O presente estudo avalia como a estrutura e a produção da comunidade de copépodes pelágicos da plataforma interna ao largo de Ubatuba (SP, Brasil) responderam às variações ambientais durante o período de julho de 2005 a junho de 2008. Durante estes três anos, a produção secundária dos copépodes foi estudada por meio da aplicação de modelos empíricos de crescimento e de estimativas de crescimento peso-específico obtidas através de experimentos de produção de ovos. Aspectos reprodutivos de 16 espécies de copépodes (9 calanóides, 3 ciclopóides e 4 harpacticóides) foram analisados neste período, através de experimentos de incubação e de métodos indiretos de obtenção de taxas de produção e viabilidade dos ovos. A comunidade de copépodes esteve representada por 70 espécies e foi caracterizada por altos valores de riqueza, diversidade e eqüitabilidade. Os copépodes apresentaram grande variabilidade nos valores médios de densidade (4726 ± 3711 ind. m-3) e de biomassa (7,42 ± 5,64 mg C m-3) e foram dominados por espécies de pequeno porte (< 1000 µm), destacando-se as fêmeas adultas de Oncaea waldemari e os copepoditos imaturos de paracalanídeos e clausocalanídeos. Quando comparada com outros ambientes tropicais e subtropicais, a região estudada apresentou valores elevados de densidade e biomassa. Da mesma maneira, a produção secundária média apresentou variabilidade temporal elevada (1,13 ± 1,11 mg C m-3 dia-1), com uma importante contribuição dos copepoditos imaturos de espécies dispersoras de ovos. No geral, os valores médios registrados foram considerados altos quando comparado com outros ambientes tropicais e subtropicais, embora a razão Produção/Biomassa média tenha sido similar às registradas nestes locais. A intrusão periódica da ACAS parece ter sido a principal responsável pelas alterações observadas na estrutura e produção da comunidade. A maioria dos meses não influenciados pela ACAS apresentou valores de densidade, biomassa e produção inferiores às respectivas médias. Entretanto, os resultados observados sugerem que as flutuações da comunidade de copépodes podem responder não apenas à intrusão da ACAS, mas também a uma complexa conjunção de fatores, incluindo as próprias relações inter e intra-específicas. Com relação à reprodução, as espécies dispersoras de ovos apresentaram taxas médias de produção de ovos similares às obtidas em outras regiões tropicais e subtropicais, enquanto que as retentoras apresentaram valores levemente inferiores. Entretanto, foram registrados picos ocasionais de produção destas últimas espécies, sugerindo que estes copépodes possuem estratégias que compensam os meses de baixa produtividade. A reprodução de algumas espécies analisadas parece ser associada a fatores intra-específicos, tais como o tamanho dos ovos e a razão entre machos e fêmeas. Além disso, as espécies dispersoras analisadas são provavelmente influenciadas pela temperatura e pelo alimento. A relação entre os tamanhos e pesos de fêmeas e ovos de 32 espécies de copépodes pelágicos mostrou que a variabilidade interespecífica observada nessas proporções é similar à tendência observada para espécies de altas latitudes. Comparando as taxas de produção estimadas a partir das equações empíricas com as obtidas experimentalmente, observa-se diferenças expressivas nas estimativas de produção secundária, o que sugere a influência de outras variáveis além daquelas consideradas pelos modelos. / The present study evaluates how the pelagic copepod community structure and production from the inner shelf off Ubatuba (SP, Brazil) responded to environmental variability from July 2005 to June 2008. During these three years copepod secondary production was studied by the application of growth empirical models and weight-specific growth estimates obtained through egg production experiments. Reproductive aspects of 17 copepod species (10 calanoid, 3 cyclopoid and 4 harpacticoid) were analyzed through incubation experiments and indirect methods to obtain production and egg hatching success rates. Copepod community was represented by 70 species and was characterized by high values of richness, diversity and evenness. Copepods had great variability in mean abundance values (4,726 ± 3,711 ind. m-3) and biomass (7.42 ± 5.64 mg C m-3) and were dominated by small size species (< 1,000 µm), especially Oncaea waldemari adult females and immature copepodites of paracalanids and clausocalanids. When compared to other tropical and subtropical environments, the copepod community in the study area had high average abundance and biomass. Mean secondary production rates had high temporal variability (1.13 ± 1.11 mg C m-3 day-1), with an important contribution from immature copepodites of broadcast spawner species. Production values were also high but mean Production/Biomass ratios were similar when compared to other tropical and subtropical environments. The periodic SACW (South Atlantic Central Water) intrusions seem to be the main responsible for the variability in community structure and production. Most months non-influenced by SACW had abundance, biomass and production values lower than the annual average. However, copepod community fluctuations may not have responded only to SACW intrusions, but also to inter- and intra-specific relations. Broadcast spawner species had mean egg production rates similar to the ones obtained in other tropical and subtropical regions, while sac spawners showed slightly lower values. Nevertheless, occasional production peaks were recorded for the latter, suggesting that these copepods have reproductive strategies to compensate for low productivity periods. Some species reproduction traits seem to be related to intra-specific factors, such as egg size and the male/female ratio. Besides, broadcast spawners were probably influenced by temperature and food. The relationship between female and egg size and weight from 32 pelagic copepod species showed that inter-specific variability observed in these proportions was similar to those observed for high-latitude species. When reproduction rates estimated from empirical equations with those obtained experimentally are compared, expressive differences in secondary production estimates emerge, which suggests the influence of other variables in addition to those accounted for by empirical models.

