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Microbial Ecology
Code: 40346
ECTS: 5.0
Lecturers in charge: doc. dr. sc. Sunčica Bosak - Lectures
Lecturers: Klara Filek - Practicum
Take exam: Studomat
English level:

1,0,0

All teaching activities will be held in Croatian. However, foreign students in mixed groups will have the opportunity to attend additional office hours with the lecturer and teaching assistants in English to help master the course materials. Additionally, the lecturer will refer foreign students to the corresponding literature in English, as well as give them the possibility of taking the associated exams in English.
Load:

1. komponenta

Lecture typeTotal
Lectures 30
Practicum 30
* Load is given in academic hour (1 academic hour = 45 minutes)
Description:
LEARNING OUTCOMES
1. Compare classical microbiological direct methods with novel molecular techniques of identification and estimation of abundances of the microorganisms from the natural environment.
2. Explain the role of microorganisms in global biogeochemical cycles of elements and food webs
3. Discuss diverse physiological and ecological adaptations of microorganisms to extreme environmental conditions
4. Apply enrichment culture methods for the isolation of bacteria from the environmental samples to the isolation of nitrogen-fixing, ammonifying, nitrifying and denitrifying bacteria
5. Distinguish different types of metabolism present in microorganisms in the Winogradky column
6. Apply correct way of citation of the scientific literature and web content in the student seminar presentations and summaries
7. Compose short summary of the scientific article from the microbial ecology indentifyying the most important and basic elements of the scientific report

COURSE CONTENT
Course aims:
This class provides a general introduction to the diversity and ecological roles of microorganisms (bacteria, archaea and eukaryotes) in natural and artificial environments.

LECTURES
1. Introduction: scope, syllabus, requirements, historical overview of the research in the field of microbial ecology; general classification of microorganisms,; instructions how to do a quality search of scientific literature and web content
2. General features of microbes (cell structure, cell wall, cell chemical composition), identification and taxonomy, quantitative methods in microbial ecology: epifluorescent microscopy and flow cytometry
3. Molecular methods of identification in microbial ecology (16s RNA, PCR, DNA fingerprinting techniques, FISH)
4. Metagenomics and taxonomy; overview of large scale metagenomical projects (human microbiome, Sargasso Sea, Global Ocean Survey)
5. Metabolic diversity of microorganisms. Biogeochemical cycles: nitrogen, phosphorous, iron
6. Biogeochemical cycles: sulfur
7. Biogeochemical cycle of carbon. Origin and role of dissolved and suspended organic matter in the water (marine environment). Microbial activity in organic aggregates in teh sea. MIcrobial food web, microbial loop.
8. Applied microbiology: biofuels, bioremediation, sanitary analysis of water, water treatment. Food microbiology: lactic fermentation, alcohol fermentation, microbiology of chocolate
9. Ecological microbial interactions (intraspecific and intespecific): predation, bacterial communication (quorum sensing), biofilms, symbioses.
10. Influence of ecological factors on growth and physiological activity of microbial communities. Extremophiles I: psychrophiles, barophiles
11. Extremophiles II: termophiles, acidophyles, poliextremophiles: Deinococcus radiodurans, microorganisms in space

PRACTICAL PART
Laboratory exercises are following course content according to the lectures
1. Quantitative methods in microbial ecology, sampling, preparation and sample analysis. Direct methods of microbial cell counting with the light microscope, filtration procedures
2. The basics of molecular methods of bacterial identification (DNA extraction, PCR, electrophoresis, sequencing, FISH) using Bacterial identification Virtual lab.
3. Nitrogen cycle I: isolation of nitrogen-fixing microorganisms
4. Nitrogen cycle II: amonification, nitrification, denitrification. Nitrogen cycle in vitro (processing environmental sample, determination of the reactants in specific reactions)
5. Nitrogen cycle III: results check of exercises 3 and 4; negative staining of capsules of nitrogen fixing bacteria, determination of the products in specific reactions
6. Organic matter and microorganisms in aquatic environments, microscopical analysis of live samples and identification of specific microbial groups in microbial loop, staining of transparent exopolimeric substances in marine sample with Alcian Blue.
7. Jogurt production from different starter cultures using various media; microscopical analysis of lactic acid bacteria and yeasts from food supplies
8. Analysis of the Winogradsky column - examination of the representatives of different metabolic types considering source of carbon, energy and electrons and their interrelationships.
Literature:
  1. Marine Microbial Diversity and its role in Ecosystem Functioning and Environmental Change Marine Board-ESF Position Paper 17 dostupno na http://www.marineboard.eu/publications/
    Prezentacije s predavanja, poveznice na razne videomaterijale dostupne unutra prezentacija.
    Originalni i pregledni znastveni članci odgovarajuće tematike.
  2. Šolić, M., Krstulović, N., 2000: Ekologija morskog bakterioplanktona. Institut za oceanografiju i ribarstvo, Split.
    Šolić, M., Krstulović, N., 2006: Mikrobiologija mora. Institut za oceanografiju i ribarstvo, Split.
    Kirchman, D.L., 2000: Microbial ecology of the oceans. Wiley-Liss, New York.
    Munn, C.B., 2004: Marine microbiology. Ecology and applications. BIOS Scientific Publishers, London
    Viličić, D., 2003: Fitoplankton u ekološkom sustavu mora. Školska knjiga, Zagreb.
3. semester
Izborni predmeti - Mandatory studij - Biology
Izborni predmeti - Mandatory studij - Molecular Biology
Consultations schedule: