Rozprawy doktorskie na temat „Estuarine systems”

Les estuaires sont constitués d'une vaste mosaïque d'habitats naturels et semi-naturels. L'objectif de cette thèse est d'étudier les végétations et les paysages végétaux des systèmes estuariens atlantique en France, en essayant de comprendre le fonctionnement et les schémas de distribution des différentes unités de végétation. La présente étude tente de mettre au point un modèle théorique commun de fonctionnement et de gradients écologiques, afin de compléter la classification et la connaissance écologique des estuaires, et une aide au suivi et à l’évaluation de l’utilisation des sols, des impacts humains, en développant un modèle spatio-temporel prédictif fondé sur la végétation réelle et potentielle, et en utilisant l'approche dynamico-caténale. Dans 8 estuaires sélectionnés, nous avons effectué des travaux sur le terrain pour une superficie totale de 98 318 ha, mettant en évidence 2 séries de végétation et 4 géopermaséries, correspondant à 131 associations végétales, 60 alliances, 43 ordres et 28 classes. Nous avons cartographié la végétation de trois estuaires représentatifs, ce qui représente une superficie totale de 74 433 ha. Un schéma synthétique des paysages végétaux estuariens est proposé, en intégrant les gradients géographiques et écologiques et les formes géomorphologiques
Estuaries generally include a wide mosaic of natural and semi-natural habitats. The objective of this thesis is to study the vegetation and Plant Landscape of French Atlantic estuarine Systems, trying to understand the functioning and the plant distribution patterns. The present study tries to carry out a theoretical common model of functioning and ecological gradients, in order to make a basis to improve their classification and ecological studies, and to Help the monitoring and assessment of land uses, land forms transformation and human impacts : developping a spatio-temporal predictive model based on actual and potential vegetation, using the dynamico-catenal approach.The study area corresponds to the Atlantic French estuaries. In 8 selected estuaries, we undertook fieldworks for a total of 98315 ha, highlighting 2 vegetation series and 4 geopermaseries, corresponding to 131 plant associations, 60 alliances, 43 ordos and 28 classes. We mapped the vegetation of three representative estuaries for a total of 74433 ha. A synthetic scheme of estuary vegetation landscape is proposed, integrating geographical and ecological gradients as well as geomorphologic forms

This thesis describes methodologies to detemiine organic and inorganic phosphorus in water and discusses biological, physical and chemical controls on the transformations of organic and inorganic phosphorus in laboratory microcosms of estuarine particle-water systems. Phosphorus is an important nutrient and the accurate determination of phosphorus species in natural waters is essential for understanding the biogeochemical cycling of the element. Chapter one reviews phosphorus impacts on water quality and relevant UK legislation, the sources, speclation and fractionation of phosphorus, the sediment/water phosphorus cycle and analytical methods for the determination of dissolved Inorganic phosphorus (DIP) and organic phosphorus (DOP) species In natural waters. Chapter two introduces the technique of segmented flow analysis and describes methods for the determination of inorganic phosphorus and total dissolved phosphorus after autoclaving. Segmented flow analysis is suitable for determining inorganic P and organic P species in freshwaters in the range of 1 - 300 pg P L"\ Calibrations were linear (R^ > 0.997) over the range 0.5 - 100 pg P L'^ with good precision (RSDs < 3 %). The LCD was 0.4 pg P L'^ for DIP and 3 pg P L'^ for DOP. The recoveries of 7 model organic phosphorus compounds (adenosine-5-triphosphate di-sodium salt (ATP), phytic acid (PTA), sodium tripolyphosphate (STP), methyltriphenylphosphonium bromide (MPT), p-nitrophenyl phosphate magnesium salt (p-NPP), p-D-glucose-6-phosphate monosodium salt (G-6-P) and cocartjoxylase (COCA)) were all > 90 %. Chapter three reports on bacterial uptake studies of phosphorus species in a plug-flow microcosm. Experiments using inert Duran and Siran beads as supports for bacterial bioflim development showed similar P uptake behaviour. Glucose-6-phosphate was almost fully utilised and converted to DIP after 3 days suggesting that labile organic phosphorus species could be a bioavailable source of P for bacteria. Phytic acid (a refractory P compound) released significant concentrations of DIP to the water column due to physical displacement. Chapter four describes phosphonjs transformations in a sediment-water flume due to turbulent resuspension events. The released DIP concentration had a strong linear relationship with shear stress in pure water and artiflcial seawater. However, no signtflcant relationship between DOP release and shear stress was observed. The sediment type and the water matrix significantly affected the magnitude of DIP and DOP release to the water column. Chapter flve extends the investigation of P exchange to constant resuspension events. The water matrix had a significant effect on the rate of DIP and DOP release from sediment and the sedimentAvaler equilibration time. Typically 6 - 12 % of total phosphorus in the sediment was released as DIP and DOP into the water column. When orthophosphate and phytic acid were added to both UHP and river water. SPM was able to buiffer theses additions. However, the SPM buffering capacity was much lower for G-6-P. The buffering capacity of the SPM for phytic acid was significant and permanent in UHP and biotic river water, whereas phytic acid was cycled in the abiotic experiments.

