River inflow is one of the most important factors influencing the density and biomass of estuarine biotic communities. The aim of this study was to obtain an understanding of the ecosystem functioning of selected estuaries on the east coast of South Africa and to represent their dynamics through ecosystem models. The responses of water column nutrients, plankton density and biomass to inlet phase changes for 16 temporarily open/closed estuaries (TOCEs) in South Africa were first determined. This analysis demonstrated that inlet phase and the duration of mouth closure were the most important factors determining plankton density and biomass of the analysed TOCEs. Estimates of planktonic standing stocks for four of these estuaries revealed that stocks can be from 26 to 10 000 times higher during the closed compared to the open phase. Also, slightly higher variability of planktonic density and biomass was recorded during the closed phase of TOCEs. The second major thrust of this study was to analyse the variability and temporal stability of planktonic and macrobenthic invertebrate density and biomass in two KwaZulu-Natal estuaries over a dry/wet cycle. The results suggest that “stable” variability and species synchronization could be the mechanisms whereby the estuarine biota of these systems compensate for environmental changes and attain a degree of environmental homeostasis. The third major thrust involved an assessment of the spatio-temporal variations in the elemental composition and stoichiometry of suspended and sediment detritus, zooplankton and macrobenthic taxa from two estuaries over a dry/wet cycle. Significant seasonal variations in the elemental composition of detritus, zooplankton and macrobenthic species were found, with the variations in the elemental content of sediment and suspended detritus being related to the seasonal changes in river inflow, while the among-taxa variability was mainly explained by feeding mode. Finally, static seasonal carbon and nitrogen ecosystem network models were developed for the East Kleinemonde, Mlalazi and Mpenjati estuaries to investigate their nutrient dynamics and ecosystem functioning. The results indicated that the East Kleinemonde and Mpenjati estuaries were mainly dependent on primary producers during the dry season, especially the high standing stocks of phytoplankton and microphytobenthos. Similarly, the dependency on detritus was higher during the wet season due to the high riverine imports during this season. Consequently, higher detritivory was recorded in all three study systems during the wet season. Cycling of nitrogen was higher than of carbon on a seasonal basis, with higher recycling of nitrogen during the dry season implying a lower availability of this element due to reduced freshwater inflow and nutrient input during the low rainfall period. System indices indicated that the organization of these systems was higher during the dry season, while the overheads on imports and exports peaked during the wet season. The ecosystem models analysed here provide an initial insight into the overall carbon and nitrogen dynamics of estuaries on the east coast of South Africa. / M.Sc. University of KwaZulu-Natal, Durban 2013.

Global climate change is predicted to affect timing and severity of disturbance events (e.g., fire, drought, hurricanes, wind storms, and inundation), but the extent of these disturbance events and their impacts on natural ecosystems may vary regionally. Rising sea level, increased frequency and intensity of tropical storms, and altered inundation regimes are likely to create changing environmental conditions in low-lying coastal ecosystems. These large scale disturbances may increase resource availability and regeneration spaces, reduce competition, and possibly increase community vulnerability to invasion. Shifting disturbance regimes and invasion together are predicted to drive long-term shifts in coastal plant community structure and ecosystem processes. However, impacts of altered environmental conditions on native and invasive plant species and the species responses to changed environmental conditions are poorly understood. The aims of this study were: (i) to assess the probability of occurrence of juveniles of the invasive exotic Triadica sebifera and co-occurring native species, Baccharis halimifolia, Ilex vomitoria, and Morella