Teses / dissertações sobre o tema "Mediterranean marine ecosystems"

Plastic pollution has been recognised as one of the major global threats for marine ecosystems. In the Mediterranean basin, plastic debris are present at concentrations comparable to the subtropical ocean gyres. Microplastics (< 5 mm) also reached the most remote environment on Earth, being reported in Antarctic surface waters and sediments. The limited knowledge on the biological impacts of the smallest fraction of plastic debris, defined as nanoplastics (< 1 μm), is of primary concern, due to their high surface reactivity and nanometric size that allow to easily interact with biological surfaces at the cellular level. Within this thesis, the bioaccumulation and toxicity of nanoplastics in Mediterranean and Antarctic marine organisms have been investigated. Polystyrene nanoparticles (PS NPs), having a nominal diameter of approx. 50 nm and different surface charge, were adopted as nanoplastics as anionic carboxylated (PS-COOH) and cationic amino-modified (PS-NH2). The characterization of their behaviour in natural sea water media was combined with cellular/whole-animal bioassays in order to define uptake, disposition and mechanisms of action under controlled laboratory conditions. The four chapters of the thesis report findings on model organisms including zooplanktonic and benthic species from the Mediterranean Sea and Southern Ocean around Antarctica, as sea urchin embryos (Paracentrotus lividus), green microalga (Dunaliella tertiolecta), brine shrimp (Artemia franciscana) and Antarctic sea urchin (Sterechinus neumayeri) and krill (Euphausia superba) respectively. Overall, we proved that NP surface charge (anionic vs cationic) drives the behaviour of PS NPs in natural sea water in terms of stability and aggregation, which differs in Mediterranean and Antarctic sea waters. Anionic PS-COOH formed large micro-sized aggregates whereas cationic PS-NH2 resulted better dispersed in Mediterranean sea waters. In Antarctic sea waters, such difference in aggregation was reduced, with PS-COOH reaching nano-sized aggregates and PS-NH2 approaching the nominal size. A similar pattern of biodistribution and toxicity was observed in marine organisms from Mediterranean Sea and Antarctica, with respect to NP surface charge. Anionic PS-COOH were mostly ingested, accumulated and excreted with no or limited effect, while PS-NH2 revealed a less clear disposition but cause high toxicity, hinder embryo development and larval growth, disrupt physiology and organism’s survival. For this latter NP, several markers of stress, were identified through up-regulation of apoptotic-related genes (caspase8, hsp60, hsp70 and p-38 mapk) in Mediterranean sea urchin embryos and moulting-related genes (clap, cstb and cb6) in brine shrimp larvae and Antarctic krill juveniles. In Antarctic sea urchin coelomocytes, both PS NPs were able to reduce the cellular phagocytic capacity, with PS-COOH inducing the strongest gene modulation in contrast to a threshold in cell defence ability upon PS-NH2 exposure. Overall, ecotoxicological data constitute a comprehensive baseline on the biological effects of nanoplastics in Mediterranean and Antarctic marine species, motivating future research using more realistic exposure scenarios towards environmental-like conditions and more specific NP-biological interactions (i.e. eco and bio-coronas).

Amb aquest treball es preté comprovar la universalitat de la relació estequiomètrica de Redfield i recercar patrons consistents de les desviacions d'aquesta raó promig en ambients oligotrofics. Per tal de dur a terme aquest propòsit s'han desenvolupat relacions estequiomètriques en el compartiment particulat i dissolt orgànic i inorgànic per el C, N, P i Si.
La estequiometria dels nutrients a l'oceà s'ha examinat al Mar Mediterrani i a l'Oceà Atlàntic subtropical, mentre que la zona costenera del Mar Mediterrani ha servit per estudiar aquestes relacions sota l'influència d'aports terrestres.
En el segon capítol de la tesi es descriuen patrons meridionals del fluxe de nitrogen i fósfor vers la capa biogènica de l'Oceà Atlàntic Central. La raó promig entre el fluxe difusiu del nitrogen inorgànic dissolt (DIN) i del fósfor (DIP) es mostra similar a la raó de Redfield al llarg de l'Oceà Atlàntic Central, però tendeix a valors per sota dels establerts per Redfield a la part sud del trajecte i superiors a la raó de Redfield al centre del gir sudtropical. La raó N:P del fluxe difusiu i la raó N:P dels nutrients dissolts inorgànics en la capa biogènica es troben fortament correlacionats, mentre que no existeix cap correlació amb els valors de la raó N:P de les aigües intermitges. Els resultats trobats en aquest capítol de la tesi indiquen que la recirculació vertical de nutrients a la capa biogènica de l'oceà Atlàntic Central és capaç d'operar amb raons estequimètriques que difereixen de Redfield i per tant els components biogènics i biolítics s'adapten a les variacions locals de la raó de Redfield. La hipòtesis que existeixen raons estequiomètriques previsibles en la reserva oceànica de material dissolt orgànic que es troben en equilibri amb la reserva del material particulat orgànic i dissolt inorgànic, es corrobora en el tercer capítol d'aquesta tesi. La majoria del carboni orgànic present en aigües oligotrofiques del Mediterrani estratificat es troba en forma d'orgànic dissolt, mentre que el POC (carboni orgànic particulat) representa un percentatge menor. El nitrogen i fósfor orgànic dissolt que comprenen el 50-80% del "pool" total de P i N a la capa biogènica, decreix en percentarge a la capa biolítica. S'ha comprovat una distribució uniforme del nitrogen disolt total (TDN). L'increment en el percentatge de N inorgànic disolt i el decreixement en percentatge de N orgànic dissolt amb la fondària, és un indicador clar de l'equilibri dinàmic que existeix entre les reaccions bioquímiques entre les reserves oceàniques. Mitjançant un sistema de balanços, s'estableix un intercanvi de nutrients (exportació-importació) entre els pools dissolt orgànic i dissolt inorgànic en el sistema. S'ha comprovat que el fluxe de nitrogen orgànic dissolt (DON) excedeix al fluxe difusiu de nitrogen inorgànic i per tant els aports atmosfèrics i terrestres són importants en aquesta regió.
En el quart capítol de la tesi es descriu el lligam existent entre el component pelàgic i els component del bentos d'una àrea litoral del Mar Mediterrani, és a dir un compartiment anabolic que produeix matèria orgànica i un de catabolic que actúa com agent oxidant de la reserva de matèria orgànica del sistema. El compartiment pelàgic es mostra heterotrofic. Al mateix temps, existeix una contribució important de material terrestre als sediments. Per contra, el compartiment bentònic és autotrofic on el dèficit en la producció grossa es compensa amb l'excés de producció neta del sistema. Mitjançant la quantificació simultànea dels fluxes anuals de sedimentació per al C, N, P i Si així com dels fluxes sediment-aigua de les espècies orgàniques i inorgàniques dissoltes, s'ha establert un sistema de balanços de matèria del sistema. El compartiment bentonic es configura com a sumider o exportador de matèria orgànica, degut als aports terrestres de carboni en el sistema.
Els patrons de distribució de nutrients derivats dels resultats dels capítols anteriors es comproven mitjançant un experiment d'addició de nutrients. En el capítol cinquè d'aquesta tesi s'estudien els canvis en la distribució de nutrients en les diferents reserves nutricionals d'un sistema quan es troba sotmès a aports controlats de nutrients. S'ha comprovat que, mentre el tamany relatiu de la reserva de nutrients inorgànics dissolts no varia amb l'increment de nutrients en el medi. Hi ha una tendència a l'increment del tamany relatiu de la reserva del material particulat, paral.lela a un decreixement simultani de la reserva de material dissolt orgànic. Aquest experiment contribueix a verificar el paper del DOM (matèria dissolta orgànica) com a principal reserva nutricional en sistemes oliogotròfics.
The stoichiometric ratios are powerful tools to model basic biogeochemical patterns of the sea when the fluxes of a single element are known. It is, therefore essential to understand the full implications of variable stoichiometries to predict the effect of the living components of the ocean on biogeochemical processes. Here, the stoichiometry between C, N, P and Si in different chemical pools (particulate and dissolved organic and dissolved inorganic matter) were examined in contrasting oceanic and littoral ecosystems, and the changes in nutrient partitioning in response to nutrient inputs was tested through experimental research.
In the Central Atlantic Ocean, the average ratio between dissolved inorganic nitrogen and phosphorus in the estimated vertical diffusive fluxes was similar to the Redfield ratio, but tended to be above the Redfield ratio at the center of the South subtropical gyre. The N:P supply ratio and the N:P ratio of dissolved inorganic nutrients in the biogenic layer were strongly correlated, but were not positively correlated to that in the intermediate waters. The vertical nutrient conveyor belt of nutrients in the upper waters operates relatively independently of the underlying waters in the Central Atlantic, so that both the biogenic and the biolythic components should be able to adapt to local variation about the Redfield ratio.
In the stratified NW Mediterranean Sea, the stoichiometry between dissolved inorganic, organic and particulate organic matter pools indicated an excess nitrogen relative to phosphorus, particularly in the biolythic layer, as well as a general silicate deficiency relative to both N and P. Most (> 80 %) of the organic carbon was present as dissolved organic carbon, with POC representing a minor percent of total organic C throughout the water column. The increasing C/N ratio of DOM with depth indicates that N is recycled faster than C in the DOM. There exists a dynamic equilibrium between the biological transformations between these pools with depth, with a dominance of DON production in surface waters and remineralization in the underlying layers, from which dissolved inorganic nitrogen is re-supplied to the biogenic layer.
Alocthonous N inputs must be important in the region since the downward DON flux exceeded the diffusive DIN supply.
The coupling between anabolic and catabolic compartments of a littoral area in the NW Mediterranean Sea are characterized. The pelagic compartment was heterotrophic, supported by significant allochthonous inputs of land material, whereas the benthic compartment was autotrophic, with the excess net benthic community production balancing the deficit in pelagic community production, leading to a system in metabolic equilibrium. Sedimentary inputs of phosphorus and silicon were compensated by sediment release of phosphate and silicate, whereas nitrogen was lost or accumulated in the sediment compartment. Carbon inputs to the benthic compartment also exceeded requirements, due to the allocthonous subsidies to the system, so that the benthic compartment stored or exported organic carbon.
Experimental nutrient additions lead to a parabolic change in C/N and C/P ratios in the dissolved organic matter with increasing nutrient inputs. The relative size of the dissolved inorganic nutrient pools did not vary, but there was a tendency towards an increase in the relative size of the particulate pool at the expense of a decrease in the relative importance of DOM as a reservoir of N, P and C, with increasing nutrient inputs.
The relative importance of different nitrogen pools was examined in relation to the total nutrient stoichiometry of the oligotrophic system. The ratio of dissolved inorganic nutrients reported in the research presented is indicative of a general deficiency in nitrogen compared to the global ratios reported in literature. The dissolved organic matter was highly depleted in P relative to N and C at all locations investigated and the resulting POC:PON ratio (11.7) of this study in the particulate pool deviates greatly from the literature values which approximates Redfield value (5.5-6). The shift of the dominance of DON towards PON at TOC/TN values higher than 20 on the oligothrophic areas of the study, gives evidence of increasing carbon export fluxes in a system dominated by particulate pool and points to the effect of the biota on the gradient-driven export to sinking carbon fluxes in the ocean.

Hydrocarbon (HC) pollution is a worldwide threat to marine natural ecosystems due to the increasing exploitation of underground marine petroleum deposits in several areas and to the high traffic of oil tankers and the presence of submarine pipes that are main transport routes for crude oil and refined products. HCs spread in the marine environment is mainly due to accidental oil spills or inadequate practices and their release affects marine ecosystems causing severe ecological and economical damages. The Mediterranean Sea is particularly endangered by hydrocarbon pollution because of its physical nature – it is an enclosed basin with a slow water exchange – and because it hosts about 20% of the global oil tanker traffic in its waters and tens of oil-related sites along its coastline. The conventional remediation strategies, comprising chemical and physical methods, are extremely expensive and invasive, therefore the development of cheaper and eco-friendly approaches is crucial to preserve human and ecosystem health. In this perspective, bioremediation (i.e. the use of living organisms to remove pollutants from a contaminated area) is a promising technology which, taking advantage of microbes’ metabolic potential to degrade a wide range of pollutants, can both reduce the costs and may represent a permanent solution. Nevertheless, there is still a scarce knowledge of the processes and the microorganisms involved in the clean-up of hydrocarbons from marine environments, hence some problems still exist concerning the in-field application of bioremediation. The aim of the present PhD thesis was to: i) investigate the overall prokaryotic diversity of pristine and oil polluted sites across the whole Mediterranean Sea; ii) depict the phylogenetic and functional diversity of hydrocarbonoclastic bacteria inhabiting pristine and polluted sites; iii) establish a large collection of bacteria showing degrading activities toward hydrocarbon compounds; iv) set up microcosm experiments to investigate the potential of bacterial bioaugmentation in bioremediation processes under laboratory scale conditions, v) test the degrading potential of selected bacterial strains and consortia under different pressure values, simulating different depths along the water column. The diversity of planktonic bacterial communities in the Mediterranean Sea was firstly evaluated on open seawater samples collected at different depths in a transect covering the main oil tanker route across the whole basin, from the Levantine Sea to the Gibraltar strait. Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that the microbiome inhabiting deep and surface water samples were sharply separated. Furthermore, the composition of the bacterial communities described in the surface layers of the water columns at different sampling stations has been significantly correlated, beside to their geographical position and depth, to the temperature and salinity values recorded for each sample. Denaturing Gradient Gel Electrophoresis (DGGE) and ARISA fingerprinting were also applied to depict the bacterial composition of highly polluted sediments collected at the Ancona harbor (Italy) and El-Max district (Egypt), showing the significant influence of the different pollutants’ concentration (i.e. hydrocarbons, heavy metals) in the selection of peculiar bacterial assemblages . This molecular approach led to the identification of bacterial species potentially useful for site-tailored bioremediation purposes. A large collection of hydrocarbon degrading bacterial strains was hence established from enrichments using contaminated sediments as inoculum and diesel, crude oil and naphthalene as unique carbon sources. The cultivation approaches adopted to enrich and isolate hydrocarbonoclastic bacteria from chronically polluted area, like the Ancona harbor, permitted to evaluate the influence of different hydrocarbon pollutants used as single carbon source in the selection of specific marine bacteria populations. The results obtained taking advantage of DGGE fingerprinting and 16S rRNA pyrosequencing applied on the enrichments showed that, under laboratory conditions, the supply of different hydrocarbon compounds led to the selection of different, and specialized, bacterial communities. A total of 248 bacterial strains have been isolated from open sea surface water collected along oil tanker routes and the chronically polluted sediments, and have been identified by 16S rRNA gene sequencing. Alcanivorax and Marinobacter, two ubiquitous marine hydrocarbonoclastic genera, were the most abundant within the established collection, representing respectively 67% and 23% of the isolates. Due to the great importance of the Alcanivorax genus for hydrocarbon remediation of marine polluted sites, all the isolates belonging to this genus were investigated at a finer level in terms of phylogenetic and functional diversity. This sub-collection, comprising 179 isolates belonging to the 4 species A. borkumensis, A. jadensis, A. venustensis and A. dieselolei, were genotyped using two different fingerprinting techniques: Internal Transcribed Spacer (ITS)-PCR and BOX-PCR. The combination of the applied techniques allowed the identification of 85 genotypes, distributed among the different sites investigated, showing clear evidence of geographic divergence. The functional diversity of these strains was furthermore investigated through the PCR amplification of the alkB gene, encoding for an alkane monooxigenase involved in the first step of hydrocarbons degradation, and subsequent Restriction Fragment Length Polymorphism (RFLP) analysis of the amplicons, allowing the identification of 16 different polymorphisms. The results demostrated the existence of a high degree of geographical divergence within the Alcanivorax genus, suggesting a potentially high metabolic diversity that could be exploited for site-tailored bioremediation interventions. Recently, the Deepwater Horizon break in the Gulf of Mexico (2010) and the subsequent huge oil spill occurred at a depth of 1500 meters, highlighted the need to get more insight on bioremediation processes occurring at high depth. This accident represents a milestone and shed a light on the importance to investigate the effect of pressure, an environmental parameter that might hamper the activity of oil-degrading strains, on growth and degradation capabilities. The capability of selected hydrocarbonoclastic strains, belonging to the species A. jadensis, A. dieselolei and M. hydrocarbonoclasticus, to adapt and degrade a model alkane molecule (dodecane) at high pressure was therefore tested. The growth of the strains at increasing hydrostatic pressure and their physiologic activities were evaluated, comparing the results with the type strain A. borkumensis SK2. Overall, the results showed a detrimental effect of pressure for all the strains in terms of growth rates, O2 consumption and CO2 production. The potential adaptation of A. borkumensis and A.dieselolei was evaluated also with less recalcitrant carbon source than alkanes (pyruvate), without showing substantial differences, except for the higher consumption of pyruvate by A. borkumensis SK2. This investigation pinpointed that the tested bacteria can survive at high hydrostatic pressures, even though both their growth and degradation capability were mostly inhibited with the increase in hydrostatic pressure. Moreover, aiming to create a baseline for future transcriptomic analyses, the complete genome of this 4 strains was sequenced and annotated: all the strains owned multiple copies of the genes involved in the degradation of hydrocarbons (alkane monoossigenase, alk and cytochrome p450, cyp450), apparently belonging to different families, highlighting the great functional potential of these strains. A second sub-collection of hydrocarbonoclastic bacteria, isolated from chronically polluted sediments, was screened for the presence of functional genes involved in the degradation/detoxification of specific pollutants (alkanes and heavy metals), the ability to grow on different HCs and the ability to produce biosurfactant and from biofilm. The results showed that several isolates, mainly belonging to the Marinobacter genus, were positive for the investigated traits, hence they could be potentially exploited for autochthonous bioaugmentation (ABA) purposes in the sites of provenience. Finally, the bacterial community response in a biodegradation process based on an ex-situ landfarming set-up was evaluated. Landfarming was performed, using a combination of biostimulation and bioaugmentation, to remediate oil-polluted sediment collected at Elefsina bay (Greece). This work was realized to determine the effect of bioaugmentation by four allochthonous oil-degrading bacterial consortia, previously isolated from 4 polluted areas located in the Southern Mediterranean, in relation to the degradation efficiency of the indigenous community. DGGE fingerprinting analysis allowed the characterization of the bacterial community dynamics, evaluating the dominant taxa through time and at each treatment. The results showed that the added allochthonous bacteria quickly perished and were rarely detected, furthermore their addition induced minimal shifts in the community structure. These data, together with the measurement of HC degradation over the experimental time, suggested that, during the landfarming, biodegradation was mostly performed by the autochthonous populations rather than by the allochthonous ones. Furthermore, biostimulation, in contrast to bioaugmentation, was proved to enhance the HCs degradation when compared to the control treatment. To conclude, the results obtained this Ph.D. project emphasized the high bacterial diversity of the Mediterranean Sea in both pristine and polluted sites and the occurrence of distribution patterns which were significantly related to several environmental parameters, including the concentration of hydrocarbons and heavy metals. Moreover, this study confirmed the great potential of the Mediterranean Sea as a source of bacterial strains harbouring degradation capabilities toward different hydrocarbon molecules and, through the ex-situ application of different bioremediation strategies (bioaugmentation and biostimulation), it demonstrated the great importance of autochthonous microbial community in remediating polluted environments.

The conservation of marine ecosystem structure and functioning is a priority target within the context of the environmental management. This is especially important in oligotrophic systems such as the Balearic Sea, where food availability is a limiting factor. For such a target is fundamental to know the array of predator-prey interactions as a basis to understand the food web trophodynamics. In this Thesis, the trophic structure of the pelagic and benthic habitats off the Balearic Islands and the feeding ecology of three taxonomic groups (cephalopods, elasmobranchs and mesopelagic fishes) playing a key role in marine ecosystems, were investigated A relatively large food web (89 species) encompassing both the pelagic and the benthic habitats were analysed. The food webs extended up to 4 trophic levels in both habitats, and most species occupied intermediate trophic levels. A high partitioning rate of trophic resources was found, which might be related to the reduction of competition for food. The energy link between the pelagic and benthic communities (benthopelagic coupling; BPC) was stronger on the shelf break, where higher hydrodinamism mix the water column and associated nutrients, than on the slope. The geographical variability of oceanographic drivers (i.e. eddies, currents) influenced the strength of the BPC. Regarding species trophic interactions, stomach contents provided evidence of mesopelagic prey coupling pelagic and benthic habitats, especially down the shelf break. Rays from the shelf consumed mainly decapod crustaceans and teleosts, whereas sharks from the slope fed primarily upon mesopelagic prey (i.e myctophids, euphausiids). Sharks and rays variation in diet was driven by species specific ontogenetic stages and habitat use. The diet of the two squid Loligo vulgaris and L. forbesii, examined for the first time in the Mediterranean, showed their highly piscivorous habits. Their prey composition revealed a lack of diet overlap as a result of their bathymetric segregation. Both squids showed shifts in diet related to size and their reproduction period. The squid L. vulgaris feed on small benthic prey until they reach a size threshold and feed on benthopelagic fish thereafter. Seasonal changes in diet in both squid species, likely related to reproduction, might help improving their individual body condition. During this period, L. vulgaris increased the consumption of highly nutritive polychaetes, whereas the adults of L. forbesii carried out movements to deeper waters to feed on lipid-rich mesopelagic prey. Mesopelagic prey are important food resources for demersal species in the Balearic Sea and, as a result of their nycthemeral movements, they have important implications for the transport of mass and energy through the water column. The trophodynamics of this group revealed that food sources (δ13C) varied little over the spatial scales sampled (location and depth) but showed high seasonality, reflecting intra-annual changes in the species composition of the phytoplankton community. By contrast, spatio-temporal variations of mesopelagic trophic interactions (δ15N) were minimal. Important niche segregation was observed between the non-migratory stomiiforms and some of the extensive migratory myctophids. Finally, the comparative analysis of the trophic ecology of deep-sea cephalopods and elasmobranchs showed that they displayed different feeding strategies with a clear resource partitioning between and within taxa. Segregation of the isotopic space indicated a contrasting food source gradient (δ13C) stretching from pelagic (squids and cuttlefishes) to nektobenthic (octopuses and elasmobranchs) sources. However, deep-sea sharks off the Balearic Islands frequently preyed on mesopelagic species, as did squids and cuttlefishes. Cephalopods, in turn, constituted an important food resource for deep-sea sharks. Squid and shark species identified as benthopelagic feeders, play a key role in the transport of energy from midwater regions to the benthic community.

