Degree Course: Marine biology and ecology Syllabus for A.Y. 2019/2020  

Mod A: Fishery biology

Marine products: ecology, thermodynamics and quantization of trophic relationships

The Mediterranean necton: hints of bio-ecology of the main species subject to fishing

Bio-statistical models: balance, growth, age.

Quantitative and dynamic reconstruction of the structure of a population

The main fishing gear: operation and technical characteristics

Statistical models of the exploitation of fishery resources

Modern fishing problems: by-catch, protected species, catch mitigation systems, Italian and European fisheries legislation

will be made available by the teacher

Introduction to Marine Biology. Main chemical-physical and hydrodynamic characteristics of the marine environment. History of the Mediterranean Sea.
Marine organisms. Morphological and physiological traits of marine organisms. Plankton; Benthos; Necton. Main orders. Biological adaptations to marine habitats.
Marine biodiversity. Protected species and habitats. Allochthonous species. Marine protected areas.
Intra-specific relationships: characteristics and adaptations.
Communication in marine animals.
Adaptations to extreme environments.
Scientific research in marine biology.

Castro P., Huber M. E. (2011) Biologia Marina. Ed. MacGraw-Hill.
Danovaro R. (2013). Biologia marina. Ed. Città Studi.


Riedl, R. (1991). Flora e fauna del Mediterraneo. Ed. Muzzio F.

Theory
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.

Practical lectures and laboratory (they could vary in relation also to the possibility to make sea excursions)

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.

Brock, Madigan, Martino, Parker, "Brock biologia dei microrganismi", CEA Ambrosiana, terza edizione 2007, volume 1 e 2
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.

Introduction to the course, knowledge verification test of basic microbiology. Classification of microorganisms. Classic characters and molecular characteristics as criteria for the classification of microorganisms. Identification of microorganisms. Physiological methods: Biolog. Molecular methods: DNA extraction; amplification; sequencing; databank comparison. Definition and construction of phylogenetic trees. Choice of method; choice of sequences and multialignment; outgroup choice. The bootstrap. Critical analysis of the results obtained. Recombinant DNA technology. Restriction enzymes and construction of a restriction map. Realization of a construct. Plasmids: cloning, expression, secretion, integration, shuttle vectors and for the study of the promoter vectors. Gene-libraries Construction. Theory of PCR. Evolution and applications. Real Time PCR; chemistry of detection systems; sybr green, hybridization probes or fret probes, hydrolysis probes or TaqMan probes. Applications: quantitative analysis; revelations of mutations; products characterization. Theoretical aspects of quantitative PCR. Calibration curve. Principles of quantification. Absolute and relative quantification. Analysis of the melting curve. Set-up of the PCR with the internal control. DNA sequencing with the Sanger method. New Generation Sequencing technologies (NGS). Prokaryotes genetic transformation. Treatment of competence. Chemistry Competence. Electroporation. Triparental conjugation. Mutations. Recombination: methods and mechanisms. Gene-conversion and unequal crossing over. Transposable elements (transposons): types structure and mechanisms of action. The Plasposon. Biofouling and quorum sensing. The sampling: theoretical and practical aspects for a correct sampling and statistically significant.
Sampling of marine microorganisms from anthropized and not anthropized environments.
Viable and total count of marine microorganisms.
Isolation, cultivation and classification (cultivation methods and molecular) of marine microorganisms.
Detection of microbial biodiversity of marine environments.
Biotechnology from the sea.
Screening for the production of metabolites / enzymes of industrial interest.
Microbiological analysis of seawater.

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.

Introduction to the course, knowledge verification test of plant biology.
Algae definition; photosynthesis in aquatic environments: problems and solutions. The role of algae in biogeochemistry and technological applications. The diversification of eukaryotic algae: endosymbiosis.
Cellular organization, anatomy, sexual and asexual reproduction, biochemistry, biotechnology and ecology of the major algal phyla:
Cyanobacteria (Cyanophyceae )
Glaucophyta
Rhodophyta (Cyanidophyceae, Porphyridiophyceae, Rhodellophyceae, Compsopogonophyceae, Bangiophyceae, Florideophyceae )
Chlorophyta: Prasinophhyceae, Chlorophyceae, Ulvophyceae, Trebuxiophyceae class and Charophycean algae.
Chromophyta: (Chrysophyceae, Synurophyceae, Tribophyceae, Eustigmatophyceae, Raphydophyceae, Bacillariophyceae, Phaeophyceae)
Cryptophyta, Prymnesiophyta, Dinophyta, Euglenophyta, Chlorarachniophyta.
Phytoplankton, macroalgal and periphyton ecology.
Introduction to the marine fungi: biology, ecology, biotecnology.
Macroalgae: collection, classification and preparation of dry macroalgae samples (Exsicata).
Microalgae: collection, microscopic observations, taxonomical classification.
Marine fungi: collection of algal samples, Isolation of algicolous fungi, microscopic observations, taxonomical classification.
Screening for the production of metabolites / enzymes of industrial interest.