cerifera in the field in relation to surrounding environmental factors, (ii) to assess the effects of elevated salinity across a typical coastal transition on germination of T. sebifera, B. halimifolia and M. cerifera, using controlled growth chamber and greenhouse experiments, (iii) to assess the effects of climate change and shifting inundation and tropical storms regimes on T. sebifera, B. halimifolia and M. cerifera, and (iv) to evaluate the role of vesicular arbuscular mycorrhizae (VAM) on spread of invasive T. sebifera in coastal transition ecosystems at the Grand Bay National Estuarine Research Reserve (GBNERR), Coastal Mississippi, southeastern USA. Results from assessing the probability of occurrence of juveniles of invasive and co-occurring native species showed that soil water conductivity (i.e., salinity) was the major factor related to the occurrence of invasive T. sebifera and native B. halimifolia, I. vomitoria and M. cerifera along the coastal transitions. Probability of occurrence of the invasive T. sebifera was significantly related to landscape factors and occurrence was highest in close proximity to roads, trails, power lines, and recreational sites, and water bodies. These results imply that future increases in salinity will negatively impact I. vomitoria, M. cerifera, and T. sebifera, leading to range contraction of these species away from the coast. However, natural and anthropogenic disturbances that often increase resource pulses and reduce competition, likely increase the dominance of T. sebifera in already invaded areas. Positive effects of landscape structures on T. sebifera occupancy highlight the role of landscape variables in promoting new invasions in coastal forests of the southeastern USA. Controlled growth chamber and greenhouse germination experiments demonstrated that germination of all species (i.e., T. sebifera, B. halimifolia, and M. cerifera) decreased with elevated salinity and that the reduction was most pronounced in soils from the most seaward zones along the coastal transition. Although native B. halimifolia was least sensitive to elevated salinity, invasive T. sebifera displayed plasticity of germination trait across different salinity levels in most inland soils. These results suggest that the phenotypic plasticity may facilitate spread of Triadica sebifera under some degree of salinity stress in more inland section of the coastal transition. A manipulative greenhouse experiment demonstrated that simulated canopy damage from intense hurricane winds and associated storm surge produced differential effects on survival and growth of native (B. halimifolia and M. cerifera) and invasive (T. sebifera) species at simulated different forest conditions common in the GBNERR. Invasive T. sebifera was by far the most shade tolerant of the three species and seedling survival under highly shaded conditions may provide it with a competitive edge over native species during community reassembly following tropical storms. T. sebifera may better utilize post-hurricane conditions (e.g., resource-rich empty spaces) and potentially increase its dominance in coastal forested ecosystems. The last experimental study revealed that invasive T. sebifera had higher VAM colonization compared to co-occurring native species both in controlled greenhouse and field experiments, and that the higher colonization leads to significant increases in aboveground biomass, supporting the hypothesis that VAM fungi strongly benefit the invasive species. These results suggest that the VAM colonization may be necessary for the initial establishment of T. sebifera along the coastal transitions. Furthermore, my research also suggested that T. sebifera was not allelopathic and did not interfere with growth of native species. Overall, the findings of this research provide insight into the impacts of climate change related shifts on performance of invasive and co-occurring native species across coastal transitions of the southeastern USA. Variation in invasive and co-occurring native species' performances under changed environmental conditions (e.g., elevated salinity and increased light availability) and improved mutualistic association between invasive T. sebifera and VAM fungi may drive increased invasion with frequent community reassembly of low-lying coastal ecosystems undergoing rapid climate change.

