Dissertations / Theses on the topic 'Mediterraean Sea'

Sea-level variability is characterized by multiple interacting factors described in the Fourth Assessment Report (Bindoff et al., 2007) of the Intergovernmental Panel on Climate Change (IPCC) that act over wide spectra of temporal and spatial scales. In Church et al. (2010) sea-level variability and changes are defined as manifestations of climate variability and change. The European Environmental Agency (EEA) defines sea level as one of most important indicators for monitoring climate change, as it integrates the response of different components of the Earths system and is also affected by anthropogenic contributions (EEA, 2011). The balance between the different sea-level contributions represents an important source of uncertainty, involving stochastic processes that are very difficult to describe and understand in detail, to the point that they are defined as an enigma in Munk (2002). Sea-level rate estimates are affected by all these uncertainties, in particular if we look at possible responses to sea-level contributions to future climate. At the regional scale, lateral fluxes also contribute to sea-level variability, adding complexity to sea-level dynamics. The research strategy adopted in this work to approach such an interesting and challenging topic has been to develop an objective methodology to study sea-level variability at different temporal and spatial scales, applicable in each part of the Mediterranean basin in particular, and in the global ocean in general, using all the best calibrated sources of data (for the Mediterranean): in-situ, remote-sensig and numerical models data. The global objective of this work was to achieve a deep understanding of all of the components of the sea-level signal contributing to sea-level variability, tendency and trend and to quantify them.

Sea-level variability is characterized by multiple interacting factors described in the Fourth Assessment Report (Bindoff et al., 2007) of the Intergovernmental Panel on Climate Change (IPCC) that act over wide spectra of temporal and spatial scales. In Church et al. (2010) sea-level variability and changes are defined as manifestations of climate variability and change. The European Environmental Agency (EEA) defines sea level as one of most important indicators for monitoring climate change, as it integrates the response of different components of the Earths system and is also affected by anthropogenic contributions (EEA, 2011). The balance between the different sea-level contributions represents an important source of uncertainty, involving stochastic processes that are very difficult to describe and understand in detail, to the point that they are defined as an enigma in Munk (2002). Sea-level rate estimates are affected by all these uncertainties, in particular if we look at possible responses to sea-level contributions to future climate. At the regional scale, lateral fluxes also contribute to sea-level variability, adding complexity to sea-level dynamics. The research strategy adopted in this work to approach such an interesting and challenging topic has been to develop an objective methodology to study sea-level variability at different temporal and spatial scales, applicable in each part of the Mediterranean basin in particular, and in the global ocean in general, using all the best calibrated sources of data (for the Mediterranean): in-situ, remote-sensig and numerical models data. The global objective of this work was to achieve a deep understanding of all of the components of the sea-level signal contributing to sea-level variability, tendency and trend and to quantify them.

Les processus caractérisant la turbulence en Méditerranée Occidentale ont été identifiés et quantifiés à partir de données de microstructure. L'accent a été mis sur le Canal de Sicile, un hot-spot pour le mélange turbulent et une région clé pour les transformations de masses d'eaux. Il module le transport de chaleur et de sel entre les deux bassins, occidental et oriental, et on y retrouve une large gamme de régimes dynamiques. La turbulence y est produite par le fort cisaillement associé à l'écoulement des eaux Levantines intermédiaires (LIW) fortement contraint par la bathymétrie et par le déferlement des ondes internes de marée. Un fort contraste entre les deux passages profonds dans le canal a ainsi été observé. La variabilité de l'efficacité du mélange a été caractérisée en fonction des régimes dynamiques rencontrés et une paramétrisation fine échelle de la dissipation d'énergie cinétique turbulente a été validée pour des régimes d'intensité turbulente faible à modérée. Les flux diffusifs turbulents verticaux calculés à partir de mesures in-situ ont permis d'estimer les changements des propriétés des masses d'eaux dans le canal. L'analyse a ensuite été étendue à tous les profils récoltés dans le bassin occidental où le rôle relatif de la double diffusion et de la turbulence mécanique sur les flux de chaleur, salinité, flottabilité et l'érosion de la LIW, a été discuté
The processes characterising turbulence in the Western Mediterranean Sea were identified and quantified using microstructure measurements. The focus was on the Sicily Channel, a hotspot for turbulent mixing and a key region for water mass transformations. It modulates the heat and salt transport from the Eastern to the Western Mediterranean Basins and exhibits a large range of dynamical regimes. Turbulence is driven by the strong shear associated to the flow of Levantine Intermediate Waters (LIW) which is constricted by the bathymetry, and by internal wave breaking of tidal origin. A strong contrast was observed between the two deep passages in the channel. The mixing efficiency variability was investigated in the context of mechanically driven turbulence over a wide spectrum of turbulence intensities. A finescale parameterisation for the turbulent kinetic energy dissipation rate was validated for weak to moderate turbulence intensity. The vertical turbulent diffusive fluxes computed from the measurements allowed an assessment of the water mass property changes incurred in the channel. The analysis was extended to all the stations sampled in the Western Mediterranean, where the relative impact of double diffusion and mechanical turbulence on heat, salt and buoyancy fluxes, as well as on the LIW, was investigated

A new methodology is being devised for ensemble ocean forecasting using distributions of the surface wind field derived from a Bayesian Hierarchical Model (BHM). The ocean members are forced with samples from the posterior distribution of the wind during the assimilation of satellite and in-situ ocean data. The initial condition perturbations are then consistent with the best available knowledge of the ocean state at the beginning of the forecast and amplify the ocean response to uncertainty only in the forcing. The ECMWF Ensemble Prediction System (EPS) surface winds are also used to generate a reference ocean ensemble to evaluate the performance of the BHM method that proves to be eective in concentrating the forecast uncertainty at the ocean meso-scale. An height month experiment of weekly BHM ensemble forecasts was performed in the framework of the operational Mediterranean Forecasting System. The statistical properties of the ensemble are compared with model errors throughout the seasonal cycle proving the existence of a strong relationship between forecast uncertainties due to atmospheric forcing and the seasonal cycle.

A new methodology is being devised for ensemble ocean forecasting using distributions of the surface wind field derived from a Bayesian Hierarchical Model (BHM). The ocean members are forced with samples from the posterior distribution of the wind during the assimilation of satellite and in-situ ocean data. The initial condition perturbations are then consistent with the best available knowledge of the ocean state at the beginning of the forecast and amplify the ocean response to uncertainty only in the forcing. The ECMWF Ensemble Prediction System (EPS) surface winds are also used to generate a reference ocean ensemble to evaluate the performance of the BHM method that proves to be eective in concentrating the forecast uncertainty at the ocean meso-scale. An height month experiment of weekly BHM ensemble forecasts was performed in the framework of the operational Mediterranean Forecasting System. The statistical properties of the ensemble are compared with model errors throughout the seasonal cycle proving the existence of a strong relationship between forecast uncertainties due to atmospheric forcing and the seasonal cycle.

[eng] The transition from mesoscale to submesoscale dynamics is investigated in the western Mediterranean Sea (WMed) using a set of ROMS model simulations. The research is structured in a series of sequential stages covering the mesoscale-tosubmesoscale range, starting from a regional overview of the WMed ocean circulation and zooming in towards local processes. The mesoscale exploration is assessed in terms of the Lorenz energy cycle (LEC), which provides a quanti cation of the kinetic-potential energy exchanges through eddymean ow interactions. The sources of eddy kinetic energy are analyzed by applying a regional formulation of the LEC to 18 years of the ROMSWMED32 numerical simulation at eddy-resolving resolution (3.5 km), which allows identi cation of whether the energy exchange between the mean and eddy ow is local or nonlocal. The patterns of energy conversion between the mean and eddy kinetic and potential energy are estimated in three subregions of the domain: the Alboran Sea, the Algerian Basin, and the Northern Basin. Results from the LEC analysis reveal that the Alboran Sea is the most energetic region in the WMed. The spatial characterization of the energy conversion routes, together with the physical and dynamical characteristics of the area, hints at two principal submesoscale mechanisms involved in maintaining balance: topographic vorticity generation (TVG) and frontogenesis (FG). The transition toward the submesoscale is explored in the Alboran Sea by means of two nested, realistic simulations covering this region with increasing horizontal resolutions ranging from 1:5 km (WMed1500) to 0:5 km (Alb500). Unbalanced submesoscale dynamics emerge in the ner solution as the model resolution is increased. The occurrence of TVG and FG in Alb500 does not display a clear spatial nor temporal variability which facilitates an overall statistical approach. Instead, our analysis is focused on particular events of FG and TVG which are considered to be representative of the Alboran Sea dynamics. TVG is explored and quanti ed using the barotropic vorticity balance equation, in which the generation of vorticity through ow-topography interaction relies on contributions from bottom stress and form drag, the latter being the principal source. FG is analyzed in a recurrent, intense density front located at the eastern edge of the permanent western anticyclonic gyre (WAG) which has a similar structure to that of the climatological Almeria-Oran front. Alb500 accurately reproduces the process of FG in this front, instigated by the straining of the mesoscale velocity eld, and the generation of ageostrophic secondary circulation, exhibiting transient downwelling events reaching peak vertical velocities of O(1) km day􀀀���1. The vertical velocity background revealed throughout the analysis of the Alb500 solution suggests that vertical motions in the Alboran Sea might stem from additional sources of perturbations in the submesoscale range, such as mixed layer instabilities, tidal e ects or topographic internal waves. Exploring these mechanisms and the possible interactions among them is beyond the scope of this Thesis; planned further analysis of the Alb500 simulation using Lagrangian techniques is likely to shed light on such processes.
[spa] La transici on de la mesoescala a la submesoescala se investiga en el Mar Mediterr aneo occidental mediante una serie de simulaciones con el modelo ROMS. El estudio se compone de varias etapas que cubren este rango de escalas, partiendo de una descripci on regional de la circulaci on en el Mediterr aneo occidental hacia los procesos que tienen lugar a escalas locales. El an alisis de mesoescala se lleva a cabo en t erminos del ciclo de energ a de Lorenz (LEC, de sus siglas en ingl es), que permite cuanti car los intercambios de energ a cin etica y potencial que tienen lugar en el uido mediante interacciones entre el ujo medio y el ujo turbulento. Las fuentes de energ a cin etica turbulenta se investigan a partir de ROMSWMED32, una simulaci on de mesoescala (3.5 km) que abarca un periodo de 18 a~nos. Una formulaci on regional del LEC permite discernir si dichos intercambios de energ a tienen un origen local o remoto. Los patrones de conversi on de energ a se investigan en tres subregiones: Mar de Albor an, Cuenca de Argelia y Cuenca de Norte. Los resultados del LEC revelan que el Mar de Albor an es la zona m as energ etica del Mediterr aneo occidental. La distribuci on espacial de las rutas de conversi on de energ a, junto con las caracter sticas geogr a cas y din amicas de esta regi on, sugieren dos mecanismos de submesoescala como principales responsables del mantenimiento del balance de energ a: generaci on topogr a ca de vorticidad (TVG, de sus siglas en ingl es) y frontog enesis (FG). La transici on hacia la submesoescala en el Mar de Albor an se investiga mediante dos simulaciones realistas anidadas que cubren esta regi on, con resoluciones que aumentan desde 1:5 km (WMed1500) hasta 0:5 km (Alb500). La din amica de submesoescala se aprecia en Alb500 seg un aumenta la resoluci on. Los procesos de TVG y FG en Alb500 no presentan una clara variabilidad espacial ni temporal que permita una descripci on estad stica de los mismos. Por tanto, el an alisis de estos mecanismos se lleva a cabo sobre eventos aislados que pueden considererse representativos de la din amica del Mar de Albor an. La cuanti caci on y el an alisis de la TVG se realiza a partir de la ecuaci on del balance de vorticidad barotr opica. La generaci on de vorticidad debido a la interacci on de la corriente con la topograf a se eval ua en t erminos del esfuerzo cortante de fondo (en ingl es, bottom stress) y del arrastre (en ingl es, form drag), siendo este ultimo la fuente principal. La FG se analiza en un intenso y recurrente frente de densidad localizado en el extremo oriental de giro anticicl onico del oeste (WAG, de sus siglas en ingl es) cuya estructura es muy similar a la del habitual frente de Almer a-Oran. Alb500 reproduce de forma precisa el proceso de FG de este frente, inducido por el aumento de tensi on del campo de velocidad geostr o ca super cial, as como el desarrollo de la circulaci on secundaria ageostr o ca asociada al frente, con episodios de intenso movimiento vertical descendente (en ingl es, downwelling) alcanzando velocidades del orden de 1 km al d a. El campo de velocidad vertical que revela el an alisis de la simulaci on Alb500 sugiere que los movimientos verticales en el Mar de Albor an pueden ser originados por otros tipos de perturbaciones de submesoescala, tales como inestabilidades en la capa de mezcla, las mareas, o bien ondas internas de origen topogr a co. La exploraci on de estos mecanismos y de las posibles interacciones que tiene lugar entre ellos va m as all a de los objetivos de esta Tesis, si bien se pretende profundizar en el estudio de dichos procesos con un futuro y exhaustivo an alisis de la simulaci on Alb500 utilizando t ecnicas lagrangianas
[cat] La transici o de la mesoescala a la submesoescala s'investiga a la Mar Mediterr ania occidental a partir d'una s erie de simulacions amb el model ROMS. L'estudi est a format per v aries etapes que abasten aquest rang d'escales, des d'una descripci o regional de la circulaci o a la Mediterr ania occidental, ns als processos que tenen lloc a escales locals. L'an alisi de mesoescala es realitza en termes del cicle d'energia de Lorenz (LEC, de les seves sigles en angl es), que permet quanti car els intercanvis d'energia cin etica i potencial que tenen lloc en un uid degut a les interaccions entre el uxe mitj a i el uxe turbulent. Les fonts d'energia cin etica turbulenta s'investiguen amb ROMSWMED32, una simulaci o de mesoescala (3.5 km) que abarca un periode de 18 anys. Una formulaci o regional del LEC permet diferenciar si aquests intercanvis d'energia s on d'origen local o remot. Els patrons de conversi o d'energia s'investiguen a tres sub-regions: Mar d'Alboran, Conca d'Alg eria i Conca del Nord. Els resultats del LEC mostren que la Mar d'Alboran es la zona m es energ etica de la Mediterr ania occidental. La distribuci o espacial de les rutes de conversi o d'energia, juntament amb les caracter stiques geogr a ques i din amiques d'aquesta regi o, suggereixen dos mecanismes de submesoescala com a principals responsables del manteniment del balan c d'energia: generaci o topogr a ca de vorticitat (TVG, de les seves sigles en angl es) i frontog enesi (FG). La transici o cap a la submesoescala a la Mar d'Alboran s'investiga a partir de dues simulacions realistes niuades que cobreixen aquesta regi o, amb resolucions que augmenten des de 1:5 km (WMed1500) ns a 0:5 km (Alb500). La din amica de submesoescala s'aprecia en Alb500 segons augmenta la resoluci o. Els processos de TVG i FG simulats amb Alb500 no presenten una clara variabilitat espacial ni temporal que faciliti la seva descripci o estad stica. Per tant, l'an alisi d'aquests mecanismes es realitza a partir d'esdeveniments a llats que es poden considerar representatius de la din amica de la Mar d'Albor an. La quanti caci o i l'an alisi de la TVG es realitza mitjan cant l'equaci o de balan c de la vorticitat barotr opica. La generaci o de vorticitat per interacci o del corrent amb la topogra a s'avalua en termes de l'esfor c de tall (en angl es, bottom stress) i de l'arrossegament (en angl es, form drag), que n' es la principal font. La FG s'analitza en un intens i recurrent front de densitat localitzat a l'extrem oriental del gir anticil onic de l'Oest (WAG, de les seves sigles en angl es) d'estructura molt similar a l'habitual front d'Almeria-Or a. Alb500 simula de forma precisa el proc es de FG d'aquest front, provocat per l'augment de tensi o del camp de velocitat geostr o ca super cial, aix com la generaci o de la circulaci o secund aria ageostr o ca associada al front, amb episodis d'intens moviment vertical descendent (en angl es, downwelling) assolint velocitats de l'ordre d'1 km per dia. El camp de velocitat vertical que mostra l'an alisi de la simulaci o Alb500 suggereix que els moviments verticals a la Mar d'Alboran podrien ser causats per altres tipus de perturbacions de submesoescala, tals com inestabilitats dins la capa de mescla, efectes de la marea, o b e ones internes d'origen topogr a c. L'exploraci o d'aquests mecanismes i de les seves posibles interaccions no es l'objectiu d'aquesta Tesi, si b e la futura i exhaustiva an alisi de la simulaci o Alb500 mitjan cant t ecniques Lagrangianes preten profunditzar en el coneixement d'aquests processos.

Thesis (M.S. in Physical Oceanography) Naval Postgraduate School, March 2000.
Thesis advisor(a): Poulain, Pierre-Marie. "March 2000." Includes bibliographical references (p. 109-111). Also available online.

Mestrado em Biologia Aplicada
A implementação da Directiva Quadro da Água tem levantado importantes questões relativas aos aspectos metodológicos da amostragem das comunidades bentónicas, tendo sido feitas várias tentativas no sentido de estandardizar as estratégias de amostragem, especialmente em águas de transição. Este estudo pretende abordar esta questão através da comparação das comunidades de macrofauna amostradas com dois métodos distintos, corer e sacos de folhas. O trabalho foi realizado no Mediterrâneo e no Mar Negro, em 10 ecossistemas de transição, distintos, sobretudo, ao nível da salinidade e tipologia de habitat. No conjunto, foram amostrados 172 taxa dos quais, 49 apenas com corers e 52 apenas com sacos de folhas. Setenta e um taxa foram comuns a ambos os amostradores. Os artrópodes são comuns aos dois amostradores, sendo dominantes nos sacos de folhas, enquanto os anelídeos caracterizam os corers. A riqueza taxonómica média por amostra foi de 4,5 nos corers e 5,2 nos sacos de folhas. Quer os corers quer os sacos de folhas apresentaram padrões semelhantes no que diz respeito às principais características estruturais da comunidade. Dos sistemas oligohalinos (<5 ‰) para os sistemas euhalinos (>30 ‰), a diversidade taxonómica (H') e a similitude de Bray-Curtis mostraram o mesmo padrão de variação. Apesar destas semelhanças, as comunidades de macrofauna bentónica amostradas com os dois dispositivos mostraram diferenças significativas que não foram relacionadas, ao nível da escala eco-regional, com o gradiente salino ou a tipologia do habitat. As diferenças entre os amostradores mantiveram-se significativas quando a análise foi realizada com base em índices bióticos, entre os quais alguns índices de qualidade ecológica. Os resultados obtidos no presente trabalho têm implicações na avaliação e monitorização do estado ecológico dos sistemas de transição, pondo em evidência o facto dos corers e dos sacos de folhas recolherem amostras caracterizadas por diferentes espécies. No entanto, a diferenças entre as lagoas mostrou-se mais importante do que a diferença entre ecótipos, isto é, grupos de salinidade.
One of the important questions in the implementation of the Water Framework Directive regards the methodological aspects about the sampling of benthic communities and many attempts are made in order to standardize sampling strategies, especially in transitional waters. The present study aims to compare the macrofauna communities colonizing leaf bags and those obtained from box-corer samples. The study was carried out in 10 transitional aquatic ecosystems located in the Mediterranean ,the Black Sea and differing mainly in water salinity and habitat typology. Overall, a total of 172 taxa were sampled; 49 taxa were found only in the sediment samples and 52 only in the bags; 71 were common to both samplers. Arthropods were a common component to both samplers, dominant in leaf bags, while annelids characterized mainly the corers. Mean taxonomic richness per sample was 4,5 in the corers and 5,2 in leafbags. Both corer and leaf-bag samples showed similar patterns of the main community structural characteristics. From the oligohaline (<5‰) to the euhaline (>30‰) systems, taxonomic diversity (H’) and Bray-Curtis similarity showed consistent patterns of variation. Despite these similarities, The benthic macrofauna sampled with the two devices showed significant differences that were not related, on ecoregional scale, to the salinity gradient or the habitat typology. The differences between samplers remained significant also when the analysis was performed on biotic indices, namely some ecosystem quality indices. The results obtained in the present work have major implication for the assessment and monitoring of ecological status in transitional waters. They evidence that the benthic invertebrates upon which the taxonomic indices are calculated and those that contribute to the functional aspects based on the study of decomposition rates, are essentially distinct. However, on the studied spatial scale, the lagoon heterogeneity (differences among lagoons) were more important than the ecotopes (i.e., salinity groups).

The main aim of this research thesis is to find and study new methodologies in order to derive an enhanced knowledge of meteorological conditions and in particular of the sea wave climatology. This applies at first locally and then to the whole extension of the Mediterranean basin. Thanks to the large amount of information stored in databases with high temporal and spatial resolution of time series of wind and wave characteristics, it is possible to improve the knowledge of marine climate. In this way, it is possible to make more accurate assessments that may concern, for example, the planning of offshore operations to be carried out safely, a study of the dispersion of pollutants in case of accident to perform rapid and targeted interventions, an accurate design of "ad hoc" structures to protect coastlines or port areas, proper functioning of measuring instruments or energy production to avoid encountering intense storm events during navigation that can create dangerous situations. Using the hindcast of MeteOcean group at DICCA (Univeristy of Genoa), four main topics have been explored. First, the study of the main tool that allows the definition of wave conditions, namely the energy wave spectrum, is addressed, including the development of the procedure of the reconstruction of the bi-dimensional spectrum, defined in the frequency-direction space. Based on the spectral data, in the second chapter a climatological analysis of the Mediterranean Sea is addressed with the aim of identifying and characterizing the major systems in the spectrum. The study of the climatology of the sea continues by exploring another point of view. In the third chapter, the aim is to select significant climatological scenarios of sea states to effectively summarise the local marine climate, introducing clustering algorithms. Using the capabilities of clustering, the fourth chapter of this research thesis concerns climatology from a spatial point of view. The aim is to divide the Mediterranean basin into climatological areas through the help of k-Means.

Knowledge about deep-sea megabenthic communities has greatly increased during the last two decades thanks to the improvement of technical diving equipment, submersibles, remotely operated and autonomous vehicles. In the last 10 years, several studies, targeting the Mediterranean deep continental shelf or mesophotic zone (40-200 m), have reported the occurrence of rich hotspots of biodiversity, namely marine animal forests, dominated by habitat-forming species such as corals and sponges thriving in dim light conditions. This bathymetric range hosts the deepest extension of shallow-water animal forests as well as proper mesophotic assemblages thriving on the so-called roche du large ecosystems. These complex aggregations play a fundamental ecological role in the marine ecosystems (refuge effect, nursery area, benthic-pelagic coupling, biogeochemical cycles) and the characterization of their diversity and distribution is considered of primary interest worldwide. Explorations have depicted not only the diversity of these forests but also their vulnerability towards mechanical impacts inflicted by demersal fishing activities, especially in the overexploited Mediterranean basin. This leads to an urgent need to quantify the damages burdening on these sensitive ecosystems and to develop easy-to-apply tools to evaluate and monitor their environmental status, in order to provide effective conservation measures. This thesis aims to address these topics focusing on the marine animal forests of the Ligurian deep continental shelf. The Ligurian Sea represents one of the most studied Mediterranean basins due to several extensive researches, which have characterized the benthic and pelagic fauna mainly through SCUBA diving (shallow waters) and trawl surveys (bathyal waters) since the beginning of the last century. On the other hand, a large knowledge gap still exists for this region regarding the deep circalittoral megabenthic communities and, overall, on the anthropic threats insisting on deep-sea communities. Indeed, considering the significant amount of professional and recreational fishermen operating at these depths in the Ligurian region, it was crucial to carry out an extensive investigation in this area. In the present study, about 80 sites have been investigated during a four-years ROV survey conducted along the Ligurian deep continental shelf representing the most comprehensive study so far for the Italian waters. ROV footage was used to characterize the benthic biocoenoses thriving on soft and hard bottoms, determine the most relevant environmental factors driving their spatial distribution, and quantify the anthropogenic disturbance. Twelve major assemblages have been identified by means of community analysis, including gorgonian and hydrozoan forests, dense keratose sponge grounds, a Dendrophyllia cornigera facies, bryozoan beds and soft-bottom meadows of sabellids and alcyonaceans, some of them reported for the first time. Forests of black corals and Paramuricea macrospina aggregations have also been reported from the video footage, although with a more scattered distribution. The distribution of these assemblages is determined by different environmental parameters, namely depth, substrate type and inclination. The abundance of marine litter herein observed is among the highest ever recorded in Europe, with maximum values up to 7900 items ha-1. Abandoned, lost or discarded fishing gears represent the 81% of the total sightings, with the highest abundance recorded on the deep rocky shoals facing the largest fishing harbors and fleets. The majority of the fishing gears observed is attributable to artisanal and recreational fishing activities, suggesting that these represent the main source of litter in the Ligurian Sea. Urban litter, mainly represented by plastic, has also been observed, generally with higher abundances nearby large cities and river mouths. A multidisciplinary approach based on ROV explorations, background fishermen interviews and on-board bycatch monitoring has also been applied to obtain quantitative data on the impact of different fishing methods adopted within two Ligurian case studies. The study areas have been selected following a bathymetric point of view to study two different deep-sea ecosystems (a deep circalittoral coralligenous shoal exploited by a small-scale fishery and a trawling ground located nearby a cold-water coral thanatocoenoses), and the investigated parameters were designed to fulfil the criteria proposed by FAO for the identification of Vulnerable Marine Ecosystems (VMEs). A fine characterisation of the megabenthic assemblages and the fishing effort was obtained, as well as the quantification of no-target catches rates (with particular attention to structuring megabenthic invertebrates and rare species), and the frequency of gear entanglement and loss. This information allowed to initiate the process to delineate Fisheries Restricted Areas (FRAs), over these sensitive deep areas. Finally, to evaluate the environmental status of megabenthic assemblages thriving on mesophotic coralligenous or rocky reefs at temperate latitudes, a multiparametric index (MACS) integrating all possible sources of ROV-based information regarding community structure and impacts has been developed and validated. This practical tool was thought to have a large-scale application within the on-going Marine Strategy monitoring programs of these ecosystems. In conclusion, a georeferenced database of the location of diversity hotspots and sites of litter accumulation has been created, in order to set the baseline for the monitoring of Ligurian mesophotic sensitive animal forests. This dataset will provide managers and stakeholders the scientific information and the tools for the creation of an extensive network of deep-sea marine protected areas in the Ligurian basin.

The sampling of met-ocean variables is crucial for a plethora of applications. In coastal areas, the management of coastal activities and shipping lanes have to account for variations on mean sea level, wave parameters and current velocities, and coastal defences need to be designed according to the severe sea states they will most likely have to face. Similarly, off-shore engineering projects are expected to stand against forces driven by waves that might occur, e.g., once in ten thousand years. The assessment of design waves relies on statistical extrapolations that need to be fed with reliable and continuous wave data. Therefore, it would be appropriate to extend as much as possible the possible ways of sampling waves. In this regard, this thesis first addresses the reliability of HF-radar wave measures, through a practical case study in the Gulf of Naples. Radar data are compared to the outcomes of two numerical models: one providing the wave parameters on a regional scale, and the other specifically developed for the area of investigation over finer resolutions. Both the models are previously validated against a buoy installed offshore the gulf (taken as reference), which is placed outside the radar domain and therefore cannot be employed for a direct comparison with the latter. The agreement between the models and the HF-radars is evaluated through error indexes computed on the significant wave heights, mean period and mean incoming directions. Results show a reasonable consistency between HF-radar and models measures, leaving room for further investigations on the use of such devices. The aforementioned study refers to hindcast data provided by the Department of Civil, Chemical and Environmental Engineering of the University of Genoa (Italy). The hindcast was developed through a third generation wave model defined over the whole Mediterranean Sea, outputting the most significant wave parameters on a hourly base in the 1979-2018 period. Such data, being continuously defined over a long period, allow also to perform reliable analysis of the extreme waves for given locations. In particular, beyond the analysis of HF-radar wave measurements, this thesis proposes two insights in the framework of the so-called extreme value analysis (EVA). First, a ``bottom-up'' approach for the identification and classification of the atmospheric processes producing extreme wave conditions is revisited, and applied to several locations selected among the Italian buoy network. A methodology is given for classifying samples of significant wave height peaks in homogeneous subsets, related to the climatic forcing driving the most severe wave states. Subsequently, the study shows how to compute the overall extreme values distribution of significant wave height starting from the distributions fitted to each single subset previously detected. From the obtained results, it is concluded that the proposed methodology is capable of identifying clearly differentiated subsets, driven by homogeneous atmospheric processes: two well-known cyclonic systems are identified as most likely responsible of the extreme conditions detected in the investigated locations. These systems are analyzed in the context of the Mediterranean Sea atmospheric climatology, and compared with those figured out by previous researches developed in similar frameworks. Then, it is proved that the high return period quantiles for the significant wave height are consistent with those resulting from the usual computational scheme of the EVA. Finally, a simple model for evaluating non-stationarity in extreme waves is discussed, and possible implications are analyzed through practical examples. This model takes advantage of a linear slope estimate that allows to quantify the rate of change of a given time series of data, lowering the weight of possible outliers. The reliability of this slope is proved against two other methods that are not bounded by the linear trend hypothesis, which in fact could represent a too limiting assumption. This study is applied to series of significant wave height annual statistics over the whole Mediterranean Sea. Trend tests are applied on the series carried out from the hindcast locations, and show that the modified linear slope is sound and reliable. Hence, it is shown how such index can be employed to evaluate for the need of non-stationary EVA rather than the common stationary ones, i.e. when significant divergences between the two models may arise. Finally, the linear slope estimates are used to assess the spatial distribution of historical long-term trend in the Mediterranean Sea, showing interesting analogies with previous works defined over similar locations.

