Le changement climatique est incontestable et affecte les océans. L'observation à long terme d'indicateurs comme le plancton peut permettre l'étude de ces changements. Le suivi du plancton dans les eaux côtières d'Europe représente une source de données importante actuellement sous-exploitée et sur laquelle cette étude est basée. Des outils analytiques ont d'abord été conçus pour résoudre des divergences taxonomiques entre les données et pour réaliser l'analyse temporelle. L'étude du plancton à L4 de 1998 à 2007 révèle de profonds changements dans la composition phytoplanctonique des blooms de printemps et d'automne, et des variations à long terme dans l'abondance des taxa dominants du zooplancton. Le phytoplancton gouverne la succession saisonnière des larves méroplanctoniques. Les changements de température de surface et de vent contrôlent les variations temporelles des communautés planctoniques. Les variations spatio-temporelles du zooplancton ont été comparées à 4 sites de 1998 à 2007 : Ston (Mer du Nord), L4 (Manche), MC (Mer Tyrrhénienne ), et C1 (Mer Adriatique). La structure des communautés est globalement stable, la saisonnalité étant la principale source de variabilité à long terme. La chlorophylle a et le vent expliquent les variations de la communauté zooplanctonique à Ston et L4 alors que c'est la température à MC et C1. Cette étude confirme l'extrême adaptabilité des communautés zooplanctoniques à un environnement variable. Elle souligne l'importance de facteurs tels que taxonomie et échelle temporelle pour l'analyse de séries, et la nécessité de maintenir les séries à long terme pour le suivi de futurs changements dans le contexte du changement climatique. / Climate change is unequivocal and dramatic changes are under way in the world's oceans. Long-term observations of indicators such as plankton can provide a better understanding of these changes. Considerable efforts have been made to monitor plankton in European coastal waters and have produced a large amount of datasets yet to be fully exploited. Analytic tools were first developed to solve taxonomic discrepancies in datasets and for temporal analyses. Time series analysis of plankton at L4 from 1988 to 2007 reveals profound changes in the composition of the spring and autumn phytoplankton blooms, and long-term variations in abundance of the dominant zooplankton taxa. Phytoplankton is driving the seasonal succession of meroplanktonic larvae. Changes in sea surface temperature and wind conditions control temporal patterns of plankton communities. Spatio-temporal patterns of zooplankton are compared at 4 sites: Ston (northern North Sea), L4 (wes tern English Channel), MC (Tyrrhenian Sea), and C1 (Adriatic Sea) from 1998 to 2007. The communities structure is on average stable and seasonal variations are the main source of long-term variability. Chlorophyll a and wind are responsible for the community patterns observed at Ston and L4 whereas temperature is the main driver at MC and C1. This study supports evidences of the extreme flexibility of zooplankton communities in adjusting to a variable environment. We highlighted the importance of factors such as taxonomy and temporal scale on time series analysis, and the necessity of maintaining long-term series to monitor future changes in the context of climate change.

Near real-time event streams are a key feature in many popular social media applications. These types of applications allow users to selectively follow event streams to receive a curated list of real-time events from various sources. Due to the emphasis on recency, relevance, personalization of content, and the highly variable cardinality of social subgraphs, it is extremely difficult to implement feed following at the scale of major social media applications. This leads to multiple architectural approaches, but no consensus has been reached as to what is considered to be an idiomatic solution. As of today, there are various theoretical approaches exploiting the dynamic nature of social graphs, but not all of them have been applied in practice. In this paper, large-cardinality graphs are placed in the context of existing research to highlight the exceptional data management challenges that are posed for large-scale real-time social media applications. This work outlines the key characteristics of data dissemination in large-cardinality social graphs, and overviews existing research and state-of-the-art approaches in industry, with the goal of stimulating further research in this direction.

Les traits fonctionnels sont de plus en plus utilisés en écologie pour expliquer les changements de composition et de structure de la communauté phytoplanctonique en fonction des contraintes environnementales. Ce succès tient au fait que les traits fonctionnels sont des caractéristiques reliées aux processus de croissance et de perte des organismes, et qu'ils déterminent ainsi l'occurrence, la dominance ou l'absence d'une espèce dans des conditions environnementales données. Parmi les traits fonctionnels, on distingue les traits morpho-fonctionnels qui présentent l'avantage d'être facilement observables et mesurables. Les approches basées sur les traits morpho-fonctionnels ont majoritairement été utilisées en lac mais pourraient toutefois s'avérer pertinentes en rivière où l'importance relative des contraintes environnementales agissant sur la communauté phytoplanctonique est très variable d'un système à l'autre. L'objectif de cette thèse a donc été de tester l'hypothèse selon laquelle la communauté phytoplanctonique en rivière pouvait être structurée selon les traits morpho-fonctionnels. Dans les rivières étudiées, nous avons montré que la communauté est structurée selon les traits morpho-fonctionnels reliés à la vitesse de sédimentation, en mettant en évidence le rôle clé de la forme des organismes, mais aussi de leur motilité et de leur densité via la présence de mucilage. A travers la sélection de différentes valeurs pour ces traits morpho-fonctionnels, nous avons pu mettre en évidence l'impact majeur de la turbulence sur la communauté phytoplanctonique de ces rivières. L'effet de ce paramètre a été testé expérimentalement en conditions contrôlées sur une communauté simplifiée afin de tester l'hypothèse selon laquelle sous l'effet de la turbulence, la composition de la structure de la communauté pouvait être prédite par les traits morpho-fonctionnels. Les résultats de cette approche expérimentale ont permis de réitérer le rôle clé de la forme dans la structure de la communauté corroborant ainsi les résultats de rivières et ont également souligné le rôle de la plasticité phénotypique. L'approche basée sur les traits a également été testée en estuaires, mais s'est cependant montré infructueuse. Plusieurs hypothèses ont été proposées pour expliquer ce résultat, notamment l'absence de trait identifié comme étant relié à la salinité. / Functional traits are increasingly used in ecology to explain changes in the composition and structure of phytoplankton community in relation to environmental constraints. Functional traits are related to growth and loss processes, and thus they determine the occurrence, dominance or absence of species in given environmental conditions. Among the functional traits, morpho-functional