Marine renewable energy developments (MRED) will result in large quantities of infrastructure being deployed in coastal habitats, and the localised exclusion of fishing. The ecological consequences of this scale of deployment are largely unknown, particularly for benthic species. Infrastructure has the capacity to act as artificial reefs (ARs), providing novel habitat, and this may viewed as a benefit of MRED, or a means to mitigate the exclusion of fishing. At present, the functioning of AR ecosystems remains poorly understood. As a measure of ecosystem function, secondary productivity can be used to assess the implications of MRED. The lack of suitable methodology, deployable at relevant scales within time and/or cost constraints, has limited benthic secondary productivity (BSP) quantifications on ARs. Techniques to measure potential BSP and particle flux were developed and applied to the Loch Linnhe Artificial Reef (functionally similar to scour protection material). Variations in BSP and mobile epifaunal densities on, and between, structures in different environments were quantified. Reefs exposed to intermediate current had the highest potential productivity. The BSP on internal areas of structures contributed to the total productive output, but the relative contribution varied according to reef location and design. BSP was primarily determined by particle supply, but the response was not consistent among locations. Mobile epifaunal densities related to reef location, but not reef design, and were highest on reefs in the deepest water and exposed to the fastest currents. The evidence presented in this thesis highlights the need to account for the receiving environment when predicting the ecological consequences of MRED, or when modelling the productive capacity of structures. Such information can be used to suggest modifications to proposed or existing structures in order to maximise their benefit to coastal ecosystems.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-04-15T14:32:54Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação - Nicolle Lagos de Melo Nogueira.pdf: 6595592 bytes, checksum: 3addd91d17b83db7049eb2c3d95ed483 (MD5) / Made available in DSpace on 2016-04-15T14:32:54Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação - Nicolle Lagos de Melo Nogueira.pdf: 6595592 bytes, checksum: 3addd91d17b83db7049eb2c3d95ed483 (MD5) Previous issue date: 2015-03-02 / FACEPE / Esta pesquisa aborda a relação do crescimento urbano e meio ambiente no bairro Barra de Jangada no município Jaboatão dos Guararapes, Pernambuco. Sustenta-se que existe uma relação entre a aceleração desse crescimento com a degradação do meio ambiente natural da região. O objetivo foi analisar a dinâmica territorial urbana e suas transformações socioespacais, utilizando material cartográfico, no bairro Barra de Jangada, que a partir de 2010 passou a receber influência do desenvolvimento econômico da região como a construção do empreendimento imobiliário Reserva do Paiva e dos investimentos do Poder Público no Complexo Industrial e Portuário Suape, localizados no município vizinho, o Cabo de Santo Agostinho. O empreendimento imobiliário Reserva do Paiva trouxe ao bairro Barra de Jangada uma nova configuração espacial e socioeconômica com empreendimentos imobiliários de verticalização para atender uma classe social de alta renda, enquanto o Complexo Industrial e Portuário Suape trouxe ao bairro uma classe social de renda inferior em busca de oportunidade de trabalho. Rotulada como “Nova Barra”, uma nova realidade espacial da orla contracena com a velha Barra de Jangada de classe social de renda mais baixa que a Nova Barra, e em boa parte destituída de infraestrutura básica. A região abriga o ecossistema litorâneo como os manguezais, além de parte da rede hidrográfica do rio Jaboatão como o seu estuário, sendo importante um estudo que sirva para discussão do planejamento urbano da região, avaliando as áreas de grande fragilidade e sua capacidade de suportar a crescente ocupação urbana, além de contribuir para gestão pública em recuperar áreas degradadas e importantes para a manutenção do ecossistema litorâneo. Para o desenvolvimento da pesquisa foram realizados revisão bibliográfica, observações in loco, coletados dados sociais do IBGE e desenvolvida uma análise multitemporal a partir do processamento de imagens com softwares livres no auxílio da gestão territorial e que mostraram a tendência do crescimento urbano da área. / This research addresses the urban relationship growth and the environment of Barra de Jangada district in Jaboatão dos Guararapes city, Pernambuco. It is argued that there is a relationship between the acceleration of this growth with the degradation of the natural environment of the region. The purpose was to analyze the urban land dynamics and its sociospatial transformations using cartographic material, in Barra de Jangada district, where from 2010 began to receive influence of economic development of the region as the construction development Reserva do Paiva and government investments in the Industrial and Port Complex of Suape, located in the Cabo de Santo Agostinho, border with Jaboatão dos Guararapes. The estate development Reserva do Paiva brought Barra de Jangadas neighborhood a new spatial and socio-economic configuration with vertical project to further a social class of high income, while the Industrial and Port Complex Suape brought the neighborhood a social class income below in search job opportunity. Called Nova Barra, a new spatial reality around beachfront acts with the old Barra of social class with the lowest income that New Barra, and largely devoid of basic infrastructure. The region is place of the coastal ecosystem as mangroves, and part of the river system of the Jaboatão river as its estuary, it is important to a study that fits discussion of urban planning in the region, assessing the areas of great fragility and its ability to support the growing urban occupation, and contribute to public management in recovering degraded areas and important for maintaining the coastal ecosystem. For the development of research were conducted a literature review, on-site observations, collected social data from the IBGE and developed a multitemporal analysis from image processing with free software to aid the territorial management which showed the trend of urban growth area.