In this thesis, the ecological role of 26 species of abundant, rare and endangered chondrichthyans present in the western Mediterranean has been studied through the study of trophic ecology and main morphological characters. Due to the number of species included, this thesis constitutes the most complete research on the trophic ecology of sharks, rays and chimeras in the Mediterranean Sea. For this purpose, different methodologies such as stomach content analysis, review of available literature and new tools such as stable isotope analysis have been combined. The results reveal the importance of chondrichthyans in the western Mediterranean as mesopredators and top predators. The small sharks Scyliorhinus canicula, Etmopterus spinax and Galeus melastomus act as mesopredators of the ecosystem and, because of their abundance, they could be considered important species in the Mediterranean Sea. S. canicula presents intraspecific changes in relation to its trophic ecology and small individuals feed on different prey than larger individuals. The same occurs with males and females, probably because they feed on different areas of the continental shelf. These three species, along with Dalatias licha, do not present changes in their trophic ecology between areas with different degrees of human impact such as the Catalan Sea and an area restricted to fishing in the Gulf of Lions. This result is probably related to the fact that S. canicula, E. spinax, and G. melastomus are opportunistic species, being able to exploit different resources including part of the fishing discards. In addition, D. licha prey mainly on these opportunistic species. It may also be that the area of the Gulf of Lions has not recovered significantly after its declaration as an area restricted to fishing and does not show substantially different characteristics to the exploited area of the Catalan Sea. Other chondrichthyans that have an ecological role similar to the small demersal sharks are the different species of skates (Rajiformes), species that feed mainly on crustaceans. Other mesopredator rays, such as Mobula mobular and Myliobatis aquila, have a unique trophic role within the studied species: M. mobular is a filter feeding species and M. aquila feeds mainly on bivalves. As top predators are the sharks Alopias vulpinus and Galeorhinus galeus, the ray Gymnura altavela, Torpediniformes, Chimaeriformes and other medium-sized sharks of the orders Carcharhiniformes, Hexanchiformes and Squaliformes. The results present in this thesis have confirmed that the chondrichthyans of the Mediterranean Sea have different ecological roles, being a very important step in the knowledge of the trophic ecology of these organisms. In addition, it has to be emphasized the use of the stable isotope analysis in blood for the first time, a non-lethal technique, for the study of the trophic ecology of the shark S. canicula. This methodology could be very useful for investigating the trophic ecology and the ecological role in sharks and rays that are rare or endangered.
En esta tesis se ha avanzado en el conocimiento del rol ecológico de 26 especies de condrictios abundantes, poco comunes y en peligro de extinción presentes en el Mediterráneo occidental, mediante el estudio de la ecología trófica y de los principales caracteres morfológicos. Por el número de especies incluidas, la presente tesis constituye el trabajo de investigación más completo sobre ecología trófica de tiburones, rayas y quimeras en el Mar Mediterráneo. Para ello se han utilizado de manera combinada diferentes metodologías como el análisis del contenido estomacal, la revisión de la literatura disponible y herramientas novedosas como el análisis de isótopos estables. Los resultados encontrados ponen de manifiesto la importancia de los condrictios en el Mediterráneo occidental como mesodepredadores y depredadores apicales. Los tiburones de pequño tamaño como Scyliorhinus canicula, Etmopterus spinax y Galeus melastomus actúan como mesodepredadores del ecosistema y por su abundancia pueden ser consideradas especies relevantes en el Mar Mediterráneo. S. canicula presenta cambios intraespecíficos en relación con su ecología trófica. Los individuos pequeños de esta especie depredan sobre presas diferentes a los individuos de mayor tamaño. Lo mismo sucede con los machos y las hembras, probablemente porque se alimentan en diferentes zonas de la plataforma continental. S. canicula, E. spinax y G. melastomus, junto a Dalatias licha, no presentan cambios en su ecología trófica entre áreas con diferente grado de impacto antrópico como lo son el Mar Catalán y una zona restringida a la pesca del Golfo de León. Este resultado probablemente está relacionado con el hecho de que S. canicula, E. spinax y G. melastomus son especies oportunistas, pudiendo explotar diferentes recursos, incluidos parte de los descartes pesqueros. Además, D. licha depreda principalmente sobre estas especies de tiburones oportunistas. Puede ser también que la zona del Golfo de León no se haya recuperado significativamente después de su declaración como área restringida a la pesca y no muestre características substancialmente diferentes a la zona explotada del Mar Catalán. Otros condrictios que tienen un rol ecológico similar a los pequeños tiburones demersales son las diferentes especies de rayas del orden Rajiformes, especies que se alimentan principalmente de crustáceos. Otras rayas mesodepredadoras, como Mobula mobular y Myliobatis aquila, tienen un rol trófico único dentro de las especies estudiadas: M. mobular es una especie filtradora y M. aquila se alimenta principalmente de bivalvos. Como depredadores apicales se encuentran los tiburones Alopias vulpinus, Galeorhinus galeus y la raya Gymnura altavela. Otros deprededaores apicales son los Torpediniformes, Chimaeriformes y otros tiburones de tamaño medio de los órdenes Carcharhiniformes, Hexanchiformes y Squaliformes. En esta tesis doctoral se ha confirmado que los condrictios del Mar Mediterráneo tienen diferentes roles ecológicos y se ha dado un paso muy importante en el conocimiento de la ecología trófica de estos organismos. Además cabe resaltar el uso por primera vez del análisis de isótopos estables en sangre, una técnica no letal, para el estudio de la ecología trófica del tiburón S. canicula. Esta metodología puede ser muy útil para estudiar la ecología trófica y el rol ecológico en tiburones y rayas poco abundantes o en peligro de extinción.

La connectivité, concept vaste et multidimensionnel, joue un rôle essentiel dans la compréhension des interactions au sein des écosystèmes, qu'ils soient terrestres ou marins. Elle fait référence aux flux de matière, d'énergie et d'organismes qui se déplacent et interagissent à travers les habitats, influençant la dynamique des populations et leur résilience face aux perturbations. Cette thèse se concentre sur l'étude de la connectivité dans les écosystèmes marins côtiers méditerranéens, et plus précisément sur la dispersion larvaire des espèces à cycle de vie biphasique. L'objectif principal de ce travail de recherche est de prédire les tendances de dispersion larvaire et de connectivité chez des espèces clés, tout en mettant un accent particulier sur le rôle des îles dans ce processus, grâce à une approche de modélisation biophysique. Ce questionnement vise à mieux comprendre la dynamique des populations et à apporter des réponses cruciales pour la gestion durable des écosystèmes marins méditerranéens. Ces systèmes complexes sont soumis aux activités humaines, qui exercent une pression importante sur les populations naturelles, notamment celles exploitées par les pêcheries. Une étude préliminaire a permis de sélectionner l’outil de modélisation le plus adapté au contexte : Ichthyop, développé par l'équipe du laboratoire MARBEC. Ce logiciel, qui modélise le transport larvaire, a été enrichi au cours de cette thèse avec des fonctionnalités spécifiques aux espèces étudiées, telles que la nage orientée et la variation des proportions de particules dans les zones de lâcher. Le cœur de cette thèse repose sur l'étude de quatre espèces modèles représentatives des écosystèmes côtiers méditerranéens : Paracentrotus lividus (l’oursin comestible), Callinectes sapidus (le crabe bleu invasif), Maja squinado (la grande araignée de mer) et Diplodus sargus (le sar commun). Chaque espèce illustre des dynamiques écologiques spécifiques, influencées par leurs comportements larvaires. Qu'elles soient exploitées ou invasives, ces espèces constituent des enjeux économiques et écologiques majeurs pour la Méditerranée. Pour Paracentrotus lividus, les simulations ont révélé des taux d’autorecrutement élevés, notamment en Corse et en Sardaigne, démontrant une connectivité régulière et durable entre ces habitats rocheux. Le modèle pour Callinectes sapidus a mis en lumière des groupes de connectivité stables dans le temps entre la Corse, la Sardaigne et la Tunisie, contribuant ainsi à la rapide expansion de cette espèce invasive en Méditerranée occidentale. Concernant Maja squinado, les simulations ont montré que sa faible capacité de dispersion larvaire, liée à une courte période larvaire pélagique (PLD), pourrait compromettre la survie des populations locales en cas de mauvaise gestion, soulignant la nécessité d'une surveillance accrue des stocks, en particulier en Corse. Enfin, pour Diplodus sargus, les résultats ont confirmé que la nage orientée des larves joue un rôle clé dans la connectivité et le recrutement, avec une validation par des données de terrain collectées sur plusieurs décennies dans les Pyrénées-Orientales. Ces conclusions soulignent l'intérêt des outils de transport lagrangiens et de la modélisation biophysique en tant que méthodes prédictives pour anticiper les tendances de connectivité. Leur puissance prédictive est, et sera encore, renforcée par leur couplage avec d'autres approches scientifiques et par l'amélioration de la qualité des données qui les alimentent
The concept of connectivity, which is both vast and multidimensional, plays a crucial role in understanding interactions within ecosystems, whether terrestrial or marine. Connectivity refers to the movement of materials, energy, and organisms across habitats, influencing population dynamics and ecosystem resilience to disturbances. This thesis focuses on connectivity in Mediterranean coastal marine ecosystems, emphasizing larval dispersal in species with biphasic life cycles. The primary objective of this research is to predict larval dispersal and connectivity patterns for key species, highlighting particularly the role of islands in this process through a biophysical modelling approach. This research project aims to enhance understanding of population dynamics and provide essential insights for the sustainable management of Mediterranean marine ecosystems. These complex systems are subject to human activities that exert significant pressure on natural populations, particularly those targeted by fisheries. A preliminary study was conducted to select the most suitable modelling tool for this context, identifying Ichthyop, developed by the MARBEC laboratory team. This software, which simulates larval transport, was enhanced during this thesis with specific features tailored to the studied species, including oriented swimming behaviour and varying proportions of particles in release zones. The core of this thesis centers around four model species representative of Mediterranean coastal ecosystems: Paracentrotus lividus (the edible sea urchin), Callinectes sapidus (the invasive blue crab), Maja squinado (the European spider crab), and Diplodus sargus (the white seabream). Each species illustrates distinct ecological dynamics influenced by their larval behaviours. Whether exploited or invasive, these species represent major economic and ecological challenges for the Mediterranean region. Simulation results indicated that Paracentrotus lividus exhibited high self-recruitment rates, notably in Corsica and Sardinia, highlighting consistent and enduring connectivity between these rocky habitats. The model for Callinectes sapidus revealed stable connectivity clusters over time between Corsica, Sardinia, and Tunisia, contributing to the rapid spread of this invasive species in the Western Mediterranean. For Maja squinado, simulations demonstrated that its limited larval dispersal capacity, associated with a short pelagic larval duration (PLD), could jeopardize the survival of local populations under poor management, emphasizing the need for increased stock monitoring, particularly in Corsica. Lastly, results for Diplodus sargus confirmed that oriented larval swimming plays a critical role in connectivity and recruitment, validated by field data collected over several decades along the coastal zones of the Eastern Pyrenees (France). These findings underscore the utility of Lagrangian transport models and biophysical modelling as predictive tools to anticipate connectivity patterns. Their predictive power will continue to be strengthened by coupling with other scientific approaches and by improving the quality of the input data

En esta tesis se revisaron las relaciones que existen entre las poblaciones de dos especies de calamares ommastréfidos Dosidicus gigas y Illex argentinus con las series temporales de la temperatura superficial del mar, clorofila a y las estimaciones de biomasa zooplanctónica, lo que resultó en la comprensión de que la temperatura puede afectar directamente a las poblaciones de organismos productores primarios y a los integrantes del zooplancton, y no así a los organismos juveniles y adultos de ambas especies de calamar. También se observó que en ambas especies la distribución y abundancia de presas potenciales es uno de los principales factores que determinan la localización y en algunos casos migraciones horizontales y verticales en el ecosistema. Para poder entender las relaciones que las especies de calamares guardan en los ecosistemas fue necesario implementar los estudios ecotróficos en los que se determinó la importancia que representan estos calamares en las redes tróficas como depredadores, así como la interacción entre especies semejantes de calamares con las que pueden compartir su hábitat. Para llevar esta investigación se seleccionaron tres áreas de importancia ecológica y comercial, la primera corresponde al océano Atlántico Sur en la plataforma Patagónica y las islas Malvinas/Falkland en las que se identificaron tres especies de calamar I. argentinus, D. gahi y O. ingens, la segunda corresponde al Noroeste del Mar Mediterráneo donde se identificó a I. coindetii y T. sagittatus y la tercera al océano Pacifico en las costas de México y Perú para D. gigas. Los resultados de este trabajo demuestran que la tendencia de las poblaciones de estas especies es afectada directamente por las presas más abundantes y disponibles en el ecosistema, así como el desarrollo de relaciones intrínsecas entre algunas especies presa y su depredador como fue el caso de D. gigas y el pez V. lucetia.
This PhD thesis was focused in the relationships between the ommastrephid squids Dosidicus gigas and Illex argentinus with the time series of sea surface temperature, chlorophyll a and zooplankton biomass. The temperature as factor affected the primary productivity and the abundance of zooplankton, and no effects were found in the populations of juveniles and adult of both squids. In this way the distribution and abundance of squid was related to other factors such as the abundance of prey resources. Then the thesis was complemented with trophic ecology studies performed in the South Atlantic Ocean (Squid species: Doryteuthis gahi, Illex argentinus and Onykia ingens), in the Northwest Mediterranean Sea (Squid species: Todarodes sagittatus and Illex coindetii), and the South Pacific Ocean (Squid Dosidicus gigas). The results showed that the biomass and distribution of squid species are close related to the most abundant and available prey resources, and also it can be found trophic dependencies between some specific prey resources as was observed for Dosidicus gigas and the mesopelagic fish Vinciguerria lucetia .

Intermittent rivers and ephemeral streams (IRES) are watercourses that naturally and periodically cease to flow. They represent more than half of the global river network and are expanding due to global change. In this thesis, I investigate the mechanisms linking flow intermittence with biodiversity and ecosystem functioning, which sustain biogeochemical cycles and energy transfer in the system. Chapter 1 analyzes the effects of hydrology, micro-habitat (surface and subsurface zones) and biotic features on organic matter decomposition and fungal biomass, in 20 streams. In Chapter 2, I assess the effect of different flow intermittence metrics (i.e., annual intermittence regime and recent aquatic status) on aquatic biodiversity, including both taxonomic and functional-trait-based metrics, in 33 streams. Chapter 3 analyzes how aquatic hyphomycete richness and composition (beta diversity and its turnover and nestedness components) are affected by a flow intermittence gradient and how these community changes affect organic matter decomposition, in 15 streams and in a microcosm approach. Finally, in Chapter 4, I explore how changes in both leaf litter quality and quantity determine the feeding preferences and growth of an invertebrate shredder. The results of Chapter 1 show that the subsurface zone contributes to maintaining microbial decomposition during non-flow periods in IRES, mainly because of the levels of fungal biomass present in the subsurface zone. In Chapter 2, I conclude that a combination of flow intermittence metrics are needed to explain the high dynamism of the invertebrate community in IRES and potentially ecosystem functioning. Moreover, this chapter shows that hydrological variables outweigh non-hydrological factors in explaining invertebrate community variation, thereby supporting the use of the former in IRES classification and bio-monitoring routines. Chapter 3 reveals that the reduction of aquatic hyphomycete richness and species turnover as a result of flow intermittence, could have negative effects on organic matter decomposition. Finally, in Chapter 4, I provide evidence on how flow intermittence reduces the quality of leaf litter, in terms of fungal richness and composition, fungal biomass and lipid content. These changes in food quality influence the consumption rates and growth of shredders, which are able to feed selectively on higher quality leaves, even though its availability is lower. Taken together, these results will help to improve the biomonitoring and management of IRES and to a better prediction of ecosystem trajectories in response to global change.

The development of offshore wind farms and marine renewable energy devices in the Mediterranean is central to both national, and international, energy strategies for countries bordering the Mediterranean Sea. The ecological impacts of marine renewable energy development in the Mediterranean region, although essential for policy makers, are as yet unknown. The Northern Adriatic is identified as a plausible site for offshore wind farm development. Using the wider region (Adriatic and Northern Ionian) as a case study, this thesis examines the likely impact to the marine environment if an offshore wind farm is established. Site suitability, based on wind speed, bathymetry, and larvae connectivity levels are investigated along with the plausibility of the turbines operating as artificial reefs in the area. As offshore wind farms may alter the larval connectivity and supply dynamics of benthic populations, a connectivity map was constructed to identify areas of high and low connectivity in the Adriatic Sea. The Puglia coast of Italy is a likely larval sink, and displays some of the highest connectivity within the region, suggesting potential inputs of genetic materials from surrounding populations. Considering offshore wind farms could operate as artificial reefs, an in-situ pilot project was established to simulate the presence of wind turbines. Macroinvertebrates colonized the new substrata within the first few months but were lower in abundance when compared to a natural hard substrata environment. Time, turbine location, and the material used for turbine construction all affected the macro-invertebrate communities. In addition, fish abundances, and diversity were lower around the simulated OWF foundations in comparison to a natural hard substrata environment, and no increases in fish abundance occurred around the simulated turbines when compared to reference sites of soft substrata. This observation was validated with the use of an ecosystem modelling software (Ecopath with Ecosim), which simulated the overall ecosystem level impacts that would occur if 50 offshore monopile wind turbines were introduced to the Northern Ionian and colonized by macroinvertebrate communities. When compared to the baseline scenario (no simulated introduction of an OWF), the introduction of new habitat had no discernible impacts to the structure or functioning of the marine ecosystem. Noticeable changes to the ecosystem were only apparent if fishing restrictions were enforced in parallel with the simulated offshore wind farm; the ecosystem appears to become more structured by top down predation. In addition seabirds are also impacted by the reduction of fishing discards as a food source. These results are the first attempt to quantify the suspected benefits of offshore wind farms operating as de-facto marine protected areas.

Firstly, I reviewed modelling approaches that were used to assess the impact of invasive alien species (IAS) in aquatic ecosystems. According to the review, multispecies/ecosystem mechanistic models dominated the applications, with dynamic and non-spatial models being the most prevalent. Most of the models included an additional human stressor, mainly fisheries, climate change and/or nutrient loading. I summarised the main features of these applications and analysed their capabilities and limitations. Based on my conclusions, I reflected on future directions of development and applications of suitable modelling tools. The review showed that the Ecopath with Ecosim (EwE) modelling approach was frequently used to assess the impacts of already established IAS and highlighted its capabilities to forecast existing, emerging and potential new IAS. As a second step, I developed two static Ecopath ecosystem models using the EwE approach and representing the food web of the Israeli Mediterranean coast in 1990s and 2010s. I characterized the structure and functioning of the ecosystem and assessed past and current impacts of IAS and fishing. I then used the time-dynamic Ecosim module of EwE to fit the 1990s model to available time series of observations between both periods and to explore the historical dynamics of the ecosystem considering the effects of IAS, fishing dynamics and sea warming. Finally, the time-dynamic ecosystem model was used to analyse alternative future simulations of ecosystem change. Particularly, and after interacting with key stakeholders, I assessed the future effects of a new set of fishing regulations currently being implemented in Israel, future changes in sea temperature following IPCC (Intergovernmental Panel on Climate Change) scenario projections and the potential increases in IAS biomass. I investigated the impacts of the stressors separately, and then I combined them to evaluate their cumulative effects. Results from the static Ecopath models highlighted that the Israeli marine ecosystem, despite productivity differences, shared some structural and functional traits with other Mediterranean ecosystems such as the dominance of the pelagic domain in term of flows, the important role of detritus through low trophic levels and the importance of the benthic-pelagic coupling. In both time periods investigated, the same keystone groups were identified with the exception of European hake in 2010s, which showed a decline in its keystone role. This may indicate that hake lost its ecological role due to population declines. Most of the functional groups identified as keystone species were previously identified as keystones in other Mediterranean ecosystems, such as dolphins, large pelagic fishes, sharks and squids. The temporal dynamic Ecosim model indicated that trophic interactions, ocean warming and fishing were important drivers of the ecosystem dynamics. In general, temporal biomass trends revealed that native demersal predators and native medium trophic level fishes largely declined over time, while an increase over time of alien species was observed. Results from ecological indicators suggested a degradation pattern of the ecosystem over time. Future scenarios using the temporal dynamic Ecosim model showed overall potential benefits of fishing effort reductions in the future, and detrimental impacts of increasing sea temperature and increasing biomass of alien species. Cumulative scenarios highlighted that the beneficial effects of fisheries reduction could be dampened by the impact of increasing sea temperature and alien species when acting together. These results support the need for reducing local and regional stressors, such as fishing and biological invasions, to retain marine ecosystems within a “safe operating space” and ensure ecosystem resilience in an ongoing warming and impacted sea.
Los ecosistemas marinos del Mediterráneo oriental han sufrido cambios ecológicos importantes debido a múltiples presiones antropogénicas, incluido el impacto de especies invasoras, la sobrepesca y el calentamiento del mar. En primer lugar, he revisado los modelos que se han utilizado para evaluar el impacto de las especies invasoras en los ecosistemas acuáticos. De acuerdo con esta revisión, predominan los modelos mecanísticos de carácter multiespecífico/ecosistémico, siendo los modelos dinámicos y no espaciales los más frecuentes. La mayoría de los modelos incluyen un impacto antropogénico adicional, principalmente la pesca, el cambio climático y el aporte de nutrientes. Además, he resumido las principales características de estos modelos y he analizado sus capacidades y limitaciones. En base a las conclusiones de esta revisión, se han mostrado posibles direcciones para futuros desarrollos de los modelos y la aplicación de modelos adecuados. En esta revisión, he observado que el modelo Ecopath with Ecosim (EwE) ha sido utilizado frecuentemente para evaluar los impactos de las especies invasoras ya establecidas. Además, la revisión ha destacado las capacidades de EwE de pronosticar los futuros impactos de las especies invasoras establecidas, emergentes y potenciales. Otras revisiones disponibles en la literatura han demostrado las capacidades de EwE para evaluar los impactos de la pesca y el cambio climático. Por lo tanto, he desarrollado dos modelos estáticos Ecopath que representan la red trófica de la costa Mediterránea de Israel en los años 1990 y 2010 para caracterizar la estructura y funcionamiento del ecosistema y evaluar los impactos de las especies invasoras y la pesca en el pasado y en el presente. Después he utilizado el módulo dinámico-temporal Ecosim para ajustar el modelo de 1990 a series temporales de datos disponibles entre ambos periodos y para explorar la dinámica histórica del ecosistema considerando el efecto de las especies invasoras, la dinámica de la flota pesquera y el calentamiento del mar. Finalmente, el módulo dinámico-temporal ha sido utilizado para realizar simulaciones futuras de cambios en el ecosistema. En particular, he evaluado los efectos de un nuevo conjunto de regulaciones de pesca que se están implementando actualmente en Israel, futuros cambios en la temperatura del mar siguiendo las proyecciones del Panel Intergubernamental sobre el Cambio Climático (IPCC por sus siglas en inglés) y posibles aumentos de la biomasa de las especies invasoras. Primero he investigado los diferentes impactos por separado y, luego, los he combinado para evaluar sus efectos acumulativos. Los resultados de los modelos estáticos Ecopath han destacado que el ecosistema marino israelí, a pesar de un patrón de productividad diferente, comparte algunas características estructurales y funcionales con otros ecosistemas mediterráneos como el dominio del hábitat pelágico en términos de flujos tróficos, el importante papel del detritus a través de niveles tróficos bajos y la importancia del acoplamiento bentónicopelágico. Los mismos grupos funcionales clave fueron identificados en ambos periodos investigados, a excepción de la merluza en 2010, lo que puede indicar que la merluza ha perdido su papel ecológico debido al declive de su población. La mayoría de los grupos funcionales identificados como especies clave ya han sido identificados previamente como tales en otros ecosistemas mediterráneos como por ejemplo los delfines, los grandes peces pelágicos, los tiburones y los calamares. El módulo dinámico-temporal Ecosim indicó que las interacciones tróficas, el aumento de la temperatura del mar y la pesca jugaron un papel clave en la dinámica del ecosistema. En general, las tendencias temporales de la biomasa revelaron que los depredadores demersales nativos (por ejemplo, la merluza) y los peces demersal nativos de nivel trófico medio (por ejemplo, los salmonetes) disminuyeron en gran medida con el tiempo, mientras que se observó un aumento de las especies invasoras con el tiempo. Los resultados de los indicadores ecológicos sugirieron un patrón de degradación del ecosistema con el tiempo. Los escenarios futuros utilizando el módulo dinámico-temporal Ecosim mostraron los beneficios potenciales generales de las reducciones del esfuerzo pesquero y los impactos negativos del aumento de la temperatura del mar y el aumento de la biomasa de las especies invasoras. Los escenarios acumulativos resaltaron que los efectos beneficiosos de la reducción de la pesca pueden verse disminuidos por el impacto del aumento de la temperatura del mar y las especies invasoras cuando actúan al mismo tiempo. Estos resultados respaldan la necesidad de reducir los impactos antropogénicos locales y regionales como la pesca y las especies invasoras, para mantener los ecosistemas marinos dentro de un “espacio operativo seguro (SOS por sus siglas en inglés)” y promover la resiliencia de los ecosistemas en un mar en continuo calentamiento y altamente impactado.
Els ecosistemes marins de la Mediterrànea oriental han patit canvis ecológics importants a causa de múltiples pressions antropogèniques, inclòs l’impacte d’especies invasores, la sobrepesca i el calentament del mar. En primer lloc, he revisat els models que s’han utilitzat per avaluar l’impacte de les espècies invasores en ecosistemes aquàtics. D’acord amb aquesta revisió, predominen els models mecanístics de caràcter multiespecífic/ecosistèmic, sent els models dinàmics i no espacials els més freqüents. La majoria dels models inclouen un impacte antropogènic adicional, principalment la pesca, el canvi climàtic i l’aport de nutrients. A més, he resumit les principals característiques d’aquest models i he analitzat les seves capacitats i limitacions. En base a les conclusions d’aquesta revisió, s’han exposat possibles direccions per futurs desenvolupaments dels models i l’aplicació de models adecuats. En aquesta revisió he observat que el model Ecopath with Ecosim (EwE) ha estat utilitzat freqüentment per avaluar els impactes de les espècies invasores ja establertes. A més, la revisió ha destacat les capacitats d’EwE de pronosticar els futurs impactes de les espècies establertes, emergents i potencials. Altres revisions disponibles a la literatura han demostrat les capacitats d’EwE per avaluar els impactes de la pesca i el canvi climàtic. Per tant, he desencolupat dos models estàtics Ecopath que representen la xarxa tròfica de la costa Mediterrànea d’Israel en els anys 1990 y 2010 per caracteritzar l’estructura i funcionament de l’ecosistema i avaluar els impactes de les espècies invasores i la pesca en el passat i el present. Després he utilitzat el mòdul dinàmic-temporal per ajustar el model de 1990 a sèries temporals de dades disponibles considerant l’efecte de les espècies invasores, la dinàmica de la flota pesquera i l’escalfament del mar. Finalment, el mòdul dinamic-temporal ha estat utilitzat per realitzar simulacions futures de canvis en l’ecosistema. En particular, he avaluat els efectes d’un nou conjunt de regulacions de pesca que s’estan implementant actualment a Israel, canvis en la temperatura del mar seguint les projeccions del panell intergovernamental sobre el Canvi Climàtic (IPCC per les seves sigles en anglès) i possibles augments de la biomass de les espècies invasores. Primer he investigat els diferents impactes per separat i, després, els he combinat per avaluar els seus efectes acumulatius. Els resultats dels models estàtics Ecopath han destacat que l’ecostema marí d’Israel, malgrat un patró de productivitat diferent, comparteix algunes característiques estructurals i de funcionals amd altres ecosistemes marins mediterrànis com el domini de l’hàbitat pelàgic en termes de fluxes tròfics, l’important paper del detritus a través de nivells tròfics baixos i la importància de l’acoplament bentònic-pelàgic. Els mateixos grups funcionals clau van ser identificats en els dos períodes investigats, a excepció del lluç en el 2010, que pot indicar que el lluç ha perdut el seus paper ecològic a causa del declivi de la seva població. La majoria del grups funcionals identificats com a espècies claus ja han estat identificats com a tals en altres ecosistemes mediterranis com ara els dofins, els gran peixos pelàgics, els taurons i els calamars. El mòdul dinàmic-temporal Ecosim ha indicat que les interaccions tròfiques, l’augment de la temperatura del mar i la pesca van jugar un paper clau en la dinàmic de l’ecosistema. En general, les tendències temporals de la biomasa van revelar que els depredadors demersals natius (per exemple, el lluç) i els peixos dersals natius de nivell tròfic mitjà (per exemple, els rogers) van disminuir en gran mesura amb el temps, mentre que es va observar un augment de les espècies invasores amb el temps. Els resultats dels indicadors ecològics van suggerir un patrò de degradació de l’ecosistema amb el temps. Els escenaris futurs van mostrar els beneficis potencials generals de les reduccions de l’esforç pesquer i els impactes negatius de l’augment de la temperatura del mar i ’augment de la biomasa de les espècies invasores. Els escenaris acumulatius van ressaltar que els efectes beneficiosos de la reducció de la pesca poden ser reduïts per l’impacte de l’augment de la temperatura del mar i les espècies invasores quan actuen al mateix temps. Aquests resultats recolzen la necessitat de reduir els impactes antropogènics locals i regionals com la pesca i les espècies invasores, per mantenir els ecosistems marins dins d’un “espai operatiu segur (SOS per les seves sigles en anglès)” i promoure la resiliència dels ecosistemes en un mar en continu escalfament i altament impactat.

This PhD project was designed to cover all the relevant issues of a restocking program for the meagre Argyrosomus regius in the Balearic Islands coastal ecosystems, ranging from the production of juveniles in captivity to monitoring survival into the wild. The long time needed by released meagres to adapt, around 3 months, seemed to imply high mortality. The reproductive study carried out with meagres in captivity conditions showed that age at maturity (i.e., 50% of probability to be mature) was 2.7 years for males and 3.5 years for females. Therefore, the meagres recaptured after spending two or more than two years at liberty were probably adults. Although there was empirical evidence that some meagres had reached the sexual maturity into the wild, we did not have evidences, as of now, that they had spawned, which would certainly increase the chance of success of the meagre restocking program. Nevertheless, reducing short-term mortality appears to be the most important challenge for increasing the chance of recovering a sustainable population of meagre in the Balearic Islands.
Este proyecto de Tesis Doctoral ha sido diseñado para cubrir todos los aspectos relevantes relacionados con el programa de repoblación de la corvina Argyrosomus regius en los ecosistemas costeros de las Islas Baleares, cubriendo desde la producción de juveniles en cautividad hasta el seguimiento de su supervivencia en el medio natural. El dilatado periodo de tiempo necesario para que las corvinas liberadas se adapten al medio natural, unos 3 meses, implica una elevada mortalidad. El estudio de las características reproductivas que se llevó a cabo con las corvinas en cautividad muestra que la edad de maduración (edad a la que el 50% de la población es sexualmente madura) es de 2.7 años en el caso de los machos y de 3.5 años para las hembras. Por tanto, los peces recapturados al cabo de unos dos años después de la liberación ya eran probablemente adultos. A pesar de que se obtuvieron evidencias empíricas de que al menos algunas corvinas alcanzaron la madurez sexual en el medio natural, no se tuvieron evidencias de que estos ejemplares se hubieran reproducido, siendo esto último un muy buen indicio de las posibilidades de éxito del programa de repoblación de la corvina. En cualquier caso, reducir la mortalidad a corto plazo parece ser el reto más importante a la hora de incrementar las posibilidades de éxito de recuperar una población sostenible de corvinas en las Islas Baleares.

In this thesis I investigated the status of the Mediterranean Sea ecosystem and the sustainability of its marine resources using an interdisciplinary approach, which combined data integration and modelling approaches. Results highlighted a series of commonalities for Mediterranean marine ecosystems: they indicate that ‘small pelagic fishes’, mainly European pilchards and anchovies, both with high biomasses and high proportions in catches, are important structuring species for the Mediterranean ecosystem (at regional, sub-regional and local scales). ‘Large pelagic fishes’ are the main keystone species for both the past and current Mediterranean ecosystem configuration, while ‘sharks’ and ‘medium pelagic fishes’ played a key role in the past, but their ecological role is currently replaced by benthopelagic and benthic cephalopods. In addition, the ‘Mediterranean monk seal’ “Monachus monachus”, where it still occurs, is the species with the highest TL followed by ‘piscivorous cetaceans’ and ‘large pelagic fish’. Looking at temporal ecosystem dynamics, biomass trends and ecological indicators (e.g., community biomass, trophic levels of the community, catch and diversity indicators) reveal that the combined effect of excessive fishing pressure and changes in primary productivity altered the Mediterranean marine ecosystem over time, especially reducing the proportions of top predators (e.g., pinnipeds, large pelagic fish) and mid trophic level organisms (e.g., small pelagic fishes) and increasing the abundance of groups at lower trophic levels (e.g., invertebrates). The Western and the Adriatic Seas are the most degraded ecosystems with biomasses declines among all the species compartments assessed (from forage fish to sharks/rays and skates, except for invertebrates that remained stable in time). The Ionian Sea was found to be the area with less biomass changes historically in comparison with available survey data. Even at a more local scale (Amvrakikos Gulf), both ecological indicators and biomass trends highlight a degradation of the demersal compartments of the food web but a relative stability of the pelagic ones mainly due to high eutrophication levels. Fishing pressure and changes in primary production (PP) play an important role in driving species temporal dynamics; yet, PP seems to be the strongest driver upon the Mediterranean Sea ecosystem. Fisheries data (mainly catch and effort) are found to be under-reported and under-estimated at regional, sub-regional and local scale. For example, fishing mortalities (and so landings data obtained from Food and Agriculture Organization [FAO] fisheries statistics) of three most important commercial species (European pilchard ‘Sardina pilchardus’, anchovy ‘Engraulis encrasicolus’ and hake ‘Merluccius merluccius’) were in fact observed in early decades (1950s), in all the Mediterranean sub-regions, between 5 and 10 times inferior from the average reference values reported in stock assessment for these fish stocks in the Mediterranean Sea. Even in the assessment of the Italian fisheries, the reconstructed of total catches were 2.6 times the landings officially reported by the FAO on behalf of Italy for the same period and same area, with unreported commercial landings (from both industrial and artisanal sectors) contributing 50% to the total catch (in relation to FAO reporting) and discards contributing another 7%. In Europe, several models and associated indicators exist that could be used in support of European policies (MSFD); yet, Ecopath with Ecosim (EwE) is the most applied tool for modelling marine and aquatic ecosystems and the one that can produce the largest number of indicators useful for the Marine Strategy Framework Directive (MSFD). Since anthropogenic pressures are rapidly expanding in the basin, this work constitutes an important first step to advance further in the regional assessment of the Mediterranean Sea ecosystem and to inform conservation plans and management actions.
En aquesta tesi he investigat l'estat ambiental del mar mediterrani i la sostenibilitat dels seus recursos marins mitjançant un enfoc interdisciplinari que combina la integració de dades i la modelització d'ecosistemes. Els resultats posen en relleu una sèrie de punts en comú dels ecosistemes marins mediterranis: el grup de "peixos pelàgics de mida petita", principalment compost per sardines i seitons, amb grans biomasses i captures, és un grup important en relació amb l'estructura de l'ecosistema mediterrani (tant a nivell regional, sub regional i a escales locals). El grup de “peixos pelàgics de gran mida” destaca per ser important com a grup clau de l'ecosistema, tant en el passat com en el present, mentre que el grup dels “taurons” i “peixos pelàgics de mida mitjana” han jugat un paper ecològic clau en el passat, però aquest és actualment reemplaçat pels grups de peixos bentopelàgicos i cefalòpodes bentònics. A més, el vell marí del mediterrani “Monachus monachus”, en aquelles zones on encara existeix, és l'espècie amb el nivell tròfic més alt, seguida pel grup de "cetacis que s'alimenten de peixos" i "peixos pelàgics de grans dimensions". Pel que fa a la dinàmica temporal de l'ecosistema, les tendències de la biomassa i dels indicadors ecològics (per exemple, la biomassa de la comunitat, els nivells tròfics de la comunitat, les captures i els indicadors de diversitat) revelen que l'efecte combinat d’una pressió pesquera excessiva i els canvis en la productivitat primària ha alterat l'ecosistema marí mediterrani a través del temps, especialment pel que fa a una reducció de les proporcions dels depredadors superiors (per exemple, pinnípedes, i peixos pelàgics de grans dimensions) i organismes de nivells tròfics mitjans (per exemple, peixos pelàgics de mida petita), i l'augment en abundància de grups d'organismes en nivells tròfics inferiors (per exemple, invertebrats). El mar mediterrani occidental i el mar adriàtic són els ecosistemes més degradats amb baixades de biomasses per a totes les espècies avaluades (des dels peixos pelàgics de mida petita als taurons i ratjades, amb excepció dels invertebrats que es mantenen estables en el temps). El mar jònic és l'àrea amb menys canvis històrics en termes de biomassa en comparació amb les dades disponibles de mostrejos. Fins i tot a una escala més local (en el Golf de Amvrakikos), tant els indicadors ecològics com les biomasses evidencien una degradació dels compartiments demersals de la xarxa tròfica, encara que s'observa una relativa estabilitat dels compartiments pelàgics, principalment a causa dels alts nivells d'eutrofització. La pressió pesquera elevada i els canvis en la producció primària (PP) juguen un paper important en la dinàmica temporal de les espècies; però, els canvis en la PP semblen ser els principals impulsors de la dinàmica temporal de l'ecosistema del mar mediterrani. Les dades pesquers (principalment la captura i l'esforç pesquer) es troben subestimats i conseqüentment registrats de forma errònia a escala regional, sub regional i local. Per exemple, la mortalitat per pesca (i per tant les dades de desembarcament que s'obtenen de les estadístiques de pesca de l'Organització per a l'Agricultura i l'Alimentació [FAO]) de tres de les espècies comercials més importants (Sardina europea “Sardina pilchardus”, anxova “Engraulis encrasicolus” i lluç “Merluccius merluccius”) per a les primeres dècades d'aquest estudi (1950), i en totes les sub regions mediterrànies analitzades, era entre 5 i 10 vegades inferior als valors de referència mitjana registrats en avaluacions de l'estoc d'aquestes poblacions al mar mediterrani. Fins i tot en l'avaluació de les pesqueries italianes, la reconstrucció de les captures totals mostra que les captures totals són 2,6 vegades més grans que els desembarcaments registrats oficialment per la FAO durant el mateix període i per la mateixa zona, amb desembarcaments comercials no declarats (dels sectors industrials i artesanals) que contribueixen al 50% de la captura total (en relació als informes de la FAO) i els descarts que contribueixen un altre 7%. A Europa hi ha diversos models i indicadors associats que podrien ser utilitzats en suport de les polítiques europees de gestió mediambiental, com la Directiva Marc sobre l'Estratègia Marina (MSFD); de totes formes, Ecopath with Ecosim (EwE) és l'eina més aplicada per a la modelització dels ecosistemes marins i aquàtics i la que pot produir un major nombre d'indicadors útils per a la MSFD. Atès que les pressions antropogèniques s'estan expandint ràpidament a la conca mediterrània, aquest treball constitueix un primer pas important per avançar en l'avaluació regional de l'estat ambiental de l'ecosistema marí mediterrani i per informar els plans de conservació i gestió presents i futurs.

Le milieu marin est un espace difficile à étudier et notre connaissance des cétacés et des oiseaux marins présente encore de nombreuses lacunes, notamment concernant leur distribution au large. Le milieu marin pélagique est caractérisé par une forte variabilité spatiotemporelle, les différents processus écologiques composant cet écosystème étant très dynamiques dans le temps et l'espace. Il est donc crucial pour ces espèces marines d'anticiper ces variations afin de se maintenir dans le milieu. Grâce à des campagnes en mer à grandes échelles réalisées en Manche, Golfe de Gascogne et Méditerranée occidentale, cette thèse vise à améliorer la connaissance de la distribution des cétacés et oiseaux marins dans ces régions, et explorer l'impact de la variabilité spatiotemporelle de l'océan sur leur écologie. Ce travail se focalise notamment sur deux échelles temporelles, les variations saisonnières et interannuelles. Dans un premier temps, nous étudierons les variations de préférences d'habitats des espèces étudiées à ces deux échelles. Les cétacés et oiseaux marins étant des espèces longévives caractérisées par de longues périodes d'apprentissage au début de leur vie, nous explorerons également comment la réponse à la saisonnalité varie en fonction de l'expérience chez une espèce commune dans la région, le fou de Bassan. Enfin, nous finirons par explorer les liens prédateurs-proies dans le Golfe de Gascogne, en considérant notamment l'accessibilité de ces proies en termes de taille et de profondeur. Ainsi, cette thèse nous permettra de discuter les implications de ce travail concernant l'écologie des cétacés et oiseaux marins, ainsi que leur conservation
Marine ecosystem is hard to study and several gaps remain in our understanding of cetaceans and seabirds, particularly regarding their at-sea distributions. The pelagic ecosystem is characterised by an important spatiotemporal variability, thanks to the space and time dynamics of its constituting ecological processes. Top predators thus have to anticipate this variability to sustain themselves in the ecosystem. Based on large-scale surveys across waters of the English Channel, Bay of Biscay and north-western Mediterranean Sea, this thesis aimed at improving knowledge regarding the distribution of cetaceans and seabirds in the area, and to explore the impact of ocean spatiotemporal variability on their ecology. This work focused on two temporal scales, the seasonal and interannual variability. We first explored the variations of habitat preferences of studied species at these two temporal scales. Cetaceans and seabirds being long-lived species characterised by long learning periods in their early life, the response to seasonality was investigated according to age and experience in northern gannets, the most abundant seabird species in the area. Finally, the predator-prey association within the Bay of Biscay was also explored, by contrasting prey accessibility in terms of size and depth. The implications of this work regarding the ecology of marine top predators, as well as their conservation, are finally discussed

