Several coralligenous reefs occur in the soft bottoms of the northern Adriatic continental shelf. Mediterranean coralligenous habitats are characterised by high species diversity and are intrinsically valuable for their biological diversity and for the ecological processes they support. The conservation and management of these habitats require quantifying spatial and temporal variability of their benthic assemblages. This PhD thesis aims to give a relevant contribution to the knowledge of the structure and dynamics of the epibenthic assemblages on the coralligenous subtidal reefs occurring in the northern Adriatic Sea. The epibenthic assemblages showed a spatial variation larger compared to temporal changes, with a temporal persistence of reef-forming organisms. Assemblages spatial heterogeneity has been related to morphological features and geographical location of the reefs, together with variation in the hydrological conditions. Manipulative experiments help to understand the ecological processes structuring the benthic assemblages and maintaining their diversity. In this regards a short and long term experiment on colonization patterns of artificial substrata over a 3-year period has been performed in three reefs, corresponding to the three main types of assemblages detected in the previous study. The first colonisers, largely depending by the different larval supply, played a key role in determining the heterogeneity of the assemblages in the early stage of colonisation. Lateral invasion, from the surrounding assemblages, was the driver in structuring the mature assemblages. These complex colonisation dynamics explained the high heterogeneity of the assemblages dwelling on the northern Adriatic biogenic reefs. The buildup of these coralligenous reefs mainly depends by the bioconstruction-erosion processes that has been analysed through a field experiment. Bioconstruction, largely due to serpulid polychaetes, prevailed on erosion processes and occurred at similar rates in all sites. Similarly, the total energy contents in the benthic communities do not differ among sites, despite being provided by different species. Therefore, we can hypothesise that both bioconstruction processes and energetic storage may be limited by the availability of resources. Finally the major contribution of the zoobenthos compared to the phytobenthos to the total energetic content of assemblages suggests that the energy flow in these benthic habitats is primarily supported by planktonic food web trough the filter feeding invertebrates.

Marine Protected Areas (MPAs) were initially created to protect the living, non-living, cultural and/or historical values from human activities. The Convention on Biological Diversity (CBD; Earth Summit in Rio de Janeiro on 5 June 1992) has set a target of protecting 10% of the coastal and marine areas by 2020, which has led to a rapid increase in the creation of MPAs worldwide. Within this context, there is a growing concern regarding the number of efficient MPAs. One of the main issues is that biological or ecological features of marine species as well as ecosystem processes are not taken into account in MPA design. Deciding criteria for species management requires considerable information collected from a number of sources, including morphometric data, genetic data and distributional data. Morphometric tools are useful to study species taxonomy, or to provide information about the morphological variability, size and growth of the species, which is essential for MPA monitoring. Genetic tools can be use to resolve species taxonomy or population structure, allowing to estimate genetic diversity and connectivity of populations at different temporal and spatial scales. Both morphometric and genetic data used in combination provide a powerful tool that should be considered in MPA assessment. However, the accurate interpretation and the integration of this information into marine spatial planning is specially challenging. The aim of this PhD thesis was to develop a protocol for monitoring Marine Protected Areas by studying the morphology and genetics of two closely limpet species (Patella rustica and Patella caerulea) across MPAs in the Western Mediterranean sea. Overall, the results of this thesis provides support the inclusion of the morphological and genetic tools into management plans, and in the guidelines for the monitoring to improve and/or maintain MPA health and effectiveness.