Aquatic sediments are, by surface, the largest habitat on Earth. A wide diversity of organisms inhabit these sediments and by their actions they have a large influence on and also mediate many ecosystem processes. Several of these processes, such as decomposition and remineralisation of organic matter are important on a global scale and are essential to sustain life on Earth. The main aim of this thesis was to use an experimental ecosystem ecology approach in order to study some of these ecosystem processes in marine sediments and how they are linked to biodiversity. Paper I and II found that an increased species richness of sediment deposit feeders increases the processing of organic matter from phytoplankton settled on the sea-floor, and that species-rich communities have a more efficient resource utilization of deposited organic matter. The results in paper IV and V also suggest that there is a link between microbial diversity in sediments and the degradation of organic contaminants. Paper V also shows that antibiotic pollution is a potential threat to natural microbial diversity and microbially mediated ecosystem services. The introduction of invasive species to ecosystems is another major threat to biodiversity and was studied in Paper II and III, by investigating the ecology of Marenzelleria arctia, a polychaete worm recently introduced in the Baltic Sea. Paper II suggests that M. arctia mainly utilize food resources not used by native deposit feeders, thus potentially increasing the benthic production in the Baltic Sea by increasing resource use efficiency. Paper III, however, show that M. arctia is protected from predation by the native benthic invertebrate predators, due to its ability to burrow deep in the sediment, suggesting that predation on M. arctia by higher trophic levels is restricted, thereby limiting trophic transfer. In conclusion, this thesis gives some examples of the importance of marine biodiversity for the generation of a few key ecosystem processes, such as organic matter processing and the degradation of harmful contaminants. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: In press.

The thesis combines laboratory experiments and field expeditions to study production, transfer and consumption of non-enzymatic antioxidants and thiamine in an aquatic food web. In particular, I (1) documented spatial and seasonal variation of tocopherols and carotenoids in the Baltic Sea pelagic food web, and (2) examined the effects of abiotic and biotic factors on tocopherol, carotenoid and thiamine concentrations in phytoplankton, zooplankton and fish. Moderate differences in temperature and salinity affected α-tocopherol, β-carotene and thiamine production in microalgae. Furthermore, the results suggest that acute stress favors the expression of non-enzymatic antioxidants rather than enzymatic antioxidants. Because production of α-tocopherol, β-carotene and thiamine differ markedly between microalgae, the availability of non-enzymatic antioxidants and thiamine is likely to be highly variable in the Baltic Sea and is difficult to predict. The transfer of non-enzymatic antioxidants from phytoplankton to zooplankton was biomass dependent. The field expeditions revealed that phytoplankton biomass was negatively associated with α-tocopherol concentration in mesozooplankton. Thus, increased eutrophication of the Baltic Sea followed by an increase in phytoplankton biomass could decrease the transfer of essential biochemicals to higher levels in the pelagic food web. This could lead to deficiency syndromes, of the kind already observed in the Baltic Sea. Astaxanthin is synthesized from precursors provided by the phytoplankton community. Thus biomass dependent transfer of astaxanthin precursors from phytoplankton to zooplankton could be responsible for astaxanthin deficiency in zooplanktivorous herring. Astaxanthin in herring consists mostly of all-Z-isomers, which are characterized by low bioavailability. Therefore, astaxanthin deficiency in salmon could be explained by the low concentration of this substance and its isomeric composition in herring.