traits display the advantage of their ease to be measured. Approaches based on morpho-functional traits were mainly used in lakes, but could however be relevant in rivers where the relative significance of environmental constraints acting on the phytoplankton community varies from one system to another. The aim of this thesis was therefore to test the hypothesis that riverine phytoplankton community could be structured according to morpho-functional features. In the rivers studied, we showed that the community is structured according to morpho-functional traits related to sedimentation rate, highlighting the key role of the shape of organisms, but also of their motility and density via the presence of mucilage. Through the selection of different values for these morpho-functional traits, we highlighted the main impact of turbulence on the phytoplankton community within these rivers. The effect of this parameter has been tested experimentally on a simplified community under controlled conditions in order to test the hypothesis that as a result of turbulence, the composition of community structure could be predicted through morpho-functional traits. The results of this experimental approach helped to reiterate the key role of the shape in community structure thus corroborating the results found in rivers. It also stressed the role of phenotypic plasticity. This approach based on features was also tested in estuaries, but was, however, unsuccessful. Several hypotheses have been proposed to explain this result, including the lack of traits identified as related to salinity.

Les réseaux complexes constituent un outil pratique pour modéliser les systèmes complexes réels. Pour cette raison, ils sont devenus très populaires au cours de la dernière décennie. De nombreux outils existent pour étudier les réseaux complexes. Parmi ceux-ci, la détection de la communauté est l’un des plus importants. Une communauté est grossièrement définie comme un groupe de nœuds plus densément connectés entre eux qu’avec le reste du réseau. Dans la littérature, cette définition intuitive a été formalisée de plusieurs différentes façons, ce qui a conduit à d’innombrables méthodes et variantes permettant de les détecter. Du point de vue applicatif, le sens des communautés est aussi important que leur détection. Cependant, bien que la tâche de détection de communautés en elle-même ait attiré énormément d’attention, le problème de leur interprétation n’a pas été sérieusement abordé jusqu’à présent. Dans cette thèse, nous voyons l’interprétation des communautés comme un problème indépendant du processus de leur détection, consistant à identifier les éléments leurs caractéristiques les plus typiques. Nous le décomposons en deux sous-problèmes : 1) trouver un moyen approprié pour représenter une communauté ; et 2) sélectionner de façon objective les parties les plus caractéristiques de cette représentation. Pour résoudre ces deux sous-problèmes, nous exploitons l’information encodée dans les réseaux dynamiques attribués. Nous proposons une nouvelle représentation des communautés sous la forme de séquences temporelles de descripteurs associés à chaque nœud individuellement. Ces descripteurs peuvent être des mesures topologiques et des attributs nodaux. Nous détectons ensuite les motifs séquentiels émergents dans cet ensemble de données, afin d’identifier les ceux qui sont les plus caractéristiques de la communauté. Nous effectuons une validation de notre procédé sur des réseaux attribués dynamiques générés artificiellement. A cette occasion, nous étudions son comportement relativement à des changements structurels de la structure de communautés, à des modifications des valeurs des attributs. Nous appliquons également notre procédé à deux systèmes du monde réel : un réseau de collaborations scientifiques issu de DBLP, et un réseau d’interactions sociales et musicales tiré du service LastFM. Nos résultats montrent que les communautés détectées ne sont pas complètement homogènes. Certaines communautés sont composées de petits groupes de nœuds qui ont tendance à évoluer ensemble au cours du temps, que ce soit en termes de propriétés individuelles ou collectives. Les anomalies détectées correspondent généralement à des profils typiques : nœuds mal placés par l’outil de détection de communautés, ou nœuds différant des tendances de leur communautés sur certains points, et/ou non-synchrones avec l’évolution de leur communauté, ou encore nœuds complètement différents. / Complex Networks constitute a convenient tool to model real-world complex systems. For this reason, they have become very popular in the last decade. Many tools exist to study complex networks. Among them, community detection is one of the most important. A community is roughly defined as a group of nodes more connected internally than to the rest of the network. In the literature, this intuitive definition has been formalized in many ways, leading to countless different methods and variants to detect communities. In the large majority of cases, the result of these methods is set of node groups in which each node group corresponds to a community. From the applicative point of view, the meaning of these groups is as important as their detection. However, although the task of detecting communities in itself took a lot of attraction, the problem of interpreting them has not been properly tackled until now. In this thesis, we see the interpretation of communities as a problem independent from the community detection process, consisting in identifying the most characteristic features of communities. We break it down into two sub-problems: 1) finding an appropriate way to represent a community and 2) objectively selecting the most characteristic parts of this representation. To solve them, we take advantage of the information encoded in dynamic attributed networks. We propose a new representation of communities under the form of temporal sequences of topological measures and attribute values associated to individual nodes. We then look for emergent sequential patterns in this dataset, in order to identify the most characteristic community features. We perform a validation of our framework on artificially generated dynamic attributed networks. At this occasion, we study its behavior relatively to changes in the temporal evolution of the communities, and to the distribution and evolution of nodal features. We also apply our framework to real-world systems: a DBLP network of scientific collaborations, and a LastFM network of social and musical interactions. Our results show that the detected communities are not completely homogeneous, in the sense several node topic or interests can be identified for a given community. Some communities are composed of smaller groups of nodes which tend to evolve together as time goes by, be it in terms of individual (attributes, topological measures) or relational (community migration) features. The detected anomalies generally fit some generic profiles: nodes misplaced by the community detection tool, nodes relatively similar to their communities, but also significantly different on certain features and/or not synchronized with their community evolution, and finally nodes with completely different interests.