Canopy-forming seaweeds are worldwide disappearing due to the combined effects of human activities and climate instabilities. Identifying the type and strength of interactions between multiple anthropogenic and natural stressors can help setting achievable management targets for degraded ecosystems and support ecological resilience through local actions. This thesis aimed to understand how algal forests change from extensive to degraded, and what factors can enhance the ability of forests to withstand or recover from stressors. I contributed to a systematic review to infer potential important synergistic stressors interactions driving the loss of canopy-forming seaweeds at a global level. We found that management of excess nutrient levels would provide the greatest opportunity for preventing the shift from canopy to mat-forming algae, because of the higher prevalence of synergistic interactions between nutrient enrichment with other local and global stressors. Then, I focused my attention on fucoid algae of the genus Cystoseira that are the most typical canopy-forming seaweeds in the Mediterranean Sea. I explored which environmental and anthropogenic factors can explain the current status of the intertidal Cystoseira populations. I found that coastal urbanization and nutrient concentration were the factors most related to the status of Cystoseira. Finally, I carried out a series of manipulative field experiments to explore the effects of nutrient enrichment and heat-wave events on intertidal C. compressa. The results showed that C. compressa is sensitive to heat-wave events and that local biodiversity and thermal history of the alga seem to play a role reducing or increasing respectively the impact of such extreme events. I also characterised the epiphytic bacteria associated to the surface of C. compressa and showed their potential influence on the responses of C. compressa to environmental stressors.

Natural systems face pressures exerted by natural physical-chemical forcings and a myriad of co-occurring human stressors that may interact to cause larger than expected effects, thereby presenting a challenge to ecosystem management. This thesis aimed to develop new information that can contribute to reduce the existing knowledge gaps hampering the holistic management of multiple stressors. I undertook a review of the state-of-the-art methods to detect, quantify and predict stressor interactions, identifying techniques that could be applied in this thesis research. Then, I conducted a systematic review of saltmarsh multiple stressor studies in conjunction with a multiple stressor mapping exercise for the study system in order to infer potential important synergistic stressor interactions. This analysis identified key stressors that are affecting the study system, but also pointed to data gaps in terms of driver and pressure data and raised issues for potentially overlooked stressors. Using field mesocosms, I explored how a local stressor (nutrient availability) affects the responses of saltmarsh vegetation to a global stressor (increased inundation) in different soil types. Results indicate that saltmarsh vegetation would be more drastically affected by increased inundation in low than in medium organic matter soils, and especially in estuaries already under high nutrient availability. In another field experiment, I examined the challenges of managing co-occurring and potentially interacting local stressors on saltmarsh vegetation: recreational trampling and smothering by deposition of excess macroalgal wrack due to high nutrient loads. Trampling and wrack prevention had interacting effects, causing non-linear responses of the vegetation to simulated management of these stressors, such that vegetation recovered only in those treatments simulating the combined prevention of both stressors. During this research I detected, using molecular genetic methods, a widespread presence of S. anglica (and to a lesser extent S. townsendii), two previously unrecorded non-native Spartinas in the study areas.

This study presents the development of a Model of Intermediate Complexity for Ecosystem assessments (MICE) for testing management scenarios for the stock of European hake (Merluccius merluccius) and Norway lobster (Nephrops norvegicus) inhabiting the Central Adriatic Sea. These two species represent the target species, as well as the predators, of this study. They are mainly fished by Italian and Croatian bottom trawl fishery, accounting for both the highest landings and commercial value among demersal species in the area. The specific circulation of the Adriatic Sea is responsible for strong nutrient recycling processes within this area, resulting in a rich fishing ground extensively exploited by Italian and Croatian fishing vessels, make it an interesting case study for the development of an Ecosystem Approach to Fisheries (EAF). Here, an EAF was developed using the MICE approach, since it is well adapted to test specific management questions, as required by this study. The MICE was developed in a step-wise manner. Firstly, single-species stock assessments for both the target species were pursued, allowing the evaluation of the state of these resources and permitting the production of the input values to be included within the MICE. Secondly, the diet of the target species were examined and prey items portioned in four groups; consumption of each prey group by each predator was modelled using a Holling Type II functional response. Finally, predator and prey dynamics were linked within the MICE model, using a modified biomass dynamic model to project them into the future and testing different management strategies. The best management scenario resulted to be the protection of adults, which produced the most beneficial results for both predators and prey groups.

No description available.