Les écosystèmes procurent de nombreux services essentiels aux sociétés humaines à travers les effets positifs de la biodiversité des communautés d'espèces. Par conséquent, identifier le rôle des organismes vivants et les facteurs influençant la diversité de leurs fonctions (ou diversité fonctionnelle), est indispensable pour prédire efficacement l'évolution des écosystèmes soumis aux pressions locales et globales.Cette thèse s'articule donc autour de deux axes: (i) établir un cadre méthodologique pour décrire la structure fonctionnelle locale et régionale des communautés, et (ii) améliorer la connaissance de l'impact des poissons sur la dégradation de la matière organique.Dans un premier temps, nous avons consolidé les outils méthodologiques permettant (i) d'améliorer la fiabilité des dendrogrammes fonctionnels, (ii) l'étude comparative des principaux indices de diversité fonctionnelle à l'échelle locale, et (iii) le développement d'une nouvelle décomposition de la diversité fonctionnelle en composantes locale (α), régionale (γ) et turnover (β). Appliqué aux communautés ichthyologiques échantillonnés le long d'un gradient de salinité, dans le système lagunaire de Patos-Mirim (Brésil), ce socle méthodologique nous a permis de révéler une structure fonctionnelle stable le long du gradient, en dépit d'une forte variabilité en composition d'espèces, ces communautés étant structurées majoritairement par un filtre environnemental agissant sur les capacités de locomotion des poissons.Dans un second temps, nous avons étudié l'impact des communautés ichthyologiques sur le cycle des nutriments. Plus précisément, nous avons estimé le potentiel de dégradation de la matière organique de plusieurs espèces de poissons, en étudiant la diversité fonctionnelle et génétique de leur flore bactérienne intestinale. Nous avons montré que les communautés ichthyologiques pouvaient influencer le recyclage des nutriments de façon non négligeable en raison d'un important potentiel de dégradation commun à la plupart des espèces étudiées, ce potentiel étant peu affecté par la diversité génétique ou les facteurs environnementaux. / Ecosystems provide many services essential to Human societies through the positive effects of biodiversity exhibited by species communities. Therefore, identifying the role of living organisms and the factors influencing the diversity of their functions (i.e. functional diversity) is fundamental to accurately predict the evolution of ecosystems undergoing local and global pressures.This thesis is organized around two axes: (i) establishing a methodological framework to describe the functional structure of local and regional communities, and (ii) improving our knowledge of the impact of fish on the degradation of organic matter.First, we have consolidated the methodological tools through (i) the improvement of functional dendrograms reliability, (ii) the comparative study of the main indices estimating local functional diversity, and (iii) the development of a new decomposition of functional diversity into local (α) and regional (γ) components, and functional turnover (β). Applied to fish assemblages sampled along a salinity gradient in Patos-Mirim lagoons complex (Brazil), this methodological framework allowed us to reveal a steady functional structure, despite a high variability in species composition, these communities being primarily structured by environmental filtering acting on fish locomotion abilities.   In a second step, we studied the impact of fish communities on nutrient cycling. More specifically, we estimated degradation of organic matter potential of several fish species by studying the genetic and functional diversity of their intestinal bacterial flora. We showed that the fish community could significantly influence nutrient cycling through an important degradation potential, common to most species studied, which is weakly affected by genetic diversity or environmental factors.

