Course: Molecular methods in soil and aquatic ecology

« Back
Course title Molecular methods in soil and aquatic ecology
Course code KBE/017
Organizational form of instruction Lecture + Lesson
Level of course Bachelor
Year of study not specified
Frequency of the course In each academic year, in the winter semester.
Semester Winter
Number of ECTS credits 3
Language of instruction Czech, English
Status of course Compulsory-optional
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Lecturer(s)
  • Chroňáková Alica, RNDr. Ph.D.
  • Bárta Jiří, doc. Ing. Ph.D.
Course content
Content of lectures: 1. Introduction to aquatic microbial ecology 2. Introduction to soil microbial ecology 3. Genetic diversity, study of diversity, taxonomy based on 16S RDNA, definition of species 4. DNA/RNA approach in microbial ecology. Definition of population structure, quantity. Analyses of DNA vs. RNA. 5. DNA fingerprint methods (PCR-RFLP, ARISA, t-RFLP, DGGE/TGGE), cloning/sequenation, on-line databases 6. Principles of new sequencing methods, pyrosequencing (DNA tagging), metagenomics 7. Quantitative analyses. Principles of qPCR, relative and absolute quantification, inhibitory effects. Use of specific and nonspecific dyes and probes 8. DNA microarrays, taxonomic and functional DNA chips. 9. Detection of microorganisms with nonspecific dyes (DAPI, Picogreen) and fluorescently labeled oligonucleotide probes (FISH, CARD-FISH, FISH-MAR). Database Probase. 10. Principle of DNA-SIP, RNA-SIP, i.e. methods of studying ctive microbial populations and their functions Content of practicals: FISH, DNA, DGGE, qPCR

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), Laboratory
  • Preparation for exam - 20 hours per semester
  • Preparation for credit - 20 hours per semester
Learning outcomes
Objective of the curse will be to give a detailed information of new trends in soil and aquatic ecology. Lectures will unravel and discuss huge microbial diversity on our planet and introduce new molecular methods to help answers basic ecological questions.
Learn new methods of the study of microbial communities in terrestrial and aquatic ecosystems Learning methods of the laboratory cultivation of cells Genomics, single-cell gen genomics Methods of the direct cell microscopy using epifluorescent microscopy Metagenomic methods and bioinformatic tools for studying the diversity of microbial communities
Prerequisites
basic knowledge of genetics and molecular biology basic knowledge of work in laboratory
KMB/608

Assessment methods and criteria
Test

Mandatory subject KMB608
Recommended literature
  • de Bruijn. Handbook of Molecular Microbial Ecology, Vol. 1 + 2. 2011.
  • Nannipier & Smalla. Nucleic Acids and Proteins in Soil. 2006.
  • van Elsas, Jansson, Trevors. .Modern Soil Microbiology, 2. edice. 2007.


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Ecosystem Biology (1) Category: Ecology and environmental protection - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Ecosystem Biology (1) Category: Ecology and environmental protection - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Ecosystem Biology (1) Category: Ecology and environmental protection - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Hydrobiology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Winter