Habitat structure is known to influence the abundance of fishes on temperate reefs. Biotic interactions play a major role in determining the distribution and abundance of species. The significance of these forces in affecting the abundance of fishes may hinge on the presence of organisms that either create or alter habitat. On temperate reefs, for example, macroalgae are considered autogenic ecosystem engineers because they control resource availability to other species through their physical structure and provide much of the structure used by fish. On both coral and temperate reefs, small cryptic reef fishes may comprise up to half of the fish numbers and constitute a diverse community containing many specialized species. Small cryptic fishes (<100 mm total length) may be responsible for the passage of 57% of the energy flow and constitute ca. 35% of the overall reef fish biomass on coral reefs. These benthic fish exploit restricted habitats where food and shelter are obtained in, or in relation to, conditions of substrate complexity and/or restricted living space. A range of mechanisms has been proposed to account for the diversity and the abundance of small fishes: (1) lifehistory strategies that promote short generation times, (2) habitat associations and behaviour that reduce predation and (3) resource partitioning that allows small species to coexist with larger competitors. Despite their abundance and potential importance within reef systems, little is known of the community ecology of cryptic fishes. Specifically on habitat associations many theories suggested a not clear direction on this subject. My research contributes to the development of marine fish ecology by addressing the effects of habitat characteristics upon distribution of cryptobenthic fish assemblages. My focus was on the important shallow, coastal ecosystems that often serve as nursery habitat for many fish and where different type of habitat is likely to both play important roles in organism distribution and survival. My research included three related studies: (1) identification of structuring forces on cryptic fish assemblages, such as physical and biological forcing; (2) macroalgae as potential tools for cryptic fish and identification of different habitat feature that could explain cryptic fish assemblages distribution; (3) canopy formers loss: consequences on cryptic fish and relationship with benthos modifications. I found that: (1) cryptic fish assemblages differ between landward and seaward sides of coastal breakwaters in Adriatic Sea. These differences are explained by 50% of the habitat characteristics on two sides, mainly due to presence of the Codium fragile, sand and oyster assemblages. Microhabitat structure influence cryptic fish assemblages. (2) Different habitat support different cryptic fish assemblages. High heterogeneity on benthic assemblages reflect different fish assemblages. Biogenic components that explain different and diverse cryptic fish assemblages are: anemonia bed, mussel bed, macroalgal stands and Cystoseira barbata, as canopy formers. (3) Canopy forming loss is not relevant in structuring directly cryptic fish assemblages. A removal of canopy forming algae did not affect the structure of cryptic fish assemblages. Canopy formers algae on Conero cliff, does not seem to act as structuring force, probably due to its regressive status. In conclusion, cryptic fish have been shown to have species-specific associations with habitat features relating to the biological and non biological components afforded by fish. Canopy formers algae do not explain cryptic fish assemblages distribution and the results of this study and information from the literature (both from the Mediterranean Sea and elsewhere) show that there are no univocal responses of fish assemblages. Further exanimations on an non regressive status of Cystoseira canopy habitat are needed to define and evaluate the relationship between canopy formers and fish on Mediterranean sea.

The present issue analyses bluefin tuna (Thynnus thunnus) and swordfish (Xiphias glaudis) diet, caught by professional long-line fishing in the middle Adriatic Sea (Pomo pit). These species represent apex predators in pelagic environment that may play key roles in determining food web structure and ecosystem dynamics. The studies about their feedings habits, based upon stomach contents analysis, are important for the comprehension of biological and ecological interaction. Over the years, many studies have been performed on the diet of tuna and swordfish in the Mediterranean Sea. This research is based on a fairly wide number of analyzed stomach contents, in comparison with the previous ones. In this work, the analysis of 340 stomach contents of bluefin tuna caught by long-line in the central Adriatic sea confirms in general the opportunistic behaviour of this species. Finding support the hypothesis that Adriatic tuna and swordfish chase their food over a wide bathymetric zone and probably near the surface at night. No indication of food preference respect to size of predator or sample season are found. It seems that the two species are able to cohabit because their trophic niche are not overlapped, changing during the time and the vertical and horizontal space.