Barsanti L., Gualtieri P. 2006. Algae, anatomy, Biochemistry and Biotecnology. Taylor & Francis. NW.

Graham L.E., Graham J.M., Wilcox L.W. 2009.Algae (second edition) Pearson Benjamin Cummings. San Francisco.

Hoek C., Mann D.G., Jahns, H.M. 1995. Algae. An introduction to phycolgy. Cambridge University press.


Rodriguez-Prieto et al., 2015. Alghe e Fanerogame del Mediterraneo. Il Castello

Ecology and evolutionary biology. Fields of study, methodological approaches, temporal and spatial scales of enquiry.
Marine communities. Ecological factors and biodiversity patterns. The tidal range: causes and consequences of the zonation. Adaptations. Biological interactions, community structure, metacommunity.
Molecular and evolutionary ecology. Principles, methods and fields of investigation. Mechanisms of the evolutionary change. Species and speciation. Phylogeography and biogeography. Diversity and divergence. Dispersal, migration, gene flow. Landscape genetics.
Population and metapopulation. Structure, diversity and demographic changes. Census size, effective size. Historical demographic survey: methods based on demographic and genetic data.
Biological invasions. Causes, vectors and invasion paths. Factors behind successful invasions. Evolution of the invaders. Eco-evolutionary consequences of invasions. Lessepsian invasions.
Variations of the coastline. Causes, time scales, magnitude of changes, effects on biodiversity at the level of population, species, communities.
Evolutionary history of the Mediterranean basin and its shores. Tectonic evolution, climate evolution, impact on biodiversity.

Bertness, Bruno, Silliman, Stachowicz, 2014. Marine Community Ecology and Conservation. Sinauer Associates.
Freeland, Kirk, Petersen, 2011. Molecular Ecology. Wiley.
Rilov, Crooks, 2009. Biological Invasions in Marine Ecosystems. Springer.
Losos, 2013. The Princeton guide to Evolution. Princeton University Press.

Fundamentals of ethology. History of animal behaviour study; the four Tinbergen questions.. Imprinting, parental care; maternal effects. Stress response. Neuroendocrine correlates of behaviour. The role of genes and environment. The role of behaviour in evolution. Preys and predators. Migration, orientation, homing. Aggression and territoriality. Mate choice and breeding systems. Animal personality. Collective behaviours. Cognitive ethology. Animal welfare.
Behavioural ecology of marine organisms. Behavioural ecology and hypothesis testing. Evolutionary convergence and divergence of behavioural traits. Behavioural plasticity. Behavioural adaptations: islands and coastal fauna; pelagic environment; the deep sea; immersion in marine mammals. Social behaviour; schooling, group dynamics and self-organization; coloniality; sexual inversion; parental care; foraging strategies; orientation, migration, homing. Basis of bioacustics. Chemical communication. Bioluminescence. Electrolocation.
Methodological aspects. Capture, tagging, sampling and monitoring; experimental design and quantification of behaviour in the field and in controlled conditions. Satellite tracking. Geolocators. Accelerometers. Radar and sonar.
Conservation and management. Behavioural ecotoxicology; endocrine disruptors; effects of anthopogenic disturbance. Effects of climate change. The behaviour of invasive species. Aquaculture and behaviour. The relevance of behaviour in the conservation and management of marine biodiversity.

J.R. Krebs, N.B. Davies (eds) 2012 Behavioural Ecology. An Evolutionary Approach- Blackwell
P. Martin, P.P.G. Bateson 2012 Measuring behaviour: an introductory guide.Cambridge University Press
J. Alcock 2013 Animal Behaviour. An Evolutionary Approach. Oxford University Press
A. Manning, M.S. Dawkins 2012 An Introduction to Animal Behaviour. Cambridge University Press

The role and importance of the sea and oceans.