In der Studie wurde die Ernährung und die Verteilung von larvalen und juvenilen Stadien von Plötze (Rutilus rutilus (L.)) und Barsch (Perca fluviatilis L.) untersucht. Untersuchungsgewässer war der Feldberger Haussee, ein geschichteter eutropher Hardwassersee, der seit über 15 Jahren biomanipuliert wurde. Der Bestand an Barschen war in diesem Gewässer im gesamten Biomanipulationszeitraum sehr gering (&amp;lt; 1% der Gesamtfischbiomasse). Längerfristig stabilisiert, aus wissenschafticher Sicht, eine hoher Bestand an piscivoren Barschen die Effekte der Biomanipulation. Ziel der Untersuchung war daher die Überprüfung der Hypothese, dass das Vorhandensein von Konkurrenz um die Ressource Zooplankton zwischen den juvenilen Barsch und Plötzen für den geringen Barschbestand verantwortlich ist (PERSSON &amp;amp; GREENBERG 1990, PERSSON et al. 1991). Die Ergebnisse der Untersuchungen ließen sich in folgenden Punkten zusammenfassen: i) Der juvenile Barsch segregierte in der Hochsommer- bis Herbstperiode in eine spezielle Nahrungsnische. Die beiden Fischarten unterschieden sich deutlich bezogen auf die Art der bevorzugten Zooplankter (0+-Barsch vorwiegend Eudiaptomus, Diaphanosoma, Leptodora; 1+/2+-Plötzen fraßen Cladocerennahrung Bosmina und in hohen Anteilen auch Daphnia). Separation und Aufteilung der Zooplanktonresourcen konnte auch für die bevorzugte Größe der Zooplankter beobachtet werden. Die hohen Wachstumsraten und der gute Konditionszustand des juvenilen Barsches sowie das Fehlen von Wintermortalität ließen konkurrenzinduzierte Mortalität als Begründung für den geringen Bestand nicht glaubhaft erscheinen. ii) Die räuberbedingte saisonale Mortalität der juvenilen Barsche in der Hochsommer- bis Herbstperiode ließ sich bei den 0+-Barschen und 1+-Barschen jeweils auf bis zu 90% einschätzen. Dadurch wurde auch ein starker Jahrgang (wie 1997) innerhalb der ersten zwei Lebensjahre auf bis zu 99% reduziert. iii) Als Alternativhypothese wurde aus den Ergebnissen der Studie und den Bedingungen am Feldberger Haussee gefolgert, dass eine Kombination von langer zooplanktivorer Phase und einem hohen Bestand an effektiven pelagischen Piscivoren (wie Sander lucioperca L.) für den geringen Barschbestand verantwortlich ist. / In the study the feeding behaviour and distribution of larval and juvenile stages of roach (Rutilus rutilus (L.)) and perch (Perca fluviatilis L.) was examined. The object of the study was the Lake Haussee, an stratified eutrophic hardwater lake that was biomanipulated for more than fifteen years. Over the whole period of biomanipulation the portion of perch population did not reach the level of one percent of the total fish biomass. From the scientific point of the view, a high biomass of piscivorous perch may stabilize the effects of biomanipulation in the long run. The aim of the study was to evaluate the hypothesis of strong competitive interaction between juvenile roach and perch for zooplankton, which could be responsible for the minor population of perch in lakes (PERSSON &amp;amp; GREENBERG 1990, PERSSON et al. 1991). The results of the study can be summarised as follows: i) In the period of midsummer to autumn juvenile perch segregated to a special food niche. In comparison to 1+/2+-roach, which fed on cladocerans (e.g. Bosmina and a high portion of Daphnia), 0+-perch preferred Eudiaptomus, Diaphanosoma and Leptodora. Thus, partitioning and separation were also observed for size-selectivity. Furthermore, the high growth rates and the good state of condition of the young perch as well as the lack of winter mortality did not indicate a competitive-induced mortality in the Lake Haussee. ii) In the period of midsummer to autumn the predator-induced seasonal mortality of juvenile perch (groups like 0+/1+) was estimated nearly up to 90 percent. Thereby, also a strong age group (like 1997) of juvenile perch was reduced up to 99 percent within the first two years of life. iii) The results of this study supported an alternative hypothesis: the morphological conditions of Lake Haussee, a prolonged zooplanktivore period of juvenile perch in combination with a strong stock of an effective pelagic piscivore predator (like Sander lucioperca L.) are responsible for the low perch stock.