Submitted by Mario BC (mario@bc.ufrpe.br) on 2016-08-09T12:53:21Z No. of bitstreams: 1 Ana Paula Pereira de Lima.pdf: 1558477 bytes, checksum: 672540b3d4430f89e746c8a120e26e7e (MD5) / Made available in DSpace on 2016-08-09T12:53:21Z (GMT). No. of bitstreams: 1 Ana Paula Pereira de Lima.pdf: 1558477 bytes, checksum: 672540b3d4430f89e746c8a120e26e7e (MD5) Previous issue date: 2016-08-22 / The continued growth of tourism has affected coastal ecosystems, especially the reef environments, negatively impacting on their organisms. high intensity tourist areas tend to have a less equal distribution of species and biological diversity lower compared to less frequented areas. This study aimed to describe the relationship between the degree of tourist use and the sanity and abundance of scleractinians corals and zoanthids in coastal reefs. For that purpose, six beaches of the coast of Pernambuco (northeastern Brazil) with different tourist use intensities were selected. The average number of visitors per beach was obtained through observations on days with different intensities of people flow (Sunday and Monday) and the beaches were classified as low use or heavy use. To measure coral cover and zoanthids were established nine transects 25m, parallel to the coast, six in midlittoral and three in the subtidal. Along each transect, three square 1x1m, with 81 points of intersection were arranged. Coral coverage, zoanthids, algae and total live coverage was calculated. All colonies that were within 50m2 each transect were counted, measured and the presence of death and bleaching were recorded. Were listed four species of zoanthids and five species of corals. The zoanthids were more abundant in areas of intense tourist use, in contrast corals were most abundant in the low tourist use, which they had higher diversity of anthozoans. The coral that had the highest number of partially bleached and dead colonies was Siderastrea stellata, besides being the most abundant in all areas. The tourist flow showed the highest relationship with the coral cover and zoanthids than with health indicators adopted for this study. However, factors such as acidification, nutrient increase and temperature fluctuations appear to act synergistically on the health of anthozoans. Changes in benthic community structure can have negative consequences for reef ecosystems, among them the phase shift, causing loss of biodiversity due to favoring the most resistant species, as algae and zoanthids at the expense of corals. Thus, due to the numerous ecosystem services, the reefs demonstrate once again being priority areas for conservation. / O contínuo crescimento da atividade turística tem afetado os ecossistemas costeiros, principalmente os ambientes recifais, impactando negativamente sobre os seus organismos. Áreas de elevada intensidade turística tendem a ter uma distribuição menos equitativa das espécies e uma menor diversidade biológica em relação a áreas menos frequentadas. O presente estudo objetivou descrever a relação entre o grau de uso turístico e a sanidade e abundâncias de corais escleractínios e de zoantídeos em recifes costeiros. Para tal, seis praias do litoral pernambucano (nordeste do Brasil) com diferentes intensidades de uso turístico foram selecionadas. O número médio de visitantes por praia foi obtido através de observações em dias com diferentes intensidades de fluxo de pessoas (domingo e segunda) e as praias foram classificadas como baixo uso ou uso intenso. Para mensurar a cobertura de corais e zoantídeos foram estabelecidos nove transectos de 25m, paralelos à costa, sendo seis no mediolitoral e três no infralitoral. Ao longo de cada transecto, três quadrados de 1x1m, com 81 pontos de intersecção foram dispostos. Foi calculada a cobertura de corais, zoantídeos, algas e a cobertura viva total. Todas as colônias que estavam dentro dos 50m2 de cada transecto foram contabilizadas, medidas e a presença de mortalidade e branqueamento foram registradas. Foram listadas quatro espécies de zoantídeos e cinco espécies de corais. Os zoantídeos foram mais abundantes nas áreas de uso turístico intenso, em contrapartida os corais foram mais abundantes nas áreas de baixo uso turístico, as quais apresentaram maior diversidade de antozoários. O coral que apresentou o maior número de colônias branqueadas e parcialmente mortas foi Siderastrea stellata, além de ter sido o mais abundante em todas as áreas. O fluxo turístico mostrou ter maior relação com a cobertura de corais e zoantídeos do que com os indicadores de sanidade adotados para o presente estudo. No entanto, fatores como acidificação, incremento de nutrientes e oscilações da temperatura parecem agir sinergicamente sobre a sanidade dos antozoários. Modificações na estrutura da comunidade bentônica podem trazer consequências negativas aos ecossistemas recifais, dentre elas a mudança de fase, ocasionando perda de biodiversidade devido ao favorecimento de espécies mais resistentes, como algas e zoantídeos, em detrimento dos corais. Assim, devido aos inúmeros serviços ecossistêmicos, os recifes demonstram mais uma vez, serem áreas prioritárias à conservação.