Explicar os padrões de diversidade de espécies e entender os processos que geram e mantêm essa diversidade na natureza é um dos grandes objetivos da Ecologia. A teoria clássica de competição prevê que duas espécies só podem coexistir quando há divergência no uso de recursos. Portanto, há um limite de similaridade imposto pela competição entre as espécies, que leva à co-ocorrência de espécies com estratégias ecológicas mais diferentes entre si. Por outro lado, o ambiente físico pode impor restrições às possíveis estratégias ecológicas das espécies. Ambientes com limitações de recursos ou condições desfavoráveis permitem apenas a sobrevivência de espécies com estratégias mais similares, um processo conhecido como filtro ambiental. Dois processos podem então gerar padrões antagônicos na estrutura das comunidades, selecionando estratégias ecológicas mais parecidas ou mais diferentes entre si. Há ainda a possibilidade de que os dois processos ou mesmo nenhum dos dois seja importante na estruturação das comunidades, levando a um padrão aleatório ou neutro. Utilizando-se das contribuições proporcionais (elasticidades) das três taxas vitais demográficas - sobrevivência, crescimento e fecundidade - para a taxa de crescimento populacional para inferir as estratégias ecológicas das espécies de árvores de uma comunidade, nos propusemos a responder a pergunta: \"Qual processo é responsável pela estruturação de comunidades de árvores tropicais?\". O trabalho foi realizado em uma parcela permanente de 10,24 hectares na Restinga da Ilha do Cardoso, São Paulo. Todos os indivíduos com mais de 15cm de perímetro à altura do peito foram marcados, identificados e tiveram seus diâmetros à altura do peito registrados para dois censos. As elasticidades das três taxas vitais para 89 espécies de árvores foram obtidas por meio de um modelo de projeção integral (IPMs). Os IPMs são ferramentas modernas mais robustas que os clássicos modelos matriciais, comumente utilizados em estudos demográficos. Definimos um espaço ecológico no triângulo onde as estratégias ecológicas das espécies são classificadas de acordo com as elasticidades das três taxas demográficas. Construímos também uma filogenia molecular específica para a comunidade baseada nos marcadores cloroplásticos rbcL e matK, com a qual obtivemos as distâncias entre todos os pares de espécies. Calculamos o sinal filogenético das estratégias ecológicas por meio da correlação entre a distância entre as espécies no espaço ecológico e suas distâncias filogenéticas. Aceitamos a premissa de conservação das estratégias ecológicas na filogenia. As espécies puderam ser classificadas em quatro grupos demográficos distintos no espaço ecológico, distribuídos principalmente no eixo crescimento-sobrevivência, o que é esperado para árvores. Não há sinal filogenético para as estratégias ecológicas, o que indica que ambos os processos ou nenhum dos dois processos é importante na estruturação dessa comunidade. Nosso trabalho traz uma nova abordagem metodológica e resultados que contradizem a literatura recente, em que a importância dos filtros ecológicos na estruturação de comunidades tropicais é repetidamente encontrada. A confirmação deste padrão para outras comunidades poderá colaborar para o melhor entendimento dos processos estruturadores das comunidades tropicais. / One of Ecology\'s biggest goals is to explain the patterns of species\' diversity and to understand the processes that generate and maintain this diversity in natural communities. Classical competition theory predicts that two species will be able to coexist only when there is divergence in the use of resources, i.e., competition imposes a limiting similarity among species that allows co-occurrence of species with divergent ecological strategies. On the other hand, the physical environment may impose restrictions to the range of possible ecological strategies of species. Environments with limited resources or adverse conditions will allow the survival of species with more specific strategies, a process known as environmental filtering. These two processes will generate opposite effects on the structure of communities, as more similar or more different ecological strategies will be selected. There is still the possibility that both processes are occurring simultaneously, or neither are important for the community. In both cases, a neutral or random pattern is expected. Using the proportional contribution (elasticities) of the three demographic vital rates - survival, growth and fecundity - to the finite rate of increase of population as a mean of inferring the ecological strategy of trees in a community, we intended to answer the question: \"What process is responsible for the structuring of tropical tree communities?\". Data was collected in a Restinga forest 10.24 ha permanent plot. All individuals with more than 15cm of perimeter at breast height were marked, identified and had their diameters at breast height registered for two censes. Elasticities of the three vital rates for 89 tree species were obtained with an Integral Projection Model (IPM). IPMs are modern tools more robust than classical matrix models, commonly used in demographic studies. We defined an ecological space in the triangle where ecological strategies are plotted according to elasticities of the three vital rates. We also generated a molecular phylogeny based on rbcL and matK chloroplast markers, and used it to obtain the phylogenetic distance between all pairs of species. We calculated the phylogenetic signal of ecological strategies using the correlation between ecological distances in the ecological space and phylogenetic distances. We assumed ecological strategies to be conserved in the phylogeny. Species could be classified into four demographic groups in ecological space, distributed mainly in a growth-survival axis. This is expected for trees. No phylogenetic signal was found for the ecological strategies. This can mean that either both processes are structuring this community, or neither is important. Our study uses a new methodological approach and presents new results that contradict recent literature, on which environmental filtering is repeatedly accounted as the main process structuring tropical communities. Confirmation of this pattern for other communities may bring further understanding of structuring of tropical communities.