The Mediterranean circulation appears to be the result of three principal forcing factors: the inflow/outflow at Gibraltar strait, the wind stress applied on the ocean surface and the buoyancy fluxes. In this thesis, the focus is on studying the role of the wind in the ocean circulation. Sub-basin scale gyres are driven in different proportions by winds and heat fluxes (Pinardi and Navarra, 1993; Zavatarelli and Mellor, 1995; Roussenov et al., 1995) and locked or modified by topography. Generally the large scale basin circulation is characterized by cyclonic gyres in the northern regions, and by an anticyclonic gyres and eddy-dominated flow fields in its southern parts, with the exception of the Tyrrhenian and the northern Ionian Sea (Pinardi et al., 2015). The decadal variability of the Mediterranean Sea shows a reversal of the current in the Ionian Sea called Northern Ionian Reversal (NIR; Pinardi et al., 2015) and can be connected to changes in the wind stress. To assess the role of the wind stress in Mediterranean circulation and on the NIR phenomenon, Perpetual Year (PY) experiments are carried out with the NEMO ocean model implemented on the SURF model platform (SURF; Trotta et al., 2015). Sensitivity experiments are performed on the physics of the model and on the wind forcing evaluating the relation between the wind stress and the Mediterranean upper circulation. A diagnostic study of the NIR phenomenon is carried through the NIR index. The NIR index uses the difference of the SSH at two points to evaluate the prevailing circulation in the northern Ionian sea. Positive values of the index are connected to anticyclonic circulation, while negative values are related to cyclonic circulation. SSH field from Reanalysis, model output and SLA Satellite observations are analysed and compared. Studies agree in setting the time of the surface reversal to 1997 and this is confirmed by the change of the NIR index sign, both in Reanalysis and Observations.

Il principale obbiettivo di questo studio è stato la descrizione della diversità della spongofauna associata alle concrezioni coralligene, il principale hot spot di biodiversità dell’intero bacino del Mediterraneo. I campionamenti sono stati effettuati in immersione in quattro siti del Mar Ligure tra 30 e 40 m di profondità: Punta del Faro (Area Marina Protetta di Portofino), Punta Manara, Isola Gallinara (stazioni Falconara e Sciusciaù) e Santo Stefano. I blocchi di coralligeno, con un volume medio di circa 20 l ciascuno, sono stati raccolti in ciascun sito e tutte le spugne presenti sulla loro superficie sono state prelevate, identificate e raggruppate in accordo con le loro caratteristiche morfo-funzionali. Gli esemplari insediati sul lato ombroso e quello illuminato dei singoli blocchi sono stati raggruppati separatamente. Inoltre due blocchi per ciascuna stazione sono stati tagliati in sezioni spesse 2 cm per consentire la raccolta e l’identificazione delle specie endolitiche. In totale 108 specie di poriferi sono state raccolte e identificate: 59 da Portofino, 54 dall’Isola Gallinara, 53 da Punta Manara e 37 da Santo Stefano. La diversità, dominanza e ricchezza specifica della comunità a spugne studiata è risultata significativamente correlata con il livello di illuminazione. In tutti i siti le spugne erano più abbondanti, sia in termini di numero di individui che di ricoprimento percentuale, sul lato ombroso dei blocchi rispetto al lato illuminato; i valori dell’indice di ricchezza specifica hanno confermato la maggiore biodiversità del lato ombroso. Su questo lato le spugne incrostanti erano le più abbondanti a causa della minore competizione con la componente algale. Al contrario il lato illuminato ospitava in prevalenza spugne massive e arborescenti che erano dunque particolarmente sottoposte all’impatto antropico. E’ possible ipotizzare che un’elevata presenza e diversità di queste specie indichi siti caratterizzati da bassi livelli di impatto. Le spugne perforatrici (8% delle specie identificate durante questo studio) rappresentano un gruppo molto importante da un punto di vista della dinamica dei substrati calcarei; il numero di specie perforanti era alto (10) in confronto con i dati riportati in letteratura (4 specie). Le spugne insinuanti, viventi nelle fessure interne alla struttura coralligena, rappresentavano il 25% delle specie individuate essendo Stoeba plicata la specie più abbondante. Cliona viridis, Jaspis johnstoni e Stoeba plicata erano le specie che raggiungevano la maggiore profondità all’interno delle concrezioni penetrando 5 cm nel substrato. Da un punto di vista biogeografico due specie, Eurypon sp. e Forcepia sp., tra quelle identificate sono probabilmente nuove; Quattro specie: Paratimea oxeata, Clathria (Microciona) haplotoxa, Eurypon denisae e Haliclona (Gellius) tenuisigma, sono nuovi ritrovamenti per la fauna italiana; 11 specie sono nuovi ritrovamenti per il Mar Ligure: Cliona burtoni, Paratimea oxeata, Acarnus souriei, Clathria (Microciona) armata, Eurypon coronula, Eurypon denisae, Eurypon sp., Forcepia sp., Mycale (P.) serrulata, Merlia normani, Bubaris carcisis, Halicnemia geniculata, Dendroxea lenis, Haliclona (Gellius) bioxeata, Haliclona (Gellius) marismedi and Haliclona (Gellius) tenuisigma; 19 specie rappresentano nuovi ritrovamenti per la comunità coralligena: Stelletta stellata, Cliona burtoni, Paratimea oxeata, Acarnus souriei, Clathria (Microciona) armata, Clathria (Microciona) haplotoxa, Eurypon denisae, Eurypon sp., Forcepia sp., Hymedesmia (Hymedesmia) baculifera, Hymedesmia (Hymedesmia) rissoi, Phorbas mercator, Plocamionida ambigua, Mycale (Aegogropila) tunicata, Mycale (Paresperella) serrulata, Merlia normani, Hymerhabdia typica, Halicnemia geniculata, Haliclona (Gellius) bioxeata and Haliclona (Gellius) marismedi. Secondo la letteratura disponibile 285 specie di poriferi sono fino ad ora descritte per le concrezioni coralligene del Mediterraneo. I nostri dati aumentano questo valore a 310 e confermano che il coralligeno è una straordinaria riserva di biodiversità ancora largamente inesplorata. Le spugne sono il più importante phylum del coralligeno e, anche se non partecipano direttamente alla deposizione della matrice carbonatica, agiscono attivamente sia nella demolizione che nel compattamento della struttura. I nostri dati chiaramente indicano che i rilievi fotografici sono largamente insufficienti a stimare la diversità dei poriferi del coralligeno: le spugne perforatrici ed insinuanti sfuggono, ad esempio, a questa analisi. Questo lavoro, che considera per la prima volta le specie epilitiche ed endolitiche potrebbe rappresentare un riferimento per ulteriori studi su questo habitat che dovrà essere inserito nei programmi di tutela dell’ambiente marino.
The main goal of this study was the description of the diversity of the sponge fauna living associated with the coralligenous concretions. This habitat represents the most important "hot spot" of biodiversity in the Mediterranean Sea. Sampling was performed by diving in four sites of the Ligurian Sea (Italy), between 30 and 40 m depth: Punta del Faro (Portofino, MPA), Punta Manara (Portofino, MPA), Gallinara Island (Falconara and Sciusciaù stations) and Santo Stefano. Coralligenous blocks with a total average volume of about 20 litres were collected from each site and all the sponge species settled on the surface of them were removed, identified and grouped according to their morphology. The species settled on the shaded and lighted side of the blocks were separately grouped. Additionally, two blocks per station were cut into slices about 2 cm thick allowing the identification of the endolithic species. A total of 108 sponge species were recorded: 59 from Portofino, 54 from Gallinara Island, 53 from Punta Manara and 37 from Santo Stefano. The diversity, dominance and species richness of the analyzed sponge assemblages of the coralligenous resulted significantly related to the level of irradiance. Sponges from all the sites were more abundant (number of individuals and % of coverage) on the shady side than on the exposed part of the concretions; the species richness indexes confirmed a higher diversity on the shady side. On the shady side the encrusting species were the most abundant probably in relation to the greater substrate availability due to the lower algal competition. On the contrary the lighted side hosted massive and arborescent sponges that are therefore vulnerable to anthropogenic impact. It is possible to hypothesize that a high abundance of these species indicates sites characterized by a good conservation status of the coralligenous communities. The boring sponges (8% of the identified species in this study) represented, from a functional and structural point of view, a group very important in the coralligenous dynamic; the number of excavating species associated to the examined structures was relevant (10) respect to the data reported in literature (only 4 species). Insinuating sponges, living in the internal crevices of the rocky structures, counts up to 25% of the total identified sponges with Stoeba plicata as the more abundant species. Cliona viridis, Jaspis johnstoni and Stoeba plicata are the species reaching the greatest depths inside the concretion, being able to penetrate up to 5 cm into the rock. Regarding the other main morpho-functional categories of the sponges, the massive species represented about 20-30% of the whole assemblage. Regarding the distributional patterns and biogeography two species Eurypon sp. and Forcepia sp. are new; four species Paratimea oxeata, Clathria (Microciona) haplotoxa, Eurypon denisae and Haliclona (Gellius) tenuisigma, are new findings for the Italian sponge fauna; 11 species represent new findings for the Ligurian Sea: Cliona burtoni, Paratimea oxeata, Acarnus souriei, Clathria (Microciona) armata, Eurypon coronula, Eurypon denisae, Eurypon sp., Forcepia sp., Mycale (P.) serrulata, Merlia normani, Bubaris carcisis, Halicnemia geniculata, Dendroxea lenis, Haliclona (Gellius) bioxeata, Haliclona (Gellius) marismedi and Haliclona (Gellius) tenuisigma; 19 species represent new records for the coralligenous community: Stelletta stellata, Cliona burtoni, Paratimea oxeata, Acarnus souriei, Clathria (Microciona) armata, Clathria (Microciona) haplotoxa, Eurypon denisae, Eurypon sp., Forcepia sp., Hymedesmia (Hymedesmia) baculifera, Hymedesmia (Hymedesmia) rissoi, Phorbas mercator, Plocamionida ambigua, Mycale (Aegogropila) tunicata, Mycale (Paresperella) serrulata, Merlia normani, Hymerhabdia typica, Halicnemia geniculata, Haliclona (Gellius) bioxeata and Haliclona (Gellius) marismedi. According to the available literature 285 sponge species have been hitherto recorded from the Mediterranean coralligenous concretions. The obtained data increase this number to 310 and confirm that the coralligenous concretions are an extraordinary reservoir of biodiversity still largely unexplored. Sponges are the most diversified phylum of the coralligenous and, even if they do not directly participate to the construction of the calcareous matrix, they act as important engineers of this structure, with both their compacting and boring activities. These data clearly demonstrated that photographic analysis largely underestimates the coralligenous sponge diversity. For example this method does not allow the record of boring sponges accounting for about 8% of the total. Taking in consideration both epi- and endolithic sponges this work represent a baseline information for the monitoring programs of this complex habitat, yet recognized at an international level, that need to be included within the priority habitat needing a complete protection.

The Mediterranean Sea is considered as a complex marine ecosystem because of its changes and the variety of the regional physical processes occurring in the area such as the thermohaline circulation, vertical mixing and deep-water formation. One of the major challenges in ocean monitoring is to understand and estimate the changes in chemical and biogeochemical properties of seawater, since they might be affected by various processes. The Mediterranean Sea is characterized by various nitrate to phosphate ratios due to the overall circulation and atmospheric and terrestrial inputs The purpose of the PhD project was focused on inorganic nutrient variability in the Western Mediterranean Sea. Thus, to investigate spatial and temporal changes in biogeochemical properties on the Western Mediterranean Sea throughout the 2004-2017 period. It is mainly based on the in-situ observation collected during various European projects, a regional comparison of biogeochemical properties at regional scale and on a climatological study at the scale of the integrality of the Western Mediterranean. We performed a careful primary and secondary quality control of nitrate, phosphate and silicate measurements and generated a new product (CNR_DIN_WMED) with unpublished oceanographic data in the Mediterranean Sea. Since there are still monitoring gaps, both in time and in space related to nutrient observations, the new data product provides a good spatial and temporal coverage. We compared biogeochemical properties between regions of the WMED, and set an inventory of average ratio characterizing each region, trying to relate the effect of the local physical mechanisms. In the final part, a climatological analysis on the WMED was embedded to quantify and investigate the spatial and temporal variability of nutrients at different depth levels. The WMED is turning to a relatively nutrient enriched basin after the Western Mediterranean transient at intermediate and deep layers.

