| Marine microbiology and laboratory
(objectives)
The course will enable students to understand the peculiar morphological, physiological and metabolic characteristics of marine microorganisms (with particular reference to prokaryotes), their role in the marine environment and interactions with other organisms. Furthermore it will allow to know the basic techniques for their sampling and manipulation in the laboratory. The course will provide a framework for understanding current issues related to marine microorganisms and their potential applications (eg the importance of microorganisms for other marine organisms, their potential in biotechnology, the danger of some microorganisms and the necessary countermeasures to cancel potential damages of these). The course will provide the necessary insights to understand the ecological peculiarities of marine microorganisms, in particular those of some extreme marine environments.
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Code
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118910 |
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Language
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ITA |
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Type of certificate
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Profit certificate
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| Module: Module A - Marine microbiology and laboratory
(objectives)
Learning results
The course will permit the comprehension of the morphological, physiological and metabolic characteristic of marine microorganisms (mainly prokaryotes); their role in marine environments and the interactions with other organisms. The course will permit to understand the principal interactions between marine microorganisms and the environment (with particular attention to some extreme marine environments) in relation with the bio-geochemical cycles. The course will supply a reference framework to comprehend modern aspect related to the marine microbial world and the potential applications of useful microorganisms.
Knowledge and understanding ability. To get the knowledge regarding the peculiarities of the marine microbial biology, their metabolism, their role in the marine environment, their interaction with other organisms, and their potential in biotechnology.
Ability to apply knowledge and understanding. To understand the issues related to the relationships between marine microorganism and environment (including other organisms). To acquire the knowledge regarding the experimental approach to study the marine microbial world.
Independent judgement. The ability to construe the results obtained by the various studies in marine microbiology. The ability to understand the role of the marine microorganisms in the environment and their influence on the biology of other organisms.
Learning ability. Ability to describe scientific topics related to marine microbiology both in written and oral forms by a specific scientific/technical language. Ability to use the methods acquired for microorganism sampling, recognition/identification and cultivation. This ability will be developed also trough the active involvement of the students in discussions during the lectures, by laboratory experiences and field activities.
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Language
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ITA |
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Type of certificate
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Profit certificate
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Credits
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6
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Scientific Disciplinary Sector Code
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BIO/19
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Contact Hours
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40
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Exercise Hours
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8
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Type of Activity
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Core compulsory activities
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Teacher
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FENICE Massimiliano
(syllabus)
1) Theory (40 hours, 5 cfu)
Introduction. Marine microbiology among the Microbiological disciplines. Topics of marine microbiology, history and objectives. Marine environments and microorganisms. The physico-chemical marine environment (notes). Methods and techniques of marine microbiology (reminders of General microbiology). Microscopy and flow cytometry. Sampling, cultivation and characterization of marine microorganisms. Identification of marine microorganisms (PCR, FISH,sequencing, etc.) Sudy of marine communities: DGGE, TRFLP, PLFA, clone libraries (notes). NGS, metagenetic and metagenomic. Diversity of marine microorganisms. Phototropic (oxygenic and anoxygenic) bacteria. Nitrifyng, anammox, S- and Fe- oxidizing bacteria. Sulfate reducing, luminescent, halophilic, methanogenic and methanotroph bacteria. Marine Archaea: Euryarchaeota, Crenarchaeota, etc. Hyperthermophilic, Hyperhalophilic and Hyperacidophilic archaea Marine microbial ecology. The microbial loop. The bio-geochemical cycles (reminders from general microbiology). Marine snow. Relationship between marine microrganisms and other marine organisms. Symbiosis, parasitism, pathogenicity. Microbiology of extreme or peculiar marine environments: estuaries and other transition zones. The deep seas, the hyperhaline environments. Marine microrganisms and human being. Biofouling and biodeterioration, Marine biotechnology. Production of enzymes bio-polymers, biodegradation. Human pathogens and marine environments. waterborne diseases and microbiological analysis of water.
2) Practical lectures and laboratory (they could vary in relation also to the possibility to make sea excursions) (8 hours, 1 cfu). Sampling of marine microorganisms. Microbial counts. Isolation, cultivation and classification of marine microorganisms. Study of marine bacterial diversity. Screening for industrial microbial metabolites. Microbiological analysis of water.
(reference books)
Brock, Madigan, Martino, Parker, "Brock biologia dei microrganismi", CEA Ambrosiana, terza edizione 2007, volume 1 e 2. Biologia dei microrgamismi di G. Dehò e E. Galli, Casa Editrice Ambrosiana, 2018. Barbieri, Bestetti, Galli, Zannoni- Microbiologia ambientale ed elementi di ecologia microbica - Casa Editrice Ambrosiana, edizione 2008 Colin Munn - Marine Microbiology: ecology and applications – Garland Science, Taylor & Francis Group, 2nd edition (2011) http://www.nature.com/nrmicro/focus/marinemicrobiology/index.html The lectures slides (PDF) are available on line. During the course, some scientific publications will be distributed and discussed.