The growing demand for strawberries has imposed challenges, especially regarding the control of pests. Many farmers report problems with reduced chemical control efficiency, probably due to selection of resistant populations of insects and mites. An alternative is the use of biological control using pathogenic fungi as a tool in integrated pest management. Metarhizium spp. (Hypocreales: Clavicipitaceae) are generalist entomopathogenic fungi with worldwide distribution and can cause diseases in a large number of hosts. Many studies on the development of Metarhizium as a biological control agent were performed, but this bulk of knowledge is in remarkable contrast to the lack of research on the fundamental ecology of Metarhizium in agroecosystems. This thesis aimed to evaluate the establishment, persistence and dispersal of these entomopathogenic fungi in strawberry crop soil in Inconfidentes, Minas Gerais, Brazil; and to study the diversity and abundance of species of Metarhizium isolated from organic and conventional strawberry crop soils, and the field margins in Brazil and Denmark. The effectiveness of new species of Metarhizium recently found in Brazil, was evaluated against two spotted spider mite, Tetranychus urticae. Applied isolates of M. anisopliae (ESALQ1037) and M. robertsii (ESALQ1426) were able to persist for up to 12 months after the application within the soil, and disperse to other plots and colonize the rhizosphere of strawberry plants. In the plots where ESALQ1037 and ESALQ1426 were applied, 25% and 87.5% of the isolates recovered after 12 months consisted of the same isolates inoculated. A new taxonomically unassigned lineage, referred to as Metarhizium sp. Indet. 5 in this study, was found in strawberry crop margins. The dominant species of Metarhizium in Brazil and Denmark was Metarhizium robertsii and M. brunneum respectively. Further, Metarhizium pemphigi was first detected in Denmark in this study. Soil in organically grown strawberries harbored a more diverse population of Metarhizium spp. compared with conventionally grown strawberries. These studies showed for the first time the potential of new species of Metarhizium as spider mite biological control agents, the lowest median lethal time (LT50 = 4 ± 0.17 days) was observed in mites treated with the isolate ESALQ1638 of Metarhizium sp. indet. 1. The best isolates were ESALQPL63 of B. bassiana, ESALQ1608 and ESALQ1638 of Metarhizium sp. indet. 1 and ESALQ3069 and ESALQ3222 of M. pingshaense based on the survival curve, total mortality, percentage of sporulated cadavers and LT50. Knowledge of the diversity of Metarhizium spp. and persistence in strawberry soil generated in this study may be useful in developing conservation strategies and maximize the natural biological pest control. / A crescente demanda por morangos vem impondo desafios, especialmente quanto ao controle das pragas. Muitos agricultores relatam problemas com a redução da eficiência do controle químico, provavelmente devido à seleção de populações resistentes de insetos e ácaros. Uma alternativa é o uso de controle biológico com fungos entomopatogênicos como ferramenta dentro do manejo integrado de pragas. Metarhizium spp. (Hypocreales: Clavicipitaceae), são fungos entomopatogênicos generalistas com distribuição cosmopolita e que podem causar doenças em um grande número de hospedeiros. Muitos estudos sobre o desenvolvimento de Metarhizium como agente de controle biológico foram realizados, mas este leque de conhecimento está em contraste com a notável falta de investigação sobre a ecologia de Metarhizium nos agroecossistemas. Esta tese teve como objetivo avaliar o estabelecimento, persistência e dispersão destes fungos entomopatogênicos em solo de morangueiro em Inconfidentes, Minas Gerais, Brasil; bem como estudar a diversidade e abundância de espécies de Metarhizium isolados do solo de cultivos orgânico e convencional de morangueiro, e das margens das plantações no Brasil e Dinamarca. A eficácia de novas espécies de Metarhizium, encontradas recentemente no Brasil, foi avaliada contra o ácaro rajado, Tetranychus urticae. Os isolados inoculados de M. anisopliae (ESALQ1037) e M. robertsii (ESALQ1426) foram capazes de persistir por até 12 meses após a aplicação no solo, além de dispersar para outras parcelas e colonizar a rizosfera dos morangueiros. Nas parcelas onde ESALQ1037 e ESALQ1426 foram aplicados, 25% e 87,5% dos isolados recuperados após 12 meses consistiam dos mesmos isolados inoculados. Uma nova linhagem não taxonomicamente identificada, referida neste trabalho como Metarhizium sp. Indet. 5, foi encontrada nas margens de morangueiros cultivados. A espécie dominante de Metarhizium no Brasil e Dinamarca foi Metarhizium robertsii e M. brunneum, respectivamente. Além disso, Metarhizium pemphigi foi detectado pela primeira vez na Dinamarca neste estudo. Solos de cultivo orgânico de morangueiro em geral apresentaram uma diversidade maior de Metarhizium do que solos de cultivos convencionais. Estes estudos revelaram pela primeira vez o potencial de novas espécies de Metarhizium como agentes de controle biológico do ácaro rajado, sendo o menor tempo letal mediano (TL50= 4 ± 0.17 dias) observado em ácaros tratados com o isolado ESALQ1638 de Metarhizium sp. indet. 1. Os melhores isolados foram ESALQPL63 de B. bassiana, ESALQ1608 e ESALQ1638 de Metarhizium sp. indet. 1 e ESALQ3069 e ESALQ3222 de M. pingshaense baseado na curva de sobrevivência, mortalidade total, porcentagem de cadáveres esporulados e TL50. O conhecimento da diversidade de Metarhizium spp. e persistência em solos de morango, gerados neste estudo, poderão ser úteis no desenvolvimento de estratégias de conservação e maximizar o controle biológico natural de pragas.