Doutoramento em Ciências do Mar
De um modo geral, os poluentes constituem uma ameaça para os ecossistemas aquáticos, originando grande preocupação nas entidades responsáveis pela gestão destas áreas. Por exemplo, o uso intensivo e continuado de poluentes em áreas agrícolas, perto de zonas húmidas costeiras, como o estuário do Mondego (Portugal), levou à execução de programas de monitorização, ao longo dos últimos 20 anos, para proteger e recuperar este sistema aquático. De acordo com informações recentes, obtidas junto de cooperativas agrícolas do vale do Mondego, Primextra® Gold TZ é o herbicida mais utilizado em campos de cultura de milho, sendo um dos 20 herbicidas mais vendidos em Portugal. Por outro lado, o cobre é largamente utilizado na formulação de pesticidas. A avaliação ecológica e de risco têm sido rotineiramente focadas na exposição individual de substâncias químicas, o que pode subestimar os riscos associados à ação tóxica de misturas. Assim, os potenciais efeitos sinergísticos, que podem levar a consequências mais graves e imprevisíveis para os ecossistemas estuarinos e marinhos, são subestimados. Apesar do recente aumento do número de estudos relacionados com a toxicidade de misturas de contaminantes orgânicos (grupo de pesticidas) e de contaminantes inorgânicos (grupo de metais), há ainda falta de informação científica sobre os efeitos destas misturas. A avaliação de risco ambiental normalmente tem como objetivo estudar os efeitos de contaminantes em endpoints, como a sobrevivência, o crescimento ou a reprodução, uma vez que a quantidade de biomassa disponível tem efeitos importantes sobre os níveis tróficos subsequentes e o funcionamento global do ecossistema. No entanto, um aspeto muitas vezes esquecido é a qualidade do alimento disponível, que tem implicações importantes na transferência de energia e de nutrientes ao longo da cadeia trófica. Portanto, para melhor compreender os efeitos das perturbações antrópicas, são necessários mais estudos sobre o efeito de mistura de substâncias orgânica-inorgânica na qualidade do alimento de espécies aquáticas não-alvo. Assim, este trabalho visa determinar os efeitos do herbicida Primextra® e do cobre, usados individualmente e em mistura, sobre a qualidade alimentar em sistemas estuarinos, considerando as respostas populacionais e bioquímicas nutricionais de organismos chave não-alvo: a diatomácea marinha (Thalassiosira weissflogii) e o copépode estuarino calanoide (Acartia tonsa). As diatomáceas como os copépodes são grupos dominantes na comunidade planctónica no estuário do Mondego, constituindo uma cadeia trófica simples: produtor primário –consumidor primário. Foram também usados náuplios de uma terceira espécie (Artemia franciscana) para determinar os efeitos tóxicos e bioquímicos individuais de ambos os poluentes e para comparar as suas respostas com as das outras duas espécies planctónicas Para isso foram desenvolvidos ensaios de toxicidade, envolvendo exposições a substâncias químicas individuais e a misturas equitóxicas, para obtenção e modelação de dados bioquímicos indicadores da qualidade alimentar: teor de ácidos gordos (FA), incluindo ácidos gordos essenciais, teor de proteína e teor de substâncias reativas de ácido tiobarbitúrico (TBARS). Esta escolha baseou-se no facto dos ácidos gordos serem uma das mais importantes moléculas transferidas através da cadeia trófica, em teias alimentares aquáticas, podendo ser usados como um bom indicador de stress. Os resultados mostraram que T. weissflogii foi a espécie mais sensível ao herbicida seguida por A. tonsa (CE50 = 0,008 mg / L e CE50 = 0,925 mg / L, respetivamente), enquanto o copépode foi a espécie mais sensível ao metal, seguido por T. weissflogii (CE50 = 0,234 mg / L e CE50 = 0,383 mg / L, respetivamente). A análise estatística dos efeitos da mistura metal-herbicida sustentou um efeito sinergístico significativo sobre a sobrevivência do copépode (relativamente ao modelo de ação independente), e um efeito significativamente antagonístico sobre o crescimento da diatomácea (relativamente ao modelo de adição de concentração). A composição em ácidos gordos das espécies zooplanctónicas respondeu com elevada sensibilidade aos dois tipos de exposição (individual e de mistura),tendo-se observado o efeito mais nocivo na concentração de ácidos gordos essenciais de A. tonsa após a exposição à mistura de metal-herbicida: o seu valor diminuiu significativamente (5 vezes) em comparação com o controlo. Os resultados dos modelos lineares generalizados, baseados na variação da composição bioquímica (total de FA, FA essenciais, teor de proteína e TBARS), para as substâncias individuais e para a mistura, revelaram que os efeitos desta foram não-aditivos, para o conteúdo de FA essenciais de ambas as espécies planctónicas. Já a qualidade alimentar de A. tonsa (consumidor primário) foi mais sensível aos stressors químicos comparativamente a T. weissflogii (produtor), quando as duas espécies foram expostas a níveis iguais de contaminação. O presente estudo sugere que a exposição simultânea a um metal e a um herbicida pode afetar negativamente a qualidade alimentar de espécies planctónicas, em diferentes níveis tróficos. Esse efeito pode, potencialmente, ser transferido para níveis tróficos superiores e causar alterações importantes no fluxo de energia através do sistema estuarino e, posteriormente, para a dieta humana.
Contaminants constitute a threat to aquatic communities and, thus to aquatic ecosystems. Pesticides are widely used to control pests and diseases in crop production. Among these agrochemicals, herbicides are commonly applied on crops to control adventive infestations. Thus, the intensive usage of pollutants in agriculture areas near ecological coastal wetlands led to the implementation of the Pesticide-Monitoring programs to recover aquatic systems, such as in the Mondego estuary, Portugal, since 1998. Nowadays, and according to the information from agricultural cooperatives of Mondego valley, the herbicide Primextra® Gold TZ is the herbicide most used in corn crops fields and is one of the 20 best-selling herbicides in Portugal, whereas copper is mainly used in pesticide`s formulation. Traditional effect and risk assessment have been routinely focused on exposures to single chemicals, which may underestimate the risks associated with toxic action of mixtures. Thus, the potential synergistic effects that may lead to more severe and unpredictable consequences for estuarine and marine ecosystems are ignored. Recently, there are an increasing number of studies dealing with toxicity of mixtures of either organic contaminants (group of pesticides) or inorganic contaminants (group of metals). However, studies with mixture experiments of metals and pesticides still remain scarce. Furthermore, environmental risk assessment typically aims to study the effects of contaminants on endpoints such as survival, growth or reproduction, since the available quantity of the biomass has important effects on the subsequent trophic levels and the overall ecosystem functioning. However, an often overlooked aspect of food availability is food quality, which has important implications on the energy and nutrient transfer through the food web. Further information about the effect of organic-inorganic mixture on the food quality of aquatic organisms, which are typical non-target species for these contaminants, is needed. This research aims to determine the effects of anthropogenic stressors on the food quality in estuarine systems by means of both, individual and mixture exposures, to the herbicide Primextra® and the metal copper, on the toxicity and nutritionally important biochemical parameters of key non-target organisms: a marine diatom (e.g. Thalassiosira weissflogii) and a estuarine calanoid copepod (e.g. Acartia tonsa) – both are dominant plankton groups in the Mondego estuary, constituting simple trophic food chain: primary producer – primary consumer. A third species, the brine shrimp Artemia franciscana (nauplii), was also added to the study to determine toxic and biochemical individual effects of both pollutants and to compare its response with the two other planktonic species. In this study a joint approach was applied, i.e. controlled laboratory experiments (toxicity tests and microcosm bioassays), involving single and equitoxic mixture exposures to chemical stressors combined with the further modelling of the obtained biochemical data: fatty acids (FA) content, including the essential FA, protein content and content of thiobarbituric acid reacting substances (TBARS) as important indicators of the food quality. Moreover, fatty acids are one of the most important molecules transferred across the plant-animal interface in aquatic food webs and can be used as good indicators of stress. The conducted lab incubations showed that T. weissflogii was the most sensitive species to the herbicide followed by A. tonsa (EC50 = 0.008 mg/L and EC50 = 0.925 mg/L, respectively), whereas the copepod was the most sensitive species to the metal in comparison to T. weissflogii (EC50 = 0.234 mg/L and EC50 = 0.383 mg/L, respectively). The statistical analysis of mixture effects revealed that the metal-herbicide mixture acted significantly synergistic on the copepod survival (relatively to the independent action model), while acted significantly antagonistic on the diatom growth (relatively to the concentration addition model). FA composition of zooplanktonic species responded with higher sensitivity to both, the individual and mixture exposures with the most harmful effect on the essential FA of A. tonsa after exposure to the metal-herbicide mixture: their amount significantly decreased (5 times) compared to the uncontaminated treatment. The results of the generalized linear models fitted to the experimentally observed responses of biochemical composition (total FA, essential FA, protein and TBARS contents) to the single substances and the mixture revealed that effects of the copper-Primextra® mixture were non-additive for the essential FA content of both planktonic species. They further showed that the food quality of the species from higher trophic level, i.e. primary consumer A. tonsa was more sensitive to the chemical stressors than for the primary producer T. weissflogii, when species were exposed to the equal levels of contamination. The study concludes that simultaneous exposure to metal and pesticide contaminants adversely affect the food quality of planktonic species at different trophic levels and this can potentially be transferred to higher trophic levels and cause important implications for the energy flow through the estuarine system and subsequently the human diet.
Verontreinigingen vormen een bedreiging voor in het water levende gemeenschappen en daarom ook voor aquatische ecosystemen. Pesticiden worden op grote schaal gebruikt om ziekten en plagen in de plantaardige productie te controleren. Onder deze landbouwchemicaliën, worden herbiciden vaak toegepast op gewassen om adventive besmettingen te controleren. Zo heeft het intensief gebruik van verontreinigende stoffen in landbouwgebieden in de buurt van ecologische wetlands geleid tot de uitvoering van Pesticide-Monitoring-programma's sinds 1998 om aquatische systemen, zoals in het Mondego estuarium (Portugal) te herstellen. Op basis van de huidige informatie uit agrarische coöperaties van de Mondego-vallei blijkt dat de herbicide Primextra® Gold TZ de meest gebruikte herbicide is in maïsvelden en dat het één van de 20 best verkopende herbiciden in Portugal is waarbij koper het voornaamste element van de samenstelling vormt. Traditionele effect- en risicobeoordeling zijn routinematig gericht op blootstelling aan enkele chemische stoffen, die de risico's van de toxische werking van mengsels kunnen onderschatten. Zo worden de potentiële synergetische effecten die kunnen leiden tot meer ernstige en onvoorspelbare gevolgen voor estuariene en mariene ecosystemen genegeerd. Recent zijn er een toenemend aantal studies gebeurd die toxiciteit van mengsels van ofwel organische verontreinigingen (groep pesticiden) of anorganische verontreinigingen (groep metalen) onderzoeken. Studies met mengselexperimenten van metalen en pesticiden zijn nog steeds schaars. Bovendien heeft milieurisicobeoordeling typisch tot doel om de effecten van contaminanten op eindpunten zoals overleving, groei of reproductie te bestuderen, omdat de beschikbare hoeveelheid biomassa belangrijke gevolgen heeft voor de hogere trofische niveaus en het algemeen functioneren van het ecosysteem. Echter, een vaak vergeten aspect van de voedselbeschikbaarheid is de kwaliteit van het voedsel, wat belangrijke gevolgen kan hebben voor de energie- en voedingsstoffenoverdracht in de voedselketen. Verdere informatie over het effect van de organische-anorganische mengsel op de voedselkwaliteit van het aquatische organismen, die vaak geen doelsoorten voor deze verontreinigingen zijn, is daarom noodzakelijk. Dit onderzoek heeft tot doel de effecten van antropogene stressoren op de voedselkwaliteit in estuariene systemen te bepalen door middel van blootstelling aan zowel individuele concentraties als mengsels van herbicide Primextra® en het metaal koper, op de toxiciteit en de nutritioneel relevante biochemische parameters van belangrijke non-target organismen: een mariene diatomee (bijv Thalassiosira weissflogii) en een estuariene calanoid copepod (bijv Acartia tonsa) - beide zijn één van de belangrijkste planktongroepen in de Mondego estuarium, die een eenvoudig trofische voedselketen voorstellen tussen primaire producent en primaire consument. Een derde soort, (de nauplii van) Artemia franciscana, werd ook toegevoegd aan de studie om de toxische en biochemische individuele effecten van beide polluenten te bepalen en om zijn respons te vergelijken met de twee andere planktonsoorten. In deze studie werd een gezamenlijke aanpak toegepast waanbij laboratoriumexperimenten (toxiciteitstesten en microcosmos bioassays), met blootstelling aan één of aan een equitoxische mengsel van chemische stressoren, werden gecombineerd met het verder modellering van de verkregen biochemische data: vetzuren, met bijzondere aandacht voor essentiële vetzuren, eiwitgehalte en de inhoud van thiobarbituurzuur reagerende stoffen (TBARS) als belangrijke indicatoren voor voedselkwaliteit. Daarenboven zijn vetzuren één van de belangrijkste moleculen overgedragen aan de plant-dier interface in aquatische voedselwebben en kunnen ze gebruikt worden als goede indicatoren van stress. De uitgevoerde labincubaties toonden dat T. weissflogii de meest gevoelige soort was voor de herbicide gevolgd door A. tonsa (EC50 = 0.008 mg / L en EC50 = 0.925 mg / L, respectievelijk), terwijl de copepoden het meest gevoelig waren voor het metaal tenopzichte van T. weissflogii (EC50 = 0.234 mg / L en EC50 = 0.383 mg / L respectievelijk). De statistische analyse van mengseleffecten bewees dat het metaal-herbicide mengsel significant synergistisch werkte op de overleving van de copepoden (ten opzichte van de onafhankelijke actiemodel), terwijl significante antagonistische effecten op de diatomeeëngroei optraden (ten opzichte van de concentratieadditiemodel). FA samenstelling van de zooplanktonische soorten reageerde met een hogere gevoeligheid op beide, individuele en mengsel, blootstellingen met de meest schadelijke gevolgen voor de essentiële vetzuren van A. tonsa na blootstelling aan het metaal-herbicide mengsel: de vetzuurconcentratie daalde aanzienlijk (tot 5 maal) ten opzichte van de onbesmette behandeling. De resultaten van de gegeneraliseerde lineaire modellen toegepast op de experimenteel waargenomen responsen van biochemische samenstelling (totale vetzuren, essentiële vetzuren, eiwit- en TBARS concentraties) tenopzichte van de afzonderlijke stoffen en van het mengsel toonden aan dat effecten van het koper-Primextra® mengsel niet additief waren voor de concentratie van de essentiële vetzuren van beide planktonische soorten. Verder bleek de voedselkwaliteit van de soort op het hoger trofisch niveau, namelijk de primaire consument A. tonsa, gevoeliger te zijn voor de chemische stressoren dan de primaire producent T. weissflogii, wanneer soorten werden blootgesteld aan gelijke verontreinigingsniveaus. De studie concludeert dat gelijktijdige blootstelling aan metalen en pesticiden verontreinigingen een negatieve invloed heeft op de voedselkwaliteit van planktonische soorten op verschillende trofische niveaus en dit kan mogelijk worden overgedragen naar hogere trofische niveaus met belangrijke gevolgen voor de energiestroom door het estuariene systeem en vervolgens ook voor het menselijke dieet.