Ecosystem-based management aims to provide a mechanism for achieving a consensus among multi-sectorial activities for sustaining goods and services and achieving ecological, economic and social objectives in an area. The present study adopts innovative methods and approaches aiming to promote a holistic approach towards collaboration and effective conservation management in Mediterranean Marine Protected Areas (MPAs). In order to understand the current management needs in the Mediterranean MPAs, a management effectiveness evaluation was conducted in the Mediterranean scale following an existing guide (Tempesta and Otero, 2013). Information was collected through a synthesis and integration of different approaches during the period 2013-2014, and MPA management was evaluated on the basis of 21 indicators that described the general categories: (i) management and legislation; (ii) conservation features; (iii) pressures; (iv) communication and outreach. Case studies were initially assessed separately and were finally compared in order to identify common challenges and good practices in MPA management that may be put forward. Some of the most important problems were the inadequate annual funding; limited surveillance and law enforcement; the inadequate stakeholder engagement and bottom-up approaches; policy gaps and long bureaucratic processes to take action; inadequate monitoring of ecological and socio-economic parameters; limited understanding of human activity threats and impacts along with defining critical thresholds that may assure good environmental status of marine ecosystems. We highly recommend that the evaluation be a cyclic process conducted by a neutral practitioner that will inform management decisions and that results should be disseminated in order to reach a high status of MPA management performance in the Mediterranean. The evaluation of MPA management effectiveness guided the next steps of the study towards addressing realistic MPA needs and providing suggestions to improve MPA management. We focused at Portofino MPA case study (Ligurian Sea, Italy) - the third smallest MPA in Italy hosting rich marine biodiversity and a significant amount of human activities. One of the future targets of the MPA’s consortium is to expand its area in order to improve its capacity to effectively protect vulnerable habitats and the species it hosts. Taking into account the past experience and the inadequate communication and up-to-date information in the area, this initiative is expected to raise conflicts and opposition from users. Hence, Portofino MPA represents a case study of particular interest and relevance with MPAs facing similar issues. Following a holistic methodological approach, an engagement process was carefully designed to provide an insight into the social networks’ characteristics directly involved in supporting stakeholder engagement for sound governance performance and co-management of resources. Enhancing stakeholder engagement from the beginning of the process is essential in order to holistically inform decisions and increase the efficiency of conservation management. It is widely accepted that stakeholder engagement may promote cooperation and the exploration of possible solutions to common problems; facilitate the mitigation of conflicts due to various interests; and enhance coordination and the enforcement of common rules in a more transparent way. A framework to examine structural patterns in social networks and identify central actors with the capacity to serve as communication hubs is suggested to boost information flow and enhance stakeholder participation in decision-making. The approach consists of two powerful tools, Stakeholder Analysis and Social Network Analysis, that their capacity to provide an in-depth knowledge of the complexity of social-ecological systems and the factors that influence the engagement process in MPA management has been recently identified. Identification of stakeholders and their relations in a social network, where information exchange and interaction occurs, may highlight important channels for communication, or indicate key stakeholders with the power to control information flow and influence perceptions. This information may be leveraged to accelerate behaviour, facilitate bridging between organisations, promote deliberation, and improve the diffusion of information in MPA management. The outcomes of the study showed that the social network of the Portofino MPA exhibits a core-periphery structure where some user groups seem to have more privileges regarding access to information and resources in the area. The core of the network keeps the network together, and central stakeholders have the capacity to act as communication hubs and facilitate a two-way information flow that will foster communication, trust and collective learning in natural resource management. However, more effort should be made towards strengthening relationships between actors that may influence or be influenced by decisions relating to the MPA. The adoption of alternative communication strategies that integrate visualisation and user-friendly web platforms, in parallel to personal communication are suggested to involve more actively marginalized actors into decisions, that will increase the network’s cohesion, mitigate the power of central actors and augment plurality and new ideas in the engagement process. Production and synthesis of quantitative and qualitative information, related to conservation features and human activities, is another important aspect in conservation management that negotiation and decisions will be based on. Management of small scale and recreational fishing is one of the most important concerns and challenges that Marine Protected Areas (MPAs) have to encounter from a socio-economic, cultural and ecological point of view. Monitoring and assessing fishing activity requires complicated approaches due to the heterogeneity of methods that combine different gears depending on the target species, the season and the characteristics of the area. Many standardized strategies of fisheries management have tried and failed to capture this spatial and temporal heterogeneity, or to provide improved understanding of fishing impacts on the ecosystem components. The present study developed a framework for the monitoring and mapping of recreational and artisanal fishing activity. The framework considers and may be adjusted depending on the MPA management capacity in terms of budget and technology available, personnel available, the level of trust that characterizes the relationship between the MPA and the fishermen, and the willingness of all relevant actors and authorities to provide or collate respectively information. Data from different monitoring strategies and sources were integrated to archive a complete dataset that described different fishing practices in the area. Simple spatial indicators that describe fishing effort were used to map and describe the footprint of each fishing practice on vulnerable habitats, and identify the areas that receive greater fishing pressure. However this is the first step in order to assess the impacts of fishing pressure on vulnerable habitats. Pressure-impact assessments were conducted using spatial analysis in order to holistically inform management decisions on vulnerable habitats such as coralligenous under pressure in Portofino MPA. The approach considers the cumulative impacts caused by different fishing practices and incorporates uncertainty regarding available information following the precautionary principle. Cumulative impacts are based on a conceptual model that identifies the pathways through which activities cause harm and describing the likelihood and consequences of an event. The vulnerability assessment quantifies these causal-chain links between biophysical attributes and to human stressors that are described in the conceptual models. The vulnerability informs on the potential risk of loosing (or degrading) a particular habitat due to a specific pressure, and can provide further support to the assessment of the cumulative impacts caused by different fishing practices operating in an MPA. Coralligenous communities, in terms of coverage, are more abundant in zone B, while Posidonia oceanica meadows dominate in zone C of Portofino MPA. However, a great percentage of the habitat lies outside the MPA borders, which confirms the desire of the MPA management board to expand the area. The areas that receive the highest amount of fishing effort were located between depths of 30-40 m receive the highest fishing pressure at the majority of zone B. The vulnerability assessment revealed that artisanal nets, and both recreational and artisanal bottom longlines, had the highest potential impact on coralligenous habitat, independently from the duration that are active on the seafloor. Other recreational activities that were considered to have high potential impact for coralligenous due to the destructive characteristics of the practice and gear used, or due to the pressure’s high intensity and frequency, were vertical jigging, bottom trolling and big game with a rod and reel. The cumulative impact assessment provided an in depth understanding of combined exposure-effect approaches and identified additional areas in zone C and in greater depths, that fishing activity is necessary to be managed more strictly. Several suggestions were enlisted in order to mitigate fishing impacts on coralligenous habitats, for instance the establishment of additional spatial and temporal closures, prohibition of destructive fishing practices, etc. while policy gaps were also identified in the current management system. The approach takes into account the heterogeneity of techniques and captures the different scale of impacts on benthic habitats in a systematic, transparent and repeatable way, and provides a useful tool that integrates ecological, management and policy interventions. An emerging threat in coastal MPAs is the loss of fishing gears that drift away driven by currents and finally end up on the seafloor covering in some cases a significant amount of fragile benthic habitats like coralligenous. In Portofino MPA this is reported as a common issue and frequently divers retrieve the lost gears and monitor it. To inform the MPA regarding which areas are more susceptible to lost fishing gear, a semi-quantitative spatial analysis was conducted using information from the sea-bottom morphology (depth, slope, Benthic Position Index, rugosity, curvature). The areas identified overlap spatially with areas of high fishing effort, while the local currents agree that most susceptible areas are located in the southern part of Portofino MPA. Although data quality regarding information coming from divers was poor, the suggested analysis may provide useful information in order to focus management actions on specific areas. Finally, the Marxan with Zones conservation planning model was applied on Portofino MPA’s present zoning plan in order to provide alternative solutions for the enlargement and re-zoning of the MPA. Different scenarios concerning the regulation of human activities such as fishing and diving activities taking place at different zones were developed. In our management plan, we set high level conservation targets based on relative EU Directives, the high conservation status of the Portofino MPA (SPAMI) and management objectives. In the present study preliminary results are shown for a single scenario where a 4-zone plan is suggested to the expanded surface area of the MPA, where diving and fishing activity are re-arranged in space and strictly regulated. The suggested zoning plan provided by MARXAN with Zones ensures that high conservation objectives are reached in Portofino MPA with the lowest possible operational cost. Overall, the present study aimed to provide a complete ecosystem-based management approach that considers the social and ecological drivers of the system as complementary components for supporting future conservation initiatives towards collaborative management of resources. The management suggestions of this study provide transparent, comprehensive and efficient plans that can improve the governance and the management of marine resources in the area. Innovative tools and methods were integrated to inform several aspects in the management of marine resources in order to promote a holistic approach towards collaboration and deliberation in MPA management. The developed methodology offers guidance on how to structure and focus efforts for collecting, synthesizing and analyzing of necessary information to inform holistically policymaking and management processes. Results provide useful advise in mitigating the cumulative impacts of human activities and deliver alternative solutions that are based on strict systematic conservation planning principles. Moreover, the study may assist the Portofino MPA to build the social conditions and a future engagement strategy where stakeholders will welcome the conservation initiative for its expansion, however particular effort should be made by the MPA management board towards this direction.

La tortuga babaua (Caretta caretta) és una espècie amenaçada, que ha experimentat una greu reducció de les seves poblacions a nivell mundial. En aquest sentit, s’han identificat molts factors implicats en la mortalitat d’aquesta espècie però, de tots ells, el més significatiu és la pesca. En el cas del mar Mediterrani occidental, tradicionalment, la captura accidental de tortugues marines havia estat relacionada majoritàriament amb el palangre de superfície, i molts estudis han confirmat que és l’art amb més incidència al sud de la Península Ibèrica. Tot i així, s’han anat identificant altres arts de pesca que generen importants captures en determinades regions, com és el cas de les Illes Balears o el mar Adriàtic, on el tresmall de llagosta o l’arrossegament, respectivament, són els arts que generen més captures. En aquest context, la manca d’informació sobre l’impacte causat per la flota de pesca professional catalana va impulsar l’inici d’aquesta tesi, amb la intenció d’estudiar la seva interacció amb la tortuga babaua a Catalunya. D’aquesta manera, l’objectiu principal d’aquesta tesi és estimar la mortalitat generada per la pesca professional al mar Mediterrani occidental, així com avaluar el paper que té aquesta espècie dins el conjunt de l’ecosistema, de manera que es puguin fer paleses les conseqüències que comporta la reducció de les seves poblacions. Els resultats descrits en aquesta tesi, mostren una elevada interacció entre les tortugues marines de l’espècie Caretta caretta o tortuga babaua i la flota de pesca professional de Catalunya. El palangre de superfície i l’arrossegament són els arts més implicats en les captures accidentals de tortugues babaues, i el Delta de l’Ebre s’ha identificat com un punt crític per a la conservació per l’espècie en el litoral català. En concret, el palangre de superfície captura tortugues presents en zones pelàgiques i l’arrossegament tortugues de la plataforma continental, en ambdós casos tortugues babaues d’origen atlàntic i mediterrani, tot i que en proporció diferent segons l’àrea. A més, al Delta de l’Ebre, on trobem la plataforma continental més extensa de tot el litoral mediterrani espanyol, és on les captures per unitat d’esforç de la flota d’arrossegament són més elevades. A partir d’aquí, s’ha mirat de veure com reduir aquest impacte. En el cas de la captura en aigües oceàniques per palangrers de superfície, s’ha mirat d’avaluar la mortalitat dels animals alliberats vius, que en són la gran majoria. En el cas de la captura per barques de bou al Delta de l’Ebre, s’ha estudiat la distribució de les tortugues babaues en l’espai i el temps per mirar d’identificar estratègies que minimitzin la captura. Finalment, s’ha comprovat que la tortuga babaua no és l’únic consumidor de meduses a la Mediterrània ans al contrari, existeix un conjunt variat de depredadors oportunistes de meduses, tots ells espècies d’interès comercial, com la tonyina o el peix espasa. Per tant, també es proposen consells necessaris per a gestionar de forma efectiva les preocupants proliferacions de meduses a la Mediterrània occidental.
The loggerhead turtle (Caretta caretta) is an endangered species that has undergone a serious reduction of populations worldwide. In this regard, many factors involved in the mortality of this species have been identified, but from all, the most significant is bycatch due to professional fishing. In the western Mediterranean, where loggerhead is the most common sea turtle species, bycatch of sea turtles has traditionally been associated mostly with drifting longlines. However, several cent studies have identified other gears as significant sources of sea turtle bycatch, at least at certain regions within the Mediterranean. At the beginning of this thesis, nothing was known about the impact caused by the Catalan professional fishing fleet on sea turtles and hence this thesis aimed to estimate the mortality generated by professional fishing in the region, identify the relative importance of different fishing gears in sea turtle bycatch, asses the post-release mortality of bycaught turtles and identify methods to reduce the bycatch levels by bottom trawlers. Furthermore, this thesis aimed to test the hypothesis that a decline in the population of sea turtles because of high levels of incidental bycatch was the reason for recent jellyfish outbreaks.