Parasitic infections contribute to natural mortality in population of free ranging sea turtles and cetaceans worldwide. Notwithstanding all host-dependant factors influencing the outcomes of parasitic infections, some parasites, spanning from protozoan to helminthic taxa, have a high pathogenic potential and can cause fatal disease in these animals. Sea turtles blood flukes (Digenea: Spirorchiidae) are a main factor in mortality of populations of green and loggerhead turtles in Atlantic and Pacific Ocean. In order to explore presence and pathology of spirorchiidiasis in the Mediterranean area, data from 168 loggerhead turtles (Caretta caretta) stranded dead along North Western Adriatic coast were collected during a six-years period. Parasitological study and pathological findings revealed the presence of eggs and adult flukes of Hapalotrema mistroides and Neospirorchis – Neogen 11, with prevalence of 15.5% and 6.0% respectively. Mild lesions were observed, including multifocal granulomatous enteritis and chronic focal vasculitis of the major vessels. Egg emboli were found widespread in the tissues, mostly attributable to H. mistroides. Sequencing of rDNA markers (28S and ITS-2) and phylogenetic analyses revealed the identity of the Mediterranean isolates with Floridian specimens. Genetic analysis on the hosts led to the conclusion that the life cycles of both genera can be entirely supported by the Mediterranean ecosystem. To estimate the infection intensity, a new rapid method was set up. Correlation between spleen egg burden and fecal egg output was studied by means of statistical tests applied to splenic tissue and fecal material, revealing the absence of correlation and the unreliability of fecal burden to assess severity of the disease in vivo. Gastrointestinal helminth community of loggerheads was also studied, revealing a species diversity typical of demersal stage turtles and similar to that observed in other neritic areas of the Mediterranean. As for cetaceans, crassicaudosis is considered one of most severe helminthic infections in these animals. Nevertheless, knowledge on the epidemiology of Crassicauda species is scarce, due to constraints of sampling free-ranging wild host species and to the difficulty of obtaining entire specimens suitable for morphologic studies. Presence and pathology of Crassicauda boopis were investigated in fin whales (Balaenoptera physalus) stranded along Italian coasts. Severe lesions linked to the presence of adult nematodes in circulatory system and kidneys were detected in five rorquals (5/7), associated with renal function impairment and arteritis of the mesenteric vessels linked to spirurid larvae migrans. Morphological studies enabled the identification of the adult nematodes as C. boopis. Sequencing of molecular barcode regions was performed on adult and larval nematodes from the whales; additionally, specimens of Crassicauda spp. isolated from toothed whales were morphologically and molecularly studied. A multigene analysis made on the barcode regions of rDNA and on the mtDNA revealed the ITS-2 spacer to be the most efficient marker in species differentiation inside the genus Crassicauda. This analysis opened new insights on the identity of the isolated larvae migrans and on the life cycles of these poorly known nematodes. Furthermore, during the parasitological examination, immature elements of the genus Pennella were recovered from one fin whale and described from a morphological point of view for the first time. Preliminary molecular data were obtained, with the aim of clarifying the taxonomy of the genus Pennella. The coccidian Toxoplasma gondii was detected in the tissues of one rorqual as well, likely associated with a chronic infection. In conclusion, these parasitological surveys highlighted the importance of a continue monitoring of the health of these endangered species avoiding underestimating the potential impact of parasitic diseases in natural mortality.
Le infestazioni parassitarie contribuiscono alla mortalità naturale in popolazioni di tartarughe marine e cetacei in tutto il mondo. A prescindere dai diversi fattori dipendenti dall’ospite che possono influenzare l’esito di tali infestazioni, alcuni parassiti, dai protozoi agli elminti, possiedono un alto potenziale patogeno, tale da essere causa primaria di morte. Infestazioni da Trematodi Digenei del sistema cardiocircolatorio (Digenea:Spirorchiidae) sono un’ importante causa di morbidità in popolazioni di tartarughe marine degli oceani Pacifico e Atlantico. Per indagare la presenza e la patologia di questa infestazione nel Mediterraneo, sono stati raccolti dati da 168 tartarughe Caretta caretta spiaggiate lungo la costa adriatica nord occidentale in un periodo di sei anni. L’approccio parassitologico, sia tradizionale che molecolare, e lo studio anatomopatologico hanno rivelato la presenza di uova e adulti di Hapalotrema mistroides e Neospirorchis – Neogen 11 con prevalenze di 15.5% e 6.0% rispettivamente. Sono state riscontrate lesioni lievi, tra cui enterite granulomatosa multifocale e vasculite cronica focale a carico dei grossi vasi. Il sequenziamento dei markers genomici (28S e ITS-2) e l’analisi filogenetica hanno permesso di verificare l’identità dei nostri campioni con quelli isolati in Florida. Analisi genetiche effettuate sugli ospiti hanno portato a concludere che il ciclo vitale di questi parassiti può completarsi all’interno del Mediterraneo. Un nuovo metodo rapido per la quantificazione dell’intensità di infestazione è stato quindi messo a punto. È stata studiata la correlazione tra l’emissione di uova nelle feci e la presenza di uova nei tessuti attraverso l’applicazione di test statistici, che hanno rivelato l’inattendibilità del valore della carica di uova fecali al fine di stimare la gravità dell’infestazione in vivo. Per quanto riguarda i cetacei, la crassicaudosi è una delle più gravi elmintiasi in questi animali ma ciononostante i dati sull’epidemiologia di Crassicauda spp. sono ancora scarsi, a causa delle limitazioni poste dal campionare queste specie ospite e alla difficoltà di ottenere campioni parassitologici integri. La presenza e la patologia della crassicaudosi sono state studiate in balenottere comuni (Balaenoptera physalus) spiaggiate lungo le coste italiane. Gravi lesioni collegate alla presenza di nematodi adulti nel sistema circolatorio e nei reni sono state trovate in cinque animali (5/7), in presenza di insufficienza renale in un caso e arterite dei vasi mesenterici associata alla presenza di larvae migrans di nematodi spiruridi. Gli studi morfologici, comparati con le descrizioni in letteratura, hanno permesso di identificare i parassiti adulti come Crassicauda boopis. Sono state sequenziate le regioni di barcoding sui parassiti adulti e sulle larve e, parallelamente, altri individui di Crassicauda spp., isolati da odontoceti, sono stati studiati morfologicamente e molecolarmente. Un’analisi multigenica sulle regioni barcode ha rivelato che il segmento ITS-2 si è rivelato il più efficiente nella distinzione di specie all’interno del genere Crassicauda. Questa analisi apre nuove questioni riguardo l’identità delle larve migrans e il ciclo vitale di questi nematodi. Durante l’esame parassitologico, elementi immaturi di Pennella spp. sono stati isolati da una balenottera e descritti morfologicamente per la prima volta. Dati molecolari preliminari sono stati ottenuti al fine di chiarire la tassonomia del genere Pennella. Toxoplasma gondii è stato isolato da un altro esemplare, associato a infezione cronica. I dati parassitologici raccolti hanno rivelato l’importanza di un continuo monitoraggio della salute di queste specie che tenga in considerazione il potenziale effetto delle parassitosi sulla mortalità naturale.

The Strait of Gibraltar limits the exchange between the Atlantic and the Mediterranean Sea and therefore plays an important role in determining the water properties of the evaporation-dominated Mediterranean Sea. On the other hand, the strait dynamics depends on the boundary conditions set by the basin. To investigate this fundamental feedback between strait and basin processes, a 3-box model of the Mediterranean with a hydraulically controlled strait was programmed. It accommodates both maximal and submaximal strait exchange and does not impose steady state budget constraints, making it particularly useful for investigating transitional and non-equilibrium situations. The model is used in an explorative study to find new dynamical aspects of the system. First, the response of the system to changing air-sea-fluxes is modelled. Increasing evaporation shifts the steady state of the system to a more saline and - as a secondary effect - slightly warmer state. Increased heat loss leads to a colder and slightly less saline basin. Besides shifting the steady state, changes in heat flux and net evaporation can also lead to a nonlinear response in which the pycnocline deepens considerably for a transitional period of decades or centuries before returning to its steady state depth. Second, the effect of rising sea levels since the Last Glacial Maximum (18kyr BP) was modelled. At times of rapid sea level rise, the long residence time leads to stronger stratification and reduced circulation in the basin, providing a possible mechanism for the formation of sapropel S1. Finally the effect of mixing in the hydraulic jump between the Mediterranean and the Strait of Gibraltar is included in the model. The entrainment of inflowing water into the outflow reduces the effective exchange between Atlantic and Mediterranean, and the system develops multiple equilibria. After a comparatively short perturbation (e.g. a 20% larger evaporation for 10 years), the system can move from the stable, well-ventilated state to an almost stagnant meta-stable state which persists for centuries before the well-ventilated state is reestablished.

The potential capacity of fertilization of surface oceans by atmospheric deposition is of scientific interest. This is especially true in the oligotrophic Mediterranean Sea. Its surface waters are extremely poor in nutrients necessary for plankton growth. At the same time, it borders with the largest and most active desert area in the world and the atmosphere over the basin is subject to frequent injections of mineral dust particles. Moreover, future scenarios foresee increases in the region's aridity, thus increasing the dust load, as well as changes in ocean stratification that will increase the potential impact of dust deposition on surface waters. Thus, it is important to study the links between deposition and plankton stimulation. In this context, the present thesis addresses relationships between desert dust deposition and phytoplankton dynamics in the Mediterranean Sea. It places especial emphasis: (1) on the seasonal and geographical patterns of both dust deposition and chlorophyll variability, (2) on the correlation between dust deposition and chlorophyll concentration, (3) on the analysis of the large deposition events and (4) on the effects on chlorophyll concentration due to very large dust deposition events occurred between 2000 and 2007. Broadly, dust deposition seasonal dynamics shows highest values in late autumn and winter in the Central and Eastern Mediterranean. While, the high dust deposition occurs close to Africa with a decreasing gradient from South to North in the basin. By contrast, the distribution of chlorophyll shows decreasing gradients both from West to East and from North to South. In addition, its broadest variability was found in the Western Mediterranean, coinciding with the highest chlorophyll concentrations on average. Positive correlations between dust deposition and chlorophyll concentration were found in large areas of the Mediterranean Sea, with a clear South to North decreasing gradient in correlation coefficient. This is especially true for the Central and the Eastern Mediterranean, where dust deposition dynamics matches with chlorophyll annual dynamics. Areas with positive correlations can be found during all seasons, although it is in spring when we see the largest correlation coefficients mainly in the Central, Eastern and Southwestern Mediterranean. Finally, 153 large dust deposition events were identified between 2000 and 2007. May of them occurred in the years 2000 and 2004, especially in autumn and winter even if they showed a high variability. The Eastern Mediterranean was more affected by the extensive events especially in winter. About the very large dust deposition events, 31 were identified during this period. They were distributed unequally over seasons and over the Mediterranean sub-basins, occurring mainly in autumn and winter in the Central and eastern Mediterranean. Chlorophyll concentration increases significantly after very large dust deposition events showing peaks in concentration between days 1 and 6 after the event, with chlorophyll increments ranging from 13% to 345% for the different outbreaks. The impact of these large events on chlorophyll shows a decreasing trend from west to east and seems to be related to the eastward increasing importance of heterotrophic bacteria with respect to phytoplankton.
La potencial capacidad de fertilización de la superficie de los océanos por deposición atmosférica es de interés científico. Esto es especialmente cierto en el oligotrófico Mar Mediterráneo. Sus aguas superficiales son extremadamente pobres en nutrientes necesarios para el crecimiento del plancton. Al mismo tiempo, limita con la mayor y más activa zona desértica en el mundo y la atmósfera sobre la cuenca está sujeta a frecuentes inyecciones de partículas de polvo mineral. Por otra parte, los escenarios futuros prevén aumentos en la aridez de la región, lo que aumenta la carga de polvo, así como cambios en la estratificación del océano que aumentará el impacto potencial de la deposición de polvo en las aguas superficiales. Por lo tanto, es importante estudiar los vínculos entre la deposición y la estimulación de plancton. En este contexto, la presente tesis aborda las relaciones entre la deposición de polvo del desierto y la dinámica del fitoplancton en el Mar Mediterráneo. Pone especial énfasis: (1) sobre los patrones estacionales y geográficos tanto de la deposición de polvo cuanto de la variabilidad de la clorofila, (2) en la correlación entre la deposición de polvo y la concentración de clorofila, (3) en el análisis de los grandes eventos de deposición y (4) en los efectos sobre la concentración de clorofila debido a los grandes eventos de deposición de polvo producidos entre 2000 y 2007. En términos generales, la dinámica estacional de la deposición de polvo muestra valores más altos a finales de otoño y en invierno en el Mediterráneo central y oriental. Mientras, la mas alta concentración de deposición de polvo se produce cerca de África con un gradiente decreciente de sur a norte en la cuenca. Por el contrario, la distribución de la clorofila muestra la disminución del gradientes tanto de oeste a este cuanto de norte a sur. Además, su variabilidad más amplia se encuentra en el Mediterráneo Occidental, coincidiendo con las más altas concentraciones de clorofila en promedio. Correlaciones positivas entre la deposición de polvo y la concentración de clorofila se encuentran en grandes áreas del Mar Mediterráneo, con un claro gradiente decreciente de Sur a Norte del coeficiente de correlación. Esto es especialmente cierto para el Mediterráneo central y oriental, donde la dinámica de deposición de polvo coincide con la dinámica anual de clorofila. Las áreas con correlaciones positivas se pueden encontrar durante todo el año, aunque es en primavera, cuando vemos los coeficientes de correlación mas altos sobre todo en el centro, este y suroeste del Mediterráneo. Por último, 153 grandes eventos de deposición de polvo se identificaron entre 2000 y 2007. La mayoría de ellos se produjeron en los años 2000 y 2004, sobre todo en otoño e invierno aunque mostraron una alta variabilidad. El Mediterráneo oriental se ve más afectado por los extensos eventos, sobre todo en invierno. Acerca de los muy grandes eventos de deposición de polvo, 31 fueron identificados durante este período. Fueron distribuidos de manera desigual durante las estaciones del año y en las sub-cuencas del Mediterráneo, se produjeron principalmente en otoño e invierno en el centro y en el este del Mediterráneo. La concentración de clorofila aumenta significativamente después de los muy grandes eventos de deposición de polvo y muestra picos de concentración entre el día 1 y 6 después del evento, con un incrementos de la clorofila que van del 13% al 345% para los diferentes eventos. El impacto de estos grandes eventos en la clorofila muestra una tendencia a la disminución de oeste a este y parece estar relacionado con la importancia cada vez mayor hacia el este de bacterias heterotróficas con respecto al fitoplancton.

