METHODS FOR ANALYSIS OF ENVIRONMENTAL MICROBIAL COMMUNITIES
Course contents summary
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 .
Structure of a microbial community - biodiversity indices of microbial communities. Traditional methods of analysis based on pure culture cultivation: isolation and identification of microbial species by biochemical and serological methods.
Molecular methods applied to microorganisms isolated in pure culture: PCR, analysis by agarose gel electrophoresis, real-time PCR, cloning, sequencing, RAPD analysis, rep-PCR, ARDRA, RISA, ARISA.
Application of molecular techniques to the study of microbial communities, without cultivation of microorganisms: isolation of environmental DNA, genetic fingerprinting techniques ARDRA, SSCP, T-RFLP, DGGE, RISA, LH-PCR, RAPD. High throughput sequencing techniques and their application to the study of microbial communities. DNA / RNA Stable isotope probing. Fluorescent in situ hybridization (FISH CARD-FISH, Raman-FISH, NanoSIMS). Microarray
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.). In silico analysis of DNA sequences, researches in databases etc will be performed in class while, in the laboratory, will be illustrated some of the most common molecular techniques (DNA extraction, PCR, digestion with restriction enzymes, electrophoresis on agarose gel).
Assessment methods and criteria
The student (attending student) will be asked to choose an article that analyzes microbial communities in a given context (eg the effect of reclamation practices and their impact on the microbial communities of a contaminated site). He will have to read the article, elaborate a presentation to illustrate the work to the teacher and other students and discuss it in class with them. It is part of the examination (and will be evaluated) also the active participation in the discussion of the presentations of other colleagues.
Upon completion of the exam, the teacher will ask a question concerning one of the subjects discussed during the course. The exam will check the student's level of competence and his autonomy of judgment. For non attending students the exam will be oral on the subjects developed by teacher in class