Submitted by Jean Medeiros (jeanletras@uepb.edu.br) on 2016-08-19T14:06:23Z No. of bitstreams: 1 PDF - Rayssa Soares da Silva.pdf: 6993577 bytes, checksum: 4b28a1b3bf1dccef7a141f2729ec2180 (MD5) / Made available in DSpace on 2016-08-19T14:06:23Z (GMT). No. of bitstreams: 1 PDF - Rayssa Soares da Silva.pdf: 6993577 bytes, checksum: 4b28a1b3bf1dccef7a141f2729ec2180 (MD5) Previous issue date: 2016-02-04 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Seagrass beds are essential habitats for the high biodiversity in coastal environments. They provide nursery, feeding and shelter areas for many organisms. Despite its importance, the seagrass beds are among the most threatened coastal ecosystems on the planet and its influence on fish populations has been little studied in Brazil. The understanding of its influence on the dynamics of fish assemblages associated with these environments and the study of the feeding habits of the species that use them supports the development of new conservation policies of these habitats. Thus, the aim of this study was to compare the composition, structure and feeding ecology of fish assemblages found in vegetated and unvegetated areas on the estuary of the Mamanguape River, Paraiba - Brazil, observing the variations in hydrological conditions between the dry and rainy periods. The values of abundance and biomass were higher in non-vegetated areas, although there was no significant difference in species diversity between study areas. Thus, the environmental stability of unvegetated areas proved to be an important factor in determining the biomass and richness patterns. In addition, it was observed that these areas are used by the species at different stages of their ontogenetic development according to the ratio of optimal foraging and the possibility of refuge from predation. Among the species captured in vegetated and unvegetated áreas on the estuary, the four most representative were selected for analysis of stomach contentes, according to their abundance. Of these, three were considered generalists and showed a high degree of individual specialization, supporting the hypothesis of niche variation proposed by Van Valen. Also, we observed the importance of intraspecific competition and the availability of food items in the intraindividual variation in the diet of the species. / Os bancos de fanerógamas marinhas são habitats essenciais para a elevada biodiversidade em ambientes costeiros, pois constituem áreas de berçário, alimentação e refúgio para diversos organismos. Apesar de sua importância, os bancos de fanerógamas estão entre os ecossistemas costeiros mais ameaçados do planeta e sua influência sobre a ictiofauna foi pouco estudada no Brasil. O entendimento da sua influência sobre a dinâmica das assembleias de peixes associados a estes ambientes e o estudo dos hábitos alimentares das espécies que os utilizam auxilia no desenvolvimento de novas políticas de conservação destes habitats. Deste modo, o objetivo deste estudo foi comparar a composição, estrutura e ecologia alimentar de assembleias de peixes encontradas em áreas vegetadas e não vegetadas do estuário do Rio Mamanguape, Paraíba – Brasil, observando as variações do regime hidrológico entre os períodos seco e chuvoso. Os valores de abundância e de biomassa foram maiores nas áreas não vegetadas, apesar de não haver diferença significativa da diversidade de espécies entre áreas estudadas. Deste modo, a estabilidade ambiental das áreas não vegetadas mostrou -se como fator importante na determinação dos padrões de biomassa e riqueza de espécies. Além disso, foi observado que essas áreas são utilizadas pelas espécies em diferentes fases do seu desenvolvimento ontogenético de acordo com a razão entre o forrageamento ótimo e a possibilidade de refúgio contra a predação. Dentre as espécies capturadas nas áreas vegetadas e não vegetadas do estuário do rio Mamanguape as mais representativas foram selecionadas, de acordo com sua abundância, para análise do conteúdo estomacal. Das quatro espécies, três delas foram consideradas generalistas e apresentaram um alto grau de especialização individual, corroborando com a hipótese da variação de nicho proposta por Van Valen. Além disso, observou-se a importância da competição intraespecífica e da disponibilidade de itens alimentares na variação intraindividual da dieta das espécies.