Dans le contexte des nouvelles exigences en termes de qualité des eaux du surface, les modèles hydro-écologiques s'avèrent être des outils indispensables pour compléter notre compréhension du fonctionnement du milieu ou prévoir l'impact sur la qualité de l'eau de nouvelles mesures. L'objectif de cette recherche est de tirer parti de l'outil de modélisation ProSe, et de le faire évaluer afin de compléter la compréhension du fonctionnement biogéochimique de la Seine. Dans une première étape, différents processus biogéochimiques sont implémentés, calibrés et validés indépendamment, grâce à des jeux de données disponibles sur un linéaire de 220 km (de Paris jusqu'à l'estuaire), à différents pas de temps, pour la période 2007-2012. Ces améliorations sont réalisées grâce à l'utilisation directe de résultats expérimentaux, à l'extrapolation de résultats de couplage entre expériences de laboratoire et modélisation biogéochimique, ou encore grâce à l'analyse de mesures haute fréquence in-situ. Le modèle ProSe est ensuite utilisé pour établir un bilan du fonctionnement biogéochimique de la Seine dans cette zone fortement anthropisée. L'effet des processus pélagiques et benthiques sur les différents cycles biogéochimiques (carbone, azote, phosphore) est quantifié, pour différentes conditions hydrologiques, en amont et en aval de la plus grosse station d'épuration de l'agglomération parisienne, qui traite les effluents de plus de 5 millions équivalent habitants. La précision spatio-temporelle du modèle est ensuite utilisée pour évaluer l'effet de la fréquence d'échantillonnage sur l'estimation des critères de qualité de l'eau au sens de la Directive Cadre sur l'Eau. Les résultats soulignent l'importance d'une représentation précise des processus physiques (hydrodynamique et processus hydro-sédimentaires) dans les modèles de qualité de l'eau pour parvenir à une simulation fiable des flux biogéochimiques dans le milieu et des échanges entre compartiment benthique et colonne d'eau. Ce travail illustre enfin toute l'utilité des modèles hydro-écologiques pour venir en appui au suivi du milieu dans le cadre des objectifs actuels d'amélioration de la qualité des milieux aquatiques. / Hydro-ecological models are essential to complete our knowledge of the functioning of aquatic systems. They can moreover be used to forecast the impact of new management strategies on the future water quality. The aim of this thesis is to use the hydro-ecological ProSe model to improve our understanding of the biogeochemical functioning of the Seine River downstream the Paris urban area. Simulated biogeochemical processes are first implemented, calibrated, and validated independently for the 2007-2012 period. For each one of these processes, appropriate methodologies are used. These methodologies include the direct use of experimentally obtained parameters, the upscaling of results from coupled laboratory experiments and stand-alone biogeochemical modelling, or the analysis of high frequency in-situ measurements. Different datasets, which are available at various time steps, allow the validation of these processes along the whole 220 km simulated stretch (from Paris to the entrance of the Seine River estuary). Once validated, the ProSe model is then used to assess the biogeochemical functioning of the Seine River along this highly anthropized stretch. The impact of pelagic and benthic processes on the different biogeochemical cycles (carbon, nitrogen, and phosphorus) is quantified for different hydrological conditions, up- and downstream the major waste water treatment plant of the Paris urban area, which treats the effluents of over 5 million population equivalent. The model is then used to assess the effect of the monitoring frequency on the estimation of the water quality as defined by the European Water Framework Directive. The results highlight the importance of a detailed representation of physical processes in hydro-ecological models for a reliable simulation of in-river biogeochemical fluxes and of exchanges at the sediment-water interface. Having in mind the present targets of the improvement of the quality of water bodies, this work illustrates the importance of hydro-ecological modelling as an essential complement to water quality monitoring strategies.