Les mucilages pélagiques marins (MPM) sont des phénomènes mondiaux sporadiques et, dans certaines régions, chroniques dans les zones côtières. Ces agrégats gélatineux, enrichis en matière organique et en microorganismes, forment des écosystèmes marins autonomes transitoires allant de 0,5 cm à plusieurs kilomètres de long. Ils correspondent à des étapes évolutives de la neige marine non-sédimentée maintenue dans la zone photique. Durant les dernières décennies une intensification des apparitions des MPM ont été recensées. Ainsi, les MPM sont devenus un sujet de préoccupation pour les populations qui exploitent les ressources côtières et dans le contexte du fonctionnement global de l'écosystème. Malgré l’intérêt scientifique grandissant au cours des dernières décennies au sujet de ces phénomènes, notamment en mer Adriatique, les causes de formation, la dynamique et le rôle respectif des microorganismes dans de tels systèmes restent énigmatiques. La plupart des études réalisées sur les MPM étaient axées uniquement sur les communautés microbiennes eucaryotes par l’utilisation de techniques microscopiques. Or de nos jours, les méthodes moléculaires permettent de se concentrer également sur l'ensemble de la communauté, y compris les procaryotes. Afin d'approfondir notre compréhension de ces phénomènes nous avons étudié un type MPM qui est apparu de manière récurrente et abondante au cours de la dernière décennie dans le sud du Golfe de Gascogne (France), le «Liga». Dans un premier temps, nous avons étudié la formation de ce MPM au travers d’une année complète en suivant la dynamique des communautés archées, bactériennes et eucaryotes par la technique de T-RFLP, technique d’empreinte moléculaire ciblant la petite sous-unité du gène codant pour ARNr. Cette approche a révélé que les communautés microbiennes du Liga étaient différentes des communautés microbiennes marines pour les trois domaines du vivant, et que ces deux communautés étaient gouvernées par des paramètres environnementaux dont la variation était saisonnière. Les archées n’ayant pas pu être détectés dans le Liga, nous nous sommes focalisés sur la structure des communautés bactériennes et eucaryotes au moyen de technologies de séquençage à haut débit. Cette méthode a révélé que le Liga était principalement composé d'espèces marines, même si ces communautés étaient significativement différentes des espèces marines. Dans le Liga, les communautés eucaryotes étaient principalement composées de dinoflagellés, de zooplancton et de cnidaires. Les communautés bactériennes étaient principalement composées d’Alphaproteobacteria et de Gammaproteobacteria. La diversité fonctionnelle du Liga fraîchement formé a été également étudiée pendant les saisons d'apparition de ce phénomène, au printemps et à l'automne. Nous avons ainsi mis en évidence que les communautés microbiennes du Liga avaient potentiellement moins de capacités de résistance au stress et que ces communautés étaient potentiellement plus virulentes que les communautés microbiennes marines. / Marine pelagic mucilage (MPM) is worldwide phenomena occurring sporadically and, in certain regions, episodically in coastal areas. These gelatinous aggregates, enriched in organic matter and microorganisms, form autonomous transitory marine ecosystems ranging from 0.5 cm to several kilometers. They correspond to evolving stages originating from the non-settling early marine snow maintained in the photic zone. During the last decades intensification of MPM events have been noticed. They became a matter of concern both for populations exploiting coastal resources and in the context of global ecosystem functioning. Although increased scientific attention has been paid during last decades to these phenomena in specific areas such the Adriatic Sea, the causes of appearance, the dynamics, and the respective role of microorganisms in such systems remain enigmatic. Most of the studies performed on MPM focused on eukaryotic microbial communities using microscopic techniques. However molecular methods allow nowadays focusing also on the whole community including the prokaryotic part. In order to deeper our understanding of these phenomena we studied a MPM that occurred recurrently and more frequently during the last decade in the south of the Bay of Biscay (France), the “Liga”. In a first step we investigated the formation of this MPM through a complete year by following the dynamics of archaeal, bacterial and eukaryotic communities using T-RFLP fingerprinting targeting the small subunit of rRNA genes. This approach revealed that Liga’s microbial communities where different from marine microbial communities for the three domains of life and that both marine mucilage and marine communities were linked with seasonal patterns. As archaea were not found in the Liga, we focused on bacterial and eukaryotic communities’ structures through high throughput sequencing. The molecular composition revealed that the Liga was mainly composed of marine species although these communities were significantly different from marine species. In the Liga, eukaryotic communities were mainly composed of dinoflagellates, zooplankton and cnidarians species and bacterial communities were mainly composed of Alphaproteobacteria and Gammaproteobacteria. Functional diversity of freshly-formed Liga was targeted during its seasons of apparition, in spring and in autumn. We highlighted that Liga’s microbial communities had less potential capabilities to resist to stress conditions and that these communities were potentially more virulent than marine microbial communities.