The Ecosystem Approach to Fisheries represents the most recent research line in the international context, showing interest both towards the whole community and toward the identification and protection of all the “critical habitats” in which marine resources complete their life cycles. Using data coming from trawl surveys performed in the Northern and Central Adriatic from 1996 to 2010, this study provides the first attempt to appraise the status of the whole demersal community. It took into account not only fishery target species but also by-catch and discharge species by the use of a suite of biological indicators both at population and multi-specific level, allowing to have a global picture of the status of the demersal system. This study underlined the decline of extremely important species for the Adriatic fishery in recent years; adverse impact on catches is expected for these species in the coming years, since also minimum values of recruits recently were recorded. Both the excessive exploitation and environmental factors affected availability of resources. Moreover both distribution and nursery areas of the most important resources were pinpointed by means of geostatistical methods. The geospatial analysis also confirmed the presence of relevant recruitment areas in the North and Central Adriatic for several commercial species, as reported in the literature. The morphological and oceanographic features, the relevant rivers inflow together with the mosaic pattern of biocenoses with different food availability affected the location of the observed relevant nursery areas.

Nell’attuale contesto di aumento degli impatti antropici e di “Global Climate Change” emerge la necessità di comprenderne i possibili effetti di questi sugli ecosistemi inquadrati come fruitori di servizi e funzioni imprescindibili sui quali si basano intere tessiture economiche e sociali. Lo studio previsionale degli ecosistemi si scontra con l’elevata complessità di questi ultimi in luogo di una altrettanto elevata scarsità di osservazioni integrate. L’approccio modellistico appare il più adatto all’analisi delle dinamiche complesse degli ecosistemi ed alla contestualizzazione complessa di risultati sperimentali ed osservazioni empiriche. L’approccio riduzionista-deterministico solitamente utilizzato nell’implementazione di modelli non si è però sin qui dimostrato in grado di raggiungere i livelli di complessità più elevati all’interno della struttura eco sistemica. La componente che meglio descrive la complessità ecosistemica è quella biotica in virtù dell’elevata dipendenza dalle altre componenti e dalle loro interazioni. In questo lavoro di tesi viene proposto un approccio modellistico stocastico basato sull’utilizzo di un compilatore naive Bayes operante in ambiente fuzzy. L’utilizzo congiunto di logica fuzzy e approccio naive Bayes è utile al processa mento del livello di complessità e conseguentemente incertezza insito negli ecosistemi. I modelli generativi ottenuti, chiamati Fuzzy Bayesian Ecological Model(FBEM) appaiono in grado di modellizare gli stati eco sistemici in funzione dell’ elevato numero di interazioni che entrano in gioco nella determinazione degli stati degli ecosistemi. Modelli FBEM sono stati utilizzati per comprendere il rischio ambientale per habitat intertidale di spiagge sabbiose in caso di eventi di flooding costiero previsti nell’arco di tempo 2010-2100. L’applicazione è stata effettuata all’interno del progetto EU “Theseus” per il quale i modelli FBEM sono stati utilizzati anche per una simulazione a lungo termine e per il calcolo dei tipping point specifici dell’habitat secondo eventi di flooding di diversa intensità. / In the current environmental context, it emerges the need to understand all the possible effects of the increase of the anthropic impact and the “Global Climate Change” on the ecosystems, considered as the main users of services and essential functions upon which whole economic and social textures are based. The forecast study of the ecosystems collides with the high complexity of them and with the lack of integrated observations. The model approach seems to be the most appropriate for the analysis of the complex dynamics of the ecosystems and the contextualization of experimental results and empiric observations. The reductionist-deterministic approach, which generally is used in the implementation of the models, has not been able to reach higher levels of complexity within the structure of the ecosystem. The biotic factor is the component that best describes the complexity of the ecosystem, because of the high dependency upon the other components and their interactions. In this thesis, it is suggested a new stochastic and model approach based on the employment of a naive-Bayesian compiler operating within a fuzzy environment. The combined employment of fuzzy logic and naive-Bayesian approach is useful to process the high degree of uncertainty of the ecosystems. The obtained generative models, called Fuzzy Bayesian Ecological Models (FBEM) are able to modelize the states of the ecosystems as functions of the high number of interactions. FBEM models have been used to understand the environmental risk for the intertidale habitat of sand beaches in case of coast flooding events forecasted from 2010 to 2100. The application has been developed within the EU “Theseus” Project, in which the FBEM models have been used also for a long term simulation and for the computation of the tipping points specific of the habitat depending on flooding events of different intensity.