Depuis le milieu des années 1990, l’utilisation de Dispositifs de Concentration de Poissons (DCP), des objets artificiels spécifiquement mis à l’eau pour agréger des bancs de poissons, est devenue de plus en plus importante pour la pêche au thon tropical à la senne. Cette utilisation massive des DCP, qui s’accompagne d’une utilisation massive de dispositifs de suivi comme les balises GPS et les balises échosondeurs, est aujourd’hui source d’inquiétude pour les stocks de thons, les prises accessoires mais aussi pour le fonctionnement des écosystèmes pélagiques. Cependant, les modalités d’utilisation des DCP et des balises GPS qui servent à les suivre restent mal connues, ce qui complique considérablement l’évaluation et la gestion des impacts de ces pratiques de pêche. Afin d’améliorer les connaissances actuelles de la pêcherie, les positions des balises GPS utilisées par les 3 armements français dans les océans Atlantique et Indien, constituant une part significative des DCP utilisés dans ces deux océans, ont été analysées. Ces données ont été combinées avec des multiples sources d’information : les livres de bord, les trajectoires VMS des senneurs français ainsi que des entretiens avec les patrons français. Elles nous permettent de mieux comprendre les stratégies de mise à l’eau des DCP et des balises, d’estimer le nombre d’objets flottants utilisés par les flottes de senneurs dans les océans Atlantique et Indien, de mesurer la contribution des DCP et des navires auxiliaires à l’efficacité de pêche des senneurs, d’identifier des destructions potentielles d’habitats par les DCP échoués and pour finir de proposer des solutions de gestion pour la pêcherie. Les résultats montrent une grande saisonnalité dans les mises à l’eau des deux océans, une croissance rapide du nombre de balises GPS au cours des 7 dernières années puisqu’elle est multipliée par 4.2 dans l’Océan Indien et 7 dans l’Océan Atlantique, des dommages possibles causés à des écosystèmes côtiers fragiles avec une probabilité d’échouage de l’ordre de 10% et finalement une augmentation de l’efficacité de pêche entre 2003 et 2014 de l’ordre de 3.8-18.8% dans l’Océan Atlantique et 10.7%-26.3% dans l’Océan Indien. Les entretiens avec les capitaines des senneurs soulignent la nécessité d’une gestion plus efficace de la pêcherie, avec entre autres l’instauration de quotas, une régulation de la capacité de la flotte de senneurs et un meilleur suivi des navires auxiliaires. Les résultats obtenus constituent les premières étapes nécessaires à une meilleure gestion de la pêche sous objet flottant / Since the mid 1990s, the use of drifting Fish Aggregating Devices (dFADs) by purse seiners, artificial objects specifically designed to aggregate fish, has become an important mean of catching tropical tunas. In recent years, the massive deployments of dFADs, as well as the massive use of tracking devices on dFADs and natural floating objects, such as GPS buoys, have raised serious concerns for tropical tuna stocks, bycatch species and pelagic ecosystem functioning. Despite these concerns, relatively little is known about the modalities of GPS buoy tracked objects use, making it difficult to assess and manage of the impacts of this fishing practice. To fill these knowledge gaps, we have analyzed GPS buoy tracks provided by the three French fishing companies operating in the Atlantic and the Indian Oceans, representing a large proportion of the floating objects monitored by the French fleet. These data were combined with multiple sources of information: logbook data, Vessel Monitoring System (VMS) tracks of French purse seiners, information on support vessels and Local Ecological Knowledge (LEK) of purse seine skippers to describe GPS buoy deployment strategies, estimate the total number of GPS buoy equipped dFADs used in the Atlantic and Indian Oceans, measure the contribution of strategies with FOBs and support vessels to the fishing efficiency of tropical tuna purse seiners, identify potential damages caused by lost dFADs and finally to propose management options for tropical tuna purse seine FOB fisheries. Results indicate clear seasonal patterns of GPS buoy deployment in the two oceans, a rapid expansion in the use of dFADs over the last 7 years with an increase of 4.2 times in the Indian Ocean and 7.0 times in the Atlantic Ocean, possible damages to fragile coastal ecosystems with 10% of GPS buoy tracks ending with a beaching event and an increased efficiency of tropical tuna purse seine fleets from 3.9% to 18.8% in the Atlantic Ocean over 2003-2014 and from 10.7% to 26.3% in the Indian Ocean. Interviews with purse seine skippers underlined the need for a more efficient management of the fishery, including the implementation of catch quotas, a limitation of the capacity of purse seine fleets and a regulation of the use of support vessels. These results represent a first step towards better assessment and management of purse seine FOB fisheries.

