimicrobial activity units [units 6-10]). Minimum pass grade: 5/10
• Practical lessons (30% of final grade): final exam (10%), multiple-choice test at the end of the semester and a final report (20%) conducted and presented 2 weeks after finishing the practical week.

To pass the subject, students must pass each section with at least a 4/10. Students who do not pass all the sections can retake those, if applicable at the end of the course. Students who participate in less than 50% of the activities cannot be assessed.

General assessment criteria

• The possession of mobile phones or similar (smartphones, tablets, etc.) while conducting the tests involves a zero in the test.
• The non-show or not fulfilling deadlines in an evaluation activity gives a zero. This qualification will be taken into account when calculating the final grade for the course.
• The final grade is the result of the weighting of the marks obtained for each of the sections.
• Students who do not pass all of the activities can resubmit those applicable during the reassessment period. Reassessment takes places during the last two weeks of the semester and cannot exceed 50 % of the final course grade.
• If a student refuses to undertake required reassessment tests, the marks obtained in the previous tests for the particular items evaluated will be kept.
• For activities that may not be taken there is no minimum mark required to calculate the final grade for the course.
• Only when there is no evidence of any submitted activities will the course be graded as "not presented".
• Subject can only be passed if practical section is passed with a quote equal or higher than 5 points.
• Final average quote for all items must be equal or higher than 5 to pass subject.

Methodology

The learning process will combine lectures, microbiology laboratory sessions and class sessions.

• Self-study activities, activities to facilitate autonomous work will be offered to the students
• Scheduled tutorial sessions will be at sutdents' disposal
• Scientific articles are used to support the class sessions
• During practical lessons, various analytical tools are used to solve problems. Students must present a short report at the end of the session.

Bibliography

Key references

• Cann, A.J. (2005). Principles of Molecular Virology (4 ed.). Academic Press.
• Madigan, M.T., Bender, K.S., Buckley, D.H., Sattley, W.M., Stahl, D.A. (2018). Thumbnail Brock Biology of microorganisms (15 ed.). Pearson.
• Paul, E. (2014). Soil Microbiology, Ecology and Biochemistry (4 ed.). Elsevier.
• Paul, E.A. (2007). Soil microbiology, ecology and biochemistry. Retrieved from https://login.biblioremot.uvic.cat/login?qurl=http%3a%2f%2fbiblioremot.uvic.cat%2flogin%3furl%3dhttps%3a%2f%2fwww.sciencedirect.com%2fscience%2fbook%2
• Prescott, L.M., Harley, J.P., Klein, D.A. (2005). Microbiology (6 ed.). McGraw-Hill.

Further reading

Teachers will provide complementary bibliography and compulsory reading throughout the course via the Virtual Campus.