Cette thèse est une contribution à l’étude de la dynamique sédimentaire dans l’écosystème de la rade de Brest. Elle a pour objectif de décrire, par la simulation numérique et l’observation in situ, le mouvement des masses d’eau et de sédiments sous l’influence de la marée à l’échelle de la rade, et l’impact de la distribution spatiale actuelle des populations de crépidules sur le transport de sédiments en suspension et l’évolution des fonds. Un modèle bidimensionnel horizontal (2DH) est mis en œuvre à partir du code TELEMAC. Il intègre la variabilité spatiale du substrat, et rend compte de la présence physique (macro-rugosité, partition de la contrainte de cisaillement) et de l’activité biologique (filtration de l’eau chargée de particules en suspension, production de biodépôts) des crépidules. Les mesures de hauteur d’eau, de vitesse du courant, et de vitesse de frottement valident de façon satisfaisante les choix de paramétrisation du modèle hydrodynamique. Les mesures de concentration de matière en suspension en rade de Brest sont sporadiques, et leur analyse est compliquée. Le modèle sédimentaire constitue un outil de compréhension. Il informe de l’évolution temporelle de la contribution de différents types de sédiments et de leur origine aux concentrations locales de sédiments en suspension et déposés. Il permet de suivre le cheminement des sédiments principalement en suspension, de quantifier les échanges entre les sous-bassins de la rade et avec le fond. L’introduction sur le fond des colonies de crépidules, sous forme de chaînes assimilées à des cylindres, induit une diminution de la vitesse du courant à l’aplomb et dans leur sillage, compensée par une augmentation en périphérie, entraînant une modification globale des zones d’érosion et de dépôt de sédiments. Localement, les macro-rugosités ont un effet antagoniste selon leur répartition: des densités moyennes augmentent le frottement de peau et les remises en suspension, tandis que des densités élevées induisent un masquage des sédiments sur le fond duquel résulte une accrétion. Par comparaison à leur impact hydrodynamique, l’activité biologique des crépidules joue un rôle secondaire sur la dynamique sédimentaire. / This thesis is a contribution to the study of sediment dynamic in the ecosystem of the bay of Brest. It aims at describing, by numerical simulations and field observations, the movement of water and sediments in the bay under tidal forcing, and the impact of the present spatial distribution of slipper limpets on suspended sediment transport and bed evolution. A two-dimensional horizontal (2DH) model is implemented based on the TELEMAC numerical system. It integrates the spatial variability of bed sediments, accounts for the physical presence (macro-roughness, form drag - skin friction partitioning) and biological activity (filtration of water carrying suspended particles, production of biodeposit) of slipper limpets. Measurements of water level, mean flow velocity, and friction velocity satisfactorily validate the choice of parameters in the hydrodynamic model. Measurements of suspended matter concentration in the bay of Brest are sporadic, and their analysis complicated. The sediment model stands as a tool for better understanding sedimentary processes. It informs the temporal evolution of the contribution of different types of sediment, and their origin, to local suspended and deposited sediment concentrations. It allows to follow the paths of sediment transport predominantly in suspension, and to quantify the exchanges of sediments between the sub-basins of the bay and with the bed. The introduction of slipper limpet colonies on the bed, in the form of chains assimilated as cylinders, induces decreasing flow velocity above and in their wake, compensated by increasing flow velocity on the outskirts, which globally modify the patterns of sediment erosion and deposition in the bay. Locally, the macro-roughness elements have an antagonist effect depending on their distribution: medium densities increase skin friction and erosion flux, whereas high densities shelter bed sediments from which results accretion. By comparison to their hydrodynamic impact, the biological activity plays a secondary role on sediment dynamic.