Made available in DSpace on 2014-12-17T14:33:07Z (GMT). No. of bitstreams: 1 RodrigoXS_DISSERT.pdf: 1797294 bytes, checksum: f032295b5b46cf49baf85e9aff88c766 (MD5) Previous issue date: 2012-04-27 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Cytogenetic studies in fish have been contributed significantly to a better understanding of the marine biodiversity, presenting information related to characterization, evolution and conservation of species e fisheries stocks. Among the marine species which cytogenetic data are less well known pelagic forms are detached, that despite the economic importance and conservation efforts have been suffering great pressure from the artisanal and industrial fisheries. The present work characterized cytogenetically six species of large pelagic fish in the Atlantic, belonging to the Order Perciformes, among them, four species of Scombridae, Thunnus albacares, T. obesus, Scomberomorus brasiliensis and Acanthocybium solandri and two Coryphaenidae, Coryphaena equiselis and C. hippurus using Classical cytogenetic methods as conventional staining, C-banding and Ag-NORs and molecular through staining fluorochromes AT and GC-specific and mapping of ribosomal multigene families, 18S and 5S. The identification of phylogenetic patterns and cytotaxonomic markers between the species and the presence of sex chromosomes in at least one species of Coryphaenidae, are particularly useful in the formulating of phylogenetic hypotheses, as well as comparisons between groups and populations / Os estudos citogen?ticos em peixes v?m contribuindo significantemente para um melhor conhecimento sobre a biodiversidade marinha, apresentando informa??es voltadas ? caracteriza??o, evolu??o e conserva??o de esp?cies e estoques pesqueiros. Entre as esp?cies marinhas cujos dados citogen?ticos s?o menos conhecidos se destacam as formas pel?gicas, que apesar da import?ncia econ?mica e de esfor?os conservacionistas v?m sofrendo grande press?o da pesca artesanal e industrial. O presente trabalho caracterizou citogeneticamente seis esp?cies de grandes peixes pel?gicos no Atl?ntico, pertencentes ? Ordem Perciformes, dentre elas, quatro esp?cies de Scombridae, Thunnus albacares, T. obesus, Scomberomorus brasiliensis e Acanthocybium solandri e duas de Coryphaenidae, Coryphaena equiselis e C. hippurus utilizando m?todos citogen?ticos cl?ssicos, como colora??o convencional, bandamento C e Ag-RONs, e moleculares, atrav?s da colora??o com fluorocromos AT e GC-espec?ficos e mapeamento de fam?lias multig?nicas ribossomais 18S e 5S. A identifica??o de padr?es filogen?ticos e marcadores citotaxon?micos entre as esp?cies e a presen?a de cromossomos sexuais em pelo menos uma esp?cie de Coryphaenidae, s?o particularmente ?teis na formula??o de hip?teses filogen?ticas, bem como em compara??es entre grupos e popula??es

A interação das tartarugas marinhas da espécie Caretta caretta e Dermochelys coriacea com o espinhel pelágico é um dos fatores que mais causa a mortalidade destes animais no oceano. Estudos com o intuito de quantificar essa interação, bem como os fatores que influenciam a mesma, são crescentes, para os quais é necessário conhecer a distribuição dos animais, e correlacioná-la com variáveis ambientais e operacionais da pesca. O presente estudo visa avaliar e quantificar os padrões espaço-temporais das capturas acidentais das tartarugas marinhas C. caretta e D. coriacea na região Sudeste/Sul do Brasil, com base em dados coletados pelo Projeto TAMAR ICMBio, entre 2003 e 2010, a partir de um programa de observadores à bordo da frota comercial com espinhel pelágico, assim como correlacioná-los com variáveis ambientais, biológicas e operacionais. Para tal, foram utilizados métodos estatísticos, como os Modelos Aditivos Generalizados para Posição, Escala e Forma (GAMLSS). Foram verificadas variações interanuais e sazonais, com destaque para maiores capturas por unidade de esforço (CPUE) no outono. A temperatura superficial do mar foi a variável abiótica de maior correlação com a CPUE de C. caretta, sendo tipo de isca, a variável operacional mais significativa. Para D. coriacea, profundidade e longitude foram os fatores que melhor explicam a CPUE. Padrões de distribuição ontogenética e áreas prioritárias de conservação para essas populações são discutidas, assim como os efeitos potenciais do aquecimento do oceano. O presente estudo deve contribuir para a definição de políticas de conservação marinha e no contexto da abordagem ecossistêmica para a pesca / The interaction between the sea turtles Caretta caretta and Dermochelys coriacea with pelagic longline is one of the factors that cause mortality of these animals in the ocean. Studies in order to quantify this interaction, as well as the factors that influence it, are increasing, focusing mostly on the turtles distribution, and how it correlates with environmental and fishing operational variables. Present study aims to evaluate and quantify the spatio-temporal patterns of the sea turtles C. caretta and D. coriacea bycatch off Southeast/South Brazil, based on data collected by Project TAMAR - ICMBio between 2003 and 2010, from an observer program on-board the commercial pelagic longline fleet, as well as to correlate them with