Neste estudo, objetivou-se caracterizar ao nível molecular os vibrios isolados de amostras de água do mar, plâncton e bivalves do Canal de São Sebastião (n=78), Baixada Santista (n=37) e Ubatuba (n=17), analisar a susceptibilidade aos antibióticos e os principais genes associados à virulência. Observou-se sensibilidade à ciprofloxaxina, meropenem e ácido nalidíxico, resistência à ampicilina e à cefalotina, e alta porcentagem de múltipla resistência (Ubatuba: 64,7%; Baixada Santista:48,6%; Canal de São Sebastião: 43%) aos antimicrobianos. Quatro isolados foram positivos para o gene de virulência stn/sto. Por MLSA, foi possível identificar V.alginolyticus, V.fluvialis, V.campbellii e V.harveyi em Ubatuba; V.fluvialis, V.alginolyticus, V.campbellii, V.rotiferianus, V.harveyi, V.diabolicus, V.atypicus, V.coralliilyticus, V.maritimus, V.parahaemolyticus e V.tubiashii no Canal de São Sebastião; e, V.alginolyticus, V.parahaemolyticus, V.rotiferianus, V.campbellii, V.harveyi, V.communis, V.maritimus, V.fluvialis, V.fortis, V.natriegens e V.navarrensis na Baixada Santista. / The aim of this study was to characterize at the molecular level Vibrio species isolated from seawater, plankton, bivalves samples from Canal de São Sebastião (n=78), Baixada Santista (n=37) and Ubatuba (n=17), to analyze antimicrobial susceptibility and the major virulence-associated genes. The results showed ciprofloxacin, meropenem, nalidixic acid sensitivity, ampicillin, and cephalothin resistance, and a significant percentage of multidrug resistance (Ubatuba: 64.7%; Baixada Santista: 48.6%; Canal de São Sebastião: 43%). Four seawater isolates were found positive for the stn/sto virulence gene. MLSA allowed the identification of V.alginolyticus, V.fluvialis, V.campbellii, V.harveyi in Ubatuba; V.fluvialis, V.alginolyticus, V.campbellii, V.rotiferianus, V.harveyi, V.diabolicus, V.atypicus, V.coralliilyticus, V.maritimus, V.parahaemolyticus and V.tubiashii in Canal de São Sebastião, and V.alginolyticus, V.parahaemolyticus, V.rotiferianus, V.campbellii, V.harveyi, V.communis, V.maritimus, V.fluvialis, V.fortis, V.natriegens, and V.navarrensis in Baixada Santista.

No description available.

La variabilité du système climatique influence la productivité et la distribution des espèces marines sur toutes les échelles de temps, de la variabilité saisonnière et inter-annuelle aux cycles glaciaires-interglaciaires. Mais ces liens entre climat et écosystèmes marins sont encore largement méconnus, de telle sorte que les prévisions des changements à venir sont difficiles. De plus, parce que les indicateurs paléoclimatiques issus des archives marines sont souvent liés au fonctionnement de l’écosystème, cette méconnaissance limite la fiabilité de la reconstruction de la variabilité climatique passée.Ce travail de thèse vise à améliorer notre connaissance de ces liens entre climat et écosystèmes marins : nous nous sommes intéressés aux changements de productivité marine au cours du dernier cycle glaciaire-interglaciaire, et nous nous sommes aussi penchés sur la réponse de l’écosystème, incluant l'ensemble des niveaux de la chaine trophique, à la variabilité inter-annuelle à décennale en climat pré-industriel. Ce travail est basé sur l’utilisation d’un modèle climatique (IPSL-CM), d’un modèle de biogéochimie marine (PISCES) et d’un modèle de niveaux trophiques supérieurs (APECOSM).Dans un premier temps, nous montrons que le lien entre l’intensité de la mousson indienne et la productivité primaire marine, en été boréal dans la mer d’Arabie, n’est pas direct. En effet, il apparait indispensable pour comprendre les changements de productivité de considérer, en plus de l'intensité