The knowledge and understanding of sediment transport is essential for the development of effective management strategies for nutrient and sediment loading in estuarine systems. Estuarine suspended sediment (in high concentrations), has the ability to adversely impact upon surrounding ecosystems, such as the Great Barrier Reef, Australia. Due to a recent decline in water and sediment quality, it has recently been mandated that a number of tropical, coastal estuarine systems in Queensland, such as the Fitzroy River estuary, have their sediment loading reduced. In order to meet these requirements, a greater understanding of the sediment transport dynamics and driving processes (such as flocculation and settling velocity) needs to be achieved, and the accuracy of estimation improved. This research project was motivated by the need to improve the general accuracy of field measurements for estuarine suspended sediment transport and dynamics. Field-based measurements (especially settling velocity) are necessary for the parameterisation of sediment transport models. The difficulty in obtaining accurate, in situ data is well documented and is generally limited to methods that isolate a water sample from its natural environment, removing all influences of estuarine turbulence. Furthermore, the water samples are often extracted from points (Eulerian) where the history of the suspended particles is generally unknown. These sampling methods typically contain intrinsic errors as suspended sediment transport is essentially Lagrangian (i.e., flows with the net motion of flow-field) in nature. An investigation into different drogue systems conducted in parallel with a study into the tidal states of the Fitzroy River estuary led to the development of a novel Lagrangian drogue device, the LAD. Additionally, the water-tracking ability of the LAD was tested and found to accurately follow a parcel of estuarine water over a slack water period. Therefore the LAD was deployed in the Fitzroy River to assist in the further understanding of complex sediment transport processes such as flocculation and settling velocity in a natural estuarine flow field. The final device (the LAD - Lagrangian Acoustic Drogue) was developed, utilizing the principals of acoustic backscatter intensity-derived SSC measurements. The investigation of a series LAD deployments (during slack water) in the Fitzroy River estuary, revealed the dominant suspended sediment processes and also gave an insight into the prevailing flow-patterns. Results showed the presence of a settling lag mechanism between low and high tide, which can initiate a net sediment flow upstream with each flood tide. The bulk settling velocity showed comparable results at both low and high water. The LAD derived bulk settling velocity as a function of concentration (SSC), yielding a strong positive correlation (r2 = 0.73). Also the importance of flocculation in the bulk settling and clear up of the water column during periods of still water (high and low tide) was demonstrated as all in situ settling velocities (0.33 - 1.75 mm s-1) exceeded single grain approximations (0.47 mm s-1). This research demonstrates the potential for Lagrangian drogue studies as an effective measuring platform for the accurate quantification of estuarine suspended sediment dynamics. The application of the LAD in the Fitzroy River has lead to a significant improvement in the understanding of the system's real sediment transport processes. This research has provided an effective and accurate technique for measuring real settling velocities for input into numerical models or for the validation of existing model outputs. Furthermore, this technique shows great potential for application in other estuarine systems.

The knowledge and understanding of sediment transport is essential for the development of effective management strategies for nutrient and sediment loading in estuarine systems. Estuarine suspended sediment (in high concentrations), has the ability to adversely impact upon surrounding ecosystems, such as the Great Barrier Reef, Australia. Due to a recent decline in water and sediment quality, it has recently been mandated that a number of tropical, coastal estuarine systems in Queensland, such as the Fitzroy River estuary, have their sediment loading reduced. In order to meet these requirements, a greater understanding of the sediment transport dynamics and driving processes (such as flocculation and settling velocity) needs to be achieved, and the accuracy of estimation improved. This research project was motivated by the need to improve the general accuracy of field measurements for estuarine suspended sediment transport and dynamics. Field-based measurements (especially settling velocity) are necessary for the parameterisation of sediment transport models. The difficulty in obtaining accurate, in situ data is well documented and is generally limited to methods that isolate a water sample from its natural environment, removing all influences of estuarine turbulence. Furthermore, the water samples are often extracted from points (Eulerian) where the history of the suspended particles is generally unknown. These sampling methods typically contain intrinsic errors as suspended sediment transport is essentially Lagrangian (i.e., flows with the net motion of flow-field) in nature. An investigation into different drogue systems conducted in parallel with a study into the tidal states of the Fitzroy River estuary led to the development of a novel Lagrangian drogue device, the LAD. Additionally, the water-tracking ability of the LAD was tested and found to accurately follow a parcel of estuarine water over a slack water period. Therefore the LAD was deployed in the Fitzroy River to assist in the further understanding of complex sediment transport processes such as flocculation and settling velocity in a natural estuarine flow field. The final device (the LAD - Lagrangian Acoustic Drogue) was developed, utilizing the principals of acoustic backscatter intensity-derived SSC measurements. The investigation of a series LAD deployments (during slack water) in the Fitzroy River estuary, revealed the dominant suspended sediment processes and also gave an insight into the prevailing flow-patterns. Results showed the presence of a settling lag mechanism between low and high tide, which can initiate a net sediment flow upstream with each flood tide. The bulk settling velocity showed comparable results at both low and high water. The LAD derived bulk settling velocity as a function of concentration (SSC), yielding a strong positive correlation (r2 = 0.73). Also the importance of flocculation in the bulk settling and clear up of the water column during periods of still water (high and low tide) was demonstrated as all in situ settling velocities (0.33 - 1.75 mm s-1) exceeded single grain approximations (0.47 mm s-1). This research demonstrates the potential for Lagrangian drogue studies as an effective measuring platform for the accurate quantification of estuarine suspended sediment dynamics. The application of the LAD in the Fitzroy River has lead to a significant improvement in the understanding of the system's real sediment transport processes. This research has provided an effective and accurate technique for measuring real settling velocities for input into numerical models or for the validation of existing model outputs. Furthermore, this technique shows great potential for application in other estuarine systems.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Engineering
Full Text

In recent years there has been an increasing awareness of the role and benefits of scientific fish farming in coastal waters for augmenting fish production of India, although a traditional practice of aquaculture has been prevailing in these waters for a long time. A comprehensive knowledge of the ecology of the different culture systems forms an integral part of the scientific farming because it directly influences the rate of production. The growth and survival of the organisms used for culture depend largely on the overall productivity of the pond, which in turn, is influenced by the various environmental characteristics of the water and the fertility of the pond soil. In short, the water and soil conditions to a great extent determine the success or failure of the culture operation. Further, the information on the various environmental characteristics of the pond water and soil, availability of essential elements and the rate of organic productivity, would not only help to adopt successful management principles and culture techniques but also to manipulate the ecosystem providing the necessary inputs for obtaining better production. Besides providing an overall picture of the productivity of the ponds, studies on soils furnish information on the inputs to enhance the fertility of soils and also help in selection of suitable sites for construction of farms.

