METHODS FOR ANALYSIS OF ENVIRONMENTAL MICROBIAL COMMUNITIES
Learning outcomes of the course unit
The course provides a multidisciplinary approach to the study of biodiversity and analysis of microbial communities. At the end of the course students will have basic knowledge relevant to the study of microbial ecosystems. In particular will know: - the main cultural and molecular techniques for the identification of micro-organisms, phylogenetic analysis methods, the principles of omics technologies applied the description of microbial communities as well as methods for the study of their functional activity .
Course contents summary
Method for microbial community description and analysis (classical and molecular)
Traditional methods of analysis of culturable microorganisms : Isolation and identification of microbial species, biochemical identification methods, serological techniques.
Molecular analysis of culturable microorganisms: PCR; Agarose gel electrophoresis; Real-time PCR; Cloning, Sequencing, RAPD, rep-PCR, ARDRA, RISA, ARISA etc
Application of molecular methods to the whole community without cultivation: DNA isolation from environment, methods of genetic fingerprinting: ARDRA, SSCP, T-RFLP, DGGE, RISA, LH-PCR, RAPD. The massive sequencing. DNA / RNA Stable isotope probing. Fluorescent in situ hybridization (FISH CARD-FISH, Raman-FISH, NanoSIMS).
Scientific literature, book's chapters available from the teacher
Lectures and class work (seminars, discussion of scientific articles on the different application of the described methods). The student will become familiar with the most recent methods of analysis of microbial communities in order to read critically scientific articles on the subject and to be able to evaluate, through these analyses, impacts on communities caused by external factors (pollution, climate change, different impacting human activities.)
Assessment methods and criteria
Oral examination in which the student must prove that he acquired knowledge about the different methods of analysis of microbial communities and how to apply. The student should also demonstrate the ability of critically reading an article on this subject