de la mousson, la structure de la mousson. En particulier, la position du Jet de Findlater par rapport à la côte de la péninsule arabique est un paramètre important puisqu'elle conditionne la dynamique d'Ekman dans la région.Dans un second temps, nous avons étudié les variations de la productivité marine au large de l'embouchure du fleuve Congo et leurs liens avec le fleuve et les changements de dynamique atmosphérique africaine. Ce travail a mis en évidence que la relation entre l'intensité de la mousson et l'intensité des alizés, souvent utilisée dans les reconstructions climatiques, n'est pas toujours vérifiée. Selon le climat étudié, l'importance des effets thermiques ou dynamiques sur les changements de précipitations et de vents simulés est différente.Dans un troisième temps, nous avons étudié l'effet de la variabilité inter-annuelle sur les changements de productivité passés et sur le signal climatique potentiellement enregistré par des indicateurs climatiques biologiques.Enfin, la dernière partie de cette thèse se focalise sur la réponse des organismes marins des haut-niveaux trophiques à la variabilité climatique à différentes fréquences. Ce travail a révélé que les organismes marins répondent de façons différentes aux variations environnementales en fonction de leur taille et de leur habitat. / Climate variability influences marine primary productivity and marine species distribution over all timescales, from seasonal to interannual variability and glacial-interglacial cycles. The links between climate and marine ecosystems are still sparsely known so that the predictions of futur changes are difficult. Moreover, because paleoclimate recorders extracted from marine archives are often linked to the functionning of the ecosystem, this lack of knowledge limits our ability to reconstruct past climate variability.This thesis work aims at improving our knowledge of these links between climate and marine ecosystems : we have looked into marine productivity changes during the last glacial-interglacial cycle, but we also examined the "end-to-end" ecosystem response to inter-annual to decadal variability in a pre-industrial climate. This work uses a climate model (IPSL-CM), a bio-geochemical model (PISCES) and a model of high trophic levels (APECOSM).First, we show that the link between Indian summer monsoon intensity and marine primary productivity in the Arabian Sea is indirect. Indeed, it appears necessary to consider the monsoon pattern, such as the Findlater Jet position, which drives the Ekman dynamics in the region, as well as its intensity to understand the productivity changes.Second, we study the marine productivity changes off the Congo river mouth and their links with the river runoff and the African atmospheric dynamics. This work shows that the relationship between monsoon intensity and trade winds intensity, often used to reconstruct past changes, is not always verified. Depending on the climate, thermal or dynamical effects are more or less prominent drivers of the simulated changes in precipitation and winds. Productivity off the Congo river mouth, which is mainly located in the subsurface, seems more affected by the ocean and atmosphere dynamics than by the river supply in nutrients.Third, we study the inter-annual variability effects over past productivity changes and over the climatic signal potentially recorded in the biological climate proxies.Finally, the last part of the thesis focuses on high trophic levels marine organisms response to climate variability at different frequencies. This study shows that marine organisms response to environmental changes varies with the organism' size and habitat.