I: Oceanic and ecological dynamics and their spatial and temporal scales

Elements of geography and representation of the earth's surface; morphology and evolution of the ocean floor principles. Origin of the sea and oceans and property of marine waters. Principles of chemistry, physics and dynamics of seas and oceans.
The boundary conditions and the influence of the environment on the continental coastal marine system. Morphology and dynamics of the coasts.

Marine oceanic and coastal habitats. The benthos zonation and Mediterranean benthic biocenosis: the classifications of Perès Picard and Riedl.

Vertical and horizontal distribution of oceanographic and ecological variables. Marine ecological dynamics: biogeochemical cycles, ecological successions. Spatial and temporal scales of physical and ecological dynamics of marine and oceanic environments: phenomena and processes at the micro, meso and macro scale.

II: Renewable and non-renewable resources, the uses of the coastal zone

The concept of natural resource. Marine renewable resources (fisheries and aquaculture, marine renewable energies) and non-renewable resources (mining and quarrying activities in the coastal and offshore area). The use of the sea and coastline. Categories and classification of coastal uses.

III: The problems of the coastal zone, marine pollution and depositional environments. Principles of protecting and preserving the marine environment. Marine management tools.

Pollution of coastal marine environment: depositional environments and contamination. Classification, destiny and cycles of pollutants. The problem of coastal erosion and the concept of physiographic units. The coastal morphotypes. Dynamics of beaches and beach nourishment. Bioaccumulation and biomagnification, changes in the trophic structure, alteration of biotic communities. Human time scales and scale of human impacts. Residence time. Climate changes. Sustainable development, natural capital evaluation and other management tools. Introduction to marine protection legislation. Case histories of different issues and at different spatial and temporal scales.

IV: Platforms and measuring instruments. Sampling equipment. Experimental methods.

The problem of sampling scales and measuring. The definition of the sampling plan and the identification of the variables to be measured: the marine environment descriptors. Issues related to environmental monitoring. Platforms and data acquisition systems and their relative spatial and temporal scales (research vessels, satellites and airplanes, underwater towed and autonomous vehicles and oceanographic buoys, stations, ARGO and drifters). Measurement tools and methods: physical-chemical characteristics and optical properties of sea water; direct and indirect measures of biomass and primary production; dynamic characteristics. Active underwater acoustic instruments (depth, ecological and geomorphological features of the seabed) and passive instruments (sounds and noise). Equipment and methods for sampling, storage and transport of samples: sea water, phytoplankton and zooplankton, bottom sediments, benthos. Instrumentation and laboratory methods in marine ecology. Methods of direct investigation by diver.

V: The restitution of the information. Data analysis and mathematical models.

The structure of the data. The calibration of the instruments. The calibration of the data. Errors, their causes, data filtering techniques. Statistical data analysis. Methods of information restitution. Databases and GIS. International data exchange and sharing of databases. Theory and application of mathematical models. Limits and opportunities for development.

Course lecture notes by Prof. Marco Marcelli. Other teaching material will be provided during the course, consisting of articles and publications.

@ Biodiversity Conservation
- Introduction to the course aims;
- Definitions, aims and goals of conservation;
- Global traits to marine biodiversity;
- The Evil Quartet

@ Conservation genetics and Population Conservation
- Patterns and mechanisms of genetic diversity: measuring genetic biodiversity; Hardy-Weinberg law; Effective population size and genetic drift; Gene flow and population subdivision
- Conservation genetics: Demography, genetic diversity and extinction; Minimum Viable Population; Extinction vortex;
- Conservation of Populations and species: Managemeny Units, Operational Taxonomic Units; Focal Species, Umbrella, Indicators, Flagship species; IUCN, Red List; Conservation Strategies (ex-situ; in-situ: restocking, stock enhancement; sea ranching)

@ Community and ecosystem diversity
- Measuring Biodiversity at the level of community and habitat;
- Biodiversity and ecosystem functioning;Preserving Functional vs. Species Diversity (FD vs. SD)
- Italian law on protected Areas; “Habitat” EU Directive 92/43/CEE, Rete Natura 2000;
- Marine Protected Areas (MPA): scope, design, management, problems and perspectives; MPA: enforcement and results; MPA Networks: connectivity, representativeness, effectiveness

F.W. Allendorf, G. Luikart, 2013. Conservation and the Genetics of Populations - 2° edition Wiley-Blackwell
M. Solan, R.J. Aspden, D.M. Paterson, 2012. Marine Biodiversity & Ecosystem Functioning. Oxford
J. Claudet, 2011. Marine Protected Areas – A Multidisciplinary Approach. Cambridge