General Microbiology (2020/2021)



Course code
4S008408
Credits
9
Coordinator
Sandra Torriani
Academic sector
BIO/19 - MICROBIOLOGY
Language of instruction
Italian
Teaching is organised as follows:
Activity Credits Period Academic staff Timetable
teoria 6 I semestre Sandra Torriani

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laboratorio [1° turno] 3 I semestre Silvia Lampis, Giacomo Zapparoli

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laboratorio [2° turno] 3 I semestre Silvia Lampis, Giacomo Zapparoli

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Learning outcomes

Module: THEORETICAL LECTURES The course is designed to introduce students to the basic knowledge of the microbial world as well as to illustrate the main methodological tools for research in microbiology, with a detailed comparison of the properties among the different type of microorganisms, both prokaryotes and eukaryotes, including bacteria, archaea, yeasts, filamentous fungi, and - in a distinct section, since non-cellular organisms – the viruses. During the first series of lectures, general themes will be addressed such as morphological and functional diversity, genetic, biochemical and metabolic features, evolutionary aspects and ecology of microorganisms, including how they interact with specific environmental factors. In the second series of lectures, microorganisms will be discussed as reference systems for fundamental studies dealing with molecular biology as well as biochemistry and metabolic regulatory mechanisms. Also elements will be provided about the methods for microbe cultivation and on strategies for the control of microbial growth and the conditioning of the metabolism. The third part of lectures will cover the detailed study of particularly important microbial groups to be defined with the Students. Module: LABORATORY PRACTICES This laboratory module is designed to guide students in the acquisition of techniques and in the development of manipulative skills all necessary for the identification and the study of both structural and functional characteristics of the microorganisms of interest, as well as for a proper handling of microbial cultures within research activities. The main objective of the module is to provide students with the basic tools, represented by traditional analytical procedures in microbiology, but also with the knowledge of advanced techniques, based on molecular methods of investigation, useful for basic research but even the definition of the correct approach to issues related to the many themes of applied microbiology.

Syllabus

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1. MICROBIAL EVOLUTION AND DIVERSITY: Origin and Evolution of the Microbial Life; Bacteria; Archaea; Eukaryotic Cell and Eukaryotic Microorganisms; Microbial Taxonomy and Systematics.
2. PRINCIPLES OF MICROBIOLOGY: Cell Structure and Function in Bacteria, Archaea and Fungi (Yeast and Moulds);
3. MICROBIAL GROWTH: Microbial Nutrition, Culture and Growth Aspects; Antimicrobial Agents and Microbial Growth Control.
4. METABOLIC DIVERSITY: Phototrophy and autotrophy (purple sulfur and nonsulfur bacteria, green sulfur and nonsulfur bacteria, cyanobacteria), Aerobic (EMP pathway, Enther-Doudoroff pathway, Hexose Monophosphate Shunt + electron transport chain and proton motive force generation) and Anaerobic Respiration (denitrification, dissimilative sulfate reduction, acetogenesis, methanogenesis), Fermentations (homolactic and heterolactic, mixed-acid, butane-diol, propionic, butanol/acetone fermentations), Chemolithotrophy (hydrogen oxidizing, sulfur oxidizing, iron oxidizing, ammonia/nitrite oxidizing bacteria, anammox process); Other biosyntheses (ammonia assimilation, nitrogen fixation).
5. VIRAL DIVERSITY: Overview of Different Viral Groups; Bacteriophages.
6. BACTERIAL GENETICS: Mutations; Genetic Recombination: Transformation, Conjugation, Transduction.
7. MOLECULAR BIOLOGY AND GENE EXPRESSION Molecular Biology of Bacteria: Cloning Vectors and Expression Vectors; Regulation of Gene Expression.
8. MICROBIAL ECOLOGY: Methods in Microbial Ecology; Major Microbial Habitats and Diversity; Nutrient Cycles; Microbial Symbioses.
9. FOCUS ON SPECIFIC MICROBIAL GROUPS (Methylotrophs and Methanotrophs, Pseudomonadales, Enteric Bacteria, Myxobacteria, both nonsporulating and endospore-forming Firmicutes, Methanogens, moulds and yeasts).
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The aim of laboratories is to demonstrate to the student some techniques of microbiological analysis of a natural source, through the use of analytical methods based on morphological, physiological, biochemical and genetical tests to evaluate the types of microorganisms present which in the source itself and to classify them by a taxonomical approach.
In the first teaching credit, it will be displayed some techniques of plate count using general-purpose media to count and isolate bacteria and fungi, microbial growth patterns in tube and plate, motility assay and culture maintaining methods.
In the second teaching credit, it will be displayed some methods used to carry out a preliminary identification of bacteria and fungi. Optical microscopy for morphological analysis of cells, sugar patterns assimilation and fermentation, cell staining methods and enzymatic assays.

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In the third teaching credit, it will be showed some molecular methods: (a) Total DNA extraction from liquid culture: i) DNA detection by means of agarose gel electrophoresis, ii) DNA quantification on BioPhotometer through analysis of 260/280 and 260/320 ratios – (b) PCR amplification of the 16S rRNA gene sequence – (c) BOX-PCR analysis and observation of BOX profiles by agarose gel electrophoresis – (d) Analysis of 16S rRNA gene sequences of sonme unknown isolates by comparison with genetic sequence data banks: i) NCBI; ii) Ez-Taxon.- e) construction of phylogenetic trees by using 16S rRNA sequences of strains belonging to Bacillus sp. and Pseudomonas sp.

Assessment methods and criteria

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MM: teoria
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Non sono previste prove in itinere. La prova d’esame consisterà in una valutazione orale del grado di apprendimento conseguito sull’intero programma del corso. L’esame consiste in tre o quattro quesiti posti ad ogni candidato. L'esame ha una durata complessiva di circa 30 minuti. La valutazione finale è espressa in trentesimi.
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At the end of the practice lessons the student should be draw up a report on the activity carried out in laboratory. The manuscript will be discussed during the test.
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MM: laboratorio
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At the end of the practice lessons the student should be draw up a report on the activity carried out in laboratory. The manuscript will be considered during the test.

Reference books
Activity Author Title Publisher Year ISBN Note
teoria Gianni Dehò e Enrica Galli (a cura di) Biologia dei Microrganismi (Edizione 3) Casa Editrice Ambrosiana 2018 978-8-808-18623-2
teoria Michael Madigan, John Martinko, Kelly Bender, Daniel Buckley, David Stahl BROCK Biologia dei microrganismi - Microbiologia generale, ambientale e industriale (Edizione 1) Pearson Italia 2016 889190094X