Two prominent factors posing a major threat to biodiversity in marine ecosystems are climate change and the establishment of invasive species, and the interaction between these two. Because of the upwelling of cold, nutrient-rich water, the coast of Portugal is a thermal refuge and distribution edge for cold-adapted species, making it a particularly important study area from a biodiversity point of view. In this study I investigated the physiological tolerance to heat stress of six different native and co-occurring non-native marine species, red algae; C. crispus and G. turuturu, brown algae; S.polyschides  and U. pinnatifida,  and mussels ; X.securis and M.galloprovincialis,  in the intertidal  rocky coast of Portugal. Dynamic ramping assays with four different durations and intensity of thermal stress was conducted for each specie to determine a so-called thermal death time (TDT) curve and the thermal tolerance parameters CTmax (the temperature that will cause death within one min) and z (the decrease in thermal decay over time) for each specie. To compare the thermal tolerance between the native vs non-native species a linear mixed effects model was applied. This study found a significantly higher thermal tolerance to extreme temperatures expressed as the upper critical temperature CTmax in the invasive red algae G. turuturu and mussel X.securis compared to its native counterparts C.crispus and M.galloprovincialis. The study found no significant difference in the thermal tolerance expressed for the kelp species S. polyschides and U.pinnatifida which had a similar response to the heat challenge. The implication from these the findings for the coast of Portugal, could be that the invasive algae and mussel might better survive an extreme event such as a heatwave then the co-occurring native, while the invasive kelp species would respond in a similar way to the heat challenge. Hence the invasive capacity might depend more on the invasion window after a stressful event and on how well the native species recover from a heat stress. The findings from this study call for further conservation, restoration and monitoring efforts in this area given the biodiversity supported by the important intertidal marine native species. Furthermore, management to avoid spread of the invasive mussel into the Portuguese. coast and limit further increase in abundance of the invasive algae species. These results are highly relevant for projections on how further climate changes might affect the invasive and native species at the coast of Portugal.

This thesis deals with the study and normative proposal for a regulation of noise pollution generated by merchant ships, which is the main cause of underwater noise pollution. It is divided into three chapters. In the first chapter, the aspects of marine acoustics are reviewed, including a revisit of hydrophones, the analysis of the distances at which sound intensities are maintained above a baseline level, and a self designed study, which leads to the conclusion that the differences in incremental trends in underwater sound intensity in previous studies are due to differences in maritime traffic. This is confirmed by highly significant statistical data obtained by binary logistic regression between hydrophonic records that have detected an increase and those that have not (p<0.0001). A compilation and bibliometric analysis has made it possible to study specifically the negative impact of ship-generated noise on marine species. In 87% of the publications consulted, including experimental data, a high or moderately high negative impact of sound on marine species was evident; only 5% of the articles reported no effects of noise pollution. The study covered a wide variety of seas and oceans, although most of the studies (31%) were conducted using cages or similar. The research was mainly conducted on fish (43%) and mammals (38%). Behavioural changes were recorded in 59% of cases, physical changes in 11%, masking in 11% and combined changes in 14%. Four levels of underwater sound intensity are proposed: Environmental zone 0 (no appreciable anthropogenic pollution), from baseline level (30 dB) to 80 dB. Zone A of acceptable (low) pollution, from 81 dB to 175 dB (threshold of potential damage). Zone B of tolerable, but potentially harmful sound intensities (between 176 dB and 195 dB) and a Zone C of risk of permanent injury (above 195 dB, permanent injury threshold); vessels generating intensities at this level should be penalised or even banned. A way forward for the future regulation of underwater noise pollution is suggested, through a concerted effort via a global track derived from the UN in collaboration with specialised global and EU organisations, including the Baltic Sea registers, and legal support from the experts of the World Commission on Environmental Law. Its implementation should be carried out through the International Maritime Organization IMO).