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / As extensas pradarias submersas formadas pelas gramas marinhas são importantes habitats da costa, onde ocorrem interações ecológicas entre diversas espécies da vegetação subaquática, invertebrados bentônicos e peixes. As gramas marinhas e algas de deriva são conhecidas como macrófitas marinhas e, por ocuparem o mesmo tipo de substrato, são normalmente encontradas juntas, proporcionando oxigênio, alimento, proteção, abrigo além de sítios de reprodução e pastagem para os animais associados a essas pradarias. Amostras de algas de deriva e de H. wrightii foram coletadas, ao longo de transectos fixos de 50 m paralelos à Ilha do Japonês, a fim de analisar a existência de relações positivas entre as espécies de macrófitas marinhas e sua macrofauna associada, comparar as duas comunidades e avaliar a estruturação da comunidade macrofaunal bêntica do local. Os transectos foram alocados de acordo com a posição do banco de grama marinha. Observou-se que a densidade de eixos e a biomassa de H. wrightii não explicam a variação da biomassa, riqueza de espécies e diversidade (Índice de Simpson) das algas de deriva. A grande movimentação das algas de deriva ao longo do banco de grama marinha faz com que elas se homogeneízem e ocupem diferentes lugares ao acaso na pradaria, muitos desses locais com baixa biomassa de H. wrightii devido à grande variabilidade na distribuição dessa espécie no local de estudo. Os descritores ecológicos da grama marinha também não tiveram relações positivas com sua macrofauna bêntica associada. A comunidade macrofaunal associada às gramas marinhas foi mais densa, rica e diversa do que a comunidade macrofaunal associada às algas de deriva. Os moluscos Anomalocardia flexuosa, Cerithium atratum, Ostrea sp, Tellina lineata e Divalinga quadrissulcata dominaram o ambiente de gramas marinhas. A maior complexidade estrutural das algas de deriva forneceu um habitat protegido mais atrativo para os crustáceos como, Pagurus criniticornis, Cymadusa filosa e Batea catharinensis. A malacofauna associada às algas não foi abundante, mas um novo registro foi a ocorrência do bivalve invasor Lithopaga aristatus, perfurando uma concha de Ostrea sp. As relações entre os descritores da biomassa algal foram comprovadas para a maioria dos descritores de sua fauna associada. As relações das macrófitas marinhas com a macrofauna total associada seguiram o mesmo padrão das relações das algas de deriva. As análises de agrupamento e ordenação mostraram que as comunidades macrofaunais bênticas do local são estruturadas de acordo com os táxons dos organismos associados mais dominantes influenciados pelo tipo de vegetação basibionte (algas de deriva ou grama marinha). Destaca-se com o presente estudo a importância de medidas de maior proteção no local para a preservação e manutenção do ecossistema da Ilha do Japonês, RJ, Brasil / Extensive submerged meadows formed by seagrasses are an important habitat of the coast, where ecological interactions among different species of the submerged vegetation, benthic invertebrates and fish occur. The seagrasses and drift algae are known as marine macrophytes and, since they often can be found occupying the same substrate, they make a viable coexistence, providing oxygen, food, protection, shelter, besides breeding and grazing sites for the animals associated with these meadows. Samples of drift algae and H. wrightii were collected, along fixed 50 meter transects parallel to the Ilha do Japonês, so as to analyze the relationships between the species of marine macrophytes and the associated macrofauna, compare both communities and assess the structure of the local benthic macrofaunal community. Transects were allocated according to the position of the seagrass bed. It was found that shoot density and biomass of seagrasses did not explain the variation in drift algae biomass, species richness and diversity (Simpson index). The constant movement of the drift algae along the seagrass bed makes the algae homogenize and occupy different places by chance on the meadow, many of these places with low biomass of H. wrigthii, due to the high variability on the distribution of this species in the study area. The descriptors of the seagrassdid not have positive relations with its associated fauna either. Macrobenthos associated with the seagrasses was denser, richer and more diverse than the macrobenthic community associated with the drift algae. The mollusks Anomalocardia flexuosa, Cerithium atratum, Ostrea sp., Tellina lineata and Divalinga quadrissulcata dominated the environment of seagrass. The greater structural complexity of drift algae provided a protected habitat more attractive for the detritivores Pagurus criniticornic, Cymadusa filosa and Batea catharinensis. Malacofauna associated with algae was not abundant, but an important record was a new occurrence of the invasive bivalve Myoforceps aristatus, drilling a shell of Ostrea sp. The relationships among the descriptors of the algae biomass were confirmed to most of the descriptors of its associated fauna. Linear relations between marine macrophytes and its total macrobenthic community followed the same pattern as drift algae linear relationships. Cluster and MDS analysis showed that the local macrobenthic communities are structured according to the taxa of the most dominant associated organisms influenced by the type of the basibiont vegetation (drift algae or seagrasses). The present study considers the importance of more protective measures at the place for the preservation and maintenance of Ilha do Japonês ecosystem, RJ, Brasil