Dissolved and suspended particulate organic carbon (DOC, POC), nitrogen (DON, PON), phosphorus (DOP, POP) and inorganic nutrient distributions and elemental ratios were measured and evaluated for the Atlantic, Southern, and Pacific Oceans. Results indicate that DOC is remineralized during mean deep-water transport from the North Atlantic to the North Pacific. Elemental ratios for both dissolved organic matter (DOM) and particulate organic matter (POM) indicate that organic N is preferentially remineralized compared with organic C, while organic P is preferentialy remineralized relative to both organic C and N. Comparison between the DOM and POM pools further suggests that surface POM may be less refractory than concurrently sampled DOM. Major compound class compositions of ultrafiltered DOM (UDOM) in the North Atlantic, North Pacific and Chesapeake Bay indicate that the majority of UDOM was comprised mainly of a molecularly-uncharacterized fraction, followed by carbohydrates, proteins and lipids. Delta14C and delta 13C results of UDOM compound classes suggest that UDOM in Bay mouth and surface open ocean waters were similarly dominated by old, marine sources, while UDOM from the freshwater endmember was influenced by much younger terrestrial sources. Results indicate that DOM is comprised of different aged organic fractions and provide evidence for a potential organic "size"-age continuum; from low-molecular weight DOM (oldest) to UDOM (intermediate age) to POM (youngest). Lipid biomarker results indicate that North Atlantic and Pacific UDOM and POM were relatively more reactive at the surface compared with greater depths, coinciding with elemental C:P and N:P ratios greater than Redfield. Factor analyses suggest that there exists a "lability continuum" spanning from surface ocean POM to riverine and deep ocean UDOM. Terrigenous organic material was found at all Bay sites although autochthonous sources of organic matter were also important. Dark microbial incubations of DOM from the Pacific Subtropical Front and South Atlantic Bight indicate that open ocean DOM is relatively refractory over short time scales (less than 2 months). Experiments with plankton leachate DOM show that this sub-pool of DOM is relatively labile and is converted to refractory DOM within days. DOP is preferentially remineralized in all experiments compared with DOC or DON.

To investigate the relationship between biological and physical mixing in forming strata, the lower mainstem of Chesapeake Bay has been contrasted with the York River Subestuary. By using radioisotope profiles from sediment cores, comparisons are made in terms of depth and rate of sediment mixing, deposition and accretion. Within the lower Chesapeake Bay two sites were selected as biologically dominated, both are located within the bay stem plains and are characterized by muddy sand and an abundance of large, deep-dwelling organisms. X-radiographs indicate complete biological reworking of sediments. 210Pb profiles reveal low sediment accretion rates within the mainstem sites (<0.1 cm y-1), but significant differences in biological mixing depths (25 vs 40 cm) and biodiffusivity (>80 vs 6--30 cm3 y-1). Within the upper York River, transient, longitudinal erosional furrows regularly form within a broad flat secondary channel. Varying furrow morphologies were observed depending on tidal flow, ranging from: (1) no bedforms during the higher flow conditions such as spring tide; to (2) large patches of meandering furrows as the mean flow decreases; to (3) large, variably spaced (5--7 m) linear furrows during the lowest mean current conditions of neap tide. A 35 month time series using kasten cores reveals that along with ∼ 25 cm differences in mixing depths due to the fortnightly time formation and destruction of furrows, a ∼ 100 cm depth scale signal of mixing exists annual to interannual time frame which is unrelated to the formation of erosional furrows. Throughout much of the energetic microtidal York River, the seabed is characterized by deep physical mixing (25--200 cm). A strong cross-estuary gradient is observed with one side, including channel, flank and shoal, dominated by frequent deep erosion and re-deposition (physical mixing), while physical mixing is reduced on the other side resulting in a greater preservation of biological mixing. Within the physically dominated side of the river, the mixed layer is characterized by 210Pb profiles with one or more segments ( ∼ 25--100 cm thick) of nearly uniform excess activity. X-radiographs reveal that the mixed layer consists of centimeter to decimeter scale units of finely to coarsely laminated strata bounded by hiatal surfaces, indicative of physical mixing. The physical mixing results in an impoverishment benthic community which is composed primarily of small, opportunistic species. Mixing in the biologically dominated side of the river is generally shallow (<40 cm), with low 210Pb biodiffusion rates (0.43--3.35 cm 2 y-1). 210Pb based particle residence time within the mixed layer are on the order of centuries. Estimates of the sediment mass in the physically mixed layer is equivalent to ∼ 70 years of river sediment yield, this is consistent with century-scale residence times. Although sediment mixing within the Lower Chesapeake Bay is controlled by biological processes and sediment mixing in much of the York River is controlled by physical processes, in both places particle residence times in the seabed are generally on the century time-frame. However, when considering the cycling of pore-water nutrients, organic matter and particle bound contaminants, the type of seabed mixing is as important as the particle residence time in determining the ultimate fate and fluxes of these constituents.

The utilisation of estuary headwater environments by young estuary- and marine-spawned fish species was investigated together with the effects of riverflow alteration, in-stream barrier effects and non-native ichthyofauna on the nursery function of these habitats. The distribution and abundance of young estuary- and marine-spawned fish were sampled using seine and fyke nets in the headwater environments of four permanently open Eastern Cape systems, namely the Great Fish, Kowie, Kariega and Sundays Estuaries. Within the suite of study systems, the first of two case studies focussed on barrier effects of in-stream structures on fish migration. This was undertaken in the Sundays River. In the second case study, predation and competition dynamics of the non-native piscivorous Micropterus salmoides on estuary-dependent fish was investigated in the estuary headwater regions of the Kowie River system. In all four estuaries, young estuary-spawned fish species dominated the ichthyofaunal community followed by marine-spawned species, despite varied freshwater inflow resulting in headwaters varying in salinity from fresh to hypersaline. Fish community structure however, differed largely between estuaries, with both freshwater abstraction and unnatural elevation of freshwater into estuaries, as a result of inter-basin transfers, affecting these communities. In-stream structures were found to effect upstream movement of fish in two ways, dependent on the type of barrier. Partial (size-dependent) and complete (species-dependent) restriction to upstream migration of fish by causeway-type instream structures were observed. Weir-type in-stream structures acted as a complete barrier to most species, regardless of fish size. Predation of estuary- and marine-spawned fish species by large sized M. salmoides was recorded, although these fish did not contribute significantly to their diet during this study. However, the main dietary components found in smaller sized M. salmoides stomachs overlap with those of juvenile estuary- and marinespawned fish species, suggesting feeding competition between the juveniles of indigenous and non-native fish species.

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Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES
Fish communities in developing countries have, in many cases, showed a decrease in the species richness and abundance over time as a result of anthropogenic impacts. We analyzed fish communities of three zones (inner, middle and outer) of the Sepetiba Bay (Southeastern Brazil) using identical sampling methods (bottom trawl) during four different time periods: 1987?1988; 1993?1995; 1998?2001 and 2012?2013. A total of 33,140 fish representing 127 species in 88 genera and 41 families were recorded. Our results revealed highly significant and consistent differences in the fish community structure among the bay zones, and a decreased in the fish richness and abundance over the time period. Changes in fish richness and abundance were related mostly to a sharp decrease that occurred in the inner bay zone, the most impacted bay area, and, to a lesser extent, in the middle zone between the two first (1987?1988 and 1993?1995) and the two latter time periods (1998?2001 and 2012?2013), whereas the outer zone remained comparatively stable over time. Spatial changes in the fish community structure among the bay zones were related to differences in salinity, transparency and depth with this latter variable, together with other factors, acting as a buffer for stabalizing community changes; however, these environmental variables explained little of the variation in the temporal changes. The most important changes over time in abundant species were the numerical decreases of the Ariid Cathorops spixii, the serranid Diplectrum radiale and sciaenid Cynoscion leiarchus, and increases of the sciaenid Micropogonias furnieri and the marine catfish Genidens genidens, with this latter species restricted to the inner and middle zones. This study adds long-term information on gradual fish community changes along spatial gradients of environmental and anthropogenic influences in embayment systems. It is perhaps timely to link conservation and management planning with historical information to protect fish biodiversity in tropical developing countries
As comunidades de peixes em pa?ses em desenvolvimento, em muitos casos, mostram uma diminui??o na riqueza e abund?ncia das esp?cies ao longo do tempo como resultado das evid?ncias dos impactos antropog?nicos. N?s analisamos as comunidades de peixes ao longo de tr?s zonas (interna, central e externa) da Ba?a de Sepetiba (Sudeste do Brasil), utilizando m?todos id?nticos de amostragem (bottom trawl) de peixes durante quatro per?odos temporais diferentes: 1987?1988; 1993?1995; 1998?2001 e 2012?2013. Registrou-se um total de 33.140 peixes representando 127 esp?cies em 88 g?neros e 41 fam?lias. Nossos resultados revelaram diferen?as altamente significativas e consistentes na estrutura da comunidade de peixes entre as zonas da ba?a e uma diminui??o na riqueza de esp?cies e abund?ncia ao longo do per?odo de estudo. As mudan?as na riqueza de esp?cies e abund?ncia foram relacionadas, principalmente, ? uma forte queda que ocorreu na zona interna da ba?a, ?rea esta mais afetada e, em menor medida, na zona central entre os dois primeiros (1987?1988 e 1993?1995) e os ?ltimos dois per?odos temporais (1998?2001 e 2012?2013), enquanto a zona exterior permaneceu relativamente est?vel ao longo do tempo. Mudan?as espaciais na estrutura da comunidade de peixes entre as zonas da ba?a foram relacionadas ?s diferen?as de salinidade, transpar?ncia e profundidade com este ?ltima vari?vel, em conjunto com outros fatores, atuando como um ?buffer? estabilizando mudan?as na comunidade; no entanto, essas vari?veis ambientais explicaram pouco a varia??o nas mudan?as temporais. As mudan?as mais importantes ao longo do tempo em esp?cies abundantes foi a diminui??o num?rica do Ariideo Cathorops spixii, do Serran?deo Diplectrum radiale e do Sciaen?deo Cynoscion leiarchus, e o aumento do Sciaen?deo Micropogonias furnieri e o bagre marinho Genidens genidens, com esta ?ltima esp?cie restrita ?s zonas interna e central. Este estudo acrescenta informa??o de longo prazo sobre mudan?as graduais nas comunidades de peixes ao longo de gradientes espaciais com influ?ncias ambientais e antr?picas no sistema de ba?a. Talvez seja oportuno vincular conserva??o e planejamento de gest?o com informa??es hist?ricas para proteger a biodiversidade de peixes em pa?ses tropicais em desenvolvimento.