L’installation des énergies marines renouvelables s’effectue dans le respect des législations environnementales françaises. La séquence Eviter-Réduire-Compenser (ERC) est ainsi appliquée pour aboutir à une non-perte nette de biodiversité. L’objectif de la thèse est de questionner l’efficacité de cette séquence, et plus particulièrement celle de la compensation écologique, en tant qu’instrument d’internalisation et de lutte contre l’érosion de la biodiversité marine. Une approche empirique qualitative a ainsi été mise en oeuvre pour (i) identifier les facteurs écologiques et sociétaux ainsi que leurs caractéristiques théoriques qui doivent permettre à la compensation d’atteindre l’objectif de non-perte nette de biodiversité ; et (ii) contrôler si ces conditions sont vérifiées en pratique dans le cas de l’éolien en mer en Europe et en France. L’analyse met en avant les enjeux juridiques, institutionnels, méthodologiques et sociétaux à relever pour permettre à la compensation écologique d’atteindre son objectif. Sur la base de ce constat, une évaluation multicritères est proposée afin de renforcer les étapes d’évitement et de réduction pour finalement mieux définir les besoins de compensation écologique en mer. L’analyse met par ailleurs en évidence un glissement d’une compensation basée sur une équivalence écologique stricte à une compensation fondée sur une équivalence écologique relâchée. Les actions de compensation tendent à être plus généralistes et/ou davantage dirigées vers les services écosystémiques que sur les composantes des écosystèmes. Associées aux mesures d’accompagnement, elles peuvent contribuer à faciliter l’acceptabilité sociale d’un projet d’aménagement. / The installation of marine renewable energies is carried out in compliance with French environmental legislation. The mitigation hierarchy is thus applied to achieve an objective of no net loss of biodiversity. This thesis aims at questioning the effectiveness of the mitigation hierarchy and more specifically biodiversity offsetting as an internalization instrument to halt the erosion of marine biodiversity. We use a qualitative empirical approach to (i) identify the ecological and societal factors as well as their theoretical characteristics that are supposed to enable the offsets achieving the objective of no net loss of biodiversity; and (ii) control whether these conditions are verified in practice for the case of offshore wind farms in Europe and France. The analysis highlights the legal, institutional, methodological and societal issues to be addressed in order to enable biodiversity offsetting to achieve the no net loss priority. On the basis of this observation, a multi-criteria assessment is carried out to reinforce the avoidance and reduction steps of the mitigation hierarchy in order to better define offsetting needs. Ultimately, the analysis shows a shift in biodiversity offsetting based on a strict ecological equivalence to a biodiversity offsetting based on a released ecological equivalence. Offsetting actions tend to be more generalist and / or more directed to ecosystem services than to ecosystem components. Associated with accompanying measures, offsetting actions can help to increase the social acceptability of a development project.

No abstract. / Coastal and marine ecosystems are some of the most heavily exploited with increasing degradation. This alarming situation appeals for urgent and effective actions. The optimal balance between use and conservation of ecosystems theoretically requires all costs and benefits to be considered in decision-making, including intangible costs and benefits such as non-market use and non-use values. The broad aim of this PhD is to examine how these economic values associated with coastal and marine ecosystem services can be measured, and how the economic valuation exercise may be considered and influence management decision- making.The first analytical part of the thesis focuses on assessing non-market use and non-use values, through econometric methods. The characterization and estimation of non-use values are complex and controversial, especially when the valuation exercise is focusing on individuals who are users of the ecosystem services being considered. An original approach based on a stated preference method, namely choice experiments, is developed then empirically applied in quantifying non-market values for marine and coastal ecosystems in two areas in New Caledonia. It allows the estimation of non-use values for populations of users in an implicit way. An in-depth analysis of the individuals’ choice heuristics during the valuation exercise is also conducted, with a focus on payment non-attendance. This issue is dealt with by comparing multiple modelling approaches in terms of: (1) inferred attendance, in relation to stated attendance; (2) attendance distribution according to several socio-economic variables; and (3) welfare estimates.After noting that the potential influence of economic valuation in decision making is unclear and largely unexplored in the literature, the second major component of this PhD aims to examine if, how and to what extent the economic valuation of ecosystem services, including measures of non-market values, influence decision-making regarding coastal and marine ecosystems management in Australia. Based on two nation-wide surveys, the perceived usefulness of the economic valuation of ecosystem services by the general public and decision-makers is studied, and the reasons why decision-makers may or may not fully consider economic values are elicited. Using a multi-criteria analysis, a part of the surveys also aims at examining the relative importance of different evaluation criteria (ecological, social and economic) when assessing the consequences of a hypothetical coastal development project on commercial activities, recreational activities and marine biodiversity.