environmental, biological and operational variables,. Statistical methods such as Generalized Additive Models for Location, Scale and Shape (GAMLSS) were applied. Interannual and seasonal variations were observed, with a higher catch per unit effort (CPUE) during fall. The sea surface temperature was the abiotic variable that most correlated with CPUE of C. caretta, being the type of bait the most significant operational variable. For D. coriacea, depth and longitude were the factors that better explained the CPUE. Ontogenetic distribution patterns and priority areas for the species conservation are discussed, as well as the potential effects of ocean warming. This study should contribute to the definition of conservation policies as well as to the ecosystem approach to fisheries context

L’étude de l’écologie alimentaire d’une espèce est une clé de la compréhension de sa biologie et de son fonctionnement dans l’écosystème. Ainsi, les interactions proies-prédateurs sont une des voies qui structurent et déterminent les dynamiques des populations et le réseau trophique à l’échelle d’un écosystème. Parmi les sites d’étude d’intérêt majeur, le milieu marin est un espace soumis à des forçages naturels et anthropiques. A l’échelle de l’Océan Atlantique Nord-Est, le Golfe de Gascogne est une vaste baie bordée par l’Espagne au sud et la France à l’est. Ce Golfe est le siège historique d’une intense activité de pêches commerciales pour lesquelles les principales espèces de petits poissons pélagiques ciblés sont la sardine, Sardina pilchardus, et l’anchois, Engraulis encrasicolus. L’objectif de ces travaux est d’analyser l’écologie alimentaire printanière, de ces deux petits poissons pélagiques dans le Golfe de Gascogne. Pour ce faire, le premier volet s’est focalisé sur le compartiment des proies mésozooplanctoniques via deux approches : la caractérisation de leurs dynamiques spatio-temporelles sur la décennie 2003-2013 et la mesure de leur contenu énergétique au printemps. Il apparaît, à cette saison, que tous les types de proies ne se valent pas énergétiquement et que notre site d’étude représente une mosaïque d’habitats alimentaires. De plus, la communauté mésozooplanctonique printanière présente une forte structuration spatiale, une évolution temporelle marquée par un changement majeur d’abondance et un contrôle par la biomasse de microphytoplancton. Le second volet de ces travaux est relatif à une approche méthodologique de l’analyse de l’écologie alimentaire de S. pilchardus et E. encrasicolus. Trois traceurs trophiques distincts ont été utilisés : les ratios isotopiques du carbone et de l’azote, la faune parasitaire et les niveaux de contamination en mercure. Pour perfectionner l’utilisation du premier de ces traceurs, une approche expérimentale a été menée sur S. pilchardus pour déterminer un facteur de discrimination trophique. Finalement, il apparaît que l’utilisation de ces trois traceurs a toujours permis de mettre en évidence une variabilité temporelle relative de l’écologie alimentaire des poissons étudiés. En revanche, aucune dynamique spatiale n’a pu être détectée via ces traceurs. / Dietary studies of marine species constitute an important key to improve the understanding of its biology and of its role in the ecosystem. Thus, prey-predator relationships structure and determine population dynamics and the trophic network at the ecosystem scale. Among the major study sites, the marine ecosystem is submitted to natural and anthropogenic constraints. In the North-Eastern part of the Atlantic Ocean, the Bay of Biscay is a large open area surrounded South by Spain and East by France. This bay is an historic place of intense fishery activities for which the main small pelagic species targeted are the pilchard, Sardina pilchardus and the anchovy, Engraulis encrasicolus. The aim of this work is to analyze the trophic ecology of these two small pelagic fish in spring in the Bay of Biscay. To do this, a first section is devoted to their prey composed by the mesozooplanktonic compartment, through a two-fold approach: the characterization of their spatio-temporal dynamics during the decade 2003-2013 and the measurement of their energetic content in spring. For this season, it appears that all prey types are not worth energetically and that the Bay of Biscay represents a mosaic of dietary habitat. Moreover, the spring mesozooplankton community presents a strong spatial structuration, a temporal evolution marked by a major change in abundance and a control by the microphytoplankton biomass. The second section of this work is relative to a methodological approach of the trophic ecology of S. pilchardus and E. encrasicolus. Three different trophic tracers have been used: isotopic ratios of carbon and nitrogen, parasitological fauna and mercury contamination levels. To improve the use of the first of these trophic tracers, an experimental approach has been conducted with S. pilchardus to determine a trophic discrimination factor. Finally, it appears that the use of these three trophic tracers has always been permitted to highlight a temporal variability of the relative trophic ecology of these fish. However, no spatial dynamics could be identified through these three trophic tracers.