A Formação Tombador, Mesoproterozoico, compreende diferentes sistemas deposicionais, depositados em um bacia sag, que abrangem desde sistemas aluviais a estuarinos. Os depósitos bem preservados e sua ampla ocorrência em escala regional (~300 km) faz com que a Formação Tombador seja um excelente caso de estudo no Proterozoico. Foram reconhecidas três sequências deposicionais, limitadas por superfícies erosivas em escala regional no topo da Formação Tombador. A Sequência I é composta na base por canais fluviais cascalhosos entrelaçados rasos, que são sotopostos por depósitos de dunas e lençóis de areia eólicos e inundações em lençol intermediário. O limite inferior desta sequência é caracterizado por uma discordância angular intra-Tombador sobre os sistemas fluvio-estuarinos, evidenciada por uma mudança abrupta de fácies e mudança nas paleocorrentes. Os sistemas fluvio-estuarinos abaixo da discordância apresentam paleocorrentes para noroeste enquanto que os sistemas fluviais acima do limite de sequências indicam um transporte para sul. Uma nova entrada abrupta de depósitos conglomeráticos relacionados a sistemas de leques aluviais sobre a sucessão fluvio-eólica, marca o limite da Sequência II. A Sequência III é caracterizada por sistemas fluvio-estuarinos na porção superior da Formação Tombador, que são progressivamente sucedidos por sistemas marinhos rasos (Formação Caboclo), definindo uma tendência geral transgressiva. As Sequências I e II refletem um soerguimento da área-fonte em resposta a movimentações tectônicas. A mudança abrupta de paleocorrentes dos fluviais basais da Sequência I indicam uma reestruturação regional das redes de drenagens, enquanto que os sistemas de leques aluviais da Sequência II sugerem sedimentos depositados por uma tectônica sin-deposicional. Os limites de sequências II e III é marcado por uma superfície erosiva regional. A discordâncias entre as sequências II e III revela um hiato significante no topo da Formação Tombador sugerindo uma origem tectônica para esta discordância.
The Mesoproterozoic Tombador Formation encompasses different depositional systems deposited in a sag basin, ranging from estuarine to alluvial. The well preserved deposits and their wide occurrence in the regional scale (~300 km) define the Tombador Formation as an excellent case study for the depositional patterns prevailing during the Proterozoic. Three depositional sequences were recognized for the Upper Tombador Formation, bounded by three semi-regional scale unconformities. Sequence I is composed of shallow, gravel-bed braided channels at its base, which are overlain by fine- to coarse-grained sandstones related to aeolian sand sheets and dunes and intermediate sheetfloods. The lower boundary of this sequence is characterized by an angular unconformity cutting fluvio-estuarine deposits, evidenced by an abrupt change of facies and fluvial palaeocurrents. The fluvio-estuarine deposits below the sequence boundary display palaeocurrents to northwest, whereas the fluvial strata above the unconformity show southeastward palaeocurrents. A new abrupt entrance of conglomeratic deposits related to alluvial fans systems overlying the fluvio-aeolian successions marks the lower boundary of Sequence II. The Sequence III is characterized by fluvio-estuarine systems in the top of the Upper Tombador Formation, that are progressively covered by shallow marine systems (Caboclo Formation), defining a general transgressive trend. The pattern of sequences I and II probably reflects the uplift of source areas in response to tectonic movements. The palaeocurrent change in Sequence I indicates a regional rearrangement of the drainage networks, while the alluvial fan systems of sequence II suggest sin-depositional tectonic pulses. The regional erosive surface between sequences II and III reveals a significant hiatus close to the Tombador Formation top, what suggests a tectonic origin for this unconformity.

Thesis (MEng)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: The Touw River estuary and Wilderness coastal lakes is a sensitive system from a flooding and ecological viewpoint and, therefore, careful consideration is placed on the hydrodynamics and salinity levels within the system. The estuary consists of a “temporary open/closed” estuary, where during closed mouth conditions, the sand bar at the estuary mouth is artificially managed in an attempt to reduce flood water levels in the system. The reason behind this management strategy is the construction of residential property along the flood plains of the estuary and coastal lakes, which in the past, had been exposed to regular cycles of inundation during flood events. In an attempt to reduce flood water levels in all water bodies and hence reduce the risk of inundation, a management policy was formulated. The past and present management plan is to maintain the sand bar at Touw estuary mouth, during closed mouth conditions, at an elevation of between +2.1m to +2.4m MSL, based on proposals made by the CSIR in 1981. Recent flood events, after the implementation of the management policy, still occasionally result in significant inundation of residential property, which has raised concern for some interested parties over the effectiveness of the management strategy. Furthermore, a growing concern was also evident over the long term wellbeing of the system from an ecological viewpoint. Historical data shows significant changes in salinity levels since the implementation of the management strategy which could impose negative long term effects on the system. In this study, numerical models were consequently constructed and applied in order to analyse the effectiveness of the current management policy and recalculate flood water levels under a number of proposed scenarios. Long term salinity changes were also analysed in an attempt to better understand salinity propagation throughout the system, using extreme hypothetical cases. Through the analysis of the simulation results, it was concluded that flood water levels in the Touw estuary were almost completely dependent on the size of the Touw River flood and the initial height of the sand bar at the estuary mouth. Whereas, water levels in the coastal lakes are almost entirely dependent on the quantity of runoff into the lakes and their initial water levels. The current management plan, involving only artificial manipulation of the sand bar at the estuary mouth, therefore has a fairly insignificant effect on flood water levels achieved in the coastal lakes. Furthermore, it was concluded that the construction of the preparatory channel is a vitally important aspect of the current management plan and that skimming of the sand bar alone is ineffective to completely mitigate the risk of residential inundation along the banks of the Touw River. The salinity modelling study provided a first indication of the salinity characteristics within the system. It was found that the penetration of seawater into the system was less prominent as the water bodies became further removed from the ocean and that a direct relationship was evident between the volume of direct freshwater inflow to a water body and the degree of salinity variation in that specific water body. In water bodies with high volumes of direct freshwater inflow such as the Touw estuary, a large degree of salinity variation is evident. However, in water bodies with no freshwater inflow, such as Rondevlei, salinity levels remain more stable and are less likely to fluctuate.
AFRIKAANSE OPSOMMING: Uit ‘n vloed- en ekologiese oogpunt is die Touwsriviermonding en Wilderniskusmere ‘n uiters sensitiewe stelsel en daar is dus deeglike oorweging gegee aan die hidrodinamika en soutvlakke in die stelsel. Die monding bestaan uit 'n "tydelike oop / geslote" monding, en tydens geslote mondtoestande word die sandbank by die riviermond kunsmatig beheer in 'n poging om vloedwatervlakke binne die stelsel te verminder. Die rede vir hierdie strategie is omdat baie residensiële eiendomme langs die vloedvlaktes van die monding en kusmere gebou is, wat in die verlede aan 'n gereelde siklus van oorstromings blootgestel is tydens vloede. In 'n poging om vloedwatervlakke in al die watermassas te verminder, en sodoende die risiko van oorstroming te verminder, is 'n bestuursbeleid geformuleer. In beide die vorige en die huidige bestuursplanne is die sandbank in die Touwsriviermond tydens geslote mondtoestande in stand gehou op 'n hoogte van tussen 2,1 m en 2,4 m MSL, gebaseer op die voorstelle wat deur die WNNR in 1981 gemaak is. Onlangse vloede wat plaasgevind het na die implementering van die beleid, het steeds van tyd tot tyd gelei tot noemenswaardige oorstromings van residensiële eiendomme, en kommer is uitgespreek deur 'n paar belanghebbende partye oor die doeltreffendheid van die strategie vir die bestuur. Daar is verder kommer uitgespreek oor die langtermyn welstand van die stelsel uit 'n ekologiese oogpunt. Historiese data toon 'n beduidende verandering in soutvlakke sedert die implementering van die bestuurstrategie met ‘n negatiewe langtermyn uitwerking op die stelsel. In hierdie studie is daar derhalwe numeriese modelle opgestel en toegepas ten einde die doeltreffendheid van die huidige bestuur van die beleid te bepaal, asook om die vloedvlakke te herbereken en te analiseer na aanleiding van 'n aantal voorgestelde scenario's. Langtermyn soutgehalte veranderinge is ook ontleed in 'n poging om die soutgehalte verspreiding deur die hele stelsel beter te verstaan, deur gebruik te maak van uiterste hipotetiese gevalle. Deur die ontleding van die simulasie resultate, is daar tot die gevolgtrekking gekom dat vloedwatervlakke in die Touwsrivier-monding byna heeltemal afhanklik was van die grootte van die Touwsrivier vloed en die aanvanklike hoogte van die sandbank by die riviermond. Watervlakke in die kusmere is egter byna heeltemal afhanklik van die hoeveelheid afloop na die mere en die aanvanklike watervlakke. Die huidige bestuursplan, wat slegs ‘n kunsmatige manipulasie van die sandbank by die riviermond behels, het dus 'n redelik onbeduidend invloed op die vloedwatervlakke wat in die kusmere bereik is. Daar is verder tot die gevolgtrekking gekom dat die konstruksie van die voorbereidende kanaal 'n uiters belangrike aspek van die huidige bestuursplan is, en dat die afskraping van die sandbank alleen oneffektief sou wees om die risiko van residensiële oorstroming langs die oewer van die Touwsrivier uit te skakel. Die soutgehalte modelleringstudie verskaf 'n eerste aanduiding van die soutgehalte eienskappe binne die stelsel. Daar is gevind dat die penetrasie van seewater in die stelsel minder prominent was as in die watermassas verder van die see af, en dat daar 'n duidelike direkte verband is tussen die volume van die varswater wat direk invloei na 'n watermassa en die mate van soutgehalte variasie in daardie spesifieke watermassa. In watermassas waar hoë volumes varswater direk invloei soos die Touwsrivier-monding, is 'n groot mate van soutgehalte variasie sigbaar. In die watermassas waar geen varswater invloei nie, soos die Rondevlei, bly soutvlakke meer stabiel en is minder geneig om te wissel.