Plastic pollution is a huge problem that is affecting all the oceans of the Earth. Plastic items end into the sea, break into tiny pieces and pollute the marine environment. The aim of this research is to increase our knowledge on this problem by comparing microplastic and zooplankton distributions. Samples from the Mediterranean Sea and Gibraltar Strait have been collected and analyzed. Plastic fragments have been extracted, weighted, photographed, measured and analyzed with a hyperspectral camera. The planktonic part of the samples has been analyzed identifying the main typology of organisms, taking pictures of the samples and analyzing them with ImageJ to take the measures. Data analysis was focused to the plastic to zooplankton ratio. The results have highlighted that most of the plastic to plankton ratios occurred in the in 1mm-10mm size range, and half of the stations in the Mediterranean sea presented values higher than 1, meaning than there is more plastic than plankton in that size range, for 50% of the Mediterranean. The ratio was higher during the day, due to the ascent of zooplankton during night. The results clearly show that the rank of greater danger is between 1mm to 10mm, and for this reason future samplings should focus on a net for this specific size range, to make sampling more simple and effective. A pollution indicator was created, based on the data collected all around the Mediterranean Sea, which could help find out future danger classifications, and choose the best adoptable strategies to solve the problem. Furthermore, the fact that the higher ratio has been found during the day can help future plastic sampling to focus on this time lapse. Concluding, the data provided by this research will be useful to better understand the degree of plastic contamination of our oceans and give updates to develop quality guidelines according to the Marine Strategy Framework Directive.

Esta tesis analiza los efectos socio-económicos de la acidificación oceánica y del calentamiento del Mediterráneo. Estas presiones ambientales vienen provocadas por el incremento de las emisiones de CO2 desde la Revolución Industrial. La combinación de estas presiones puede tener consecuencias negativas sobre hábitats y especies (p.e., coralígeno, bivalvos y gorgonias) junto con pérdidas económicas para la acuicultura y el turismo. Esta tesis ha investigado dichas pérdidas, desarrollando las siguientes actividades: 1) desarrollo del marco conceptual para el estudio del impacto socio-económico de la acidificación en el Mediterráneo; 2) diagnóstico de la vulnerabilidad potencial de la acuicultura de moluscos del Mediterráneo respecto a varias presiones ambientales, según las percepciones del sector; 3) valoración del impacto de la acidificación y calentamiento del mar sobre los beneficios recreativos del buceo en zonas marinas protegidas (ZMP) del Mediterráneo compuestas por el coralígeno y gorgonias; y 4) transferencia de valores ambientales, en concreto, costes en términos de bienestar y pérdidas de ingresos turísticos a causa de estas presiones, utilizando un modelo ecológico para varias ZMP de la región Euro-Mediterránea. Las principales conclusiones son cinco: primero, la acidificación y el calentamiento del mar son perceptibles en el Mediterráneo y pueden verse acentuados durante el presente siglo. Hábitats coralígenos, arrecifes de vermétidos y praderas de Posidonia, y otras especies (p.e., especies planctónicas, bivalvos, gorgonias) son vulnerables respecto a ambas presiones. Los servicios ecosistémicos potencialmente afectados incluyen la provisión de alimentos, el soporte de actividades recreativas, la protección costera y la captura de carbono. Los sectores amenazados incluyen la pesca, la acuicultura o el turismo. Segundo, los cuestionarios a productores y ZMP indican que la acidificación es un fenómeno poco conocido y que existe una alta incertidumbre sobre sus consecuencias futuras. Muchos de los encuestados la consideran como una amenaza menor en comparación con olas de calor, el incremento gradual de la temperatura del mar o los brotes de algas tóxicas. Las olas de calor constituyen una importante preocupación para el sector acuícola, debido a experiencias recientes. Tercero, la acidificación y el calentamiento del mar pueden perjudicar zonas de buceo del Mediterráneo con hábitat coralígeno. Los resultados de un experimento basado en la elección de alternativas, realizado en la ZMP de las Islas Medes (España), indican posibles pérdidas en términos de bienestar de los buceadores para los escenarios de reducción de 50% y 100% de las gorgonias (p.e., coral rojo, gorgonia roja), de -17€ y -60€/inmersión, respectivamente. Además, el análisis de las probabilidades de selección (o rechazo) de experiencias de buceo según escenarios climáticos indica la posible pérdida de ingresos turísticos, hecho que puede perjudicar las economías locales y la financiación de las ZMP. Cuarto, estos resultados fueron extrapolados para otras ZMP similares del espacio Euro-Mediterráneo. El análisis mediante transferencia de valores ambientales se llevó a cabo junto al uso de costes en términos de bienestar y pérdidas de ingresos turísticos a partir de los resultados de un modelo ecológico para el hábitat coralígeno. Dicho modelo indica que las condiciones para la presencia del hábitat coralígeno serán probablemente menos favorables en el futuro. Las estimaciones de los costes en términos de bienestar y pérdidas de ingresos asociados alcanzarían máximos de 36,6 y 20,780 millones de euros, respectivamente. Por último, el análisis de los efectos socio-económicos de la acidificación y calentamiento del mar se enfrenta a varios desafíos. Entre otros, la incertidumbre de sus efectos sobre especies, hábitats y procesos ecológicos, y la consecuente dificultad para traducirlo a términos económicos; el desconocimiento de las sinergias con otras presiones ambientales; y la falta de conocimiento sobre el potencial de adaptación de los ecosistemas y sectores económicos.
This thesis has assessed the socio-economic effects of ocean acidification (OA) and sea warming in the Mediterranean Sea. These pressures share a common driver, namely the increase in anthropogenic emissions of CO2 since the Industrial Revolution. Their combination can be detrimental to endemic habitats and species, inter alia, coralligenous, bivalve molluscs and gorgonians. This, in turn, represents potential economic losses for bivalve mollusc aquaculture and scuba diving tourism sectors. This thesis has investigated such losses. To this end, the following tasks were undertaken: 1) development of a framework for studying the socio-economic impacts of OA in the Mediterranean Sea; 2) assessment of the potential vulnerability of Mediterranean bivalve mollusc aquaculture to climatic and non-climatic pressures by addressing the perceptions of the sector; 3) valuation of the impact of OA and sea warming on recreational benefits associated with diving in Mediterranean Marine Protected Areas (MPAs), featuring coralligenous habitat and gorgonians species; and 4) value transfer of welfare costs and tourism revenue losses due to both pressures by using an ecological model for various EU-Mediterranean MPAs. The main conclusions cover five insights. First, OA and sea warming are already perceivable in the Mediterranean Sea, and can become more pronounced throughout the century. Unique habitats like coralligenous, vermetid reefs and Posidonia oceanica meadows, and various groups of species (e.g., planktonic species, bivalve molluscs, gorgonians) are found to be vulnerable to both pressures. Likely ecosystem services to be affected include provision of food, the support of recreation activities, coastal protection, and carbon sequestration. Sea-based market activities such as fisheries (capture and aquaculture) and tourism, are sensitive to both pressures. Second, the results obtained from the questionnaires distributed among bivalve mollusc producers and representatives of Mediterranean MPAs show that OA is still poorly known, and that there is a high uncertainty about what it might imply in the future. Many respondents consider OA a low threat in comparison with other stressors, such as summer heat waves, a gradual increase in sea surface temperatures, or harmful algal blooms. Summer heat waves is a matter of great concern to the bivalve mollusc aquaculture sector, as it has already experienced various extreme events of this kind in the past years. A third insight is that OA and sea warming could affect the recreational value of Mediterranean diving areas with coralligenous. Results from a choice experiment for the MPA of Medes Islands (Spain) show potential welfare losses of scuba divers for scenarios involving a decrease of 50% and 100% in gorgonians (e.g., red coral, red gorgonian, white gorgonian) to equal -€17 and -€60/dive, respectively. In addition, the analysis of choice probabilities for selecting (or rejecting) dive experiences under various climatic scenarios indicate potential losses in tourism revenues, which in turn may affect local economies and funding of the MPA. Fourth, the previous results were extrapolated to other, similar EU-Mediterranean MPAs. This value transfer analysis combined information about welfare costs and tourism revenue losses with estimates generated by an ecological model of habitat suitability. The results show a likely decrease in the suitability of the coralligenous in the majority of the studied areas. Estimates for total welfare costs and tourism revenue losses were up to €36.6 and €20.780 million, respectively. Finally, assessment of the socio-economic effects of OA and sea warming presents various challenges associated with, inter alia, the uncertainty about the effects of these pressure on species, habitats and ecological processes, and the consequent difficulty to translate these into economic effects; the lack of understanding about the synergetic effects between multiple environmental pressures; and the uncertainty about the potential adaptation of ecosystems and economic sectors to future ocean conditions.

This research presents a detailed study of the planktonic foraminiferal records of eleven sediment cores taken from a west-east transect in the Mediterranean Sea. Correlations are based on biostratigraphy, oxygen isotope stratigraphy and assisted by AMS 14C dating. This study assesses the potential to define a foraminiferal biostratigraphy of basin-wide validity. Principal Component Analysis (PCA) is used to determine variabilities in the planktonic foraminiferal records. The first principal component groups species on its positive and negative sides in such a way that this axis may be interpreted as an expression of SST variations. This interpretation is corroborated by its close similarity to oxygen isotope records. Mean PCA scores confirm previous observations that the temperature gradient in the eastern Mediterranean basin follows the same eastward increasing trend at glacial times as it does today. In contrast, the inferred sea surface temperatures (SST) from the western Mediterranean basin suggest a reversed gradient compared to the present. Preliminary results are discussed from the unprecedented high resolution marine records from two eastern Mediterranean cores. Based on PCA and planktonic foraminiferal ratios of warm, oligotrophic mixed layer species relative to cool, more eutrophic species, a series of cool episodes is observed throughout the Holocene. The cyclicity of these events is calculated at approximately 1300 years, a figure comparable with Holocene climate fluctuations recognised previously in the North Atlantic Ocean and the Greenland Ice Sheet. Micropalaeontological investigation of two western Mediterranean cores shows for the first time that abrupt cold spells, associated with Atlantic Heinrich-events, affected the Mediterranean Sea. Unusually high abundances of the subpolar species N. pachyderma (leftcoiling) in the Gulf of Lions reflect a thriving of a normally rare taxon in the western Mediterranean, in response to distinct, short term, episodes of favourable habitat development.

The study of tides and their interactions with the complex dynamics of the Mediterranean Sea represents a crucial and important challenge in ocean modelling. In this work, the main semidiurnal and diurnal tides have been implemented in the NEMO model, with a horizontal resolution of 1/24◦, never achieved so far in this regional configuration. Both the equilibrium tide and the Atlantic tides contribute to tidal propagation in this semi-enclosed Sea. Consequently a Mediterranean Sea tidal configuration requires high resolution to solve the Strait of Gibraltar and a careful nesting on a global tidal model. On this purpose, a modelling chain is used in this work, to downscale tidal currents to the Med Sea model lateral open boundary. Tides are also very sensitive to both a reliable bathymetry and coastline, especially at the Strait of Gibraltar and to an appropriate calibration of the parameterization of the bottom friction. A barotropic- equivalent model is used to set up the configuration and to perform several sensitivity tests, then the tidal forcing is added to a complete and realistic baroclinic tidal model, which allows to study the interactions of tides with the complex dynamic of the basin. In general, modelled M2, S2, K1 and O1 waves result in good agreement with the observations. This study confirms that the interaction of the barotropic tide with the topography of the Strait of Gibraltar generates an internal tidal variability which produces an enhancement of vertical mixing at the entrance of the Mediterranean Sea. The strength of this Mediterranean tidal model is its capability to simulate from the synoptic scale to the mesoscale, an essential characteristic to understand properly the dynamics of the Mediterranean Sea and despite their moderate intensity, the important role that tides play.

ABSTRACT The main objective of this thesis is to carry out a complete analysis of all the key factors that positively or negatively affect the conservation of archaeological material in order to find the best possible way for the implementation of in-situ conservation of shipwrecks in the Mediterranean Sea. It must be kept in mind that in-situ conservation in the Mediterranean Sea is a very complicated process that requires a multidisciplinary approach and analysis of the most important parameters and factors. For this reason it was necessary to break down the entire problem into its basic components (definition, value and importance of the process of formation of shipwreck sites, the greatest threats that jeopardize it) in order to better understand and find a more efficient method for protection and in-situ conservation of shipwreck sites. In addition, this complex analysis will be supported from the theoretical point of view, as well as by the latest researches conducted in the area of the Mediterranean Sea in order to determine the real potential for the conservation of shipwrecks. It is known that the Mediterranean Sea does not provide good conditions for conservation and that the main problems associated with in-situ conservation in the Mediterranean Sea are related to natural environmental conditions, more precisely, physical and biological impacts, but also the human factors that have the greatest influence on the degradation of a shipwreck. For this reason, a large part of the thesis will be devoted to the analysis of these factors and the potential danger that they pose to a shipwreck site. It is highly important to understand how significant their impact on the degradation of archaeological shipwreck sites is, and that the future protection methods and in-situ conservation will mostly depend on them. Also, will be necessary to provide an argumentative reflection and comparative analysis of the methods and results of studies that have been applied in other areas. For this reason, the importance of projects that were carried out in the Baltic Sea in recent decades must be noted. Discoveries and conclusions from these projects have made a great contribution in the field of in-situ conservation and gained experience and knowledge have enabled the use of this method even in conditions that are significantly different from the Baltic, like, for example, in the area of the Mediterranean Sea.