Made available in DSpace on 2016-04-28T20:16:19Z (GMT). No. of bitstreams: 1 2006-Aline Rodrigues Paraguassu.pdf: 983519 bytes, checksum: 0c74cca0a30825c36292d89b35424d4e (MD5) Previous issue date: 2006-02-21 / Funda??o Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / From April 2002 to July 2003, 296 freshwater fishes from Lajes Reservoirs in the State of Rio de Janeiro, Brazil (22?42 - 22?50 S, 43?53 - 44?05 W) were necropsied to study their community metazoan parasites: 39 Astyanax bimaculatus (Linnaeus, 1758), 79 A. fasciatus (Cuvier, 1819), 65 Geophagus brasiliensis (Quoy & Gaimard, 1824), 23 Hypostomus affinis (Steindachner, 1877), 26 Hoplias malabaricus (Bloch, 1794), 30 Loricariichthys castaneus (Castelnau, 1855) and 34 Trachelyopterus striatulus (Steindachner, 1877). The majority specimens of G. brasiliensis (81.5%), H. affinis (95.6%) and H. malabaricus (84.6%) was parasitized by one or more metazoan species. In A. bimaculatus, A. fasciatus, L. castaneus and T. striatulus 41%, 39.2%, 56.7 and 14.7% of specimens were parasitized, respectively.Ten different metazoan parasites species were collected: 2 in A. bimaculatus, 3 in A. fasciatus, 6 in G. brasiliensis, 3 in H. affinis, 4 in H. malabaricus, 4 in L. castaneus and 1 in T. striatulus. Six species were common in at least two communities. The glossiophonid was collected in 6 communities. The larval stage of digeneans were the majority of the parasite specimens collected in H. malabaricus and L. castaneus with 45.9% and 80.4%, respectively. In A. bimaculatus and A. fasciatus the nematodes were the majority of the parasite specimens collected, while in G. brasiliensis and H. affinis the hirudine glossiophonid was the majority of the parasite specimens collected. Only one spcecies of monogenean was collected in T. striatulus. The parasite of 7 host species showed the typical aggregate pattern of distribution. Two cases of negative correlation between host s total length and prevalence and parasite abundance were found. The parasite community of L. castaneus showed the higher values of mean intensity, index of dispersion and higher values of diversity. While the parasite community of H. affinis showed the higher values of mean abundance and the mean parasite species richness. Only in A. fasciatus and L. castaneus the abundance and parasite species richness showed positive correlations with the host s total length. Geophagus brasiliensis was the species with higher number of species: ectoparasites (3), adult endoparasites (1) and larval stage of endoparasites (2). The parasite communities of the studied fishes showed scarcity of significant correlation of parasitic abundance, scpecies richness and diversity and the size of the host. The low scpecies richness and diversity of parasite communities could be attribute by oligotrophic characteristics of the Lajes Reservoirs. / Entre abril de 2002 e julho de 2003, foram necropsiados 296 esp?cimes de peixes: 39 Astyanax bimaculatus (Linnaeus, 1758), 79 A. fasciatus (Cuvier, 1819), 65 Geophagus brasiliensis (Quoy & Gaimard, 1824), 23 Hypostomus affinis (Steindachner, 1877), 26 Hoplias malabaricus (Bloch, 1794), 30 Loricariichthys castaneus (Castelnau, 1855) e 34 Trachelyopterus striatulus (Steindachner, 1877) provenientes do Reservat?rio de Lajes (22?42 - 22?50 S, 43?53 - 44?05 O), Estado do Rio de Janeiro, Brasil, para estudo das suas comunidades parasit?rias. A maioria dos esp?cimes de G. brasiliensis (81,5%), H. affinis (95,6%) e H. malabaricus (84,6%) estavam parasitados por pelo menos uma esp?cie de metazo?rio. Em A. bimaculatus, A. fasciatus, L. castaneus e T. striatulus 41%, 39,2%, 56,7% e 14,7% dos esp?cimes estavam parasitados, respectivamente. Foram coletadas 10 diferentes esp?cies de metazo?rios parasitos: 3 digen?ticos, 1 monogen?tico, 2 nemat?ides, 1 cop?pode, 1 hirud?neo, 1 bivalve e 1 is?pode. Seis esp?cies de metazo?rios parasitos foram comuns a pelo menos duas comunidades. O glossiphon?deo foi encontrado em seis das sete comunidades estudadas. Os est?gios larvais de digen?ticos corresponderam ? maioria dos esp?cimes coletados em H. malabaricus e L. castaneus com 45,9% e 80,4%, respectivamente. Em A. bimaculatus e A. fasciatus os nemat?ides corresponderam a maioria dos esp?cimes coletados, enquanto em G. brasiliensis e H. affinis o glossiphonideo correspondeu a maioria dos esp?cimes coletados. Apenas uma esp?cie de monogen?tico foi coletada em T. striatulus. As comunidades de metazo?rios parasitos dos sete peixes estudados apresentaram t?pico padr?o de distribui??o agregada. Apenas o glossiphonideo apresentou correla??o negativa entre a abund?ncia e a preval?ncia parasit?rias e o comprimento total em H. malabaricus e L. castaneus, respectivamente. A comunidade parasit?ria de L. castaneus apresentou os maiores valores de intensidade m?dia, ?ndice de dispers?o e diversidade. Enquanto a comunidade parasit?ria de H. affinis apresentou os maiores valores de abund?ncia m?dia e riqueza parasit?ria. Apenas em A. fasciatus e L. castaneus a abund?ncia e a riqueza parasit?ria apresentaram correla??o positiva com o comprimento total do hospedeiro. Geophagus brasiliensis foi o hospedeiro com o maior n?mero de esp?cies de parasitos: ectoparasitos (3), endoparasitos adultos (1) e est?gios larvais de endoparasitos (2). As comunidades parasit?rias dos peixes estudados apresentaram escassez de correla??o entre a abund?ncia, riqueza parasit?ria e diversidade com o comprimento total dos hospedeiros. Os baixos valores de riqueza e diversidade das comunidades parasit?rias podem ser atribu?dos as caracter?sticas oligotr?ficas do Reservat?rio de Lajes.