Coastal flooding is a natural hazard causing devastation to many regions throughout the world, induced by the coincidence of high spring tides, large storm surges and waves. To reduce the risk posed by coastal inundation, warning systems have been developed to enable preparations to an expected threat. Although current operational predictions provide invaluable warnings, uncertainty in model formulations and input datasets, can lead to errors in forecasts. In order to provide coastal managers with the best possible information with which to make decisions, recent research has begun to focus on the movement from deterministic to probabilistic forecasting, which aims to explicitly account for uncertainty in the system. This research described the implementation of a regional tide-surge-wave model for the Solent-Southampton Water estuarine system, a region that is likely to experience increased risk of coastal flooding in the coming century. The accuracy of the model predictions were examined relative to in-situ measurements and those obtained from independent systems. Using the model, sources of error were examined and their effects upon the model predictions quantified, with particular reference made to the spatial variability throughout the region. In light of recent research, a probabilistic modelling approach, utilising a Monte Carlo technique used to provide a forecast capable of representing the uncertainty in the system, within a suitable time-frame for real-time flood forecasting that included an hourly Kalman filter data assimilation update. The findings presented in this thesis will be of interest to coastal modellers working in complex estuarine environments where the influences of tide-surge-wave interactions upon model predictions are uncertain. Furthermore, the application of a computationally efficient model, presented here, will provide a useful comparison with traditional physically-based systems to those wishing to quantify uncertainty in regions where computational resources are low

A região costeira do Brasil é historicamente impactada por atividades antrópicas, que liberam contaminantes, como os metais pesados. Nos estuários de Paranaguá (PR), Cananéia e Santos (SP), tais atividades estão presentes em diferentes níveis. Neste estudo foram investigadas as concentrações de arsênio, cádmio, chumbo, cobre, cromo, níquel, selênio, zinco e mercúrio, além de isótopos estáveis de carbono e nitrogênio, em sedimentos, fragmentos vegetais e organismos marinhos, como invertebrados bentônicos, peixes bentívoros e mamíferos marinhos, coletados nos três estuários. As amostragens foram realizadas em 2015, sendo as análises de isótopos realizadas por EA-IRMS e as análises de metais pesados realizadas por ICP OES-VGA e ICP-MS. As razões isotópicas permitiram a distinção entre fontes de matéria orgânica e nível trófico. Exemplares da ictiofauna e de cetáceos analisados não apresentaram distinção entre os níveis tróficos 3 e 4, indicando uma dieta generalista para estes animais e potencial compartilhamento de nicho trófico. Os metais apresentaram maiores concentrações nos sedimentos do estuário de Santos, coincidindo com o local com maior intensidade de atividades antrópicas. Comparando os estuários há maior acumulação de: Cr, Cu, Zn e Hg em Paranaguá, As e Pb em Cananéia, e Cd, Ni e Se em Santos, resultados justificados por atividades antrópicas, fontes naturais e características geoquímicas de cada região. A tendência de biomagnificação de Se foi observada nas teias tróficas de todos os estuários, e de Zn e Hg nas teias de Paranaguá e Cananéia. Entretanto, As, Cr, Cu, Ni e Pb demostraram tendência a biodiluição nas teias tróficas estudadas, com maior bioacumulação em invertebrados bentônicos. Portanto, este estudo traz um panorama atual da distribuição espacial e trófica de metais pesados nos estuários, colaborando com o monitoramento e ações de gestão costeira.
The coastal region of Brazil is historically impacted by anthropic activities, which release contaminants such as heavy metals. In the estuaries of Paranaguá (PR), Cananéia and Santos (SP), these activities are present in different levels. In the present study, concentrations of arsenic, cadmium, lead, copper, chromium, nickel, selenium, zinc and mercury were investigated, as well as stable carbon and nitrogen isotopes in sediments, plant fragments and marine organisms such as benthic invertebrates, benthivorous fish and marine mammals, collected in the three estuaries. Samples were collected in 2015, with isotope analysis performed by EA-IRMS and heavy metal analysis performed by ICP OES-VGA and ICP-MS. Isotopic ratios allowed the distinction between organic matter sources and trophic level. The specimens of the ichthyofauna and cetaceans analyzed did not present distinction between trophic levels 3 and 4, indicating a generalist diet for these animals and a potential sharing of trophic niche. The metals have presented higher concentrations in the sediments from Santos estuary, what coincides with the place with greater intensity of anthropic activities. Comparing the estuaries, there is more bioaccumulation of Cr, Cu, Zn and Hg in Paranaguá, As and Pb in Cananéia, and Cd, Ni and Se in Santos; results which are justified by anthropic activities, natural sources and geochemical characteristics of each region. A biomagnification tendency of Se was observed in the trophic webs of all estuaries, and Zn and Hg in the Paranaguá\'s and Cananéia\'s webs. However, As, Cr, Cu, Ni and Pb displayed a tendency to biodilution in the studied trophic webs; with a higher bioaccumulation in benthic invertebrates. Therefore this study provides a current overview of the spatial and trophic distribution of heavy metals in the estuaries. Thus, it is collaborating with the monitoring and actions of coastal management.

En la presente tesis se aborda el desarrollo de un modelo de calidad del agua orientado al estudio de sustancias prioritarias y peligrosas teniendo en cuenta los efectos de la dinámica sedimentaria a fin de facilitar la gestión de zonas estuarinas. Además, con el objeto de poder llevar a cabo la integración del modelo desarrollado dentro de un Sistema de Información Geográfica, se establecen los procedimientos metodológicos necesarios. La conjugación de estas tareas permitirá fusionar los beneficios de ambos instrumentos bajo un único entorno a fin de obtener una herramienta de gestión de vertidos que aporte respuestas técnicas tomando en consideración las exigencias legislativas de la normativa vigente.
This thesis tackles the development of a water quality model devoted to priority and hazardous substances considering, as well, the effects derived from the sedimentary dynamics with the aim to simplify the management of estuarine areas. Moreover, with the aim to integrate this model into a Geographical Information System, the required methodological procedures are established. The combination of both tasks will allow the integration of the benefits from both tools within a unique environment that will allow the discharges management providing technical answers taking into consideration the legislative requirements.