Los objetivos de la tesis fueron estudiar los factores que pueden explicar la variabilidad existente en la distribución e intensidad de la pesca artesanal en torno a una reserva marina (RM), valorar el efecto de la protección sobre la pesca y analizar y valorar los efectos bio-económicos de configuraciones alternativas de diseño y gestión. Los resultados revelaron que las embarcaciones artesanales calan más artes, de menor longitud, en zonas de elevada diversidad de hábitats. El rendimiento pesquero depende del nivel de protección, la distancia a la RM y la diversidad de artes por unidad de área. La protección está teniendo resultados positivos sobre las poblaciones de peces explotadas y beneficiando a la economía local. El aumento de superficie protegida, distribuido en varias reservas integrales en emplazamientos adecuados, distanciadas unas decenas kilómetros, más que la reducción del esfuerzo, tendría efectos positivos sobre el poblamiento de peces y la economía local.
The aim of the present work is to study the factors that may explain the variability in distribution and intensity of artisanal fishing around a marine reserve, evaluate the reserve effect and analyze and assess the biological and economic effects of alternative configurations of a marine protected area. The results revealed that artisanal vessels used more fishing gears, but shorter, in high habitat diversity areas. The fishing yield depends of protection level, distance to marine reserve and diversity of fishing gears per unit area. The protection measures have had positive results on exploited fish populations and in the local economy. The increase of protected area surface, distributed on several no take zones at appropriate locations, a few kilometers apart, more than the reduction of the fishing effort, would have positive effects on the population of commercial fishes and the local economy.

L'étude de l'impact que les structures hydrodynamiques à mésoéchelle peuvent avoir sur la distribution spatiale des organismes planctoniques et le transport de matière entre la zone côtière et le large est essentielle à la compréhension du fonctionnement de l'écosystème planctonique dans l'océan côtier. L'influence des tourbillons anticycloniques et des processus physiques associés sur l'écosystème planctonique pélagique est examinée au moyen d'un modèle couplé physique-biogéochimie. Dans un premier temps, les sorties du modèle sont confrontées à des données in situ et satellitales afin de vérifier le réalisme du modèle. Pendant la majeure partie de la simulation, et plus particulièrement sur la partie ouest du golfe de Lion pendant la période estivale, l'erreur commise par le modèle sur l'estimation de la chlorophylle de surface (proxy du phytoplancton) est inférieure à celle donnée par le calcul issu de la télédétection. Ensuite, la distribution du plancton en présence d'un tourbillon a été étudiée. Dans les sorties du modèle, un filament avec une forte concentration en chlorophylle est systématiquement observé sur le bord nord/nord-est de la structure, est confirmé par des données satellitales. Enfin, grâce à une simulation longue sur la période 2011-2004, plusieurs tourbillons ont été comparés du point de vue de leur impacts sur les échanges entre la côte et le large de matière et plancton. L'intensité et la direction de ces échanges sont hétérogènes et dépendent des forçages physiques qui ont donné lieu à la génération de ces tourbillons
The role that mesoscale physical structures play in driving plankton community shifts and transporting matter is key to the understanding of food web dynamics at the regional scale

Le bassin méditerranéen est reconnu comme un "point chaud" de biodiversité soumis à de fortes pressions anthropiques. En domaine marin, les habitats coralligènes participent grandement à cette biodiversité et leur situation côtière les rend accessibles aux hommes. La thèse porte sur l'identification et l'évaluation de leurs services écosystémiques. J’ai utilisé le concept de \textit{service écosystémique} à une échelle locale : la Baie de Marseille (anthropisée) et le Parc national de Port-Cros (sous pression humaine minimale). Le premier volet de la thèse porte sur l'identification et la description des services rendus par les habitats coralligènes dans les zones d’étude. Les services les plus évidents (production de ressource alimentaire, production de corail rouge et sites de plongée) font l’objet d’une étude plus approfondie. Le deuxième volet de la thèse teste le concept de cascade de service écosystémique d'Haines-Young et Potschin pour décrire les éléments et fonctions de l'écosystème impliqués dans chaque service, les bénéficiaires et les types de valeurs économiques qui en sont issus, et des indicateurs pour mesurer chaque niveau de la cascade. Le troisième volet de la thèse porte sur une analyse de l'activité de plongée sur les habitats coralligènes de la baie de Marseille. Le dernier volet de la thèse est une étude des préférences déclarées dans les secteurs de Marseille et Port-Cros concernant les services rendus par les habitats coralligènes, grâce à la méthode des choix discrets. Ce dernier volet comprend une étude de l’impact de la connaissance initiale et de l’apport d’information dans la formation des préférences
The Mediterranean basin is recognized as a "hotspot" of biodiversity subjected to strong anthropic pressures. In the marine domain, coralligenous habitats greatly contribute to the basin’s biodiversity and their coastal location makes them accessible to humans. The thesis attempts to identify and economically evaluate some of those ecosystem services. I used the concept of \textit{ecosystem service} at a local scale, focusing on the Bay of Marseille (anthropized) and the Port-Cros national park (under minimal human pressure). The first part of the thesis deals with the identification and description of the services rendered by coralligenous habitats in the study areas. The second part of the thesis describes the provisionning services through the application of the concept of ecosystem service cascade as developed by Haines-Young and Potschin. This approach helps to identify the elements and functions of the ecosystem involved in each service, the human beneficiaries and the types of economic benefits associated with the services. This chapter also proposes variables to measure each level of the cascade. The third part of the thesis deals with an analysis of the relationship between the presence of coralligenous habitat and the frequency of dives in the Bay of Marseille. The last part of the thesis employs the method of discrete choices experiment to study the declared preferences in the study areas of Marseille and Port-Cros concerning the services rendered by the coralligenous habitats. This analysis provided insight into how preferences can evolve as initial knowledge is enhanced through the provision of additional information

Les lagunes côtières présentent une forte importance écologique, économique et sociale. Toutefois, elles sont particulièrement vulnérables face aux pressions anthropiques et aux changements climatiques, notamment en région méditerranéenne. La conservation des lagunes est donc fondamentale pour la protection des systèmes littoraux et le bien-être des populations humaines. Cette thèse vise à apporter un soutien aux politiques publiques pour la restauration et la conservation des lagunes côtières, mais également à rechercher de potentielles valorisations des ressources. Les travaux ambitionnent d’approfondir les connaissances sur les trajectoires d’évolution des communautés phytoplanctoniques et des lagunes côtières du littoral corse, (i) en questionnant l’évolution des variations saisonnières face aux paramètres abiotiques, mais également l’impact des variations de salinité, notamment dans le cadre du changement climatique, sur de grandes et/ou de petites lagunes et (ii) en testant différentes approches intégrées avec la prise en compte de l’impact de l’homme, du bassin versant jusqu’à la mer.Les communautés phytoplanctoniques de six lagunes du littoral corse (Diana, Urbino, Biguglia, Arasu, Santa Giulia, Balistra) sont étudiées dans ce cadre. Les analyses sur le long terme grâce aux données historiques disponibles, les suivis in situ et les expérimentations réalisées ont permis d’identifier des dynamiques saisonnières marquées des communautés phytoplanctoniques et des éléments centraux pour la gestion des milieux lagunaires. La tendance vers une dominance des dinoflagellés, l’émergence d’espèces tolérant le stress (e.g. salinités extrêmes), parfois potentiellement toxiques, l’augmentation des blooms phytoplanctoniques ainsi que des modifications des cycles saisonniers ont été mis en évidence sur des lagunes de grandes et de petites tailles. Ces phénomènes sont liés principalement à des impacts d’origine anthropique (pollution, rejets urbains, usage de l’eau, tourisme…), des altérations hydrologiques engendrées par des interventions humaines, et le changement climatique.L’étude d’autres compartiments biotiques et abiotiques de l’écosystème, comme l’invasion biologique, la production halieutique ou le fonctionnement hydrogéologique, a confirmé la nécessité d’appliquer une approche écosystémique, du bassin versant jusqu’à la mer, pour comprendre le fonctionnement global du système. La prise en compte de l’Homme dans l’étude des trajectoires écologiques a été aussi mise en évidence, soulignant que les lagunes doivent être considérées comme des socio-écosystèmes. Cette vision holistique est fondamentale pour envisager une gestion optimale intégrée de la complexité du système.Cette thèse apporte de plus un regard nouveau sur les lagunes de petites surfaces à l’échelle du littoral méditerranéen qui sont très réactives aux changements et qui peuvent être considérées comme des sentinelles de l’évolution climatique.Parallèlement, l‘étude d’une souche de diatomée issue de l’étang de Diana a démontré des caractéristiques écophysiologiques et chimiques prometteuse pour de potentielles applications biotechnologiques dans le domaine de l’aquaculture, en raison de son origine lagunaire.L’ensemble de ces résultats sur les trajectoires d’évolution passées et futures a permis de marquer la complexité et la vulnérabilité des lagunes côtières (et celles de petites surfaces en particulier) face aux menaces croissantes et des interrogations sur leur avenir. Ce travail fournit donc des éléments d’appui pour la gestion des lagunes et de valorisation des ressources liées à ces milieux, en proposant une gestion intégrée et interdisciplinaire pour une conservation durable de ces écosystèmes et des services fournis, notamment dans le cadre du changement climatique
Coastal lagoons are of high ecological, economic and social importance. Nevertheless, they are particularly vulnerable to anthropogenic pressure and climate change, especially in the Mediterranean region. Lagoons’ conservation is hence fundamental for the protection of littoral systems and the well-being of human populations. This thesis aims to provide support for public policies for the restoration and conservation of coastal lagoons, but also to look for potential resources’ valorisation. The works aim to deepen knowledge on the evolution trajectories of phytoplankton communities and coastal lagoons of the Corsican coast, (i) by questioning the evolutions of seasonal variations linked to abiotic factors, but also the impact of salinity variations, particularly in the context of climate change, on large and/or small lagoons, and (ii) by testing different integrated approaches taking into account the human impact, from the watershed to the sea.Phytoplankton communities of six Corsican lagoons (Diana, Urbino, Biguglia, Arasu, Santa Giulia, Balistra) are studied in this framework. Analysis of long term historical datasets available, in situ monitoring and experimental essays performed allowed the identification of marked seasonal dynamics of phytoplankton communities and central elements for coastal lagoons’ management. The trend towards the dominance of dinoflagellates, the emergence of stress-tolerant (e.g. extreme salinities), sometimes potentially toxic, the increase in phytoplankton blooms as well as changes in the seasonal cycles have been highlighted in large and small sized lagoons. These phenomena are mainly linked to anthropogenic impacts (pollution, urban wastewater, water use, tourism…), hydrogeological alterations caused by human interventions, and climate change.The study of other biotic and abiotic compartments of the ecosystem, like biological invasion, fish production or hydrogeological functioning, has confirmed the need to apply an ecosystem-based approach, from the watershed to the sea, in order to understand the overall functioning of the system. The consideration of Humans in the study of ecological trajectories has also been highlighted, emphasizing that lagoons should be considered as social-ecological systems. This holistic vision is fundamental to consider an optimal integrated management of the complexity of the system.Moreover, this thesis provides a new perspective on small surfaced lagoons on the Mediterranean coast scale, which are very reactive to change and can thus be considered as sentinels of climate change.At the same time, the study of a diatom strain from the Diana lagoon has demonstrated promising ecophysiological and chemical characteristics for potential biotechnological applications in the aquaculture domain, due to its lagoon origin.The overall results on the past and future evolution trajectories have highlighted the complexity and vulnerability of coastal lagoons (and those of small surface areas in particular) in the face of growing threats and some questions about their future. This work provides hence some supporting elements for the lagoon management and the valorisation of resources linked to these environments, by proposing an integrated and interdisciplinary management for the sustainable conservation of these ecosystems and of the services provided, particularly in the climate change context