L'objectif principal de cette thèse est la caractérisation des dynamiques hautes fréquance en milieu côtier et en particulier leurs extrêmes, par l'intermédiaire de l'étude de série temporelle biogéochimiques à long terme enregistrées par des systèmes automatisés. Les bases de données hautes fréquences utilisées dans cette étude proviennent majoritairement du programme MAREL, qui a été mise en oeuvre par l'IFREMER. Des séries temporelles basses fréquences provenant des programmes de surveillance du littoral SOMLIT (CNRS, INSU) et SRN (Ifremer) sont mises à contribution pour appuyer l'importance des systèmes automatisés. La méthode EMD (Empirical Mode Decomposition) nous a servi de base dans de nombreuses analyses pour étudier ces séries temporelles. Nous avons aussi utilisé des méthodes plus classiques empruntées aux domaines de l'analyse numérique et de la turbulence. Cette études se décompose en 3 parties, et plusieurs annexes. Les matériels et méthodes sont présentés dans la première partie. Dans la seconde partie, la méthode EMD nous a permis de mettre en avant les fortes fluctuations contenues dans les blooms, ainsi que de mener des analyses spectrales grâce à un couplage avec la transformée de Hilbert. L'analyse en composante principale (ACP) a mis en avant les principaux forçages exercés sur la production primaire et les profils de température SOMLIT laissent supposer un impact de la stratification sur l'intensité des blooms. Dans la troisième partie, nous avons mené une étude comparative entre les données basses fréquences et hautes fréquences. Et deux méthodes de cross-corrélation (TDIC et co-spectre) nous ont permis de définir une échelle caractéristique de transition entre les températures de la Manche occidentale et orientale. En annexe, nous avons testé la robustesse de différentes méthodes d'analyses spectrales quant au manque de données dans les séries temporelles, qui est un problème inhérent aux bases de données enregistrées par des systèmes automatisés, et nous avons reproduit un article qui est en cours de soumission. / The main objective of this thesis is the characterization of high frequency dynamics in coastal areas and in particular their extremes, through the study of long-term biodeochemical time series registered by automated systems. The majority of high-frequency data sets used in this study came from MAREL program. The low-frequency time series from coastal monitoring programs SOMLIT (CNRS, INSU) and SRN (Ifremer) are employed to support the importance of automated systems. The EMD (Empirical Mode decomposition) method has provided a basis for us to study several of these time series. We also have used some methods more classical borrowed from numerical analysis field and turbulence. This study is organized in three chapters, and several appendices. The first chapter is devoted to the material and method. In the second chapter, using the EMD method we have highlighted the strong fluctuations contained in the blooms, and we have performed spectral analyzes. The principal component analysis (PCA) highlighted the main forcing exerted on primary production and SOMLIT temperature profiles suggest an impact of stratification on the intensity of blooms. In the third chapter, we conducted a comparative study between low-frequency and high-frequency data. Two cross-correlation methods (TDIC and co-spectra) allowed us to define a characteristic transition scale between the temperatures of the western and eastern English Cahnnel. In appendices we tested the robustness of different spectral analysis methods about the missing data in the time series, which is an underlying problem in the database registered by automated systems, and we reproduce a paper, which is under submission.