Orientadores : Profª. Drª. Eunice da Costa Machado e Prof. Dr. Tom Moens
Dissertação (mestrado) - Universidade Federal do Paraná, Setor de Ciências da Terra, Programa de Pós-Graduação em Sistemas Costeiros e Oceânicos. Defesa: Pontal do Paraná, 05/02/2014
Inclui bibliografia
Resumo: As variações das fontes de carbono orgânico e suas variações espaciais são importantes para compreender o balanço das diferentes formas de carbono orgânico nas regiões costeiras. Amostragens foram feitas ao longo de gradientes de salinidade e nas duas desembocaduras do Complexo Estuarino de Paranaguá (CEP), objetivando analisar a distribuição espacial do Carbono Orgânico Particulado (COP) e do Carbono Orgânico Dissolvido (COD), as variações das saturações do CO2 e O2, análises metabólicas do estuário, fluxos de difusão do CO2 e as exportações do COP e do COD para a área costeira adjacente ao CEP. O sistema está localizado no estado do Paraná, região sul do Brasil, compreendendo uma área de 612km2 e um volume de 2x109m3. Amostras foram coletadas durante campanhas amostras, ao longo de gradientes de salinidade dos eixos Norte-Sul e Leste-Oeste, e nas desembocaduras Norte e Sul do sistema. As amostras de carbono orgânico foram analisadas através do método de combustão em alta temperatura HTC no equipamento TOC-5000 Shimadzu; os fluxos de difusão, na interface ar-água foram estimados de acordo com Carmouze (1994) e as exportações foram baseadas em fundeios de medição como equipamento S4 Current Meter, medindo as correntes e descargas de água durante um ciclo complete de maré. Os resultados apresentaram variações nos valores de concentração de carbono orgânico: máximo de 13.56mg.L-1, mínimo de 3.84mg.L-1, com uma média de 6.59mg.L-1 para o eixo Leste-Oeste; e 19.37mg.L-1, 5.44mg.L-1 e 8.59mg.L-1 para o eito Norte-Sul (valores máximo, mínimo e médio, respectivamente). Ao longo dos transectos de salinidade (em direção às desembocaduras do sistema estuarino), a concentração do carbono orgânico foi constante, enquanto a absorbância do CDOM diminuiu, inferindo na existência de diversas fontes de material orgânico para o sistema. As saturações do CO2 e O2 fora relacionadas com a salinidade e também se mostraram correlacionadas com a absorbância do CDOM nos comprimentos de onda de 320 e 443nm (61% e 47% para o O2; 63% e 46% para o CO2, respectivamente). Os eixos Leste-Oeste e Norte-Sul exibiram médias de fluxo de difusão de 1.74 e 2.72mM.m-2.h-1. As exportações de COD e COP na desembocadura Norte foi de 21.39kg.s-1 e 8.30kg.s-1, respectivamente; enquanto para a desembocadura Sul, as médias foram de -1.57kg.s-1 (em direção ao estuário) e 26.40kg.s-1, respectivamente. A presença de substâncias húmicas no sistema afeta a produção primária, e consequentemente afeta as saturações de CO2 e O2. O estuário demonstrou um metabolismo heterotrófico, exportando grandes quantidades de CO2 para a atmosfera e grandes quantidades de carbono orgânico, até mesmo quando comparado com alguns dos maiores rios do planeta.
Abstract: Variations of organic carbon sources and its spatial variations are important to comprehend the balances of the different organic carbon phases in the coastal zones. Surveys were made along the salinity gradients and mouths of the Paranaguá Estuarine Complex (PEC), objecting to analyze the spatial distribution of Particulate Organic Carbon (POC) and Dissolved Organic Carbon (DOC), variations of CO2 and O2 saturations, metabolic analysis of the estuary, the CO2 diffusive fluxes and the POC and DOC exportations to the adjacent coastal waters of the PEC. The system is located in the Paraná State, south of Brazil, comprising 612km2 and a water volume in the order of 2 x 109m3. Samples were collected, during four sampling campaigns, along the salinity gradients in the two axes, North-South and East-West axes, and in the Northern and Southern Mouths of the system. The organic carbon samples were analyzed by HTC TOC-500 Shimadzu equipment; diffusive fluxes at the air-water interface were estimated according to Carmouze (1994) and the exportations were based on the anchoring of the S4 Current Meter, measuring currents and water discharge for an entire tidal cycle. The main results showed a variation of the organic carbon concentration values: maximum of 13.56mg.L-1, minimum of 3.84mg.L-1 with a mean of 6.59mg.L-1 for the East-West Axis; and 19.37mg.L-1, 5.44mg.L-1 and 8.59mg.L-1 for the North-South Axis (maximum, minimum and mean values, respectively). Along the salinity transects (direction to the mouth of the estuarine system), the absorbance of CDOM diminishes, which infer different sources of organic matter to the system. The saturations of CO2 and O2 were related with the salinity and also showed correlations with the absorbance of CDOM at 320 and 443nm (61% and 47% for O2; 63% and 46% for CO2, respectively). The East-West and North-South axes exhibited mean diffusive fluxes of 1.74 and 2.72mM.m-2.h-1. The exportations of DOC and POC at the Northern Mouth had an average flux of 21.39kg.s-1 and 8.30kg.s-1, respectively; while the Southern mouth had an average flux of -1.57kg.s-1 (towards the estuary) and 26.40kg.s-1, respectively. The presence of humic substances in the system affects the primary production, consequently affecting the CO2 and O2 saturations. The estuarine system reflects a heterotrophic metabolism, exporting high amounts of CO2 to the atmosphere and high quantities of Organic Carbon to the adjacent ocean, even when compared to the major rivers in the world.

A fim de avaliar a influência do sistema estuarino de Santos sobre os Nematoda da plataforma continental adjacente, a densidade, composição genérica e diversidade desse grupo foram analisadas e relacionadas com o tipo de sedimento, teor de matéria orgânica e biomassa de fitopigmentos. Para isso, o sedimento foi coletado em seis estações, no inverno/2005 e verão/2006, com um amostrador do tipo box-corer, do qual foram retiradas amostras para a meiofauna com um tubo de 4,9 cm2 de área superficial e 10 cm de altura. Os Nematoda representaram mais de 95% da meiofauna, com densidades médias de 2472±1794 ind.10cm-2 no inverno/2005 e de 2606±2017 ind.10cm-2 no verão/2006. A influência do sistema estuarino de Santos restringiu-se às áreas na saída da baía de Santos e do canal de Bertioga e deu-se através do aporte de sedimentos finos e de matéria orgânica, que foi mais evidente no verão devido à maior pluviosidade. Nessas áreas foram observadas menores densidades e maior abundância de gêneros depositívoros, como Sabatieria e Terschellingia e da família Xyalidae. Nas outras estações rasas com sedimento arenoso, bem selecionado e com biomassa de clorofila-a relativamente alta, as densidades foram as mais altas e predominaram Chromadorita e Microlaimus, herbívoros/comedores de epistrato. Nas estações mais profundas, com sedimento mais finos, a densidade e diversidade foram menores e Sabatieria foi dominante. Portanto, além do sistema estuarino, a profundidade e o hidrodinamismo local, que determinam as condições sedimentares e tróficas, foram fatores importantes para as associações dos Nematoda.
To assess the influence of Santos estuarine system on the nematodes of the adjacent continental shelf, the density, composition and generic diversity of this group were analyzed and related to the sediment type, organic matter content and phytopigments biomass. The sediment was collected at six stations, in the winter of 2005 and summer of 2006, with a box-corer from which meiofauna samples were taken with a 4.9 cm2 superficial area and 10 cm height corer. Nematodes represented more than 95% of the total meiofauna, and their average densities were 2,472±1,794 ind.10cm-2 in the winter/2005 and 2,606±2,017 ind.10cm-2 in the summer/2006. The influence of Santos estuarine system was restricted to the closest areas to Santos bay and Bertioga channel and it was observed through the contribution of fine sediments and organic matter, which was more evident in the summer due to higher rainfall. In these areas, lower nematodes densities were found as higher abundance of deposit feeders genera, like Sabatieria and Terschellingia, and from the Xyalidae family. In the other shallow stations with well sorted sands and relatively high chlorophyll-a biomasses, densities were the highest and Chromadorita and Microlaimus, herbivorous/epistrate feeders, were predominant. In the deepest stations with finer sediments, the densities and diversities were the lowest and Sabatieria was dominant. Therefore, apart from the estuarine system, the depth and local hydrodynamics, which determines the sediment and trophic conditions, were important factors for the nematodes assemblages.