It is common knowledge that the marine environment is facing a great challenge nowadays against the smallest fraction of marine litter known as microplastics (MP; < 5 mm) and nanoplastics (< 1µm). The Mediterranean Sea, due to its geographic conformation, is recognized as one of the main areas with a high accumulation of both MPs and nanoplastics. The most affected compartment seems to be the sediments, especially those bordering marine coastal areas, which act as a long-term sink of legacy and emerging contaminants of anthropogenic origin. How MPs and nanoplastics interact with marine species and in particular with benthic organisms is a research topic not yet completely understood. This knowledge-gap results in the absence of a fitting ecological risk assessment with consequent severe damages to the marine ecosystems. Among the benthic organisms of environmental concern, the sea urchin Paracentrotus lividus could be a target of MPs and nanoplastics with consequences on its ecological role and function in Mediterranean coastal areas. It is widely recognized as the key species of the Mediterranean benthic communities being grazer who defines structural complexity as well as the dynamic supply of energy, mass, and nutrients from detritus to higher trophic levels. In order to fill current knowledge gaps on the impact and interaction of MPs and nanoplastics on benthic species populating Mediterranean coastal areas, the aim of the present study was to explore mechanisms of uptake, biodisposition and clearance, and toxicological responses of selected MPs and nanoplastics in different organs and cells of the sea urchin P. lividus. In addition, a special focus was reserved on the nanoscale dimension of plastics (<100 nm), by looking at the mechanisms of the bio-nano interactions between nanoplastics and the sea urchin immune cells. The research described here has been divided in 4 chapters in which findings on polystyrene (PS) MPs and nanoparticles (PS NPs) in P. lividus have been obtained by using 3 approaches: 1) an in vivo study has been designed in order to identify mechanisms of uptake, toxicity and immunological response of either virgin or colonized MPs of different sizes; 2) an in vitro study has been performed to examine the cellular trafficking of PS NPs having negative surface charges in immune cells coupled to the evaluation of immune function and ultrastructural properties; 3) a field study was performed to assess the occurrence of MPs in wild specimens collected from various locations in the Gulf of Naples (Italy). Concerning the in vivo study, adult specimen’s sea urchins were exposed to two different sizes of PS MPs, 10 and 45 µm (10 MPs mL-1), for 72h. A size-dependent MPs uptake in sea urchins was observed; while the smallest MPs resulted located in the aquifer system, the largest ones were mainly found in the digestive system. As far as the observed effects upon exposure, PS MPs regardless of their different size both affected the immune response in terms of quantity/quality of cells, antioxidant capacity, reactive oxygen and nitrogen species. Another important finding concerns the evidence that the naturally occurring colonized MPs are higher internalized by sea urchins compared to virgin ones after 48h of exposure. Colonized microplastics were obtained by 1-week incubation in unfiltered natural sea water (NSW) collected from a coastal site in the Gulf of Naples. The biofilm formation on MPs surface targets immune cells in terms of counts and morphology as well as redox status. Therefore, it can be concluded that colonized PS MPs exhibit greater effects on sea urchin immune cells compared to virgin ones as those most commonly used in ecotoxicological studies. These results encourage the use of colonized rather than virgin MPs for a more environmentally relevant risk assessment, since once released in marine waters MPs are soon colonized both chemically and biologically. Regarding the bio-nano interactions, our in vitro study with sea urchin’s immune cells confirmed the role of surface charges (negative vs positive) as drivers of ecotoxicity. Precisely, immune cells were exposed to negatively charged PS NPs (PS-COOH; 50nm) (0, 5, 25 µg mL-1) and to PS NPs (PS-NH2; 50nm) (25 µg mL-1) for 4h. In detail, our study showed a fast uptake by phagocytes of negatively charged PS NPs and sequestration into lysosomal compartments associated with low acute toxicity in comparison with their positively charged counterparts as amino-modified PS NPs (PS-NH2). In the field study, the occurrence of MPs, mostly microfibers (MFs), in adult sea urchin specimens sampled in four sites in the Gulf of Naples was demonstrated. MFs were found both in gonads, coelomic fluid and digestive system of wild sea urchins, although in the latter in higher amounts. Polyester-based fibers were the most abundant together with natural fibers such as cotton. Potential sources could be represented by fishing lines and textiles whole fibers could be released by the sewage treatment plants. Overall these findings provided for the first time the evidence of the multisided interactions between MPs/nanoplastics and the sea urchin P. lividus with important ecological implications. This thesis provided key answers to the scientific existing gaps by establishing how MPs uptake and biodistribution occur and how these are transformed according to their surface biological characteristics. Furthermore, the key factors for estimating how the sea urchin immune response counteract exposure to MPs as well as toxicokinetic/toxicodynamic elements underlying the bio-nano-interaction have been revealed. The use of the adult sea urchin P. lividus as a suitable model has been proved to be instrumental in shedding light on the potential effects of MPs and nanoplastics on benthic marine grazer species thus stimulating future research in deepening the understanding of the potential impacts on marine communities and ecosystems.

The Mediterranean Sea is a semi-enclosed sea, connected to the Atlantic Ocean through the Gibraltar Strait and subdivided in two different regions by the Sicily Strait. The geographical extension of the basin, the surface heat flux, and the water inflow from the Gibraltar Strait are some of the basic factors determining its horizontal and vertical circulation. In the Mediterranean strong salinity and temperature zonal gradients contribute to maintain the zonal-vertical circulation, while meridional-vertical cells are equally forced by winds and deep water mass formation in three regions, the Gulf of Lyon, the southern Adriatic and the Cretan Sea areas. The objective of this thesis is to study how these cells combine together to form the Mediterranean conveyor belt system. This has never been attempted before so the conclusions are necessarily preliminary. In the first part we discuss the vertical zonal and meridional circulation by reconstructing the Wust Mediterranean vertical salinity and temperature structures in an attempt to evaluate the water mass structure consistent with modern data. Our results confirm that Wust depicted vertical circulation from scarce data is reproduced by the past 27 years observations. The structure of both meridional and zonal circulations was discussed using velocity vertical streamfunctions with two different methods. The first one, eulerian, allowed us to observe vertical structures that were already reported in the literature. Recent studies in the Atlantic Ocean have shown that gyres and eddies have an important influence in the isopycnal vertical circulation. This is called the residual circulation which was computed in this study for the first time. A possible interpretation of horizontal connection between the meridional and zonal cells was discussed using horizontal streamfunction. In the last part of the thesis we have been developing an idealized numerical model to study the vertical circulation in the Mediterranean.

La Méditerranée Nord-Occidentale (MNO) est marquée par un processus de formation d’eau profonde en hiver qui induit une forte floraison phytoplanctonique au printemps. L'objectif de cette thèse a été de caractériser la dynamique de la communauté mesozooplanctonique à l'échelle régionale de la MNO, y compris dans la zone de convection profonde (ZCP), en évaluant ses stocks, sa composition taxonomique, sa structure en taille et ses liens trophiques avec le phytoplancton, en relation avec l'environnement hydro-biogéochimique. Trois campagnes océanographiques ont été menées en saisons contrastées: hiver, printemps et été, fournissant un jeu de données unique à cette échelle régionale. Le zooplancton est caractérisé par de faibles abondances et biomasses en hiver, surtout dans la ZCP, puis par une augmentation générale printanière, en abondance et en biomasse. Des différences spatiales s’observent, la ZCP présentant les plus forts changements de biomasse de l’hiver au printemps. Les valeurs d'été sont similaires aux valeurs hivernales et sont assez homogènes dans la zone d'étude. L'impact du broutage estimé n'est pas suffisant pour contrôler globalement la floraison printanière. Cependant, au printemps, toute la MNO, à l'exception de la ZCP, subit un contrôle top-down du zooplancton sur le phytoplancton, tandis que dans la ZCP, les valeurs de chlorophylle-a restent élevées malgré la forte demande en carbone du zooplancton, ce qui indique un contrôle bottom-up. Cette étude montre que la ZCP est probablement une zone d'intense transfert d'énergie vers les niveaux trophiques supérieurs ainsi que d'export de matière organique en MNO
The North-Western Mediterranean Sea (NWMS) is characterized by a deep water convection process in winter, which induces a large phytoplankton bloom. The main objective of this thesis was to characterize the dynamics of the mesozooplankton community at the regional scale of NWMS including the deep convection zone (DCZ), by assessing its stocks, taxonomy and size structure, and by evaluating its phytoplankton-zooplankton trophic links in connection to the hydrological and biogeochemical environment. Three oceanographic cruises were conducted to map the NWMS in contrasting seasons: winter, spring, and summer. This represents a unique data set of zooplankton at this regional scale. The NWMS was characterized in winter by low zooplankton abundance and biomass. In spring, a general increase was found. Spatially DCZ was characterized by lowest stocks in winter and the highest in spring. In summer, biomass and abundance were similar to winter values and were quite homogenous over the study area. The estimated zooplankton grazing impact was not sufficient to globally control the spring phytoplankton bloom. However, in spring, all areas except the DCZ incurred top-down control by zooplankton on the phytoplankton stock. In the DCZ, the chlorophyll-a values remained high despite the high zooplankton biomass and carbon demand, indicating a sustained bottom-up control. This study indicates that the deep convection zone is likely an area of both enhanced energy transfer to higher trophic levels and organic matter export in NWMS

A climatological field is a mean gridded field that represents the monthly or seasonal trend of an ocean parameter. This instrument allows to understand the physical conditions and physical processes of the ocean water and their impact on the world climate. To construct a climatological field, it is necessary to perform a climatological analysis on an historical dataset. In this dissertation, we have constructed the temperature and salinity fields on the Mediterranean Sea using the SeaDataNet 2 dataset. The dataset contains about 140000 CTD, bottles, XBT and MBT profiles, covering the period from 1900 to 2013. The temperature and salinity climatological fields are produced by the DIVA software using a Variational Inverse Method and a Finite Element numerical technique to interpolate data on a regular grid. Our results are also compared with a previous version of climatological fields and the goodness of our climatologies is assessed, according to the goodness criteria suggested by Murphy (1993). Finally the temperature and salinity seasonal cycle for the Mediterranean Sea is described.

Il mare profondo rappresenta l’ambiente più grande del nostro pianeta, ma anche il meno esplorato. A causa dei cambiamenti climatici e dei crescenti impatti antropici, l’esistenza dei beni e servizi che questo ambiente fornisce è a rischio. Stime monetarie di tali benefici sono carenti. Elevata è la biodiversità che il mare profondo e, più in generale, gli oceani ospitano. Dalla letteratura emerge una grande variabilità della disponibilità a pagare (DAP) delle persone per la tutela della biodiversità marina. L’area geografica, le specie investigate e l’ammontare dei costi sono le variabili che maggiormente influenzano tale DAP. Molte delle relazioni tra la DAP e le variabili esplicative risultano non lineari. Una migliore comprensione della percezione che le persone hanno del mare profondo può facilitarne la valutazione economica. Utilizzando la metodologia Q, emergono punti di vista che differiscono per l’importanza attribuita a specie e habitat. L’uso di diverse condizioni di istruzione e le conoscenze scientifiche sono fattori importanti nel determinare la percezione che gli intervistati hanno del Mar Mediterraneo profondo, sebbene non sufficienti a spiegarne interamente la soggettività. Una grande eterogeneità nelle preferenze espresse da cittadini italiani, riguardo la loro DAP per la salvaguardia di tale ambiente, emerge da un esperimento di scelta discreta. Solamente alcuni dei soggetti intervistati, maggiormente sensibili verso la tutela delle risorse naturali, appaiono disponibili ad una donazione per la protezione del Mar Mediterraneo profondo, in particolar modo di ambienti a coralli. Persone con un elevato reddito, e che in passato hanno effettuato donazioni per la salvaguardia dell’ambiente, sono particolarmente disponibili a finanziare la ricerca scientifica sul Mar Mediterraneo profondo. Nessuna DAP emerge, invece, per ridurre il riscaldamento globale.
The deep sea represents the largest (but the least explored) biome on Earth. It is increasingly affected by anthropogenic stressors and climate changes, threatening the provision of crucial ecosystem services in the future. The monetary value of those benefits remains scarcely assessed. The deep sea and, more generally, oceans host a high biodiversity. A great variability in the people’s willingness to pay (WTP) for marine biodiversity emerges from the literature. Price vector, investigated species and location of studies represent the variables that most influence such WTP. Non-linear relationships between the WTP and most of the explaining variables are observed. A better understanding of people’s perception of deep sea may support its (non-market) valuation. Applying Q methodology, different perspectives on Mediterranean deep sea are revealed. The importance attributed to species and habitats vary between the points of view. The use of different conditions of instruction and the respondents’ expertise are important factors in determining the perception of Mediterranean deep sea, even if they cannot completely explain the participants’ subjectivity. A great heterogeneity in the preference of Italian citizens for preserving the Mediterranean deep sea emerges from a discrete choice experiment. Many respondents refuse to pay for supporting the protection of biodiversity and the scientific research on that remote and unfamiliar environment. By contrast, participants with a high awareness of the importance of natural resources are willing to pay for protecting, in particular, deep-water corals. High income and past donations for environmental protection positively influence the respondents’ willingness to fund further scientific researches on the Mediterranean deep sea. Overall, the global warming is of little concern for the participants, who are not willing to pay for limiting the temperature rise.

L’incremento in volume e complessità dei dati paleo rende il Big Data Analytics (BDA) un settore fondamentale della scienza che fornisce strumenti di ricerca innovativi, fondamentali per i risultati scientifici dei prossimi decenni. Per la prima volta, la deposizione del sapropel S1 è stata studiata attraverso le tecniche BDA. I saproprel sono sedimenti scuri ricchi in sostanze organiche, che si sono depositati nel mar Mediterraneo orientale durante gli ultimi 13.5 miliardi di anni (Miocene-Pliocene-Pleistocene-Olocene). Differenti ipotesi sono state proposte per spiegare la deposizione dei sapropel ma, nonostante questo, ad oggi non siamo a conoscenza dei precisi processi che determinano la sua deposizione. Lo scopo di questa tesi è quello di approfondire le conoscenze riguardanti i processi che hanno causato la deposizione di S1 ed il modus operandi del mar Mediterraneo orientale durante questo evento. Considerando la ricchezza dei dati paleo in letteratura riguardanti la deposizione di S1, abbiamo prima di tutto ideato, e successivamente sviluppato, il database BEyOND, che contiene un’ampia quantità di dati paleo relativi agli ultimi 20.000 anni di storia del mar Mediterraneo. Questa prima fase del lavoro ha incontrato difficoltà dovute alla mancanza di dati standardizzati, un aspetto che si è rivelato essere una delle principali problematiche di quando si lavora con un grande volume di dati. I risultati ottenuti attraverso la combinazione di carote raccolte in differenti bacini (Mar Adriatico, Egeo, Ionio e Levantino) ed a differenti profondità, hanno mostrato una deposizione sincrona di S1 in tutto il Mediterraneo orientale tra 10.1 e 6.5 cal. ka BP, con piccole differenze di 100-130 anni in profondità che mostrano una deposizione dipendente da quest’ultima. Questo sincronismo si è riflesso dal grande apporto d’acqua dolce avvenuto in tutto il Mediterraneo. Questo apporto d’acqua, insieme ai diversi eventi freddi osservati a 9.5, 8.5 (in relazione all’evento 8.2 ka), e 7.5 cal. ka BP, conferma la stretta interazione dei sistemi climatici fra le medie (Atlantico nord) e basse latitudini (il monsone del nord di Africa). Gli eventi freddi, precedentemente citati, incrementarono la circolazione dell’acque intermedie con la conseguente formazione delle acque profonde, che migliorarono le condizioni di ossigeno nei fondali marini. Le differenti condizioni di ossidoriduzione ed il variabile contenuto di TOC osservato fra i bacini, inoltre, non sono rappresentativi delle forzanti locali ma sono correlati alle differenti profondità dell’acqua. Infine, è stato osservato che l’iniziale deposizione di S1 non è avvenuta in condizioni anossiche, poiché queste condizioni si sono manifestate dopo 400-500 anni dall’inizio di S1. Questi risultati sono in linea con il progressivo deterioramento della ventilazione delle acque profonde dei fondali del Mediterraneo orientale.
The growing complexity and volume of paleodata make Big Data Analytics (BDA) a fundamental field of science that will provide ground-breaking research tools that will be instrumental to the scientific accomplishments of the next decades. For the first time, the sapropel (S1) deposition has been studied through BDA techniques. Sapropels are organic-rich dark sediments deposited during the last 13.5 million years (Miocene-Pliocene-Pleistocene-Holocene) in the eastern Mediterranean Sea. Even though several mechanisms have been proposed that might have led to the deposition of sapropels, but until now, we not know the precise process of it. The goal of this thesis was to use the novel Data Analytics (DA) techniques to contribute to identify the mechanisms leading to S1 deposition, and deepening our understanding of the modes of operation of the eastern Mediterranean Sea throughout S1. Taking advantage of the great wealth paleodata in the literature at the time of S1 deposition, we designed and developed the BEyOND database, which provides a large amount of paleodata record of the Mediterranean Sea past 20.000 years history. This first step revealed the need for data standardization as the main issue when working with a huge data volumes. The results obtained by combination of cores collected at different water depths and located across the eastern Mediterranean Sea (Adriatic, Aegean, Ionian, and Levantine Seas) shown a synchronous S1 deposition in the whole eastern Mediterranean Sea between 10.1 and 6.5 Cal. ka BP with slight differences of the order of 100-130 years, showing a depth-dependent deposition. This synchronism was reflected in the large input of freshwater in the whole eastern Mediterranean Sea that, together with the cold events observed at 9.5, 8.5 (related to 8.2 ka event), and 7.5 Cal. ka BP, confirm the close interplay between mid- (North Atlantic) and low-latitudes (North African Monsoon) climate systems. These cold events caused activation/enhancement of the intermediate waters circulation and the subsequent resumption of deep-water formation that improved the oxygen conditions. Furthermore, the different redox conditions and TOC contents observed among the sub-basins are not representative of the local forcings but correlate to different water depths. Finally, the S1 onset did not occur under anoxic waters, as these were settled 400-500 years after S1 onset, in line with the progressive deterioration of deep water ventilation.