Understanding and modeling microbial responses and feedbacks to climate change is hampered by a lack of a framework in the pelagic environment by which to link local mechanism to large scale patterns. Where terrestrial ecology draws from landscape theory and practice to address issues of scale, the pelagic seascape concept is still in its infancy. We have applied the patch mosaic paradigm of landscape ecology to the study of the seasonal and interannual variability of the North Pacific to facilitate comparative analysis between pelagic ecosystems and provide spatiotemporal context for eulerian time-series studies. Using multivariate, 13-year climatologies of sea surface temperature, photosynthetically active radiation, and chlorophyll a derived from remote sensing observations, we classified hierarchical seascapes at monthly and interannual scales. These dynamic, objectively-determined seascapes offer improved hydrographic coherence relative to oceanic regions with subjectively defined and static boundaries (Chapter 2) and represent unique biogeochemical functioning (Chapter 2) and microbial communities (Chapter3). Furthermore they provide consilience between satellite studies and in situ observations (Chapter 4) and allow for objective comparison of ecosystem forcing (Chapters, 4 and 5). In Chapter 2, we rigorously tested the assumption that satellite-derived seascapes describe regions of biogeochemical coherence. The seasonal cycle of the North Pacific was characterized at three levels of spatiotemporal hierarchy and broader relevance of monthly ���resolved seascapes was assessed through analysis of variance (ANOVA) and multiple linear regression (MLR) analyses of nutrient, primary productivity, and pCO��� data. Distinct nutrient and primary productivity regimes were well-characterized in the coarsest two levels of hierarchy (ANOVA, R�� = 0.5-0.7). Finer scale partitioning was more relevant for pCO���. MLR analyses revealed differential forcing on pCO��� across seascapes and hierarchical levels and a 33 % reduction in mean model error with increased partitioning (from 18.5 ��atm to 12.0 ��atm pCO���). In Chapter 3 we verified the seascapes with in situ collections of microbial abundance and structure. Flow cytometry data was collected from two long term time series and several cruises spanning thousand kilometers of the NE Pacific; these data allowed us to quantify spatiotemporal patterns. In addition, multiple response permutation analysis revealed differences in community structure across discrete seascapes, in terms of both absolute and relative abundances. Principal component analysis of the assemblage supported seascape divisions and revealed structure along environmental gradients with strong associations with chlorophyll a and sea surface temperature and, to a lesser extent, with mixed layer depth and mean photosynthetically active radiation in the mixed layer. Differences of assemblage structure between seascapes and strength of environmental forcing were strong in the subarctic and transition zones, but less pronounced in the subtropics, suggesting satellite-detected changes in bulk properties that may be associated with local physiology or interannual shifts in seascape boundaries. Based on the work presented in Chapter 4, we discovered that interannual shifts in the boundaries of a transition seascape and two distinct oligotrophic subtropical seascapes affect the variability observed at benchmark time series Station ALOHA; the latter two seascapes oscillate in their contributions to the expansion of the entire subtropics. On interannual scales, in situ phytoplankton abundance (as measured by chl-a), net primary productivity (NPP), and the relative abundance of eukaryotic phytoplankton and Synechococcus sp. increased during periods of encroachment by the transition seascape. Conversely, the relative abundance of Prochlorococcus increased and chl ���a and NPP decreased when the highly oligotrophic seascape encroached on Station ALOHA. The dynamic range (~6 million km��) of subtropical expansion is born almost entirely by the transition zone - resulting in a transfer of ~1.2 Pg of total primary C production between a system primed for export production and one dominated by the microbial loop. In Chapter 5, we investigated multiple factors that contribute to the effectiveness of the biological pump in the transition seascape. Near-continuous measurements of net primary production (NPP), net community production (NCP) and several ecophysiological variables were collected in across subarctic, transition, and subtropical seascapes of the Northeast Pacific during August and September of 2008. Mesoscale processes and shifts in community structure contributed to high export efficiency in the subtropical seascape; the convergence of assemblage structure, high biomass, moderate NPP: NCP and high NCP contributed to biologically mediated air-sea exchange in the transition seascape. Furthermore, NPP and NCP were strongly spatially coupled in both the transition (r[subscript 1, 39]=0.70; p<0.0001) and subtropical seascapes (r[subscript 1, 45]= 0.68, p<0.0001), suggesting the possibility for empirical modeling efforts. This dissertation provides a first step to characterize the seascape variability in the NE Pacific and to understand the modulation of primary and export production in a critical transition region. The multivariate seascape approach described here provides spatiotemporal context for in situ studies and allows objective comparisons of systems' responses to climatic forcing. An integrated ocean observing system will require insight from in situ observations and experiments, ecosystem models, and satellite remote sensing. The results highlighted in this dissertation suggest that the pelagic seascape framework, through its capacity to scale both context and mechanism, may serve as an important and unifying component of such an observing system. / Graduation date: 2013