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Dates of beginning and end of teaching activities
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From to |
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Delivery mode
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Traditional
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Attendance
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not mandatory
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Evaluation methods
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Oral exam
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| Module: Module B - Marine microbiology and laboratory
(objectives)
The course will enable students to understand the peculiar morphological, physiological and metabolic characteristics of marine microorganisms (with particular reference to prokaryotes), their role in the marine environment and interactions with other organisms. Furthermore it will allow to know the basic techniques for their sampling and manipulation in the laboratory. The course will provide a framework for understanding current issues related to marine microorganisms and their potential applications (eg the importance of microorganisms for other marine organisms, their potential in biotechnology, the danger of some microorganisms and the necessary countermeasures to cancel potential damages of these). The course will provide the necessary insights to understand the ecological peculiarities of marine microorganisms, in particular those of some extreme marine environments.
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Language
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ITA |
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Type of certificate
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Profit certificate
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Credits
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5
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Scientific Disciplinary Sector Code
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CHIM/11
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Contact Hours
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40
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Type of Activity
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Core compulsory activities
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Teacher
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BARGHINI Paolo
(syllabus)
Introduction to the course, verification test of general microbiology knowledge. Recombinant DNA technology; restriction enzymes: definition and properties; restriction maps; DNA cloning. Cloning vectors: definition and applications; cloning vectors of first, second and third generation; phage and cosmid vectors. Vectors for special purposes: expression vectors, description and salient features; secretion vectors, description and salient features; shuttle carriers, description and salient features; integration vectors, description and salient features; vectors for the study of promoters, description and salient features. Artificial chromosomes. Mutations: origins and effects of mutations. Recombination as mutual exchange of genetic information. Transposable genetic elements. Technique for the isolation and sequencing of genes: the use of transposons. The plasposon. Description and use of the plasposon. Introduction to PCR; the stages of PCR; detailed description of the polymerase chain reaction; cloning of amplicons. PCR evolution; Reverse Transcription-PCR; Real Time-PCR. Monitoring the reaction. Amplification efficiency concept. Quantitative PCR; DNA quantification, Crossing point and calibration curve. Quantification principles. Melting Curve analysis. Pathogen research. Sequencing with Sanger method. Automatic sequencing and related problems. New massive sequencing technologies (NGS). New DNA editing technology: CRISPR-Cas. Classification and nomenclature of microorganisms: Classic characters (morphological, physiological / metabolic, ecological, genetic analysis) and molecular characters (comparison of proteins, composition in DNA bases, hybridization of nucleic acids, sequencing of nucleic acids). Southern Blotting. 16S-rDNA sequencing, comparison in database. Affiliation: physiological methods (Biolog) and molecular methods. Identification workflow. Phylogeny and phylogenetic trees. How to build a phylogenetic tree: choice of sequences, algorithm and outgroup. Bootstrapp. Critical analysis of the results. Case study: arctic bacteria. Taxonomic identification. Comparison of molecular and metabolic methods. General aspects on the analysis of microbial communities. Quorum Sensing (QS): definition and physiological aspects of QS. Molecular mechanisms underlying QS. Ecological meaning of the QS. Main classes of QS signal molecules in Gram + and Gram-. Polyglot bacteria. QS in competition and collaboration. Inter-Kingdom communication. Biofilm: definition, structure, modalities and mechanisms of biofilm formation. Biofilm and antibiotics. Use of furanoni against biofilm. Biofouling: definition, structure, modalities and mechanisms of biofouling formation. Problems related to biofouling. TBT in antifouling paints. Experimental project: identification of molecules with antifouling action. Chromatography. Bases of the chromatographic process. Display of separation. Concepts of: retention time; theoretical plates and height of theoretical plates; optimal separation. Solute-phase interaction. Separation mechanisms and related chromatography: adsorption; spreading; ion exchange; exclusion; affinity. Planar and column chromatography. HPLC.
(reference books)
Colin Munn. Marine Microbiology: Ecology and Applications. Garland Science
Brock Biologia dei microorganismi: microbiologia generale, ambientale e industriale. 14° edizione (2016). Casa Editrice Ambrosiana.
Roberto Danovaro - Biologia Marina: biodiversità e funzionalità degli ecosistemi marini. CittàStudi Edizioni.
Barbieri, Bestetti, Galli, Zannoni- Microbiologia ambientale ed elementi di ecologia microbica - Casa Editrice Ambrosiana, edizione 2008.
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Dates of beginning and end of teaching activities
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From to |
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Delivery mode
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Traditional
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Attendance
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not mandatory
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Evaluation methods
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Oral exam
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