Questa tesi studia l’applicazione di simulazioni numeriche relative ad eventi estremi, sia atmosferici che oceanici, che si verificano nel bacino del Mediterraneo e che sono fortemente influenzati dall'interazione aerea-mare. Nella prima fase di questo lavoro viene proposta la caratterizzazione fisica degli eventi studiati. I fenomeni studiati sono: i) un evento di Cold Air Outbreak (CAO) avvenuto nell'inverno del 2012 nell'area del Mediterraneo centrale, e in particolare nel nord dell'Italia; ii) un evento di Dense Waters Formation (DWF) prodotta da questo evento CAO; e iii) un evento di "Tropical-Like Cyclone" (TLC) (chiamato "ROLF") che si è sviluppato sulle isole Baleari tra il 6 e il 9 novembre 2011. Inoltre vengono proposti i risultati preliminari di uno studio su un Flood Flash formato sulla Laguna di Venezia. Discuteremo le caratteristiche fisiche che governano questi fenomeni, in particolare l'interazione oceano-atmosfera. Dopo aver descritto questi fenomeni, proponiamo alcune considerazioni sulle applicazioni numeriche necessarie per una corretta simulazione di questi fenomeni, basandoci principalmente su tre approcci numerici. Il primo approccio numerico utilizzato è del tipo "Uncoupled", che consiste nell'uso di modelli atmosferici non accoppiati con modelli oceanici ricavano i dati di SST da datasets satellitari. Il secondo approccio utilizzato si riferisce all'uso di modelli accoppiati di atmosfera-oceano, mentre il terzo presenta l'accoppiamento completo tra atmosfera-oceano ed onde. Lo scopo di queste tecniche di modellizzazione è cercare di descrivere con maggiore precisione i flussi di momento e di calore che si esplicano all’interfaccia aria-mare e che caratterizzano e guidano l’evoluzione di alcuni fenomeni estremi, atmosferici ed oceanici. I risultati mostrano che l'uso di modelli accoppiati fornisce risultati migliori se comparato ad applicazioni non accoppiate, suggerendo spunti significativi per lavori futuri anche nel campo climatologico.
This thesis is the result of the work carried out in the three years of course, dealing with the issue of the application of numerical simulations related to extreme events, both atmospheric and oceanic, that appear over the Mediterranean basin and that are strongly influenced by the air-sea interaction. In the first phase of this work the physical characterization of the studied events is proposed. The phenomena studied are i) a case of Cold Air Outbreak (CAO) formed in the winter of 2012 on the central Mediterranean area, and in particular in the north of Italy; ii) a Dense Waters Formation (DWF) produced by this CAO event; and iii) one event of "Tropical-Like Cyclone" (TLC) (called “ROLF”) that developed on the Balearic Islands between the 6th and the 9th of November 2011. Moreover, preliminary results about a Flash Flood formed over the Venice Lagoon are showed in the end of this manuscript. We will discuss the physical characteristics that govern these phenomena, in particular the interaction between sea and atmosphere. After describing and studying the above mentioned phenomena, we propose some considerations regarding the numerical applications that are needed in order to obtain better results. The modeling techniques used for this thesis are mainly three. The first approach used is a classical "Uncoupled", which consists in the use of atmospheric models uncoupled to ocean models and wave models that exploit SST satellite data. The second approach used refers to the use of "Coupled" ocean-atmosphere models, and the third presents the ocean-wave atmosphere coupling. The purpose of these modeling techniques is to try to describe accurately the momentum and heat fluxes that appear at the air-sea interface, and that characterize, very often, some atmospheric and oceanic phenomena. Results show that the use of coupled models provide improved results, having this approach a direct impact mostly on some heat and momentum fluxes and the SST evolution, fundamental in some applications. Moreover, other indirect implications brought along by the use of coupled models, that are often important at the basin scale and regarding also the case of deep marine ventilation, are presented and discussed (Benetazzo et al., 2013, Carniel et al., 2016, Ricchi et al., 2016, Ricchi et al., 2017, Bonaldo et al., 2017).

Riverine influences in the Mediterranean Sea are investigated by means of numerical experiments performed with an ocean general circulation model implemented in the basin, along with the model capability to correctly reproduce the thermohaline properties of the basin through an improved representation of the riverine inputs. As a first step, an improved implementation of the Dardanelles Strait inflow into the Mediterranean Sea is performed, moving from a river-like parameterization to a lateral open boundary condition implementation. The river runoff impacts on the Mediterranean Sea are then evaluated by means of sensitivity experiments considering an increased number of river runoff sources, different riverine outflow salinity values, a modified mixing at river mouths and a different vertical mixing scheme adopted in the ocean model. With the purpose of further improving the representation of the estuarine processes affecting the riverine outflow salinity and volume flux, which cannot be resolved by the current resolution of the Mediterranean Sea ocean model, an Estuary Box Model simulating the estuaries dynamics is implemented at each river and 1-way offline coupled with the Mediterranean Sea ocean model. The results of the performed numerical experiments are validated with respect to in situ and satellite observations to evaluate the capability of the model to correctly represent the thermohaline properties of the Mediterranean Sea. In addition, the riverine influences are evaluated assessing the impacts of the tested river runoff forcings on the mixed layer depth, the circulation pattern, the sea surface height and the water volume transport through the major straits of the Mediterranean Sea, comparing the numerical results with available climatological data sets and reference literature.

Air-sea interactions are a key process in the forcing of the ocean circulation and the climate. Water Mass Formation is a phenomenon related to extreme air-sea exchanges and heavy heat losses by the water column, being capable to transfer water properties from the surface to great depth and constituting a fundamental component of the thermohaline circulation of the ocean. Wind-driven Coastal Upwelling, on the other hand, is capable to induce intense heat gain in the water column, making this phenomenon important for climate change; further, it can have a noticeable influence on many biological pelagic ecosystems mechanisms. To study some of the fundamental characteristics of Water Mass Formation and Coastal Upwelling phenomena in the Mediterranean Sea, physical reanalysis obtained from the Mediterranean Forecating System model have been used for the period ranging from 1987 to 2012. The first chapter of this dissertation gives the basic description of the Mediterranean Sea circulation, the MFS model implementation, and the air-sea interaction physics. In the second chapter, the problem of Water Mass Formation in the Mediterranean Sea is approached, also performing ad-hoc numerical simulations to study heat balance components. The third chapter considers the study of Mediterranean Coastal Upwelling in some particular areas (Sicily, Gulf of Lion, Aegean Sea) of the Mediterranean Basin, together with the introduction of a new Upwelling Index to characterize and predict upwelling features using only surface estimates of air-sea fluxes. Our conclusions are that latent heat flux is the driving air-sea heat balance component in the Water Mass Formation phenomenon, while sensible heat exchanges are fundamental in Coastal Upwelling process. It is shown that our upwelling index is capable to reproduce the vertical velocity patterns in Coastal Upwelling areas. Nondimensional Marshall numbers evaluations for the open-ocean convection process in the Gulf of Lion show that it is a fully turbulent, three-dimensional phenomenon.

Sea water samples were collected from different sampling stations along the Lebanese coast in the summer of 1994. Chemical, biological and physical analysis were conducted to assess the recreational water quality in Lebanon.
Some 125 samples were then analyzed for the presence of Cadmium and Mercury by atomic absorption spectrophotometry. Cadmium content, holding a mean 0.77 $ mu$g/L, was generally low for most areas with only a few elevated readings in Tripoli (1.89 $ mu$g/L), Checca (1.83 $ mu$g/L), Kaslik (0.79 $ mu$g/L), Beirut (1.19 $ mu$g/L) and Ramlet Al-Bayda (1.77 $ mu$g/L). Mercury content, holding a mean value of 0.06 mg/Kg (wet weight), was below the accepted tolerance limit of 0.5 mg/Kg for all sampling sites.
Some 128 samples were then analyzed for fecal coliforms (Escherichia coli and Streptococcus feacalis). Approximately, 50% of the sampling stations showed satisfactory results (less than 100 colonies/100 ml). High counts of fecal coliforms, over 500 colonies/100 ml, collected at Dora, Ramlet Al-Bayda and Antelias, reveal poor sea water quality and a public health hazards to swimmers and fishermen.
Some 36 samples were collected and analyzed for dissolved oxygen (DO), pH, salinity and temperature. For all sites sampled, DO averaged 4.03 mg/L, pH averaged 7.97, salinity averaged 38.77 ppt and temperature averaged 27.9$ sp circ$C.
The degree of pollution was found to be related to population density, industrial and human activity, continental runoffs and hydrological and meteorological conditions.

Sea level variation is one of the parameters directly related to climate change. Monitoring sea level rise is an important scientific issue since many populated areas of the world and megacities are located in low-lying regions. At present, sea level is measured by means of two techniques: the tide gauges and the satellite radar altimetry. Tide gauges measure sea-level relatively to a ground benchmark, hence, their measurements are directly affected by vertical ground motions. Satellite radar altimetry measures sea-level relative to a geocentric reference and are not affected by vertical land motions. In this study, the linear relative sea level trends of 35 tide gauge stations distributed across the Mediterranean Sea have been computed over the period 1993-2014. In order to extract the real sea-level variation, the vertical land motion has been estimated using the observations of available GPS stations and removed from the tide gauges records. These GPS-corrected trends have then been compared with satellite altimetry measurements over the same time interval (AVISO data set). A further comparison has been performed, over the period 1993-2013, using the CCI satellite altimetry data set which has been generated using an updated modeling. The absolute sea level trends obtained from satellite altimetry and GPS-corrected tide gauge data are mostly consistent, meaning that GPS data have provided reliable corrections for most of the sites. The trend values range between +2.5 and +4 mm/yr almost everywhere in the Mediterranean area, the largest trends were found in the Northern Adriatic Sea and in the Aegean. These results are in agreement with estimates of the global mean sea level rise over the last two decades. Where GPS data were not available, information on the vertical land motion deduced from the differences between absolute and relative trends are in agreement with the results of other studies.

Salps are marine pelagic tunicates that have evolved opportunistic skills to bloom under favorable conditions and persist during adverse periods. They experience population outbursts (blooms) which, combined with their efficient feeding mechanism, produce several ecological and societal consequences. Although salp blooms are common in the Catalan Sea during spring and autumn, their causes and effects on the ecosystem have never been studied in this area before. The general aim of the present thesis is to understand the spatial and temporal processes leading to salp blooms and estimate their trophic impact in the Catalan Sea, northwestern Mediterranean Sea. For this purpose, mechanistic (matrix models) and statistical models (GAMs) combined with in situ observations allowed us to propose the simplest mechanisms to account for bloom development. In contrast to previous hypotheses, we found that changes in female reproduction drive the population to latency under unfavorable conditions and trigger the bloom when conditions improve (Chapter 1). From a spatial scale, hydrodynamic factors mainly drove high local salp abundances, although biological variables (predator abundance) had secondary importance (Chapter 2). We observed the coexistence of contrasting diel vertical migration (DVM) patterns in a salp (nocturnal and diurnal migrations), which explains controversial conclusions in previous studies, but brings new questions about the drivers of DVM in salps (Chapter 3). The two species found produced contrasting trophic impacts: Thalia democratica was less abundant and its effect on the ecosystem seemed to be negligible while, Salpa fusiformis ingested a maximum of 69.92 mg C m-2 day-1 and defecated 35.76 mg C m-2 day-1, contributing to the transport of organic matter to the deep ocean (Chapter 2). Our findings contribute to general knowledge in salp ecology. They lead us to consider evolutionary demographic studies to understand the potential benefits of their life cycle as an adaptation to environmental change and the mechanisms which maintain genetic variability after bloom-latency periods.
Les salpes són tunicats pelàgics marins que han desenvolupat característiques oportunistes per a proliferar quan les condicions són favorables i mantenir-la en períodes adversos. Les altes abundàncies assolides durant un bloom, en combinació amb els seus mecanismes d’alimentació altament eficients, tenen un efecte notable pels ecosistemes així com per a la societat. Tot i que els blooms de salpes són comuns a la costa catalana durant primavera i tardor, les seves causes i el seu paper en l’ecosistema no s’han estudiat mai al mar Català. L’objectiu general de la present tesi és entendre els processos espacials i temporals que condueixen a formar les agregacions de salpes i estimar el seu paper en el mar Català, nord-oest del Mediterrani. Per assolir aquesta fita, s’han combinat models mecanístics (models matricials) i estadístics (GAMs) amb observacions in situ que ens han permès proposar els mecanismes més simples que expliquen el desenvolupament d’un bloom. Hem vist que canvis en la reproducció de les femelles serien els responsables del fre del creixement poblacional durant el període de latència i el detonador del bloom quan les condicions es tornen favorables (Capítol 1). Des d’un punt de vista espacial, l’abundància local de salpes està influenciada principalment per factors físics tot i que les variables biològiques juguen un paper secundari (Capítol 2). Per primer cop s’ha observat la coexistència de patrons diferents de migració vertical diürna (DVM) en una salpa (migració diürna i nocturna en Salpa fusiformis), la qual cosa explica les conclusions contradictòries d’estudis anteriors, però obre noves preguntes sobre els mecanismes de la DVM en salpes. Les dues especies presents en l’estudi produïren impactes tròfics molt diferents: l’impacte de Thalia democratica, va ser quasi negligible degut a la seva baixa abundància mentre que S. fusiformis va ingerir un màxim de 69.92 mgC m-2 dia-1 i defecar 35.76 mgC m-2 dia-1, incrementant considerablement el flux de matèria orgànica cap a l’oceà profund (Capítol 2). Els resultats d’aquesta tesi contribueixen a l’ecologia general de les salpes i ens han portat a la necessitat de plantejar estudis de demografia evolutiva per entendre l’efecte del seu cicle de vida en l’adaptació de la població a canvis ambientals i en el manteniment de la variabilitat genètica entre períodes de latència-bloom.