Entre les fleuves Amazone et Orénoque, la frange côtière atlantique de l’Amérique du Sud (1500 km) est considérée comme la plus vaseuse au monde, conséquence des apports de sédiments en suspension de l’Amazone. Malgré la forte variabilité et l’instabilité de ces vasières uniques au monde, elles apparaissent comme des écosystèmes très productifs et sont des habitats clés dans l’accomplissement du cycle de vie des espèces de poissons et d’oiseaux qui les exploitent. Cependant, les connaissances sur les communautés biologiques qui y sont associées restent au niveau exploratoire. Ce travail de thèse vise donc à décrire la structure de l’endofaune benthique intertidale des vasières guyanaises et à définir son fonctionnement dans des environnements vaseux tropicaux très instables. Comme prévu, la forte instabilité des sédiments a entraîné une très faible diversité des assemblages de la macrofaune et de la méiofaune. Néanmoins, les communautés benthiques des vasières guyanaises ont montré une abondance remarquablement élevée avec la dominance d'espèces opportunistes de petites tailles. 39 taxons de la macrofaune ont été trouvés tandis que la méiofaune était moins diversifiée avec la présence de 34 taxons. Le tanaidacée Halmyrapseudes spaansi et le polychète Sigambra grubii sont les deux espèces de macrofaune les plus abondantes, largement réparties le long de la côte guyanaise. De même, le nématode Pseudochromadora spp., suceur d’épistrate, et Halomonhystera sp. 1 (non deposit feeders) étaient les deux espèces de méiofaune les plus abondantes sur chacune des stations. La distribution des communautés benthiques sont spécifiques aux sites d’étude et varie saisonnièrement. Les assemblages en zone estuarienne (Sinnamary) étaient plus diversifiées que dans la zone de vasière nue (Awala), alors que les abondances des communautés benthiques étaient toujours plus élevées en saison humide qu’en saison sèche. Les facteurs abiotiques et biotiques ont influencé significativement les communautés benthiques. Néanmoins, les changements dans la structure de la communauté benthique induits par la disponibilité des sources alimentaires (chl a) et la pression de prédation étaient tout aussi importantes que les variations des assemblages imposées par les paramètres abiotiques (teneur en eau, salinité ...). En particulier, une forte corrélation a été trouvée entre la méiofaune et le microphytobenthos. Les mesures isotopiques de différents compartiments des vasières ont non seulement révélé le rôle central du microphytobenthos dans la composition du régime alimentaire de la méiofaune, mais ont également montré l'importance écologique de la méiofaune comme principale source de nourriture pour les petits oiseaux limicoles et les poissons côtiers. La méiofaune et le microphytobenthos rentrent dans le régime alimentaire de trois poissons côtiers en grande proportion, alors que les oiseaux limicoles migrateurs présentaient une plus grande diversité de proies. Cependant, la contribution relative des tanaidacées dans le régime alimentaire des oiseaux limicoles était étonnamment faible. Le travail de thèse a permis d'améliorer notre compréhension de la structure de l’endofaune benthique intertidale des vasières guyanaises et de définir son fonctionnement dans des environnements vaseux tropicaux très instables. Ce travail a permis de construire, pour la première fois, un modèle conceptuel de réseau trophique des vasières intertidales mobiles guyanaises. / Locating between the Amazon and Orinoco Rivers, the 1500 km-long Atlantic coastline of South America are considered as the muddiest areas in the world due to the large discharge of suspended sediment from the Amazon. Despite the extreme morphodynamics of these ecosystems, the Guianas mudflats are important feeding zones for many shorebirds and fish. However, the state of knowledge on benthic organisms associated with these highly unstable environments is still at an exploratory stage. This study, therefore, aims to describe the structure and dynamics of the intertidal benthic infauna in the Guianas mudflats and to define its functioning in such highly unstable tropical muddy environments. As expected, the high instability of the sediment resulted in very low diversity of both macrofauna and meiofauna assemblages. Nonetheless, the infauna communities of the Guianas mudflats showed remarkably high abundance with the predominance of small-sized opportunistic species. A total of 39 operational taxonomic units of macrofauna was recorded while meiofauna was less diverse with the occurrence of 34 taxa. The tanaid Halmyrapseudes spaansi and the polychaeta Sigambra grubii are the two most abundant macrofauna species, which widely distributed along the Guianas coast. Likewise, the nematodes epistrate feeder Pseudochromadora spp. and non-deposit feeders Halomonhystera sp. 1 were the principal components of meiofauna communities in every station. The distribution patterns of the infauna were both site-specific and seasonal variation. The assemblages in estuarine habitat were more diverse than in the bare mudflat habitat, while infauna abundances in the WS were always higher than in the DS. Both abiotic and biotic factors significantly influenced the benthic communities. Nevertheless, the changes in benthic community structure induced by food source availability (chl a) and predation pressure were more prominent than the assemblage variations imposed by abiotic parameters (mud content, salinity…). Particularly, the tight coupling between meiofauna and MPB was observed in both distribution patterns and trophic structures. The isotopic measurements of different intertidal compartments not only revealed the pivotal role of MPB on structuring meiofaunal coummunities, but also indicated the ecological importance of meiofauna as the main food source for the small shorebirds and coastal fish. Meiofauna and MPB entered the diet of three coastal fish in great proportion, whereas the migrating shorebirds showed a wider diet breadth. The isotopic ratios were perfectly matched with the feeding guilds assigned by morphological features. However, the relative contribution of tanaids to the top epibenthic predators were surprisingly lower than expected. The thesis has increased our understanding of the Guianas infauna communities, and revealed for the first time a conceptual food web model of these unique intertidal mudflats.