Shallow-water corals of the Mediterranean Sea are facing a dramatic increase in water temperature due to climate change. In many cases, a shift toward environmental conditions outside the normal range of variability may cause suboptimal physiological performance, such as enhanced respiration, higher susceptibility to pathogens, bleaching, reduced calcification and tissue necrosis. However, not all corals are thought to be affected equally, because physiological performances and responses are the principal determinant of a species tolerance to environmental variability and may change the ability of corals to cope with changing conditions. In this study, transcriptional profiles of four genes involved in apoptosis (bax and bcl-2), redox regulation (sod) and energy metabolism (gapdh) have been analyzed in three common shallow-water Mediterranean scleractinian, namely Astroides calycularis, Balanophyllia europaea and Leptopsammia pruvoti. The main aim was to assess the contribution of these cytoprotective mechanisms to the physiological plasticity of the species, that possess different growth modes (solitary vs colonial) and trophic strategies (zooxanthellate vs azooxanthellate). Using quantitative real-time PCR, expression profiles after an acute heat-shock exposure (2h at 32°C + 0-24 h post-stress recovery) were assessed, and a potential timeline for the events occurring in the investigated species was disclosed. The overall transcriptional response to heat stress aligns with relative differences in stress susceptibility of the species and suggests a contribution of trophic strategy in the degree of coral resilience to stress. Understanding the overall molecular processes is demanding for corals inhabiting the Mediterranean (a biodiversity “hot spot”), in light of projected scenarios of anthropogenic global change.

La descàrrega d’aigua subterrània al mar (SGD, en les seves sigles en anglès) es defineix com a qualsevol flux d’aigua a través del marge continental des del substrat marí cap a la columna d’aigua del mar. La SGD inclou, doncs, aigua dolça d’origen continental i aigua salada que recircula a través de l’aqüífer costaner. A banda de la seva importància en el cicle hidrològic, com a font d’aigua dolça que pot alimentar, per exemple, zones humides, la SGD és considerada una font important de diversos compostos dissolts d’origen terrestre (com ara nutrients, metalls traça o contaminants) cap a l’oceà costaner. Aquests fluxos d’elements dissolts associats a la SGD poden tenir una gran influència en els cicles biogeoquímics dels ambients costaners marins, especialment en zones oligotròfiques i regions semi-àrides, com ara el Mar Mediterrani. Malgrat la importància de la SGD pel desenvolupament dels cicles biogeoquímics marins, els estudis sobre el paper de la SGD com a font de compostos dissolts als ecosistemes costaners del Mar Mediterrani són escassos. A més, a escala de tot el Mar Mediterrani, no existeixen estimacions de la magnitud de la SGD ni dels fluxos de compostos químics associats. L’objectiu principal d’aquesta Tesi Doctoral és avaluar la importància de la descàrrega d’aigua subterrània al Mar Mediterrani, així com el paper que juga com a font de compostos dissolts al mar i la utilitat dels isòtops de radi (Ra) com a traçadors per quantificar la SGD. Amb aquesta finalitat, s’han estudiat tres ambients Mediterranis costaners amb característiques hidrogeològiques diverses: i) una zona humida litoral alimentada per aigua subterrània provinent de diversos aqüífers (Marjal de Peníscola, Castelló); ii) un port natural semi-tancat, amb descàrregues d’aigua subterrània provinents d’un sistema calcari carstificat, i influenciat per la resuspensió freqüent de sediments (Port de Maó, Illes Balears); i iii) una badia oberta al mar amb descàrrega difusa d’aigua subterrània a través d’un aqüífer detrític superficial (Badia de Palma, Illes Balears). A banda d’aquestes tres zones d’estudi, també s’ha dut a terme un estudi general a tota la conca amb la finalitat d’obtenir una primera estimació de la SGD a tot el Mar Mediterrani, així com dels fluxos de nutrients associats a aquesta descàrrega. Els resultats derivats d’aquests estudis aporten nous coneixements en l’aplicació dels isòtops de Ra com a traçadors de SGD i realcen la seva idoneïtat en un ampli ventall de sistemes amb característiques hidrogeològiques diverses. Els isòtops de Ra han estat utilitzats amb èxit per a quantificar fluxos de nutrients cap al mar i, per primera vegada al Mar Mediterrani, s’ha quantificat els fluxos de metalls traça associats a la SGD, evidenciant la rellevància de la SGD com a font d’aquests compostos en ambients marins. L’avaluació de la SGD a tota la conca ha permès estimar la descàrrega d’aigua subterrània a tot el Mar Mediterrani ((0.2 – 4.3)·1012 m3·yr-1), demostrant que la SGD és un procés rellevant a llarga escala i d’una magnitud, per exemple, superior a les entrades d’aigua fluvial. A més, s’ha estimat que la SGD representa una font important de nutrients dissolts a tot al Mar Mediterrani, d’una magnitud comparable a les fonts externes considerades tradicionalment (i.e. aportacions atmosfèriques i del rius). Aquesta nova concepció de la magnitud de la SGD i dels seus fluxos associats demostra la rellevància de la SGD en els cicles biogeoquímics del Mar Mediterrani, accentuant la necessitat d’incloure aquests procés en futurs estudis marins, tan costaners com globals.
Submarine groundwater discharge (SGD) is defined as any flow of water through the continental margin from the seabed to the coastal ocean, including fresh meteoric groundwater and seawater recirculating through coastal aquifers. SGD has been recognized as a major component of the hydrological cycle and a significant source of various dissolved terrestrial compounds (e.g. nutrients, trace metal, carbon, contaminants) to the coastal ocean. These fluxes of chemical elements via SGD may have a profound impact on the biogeochemical cycles of the receiving water bodies. This can be especially relevant in oligotrophic and semi-arid regions, such as the Mediterranean Sea. However, and despite the potential importance of SGD in regulating coastal biogeochemical cycles of the Mediterranean Sea, there is still a lack of detailed assessments on the relevance of SGD as a source of chemical constituents into this basin. Indeed, the magnitude of SGD to the entire Mediterranean basin and its associated fluxes of dissolved compounds have never been evaluated. The main objective of this PhD Thesis is to evaluate the importance of SGD in the Mediterranean Sea by using radium (Ra) isotopes, paying attention to the role that SGD plays as a source of dissolved chemical compounds to the sea and to the use of Ra isotopes as SGD tracers. To this aim, contrasting Mediterranean coastal environments were selected, including: i) a coastal wetland nourished by groundwater inflowing from several aquifers (Peníscola marsh, Castelló); ii) a semi-enclosed embayment highly influenced by bottom sediments (Port of Maó, Minorca, Balearic Islands); and iii) a detrital bay open to the sea (Palma Bay, Majorca, Balearic Islands). Aside from these three specific sites, the first appraisal of the magnitude of SGD into the entire Mediterranean Sea was also conducted, demonstrating its significance as a source of dissolved compounds in a basin-wide scale. Results from these studies provide new insights into the use of Ra isotopes as tracers to quantify SGD and underline their suitability in a wide range of Mediterranean hydrogeological settings. We successfully applied them to estimate SGD-driven fluxes of dissolved nutrients and, for the first time, trace metals to a coastal Mediterranean area, stressing the role SGD may play as a source of these constituents to the marine environment. We show that SGD is a volumetrically important process in the Mediterranean Sea, contributing up to (0.2–4.3)·1012 m3·yr-1, a magnitude that is significantly larger than riverine discharge. SGD also represents a major source of dissolved nutrients to the basin, rivaling the conventional external sources (i.e. atmospheric deposition and river discharge). This new understanding of the magnitude of SGD and its associated chemical fluxes demonstrates the profound implications of SGD in the biogeochemical cycles of the Mediterranean Sea, emphazising the need for its consideration in coastal and basin-wide studies.

The response of phytoplankton to various ecological forcings was examined in the upper waters of the NW Mediterranean (MED) and the subtropical North Atlantic (NA) from field observations, analysis of historical data sets and numerical simulations. Particular emphasis was given to the role played by the water column structure in controlling the nitrogen diffusion and new production. Using numerical simulations, the effects of different levels of heating of surface waters and nutrient concentrations in waters below the euphotic zone were examined.
Spring microplankton metabolism of surface mixed waters in MED was studied. The system was heterotrophic explained by dark community respiration (DCR) rates higher than gross primary production (GPP) rates. The GPP to DCR ratio was ~0.53, indicating that the system was far from balance between carbon production (photosynthesis) and consumption (respiration), probably caused by organic matter accumulation in the mixed layer favouring respiration over production processes.
Summer primary production and nitrogen fluxes in stratified water layers in NA were analysed. The nitrogen flux fuelling new primary production was closely linked to vertical turbulent diffusion at the nitracline rather than at the thermocline. Upward diffused nitrogen inducing new production explaining 21% of total primary production. The vertical turbulent diffusion model used to estimate new production did not explain new production in the Canary Current zone, where laterally advected nutrients from coastal upwelling areas altered the vertical nitrate gradients.
A numerical ecological model of the pelagic domain was developed to assess the plankton response to different environmental pressures. The model represents the vertical dimension of the upper and intermediate water layers of the open ocean. A comparative study of the plankton functioning in MED and NA sites was carried out using the model. The nitrate entering the euphotic zone through the lower boundary explained the low but continuous primary production in the two systems. The latitudinal variability of plankton scenarios implied a year round different solar heating of the upper waters, altering both phytoplankton photosynthesis and mixed layer processes in the water column, with the latter dominating over the former in controlling the phytoplankton biomass. The balance of light availability and nutrient concentration controlled the chlorophyll maximum depth, but the zooplankton grazing prevented this maximum to reach greater concentrations. The model structure and functioning makes it suitable for comparative ecological studies and is expected to be applicable to other studies related to coastal and marine environmental issues.

Les bactéries magnétotactiques (MTB) sont un groupe de bactéries caractérisées par leur capacité à synthétiser des magnétosomes et à nager le long de lignes du champ géomagnétique. Les Procaryotes Multicellulaires Magnétotactiques (MMP) représentent les MTB les plus évoluées. Deux morphotypes de MMP ont été découverts: sphérique (sMMPs) et ellipsoïdal (eMMP). Dans cette thèse, j'ai tout d'abord révélé une diversité inattendue d'eMMP de la mer Méditerranée. Quatre nouvelles espèces ont été détectées, ce qui augmente le nombre total d'eMMP identifiés en Méditerranée d’une espèce appartenant un genre à cinq espèces affiliées à deux genres. J'ai également effectué une analyse approfondie de l'architecture des eMMPs en utilisant plusieurs approches microscopiques. Les eMMP sont composés d'une couche de cellules entourant une lumière centrale. Les cellules sont disposées axisymétriquement le long du grand axe des eMMP et sont radialement symétriques le long du petit axe. Leurs membranes juxtaposées relient étroitement les cellules en une entité multicellulaire. Les eMMP se reproduisent par constriction unilatérale des cellules constituantes, de la périphérie vers le centre et par fission binaire unidirectionnelle des globules ellipsoïdaux. J'ai identifié deux bactéries magnétotactiques Nitrospirae pour la première fois collectées en milieu marin. Elles ont une morphologie sphérique, une motilité similaire. Elles synthétisent des magnétosomes en forme de balle, composés de magnétite et disposés en plusieurs de chaînes. Les deux nouvelles espèces de MTB Nitrospirae élargissent la distribution des MTB Nitrospirae de l’eau douce au milieu marin
Magnetotactic bacteria (MTB) are characterized by synthesizing magnetosomes and swimming along geomagnetic field lines. Multicellular Magnetotactic Prokaryotes (MMPs) is the most evolved MTB. Two morphotypes of MMPs have been discovered: spherical (sMMPs) and ellipsoidal (eMMPs). In this thesis, I revealed a high diversity of eMMPs from the Mediterranean Sea. Four new eMMPs species have been detected, extending the total number of identified eMMPs in the Mediterranean Sea from one species of one genus to five species of two genera. I also performed a comprehensive analysis of eMMP architecture. The eMMPs was composed of one layer of cells that surround a central lumen. The constituent cells are arranged axisymmetrically along the long axis of eMMPs and radial symmetric along the short axis. The juxtaposed membranes connect cells into a multicellular entity. The eMMPs reproduce through periphery–core unilateral constriction of constituent cells and unidirectional binary fission of the ellipsoidal MMPs. I have also identified two Nitrospirae MTB collected, for the first time, from marine environment. They have similar morphology, motility but different colors. They synthesized multiple bundles of bullet-shaped magnetite magnetosomes. The two novel Nitrospirae MTB species expand the distribution of Nitrospirae MTB from freshwater to marine