O Rio Ribeira nasce no estado do Paraná e tem sua foz no município de Iguape estado de São Paulo. Possui 470 km de extensão e recebe o nome de Ribeira de Iguape em sua porção final, onde existe uso intensivo do solo para a agricultura (bananicultura), atividades industriais como mineração, eliminação de esgoto e um pouco de pecuária. Estas atividades contribuem com o aporte de nutrientes nitrogenados e fosfatados para o corpo hidrológico, atingindo o Complexo Estuarino-Lagunar de Cananéia-Iguape por meio do Canal do Valo Grande, em Iguape. O presente trabalho caracterizou o sistema hídrico por meio de parâmetros hidrológicos e hidroquímico como: temperatura da água, salinidade, pH, oxigênio dissolvido, material em suspensão, teores de nitrogênio e de fósforo, matéria orgânica em suspensão e turbidez. Foi realizado um diagnóstico do setor norte do sistema em relação às condições estuarinas naturais presentes no setor sul, correlacionando os valores observados de componentes nitrogenados e fosfatados com a carga estimada de fertilizante empregada nos cultivos de banana, principal cultura da área estudada. Entre Registro e Iguape, a bananicultura localizada na região marginal ao rio foi estimada, com o uso de imagens, em aproximadamente 744 hectares. Foram feitas quatro coletas (invernos 2012 e 2013, verões 2013 e 2014) com 20 estações ao longo do Rio-Valo Grande-Sistema Estuarino Lagunar de Cananéia Iguape. No setor norte foram obtidos os mais altos teores de nitrato, 15,72 µmol L-1 no rio e 14,59 µmol L-1 no Valo Grande indicando o grande aporte deste nutriente via rio e com contribuição significativa da adubação da cultura da banana. Quanto ao fosfato, os valores foram extremamente altos em toda a amostragem no setor norte, sobretudo no Inverno de 2012, onde o máximo teor foi de 12,45 µmol L-1 no Rio. Este aporte alto é contínuo e deve receber contribuição suplementar via afluentes, com forte indicativo da proveniência da exploração de rochas fosfatadas, na região de Cajati, cujos efluentes podem atingir o Rio Ribeira de Iguape por meio do Rio Jacupiranga. As cargas de N e P provenientes da agricultura foram de 44,22 t ano-1 para N (1,6% da carga total do rio) e 5,36 t ano-1, para P (0.12% da carga total do rio). O desbalanceamento da entrada de P na relação N:P mostra esta entrada suplementar de P no norte do sistema indicando a forte influência antrópica na região em relação aos dois nutrientes, mas com maior carga para P e uma diluição em relação ao sul que deve ser monitorada.
The Ribeira River rises in the state of Paraná- Brazil and outfalls in Iguape, state of São Paulo (Brazil). The river is 470 km long, and in its final portion, which is aproximately 70 km long, is called Ribeira de Iguape River. In this area an intense use of the soil can be found regarding the growth of bananas crops, there are also industrial mining activities, sewage disposal and some livestock. These activities contribute to the supply of nitrogenous and phosphate nutrients input for the hydrological body, which further reaches Cananéia-Iguape Estuary-Lagoon Complex through Valo Grande Channel, in Iguape. This study characterized the water system through hydrological and hydrochemical parameters such as water temperature, salinity, pH, dissolved oxygen, suspended matter and turbidity. It was conducted a diagnosis of the northern sector of the system in relation to the natural estuarine conditions present in the south sector. The observed values of nitrogen and phosphate were correlated with the estimated load of fertilizer used in banana plantations, which is the main crop in the study area. The banana plantation located in the river\'s margins, between the cities of Registro and Iguape, was estimated with the use of images, and resulted in approximately 744 hectares. Four campaigns of water sampling were made: winter of 2012 and 2013; summers 2013, 2014) with 19 stations along the River - Valo Grande channel - Cananéia Iguape Estuarine Lagoon System. Highest levels of nitrate were obtained in the river sample of 15.72 µmol L-1, and 14.59 µmol L-1 in the Channel, indicating the great contribution of this nutrient via river and significant contribution of the banana crop fertilization. Regarding the phosphate levels, they were extremely high throughout the sampling in the northern sector, especially in winter 2012, where the maximum level was 12.45 µmol L-1 in the River. This high contribution is ongoing and might receive additional contribution via tributaries, with strong indication of provenance from exploiting phosphate rocks, in the region of Cajati- SP, where effluent can reach the Ribeira de Iguape River through Jacupiranga River. The agricultural load of N and P were estimated in 44.22 t N year-1 (1.62% of total river load) and 5.36 t year-1 P (0.15% of total river load). The imbalance of P input in N:P shows this additional input of P- Phosphate in the north of the system, indicating the strong anthropogenic influence in the region in the two nutrients, but with higher load for P and a dilution towards south, which should be monitored.

Le concept de réseau d'interactions est central en Écologie et différents modèles et méthodes ont été utilisés. Ce travail de thèse met en relation deux approches développées par des courants séparés : l'étude des matrices de communauté et les analyses entrée-sortie. Il confronte leurs hypothèses aux propriétés fondamentales des écosystèmes estuariens. Il précise explicitement les liens entre les différentes matrices, ainsi que la signification des mixed trophic impacts. Les matrices de la storage et de la throughflowanalyses sont reliées à des jacobiennes de modèles à compartiments dont les flux sont contrôlés par les compartiments donneurs ou receveurs. Contrairement à ce qui est le plus souvent présenté dans la littérature, l'analyse des mixed trophic impacts est ici interprétée en terme de présence-absence du compartiment considéré. Avec les données disponibles sur les réseaux trophiques de cinq estuaires européens, des matrices qualitatives et quantitatives sont construites afin de réaliser des analyses de sensibilité. Ces premières explorations montrent des niveaux d'incertitudes très élevés, et ceci même pour le signe des prédictions. Par ailleurs, ce travail de thèse approfondit les possibilités d'étude de dynamiques transitoires à partir de la matrice de communauté. Il souligne des éléments importants qu'il est nécessaire de prendre en compte lorsque ces approches sont choisies
Networks are a key concept in ecology and a number of models and methods have been used. This PhD dissertation links two approaches, the community matrix and input-output analyses, which have been developed by separate streams of theory. It compares their assumptions with important features of estuarine systems. It explicitly analyses the links between the matrices and the significance of the mixed trophic impacts analysis. Matrices of storage and throughflow analyses are linked to Jacobian matrices of donor or recipient controlled compartment models. Unlike most of what can be seen in the litterature, here the mixed trophic impacts are interpreted as the effects of a compartment being present or absent. Using available data in the case of five European estuaries, qualitative and quantitative matrices are built in the aim of performing sensitivity analyses. First explorations reveal high levels of uncertainties, even in the sign of the predictions. Furthermore, this work examines in more details the possibilities to explore transient dynamics from the community matrix. This PhD dissertation emphasises important features which are necessary to consider when choosing such approaches

A composição, distribuição, abundância, biomassa e produção secundária do zooplâncton do Sistema estuarino de Santos foram estudadas na baía de Santos (4 estações), canal de Santos (3 estações) e canal da Bertioga (4 estações), entre novembro de 2004 e outubro de 2005, em relação à temperatura, salinidade, material em suspensão, nutrientes dissolvidos e clorofila-a. Nas 114 amostras analisadas, o zooplâncton foi constituído de 101 táxons distribuídos em 10 filos: Arthropoda (subfilo Crustacea), Annelida (classe Polychaeta), Bryozoa, Chaetognatha, Chordata (subfilo Tunicata), Cnidaria, Ctenophora, Echinodermata, Mollusca e Phoronida, sendo o primeiro dominante. Os copépodes constituíram, em média, 85,5% do zooplâncton total. A comunidade zooplanctônica das três áreas incluiu táxons estuarinos, costeiros e oceânicos, sendo dominantes Oithona hebes, Oithona oswaldocruzi, Acartia lilljeborgi, Acartia tonsa, Bestiolina similis, Balanus spp. (náuplios), Paracalanus quasimodo, Paracalanus spp. (copepoditos), Parvocalanus scotti, Euterpina acutifrons, Pseudodiaptomus acutus, Oikopleura dioica e as larvas de Polydora spp., Aonides spp., Spionidae e Bivalvia. A abundância, biomassa e a produção secundária zooplanctônica foram maiores no canal da Bertioga, enquanto a produtividade foi maior na baía de Santos. Esses fatores estiveram associados, principalmente, à salinidade, temperatura da água e material em suspensão total.
The zooplankton´s composition, distribution, abundance, biomass and secondary production of Santos estuarine system were studied on Santos bay (4 stations), Santos channel (3 stations) and Bertioga channel (4 stations) between November 2004 and October 2005 in relation to temperature, salinity, suspended matter, dissolved nutrients and chlorophyll-a. On the 114 analyzed samples, zooplankton was constituted of 101 taxa distributed among 10 phyla: Arthropoda (subphylum Crustacea), Annelida (class Polychaeta), Bryozoa, Chaetognatha, Chordata (subphylum Tunicata), Cnidaria, Ctenophora, Echinodermata, Mollusca and Phoronida, being Arthropoda the dominant phylum. Copepoda (subphylum Crustacea) constituted on average 85,5% of total zooplankton. The zooplankton community among the three areas included estuarine, coastal and oceanic taxa, being Oithona hebes, Oithona oswaldocruzi, Acartia lilljeborgi, Acartia tonsa, Bestiolina similis, Balanus spp. (naupli), Paracalanus quasimodo, Paracalanus spp. (copepodite), Parvocalanus scotti, Euterpina acutifrons, Pseudodiaptomus acutus, Oikopleura dioica and the larvae of Polydora spp., Aonides spp., Spionidae and Bivalvia dominant. The abundance, biomass and zooplanktonic secondary production were higher on Bertioga channel, whereas the productivity was higher on Santos bay. These factors were associated mainly to salinity, water temperature and total suspended matter.

Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.
Title from electronic title page (viewed Jun. 23, 2010). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Marine Sciences Physical Oceanography." Discipline: Marine Sciences; Department/School: Marine Sciences.

The following is a compilation of field data collected in 2011 and 2012 in Apalachicola, FL as part of a five year study assessing the ecological effects of sea level rise in the northern Gulf of Mexico. Many coastal communities, both natural and developed, will soon be working to mitigate the effects of sea level rise, if they are not already doing so. This thesis investigates the natural patterns of the Apalachicola estuarine system through the collection and analysis of in situ water, sediment, and biomass samples. Additionally, results of the field samples are presented and recommendations for additional sampling are given. The field methods and procedures developed in this study were designed to be repeated in other estuaries to build upon the work that has been conducted in Apalachicola. Water samples were tested for total suspended solids (TSS) and compared against hydrodynamic (tidal circulation and streamflow) and meteorological (wind and precipitation) characteristics. Streamflow was determined to influence a seasonal base level concentration of TSS. Wind strength and direction consistently influenced small TSS concentration fluctuations, an effect amplified by the shallow nature of the estuary. Tidal circulation appeared to have minor influences on TSS concentration fluctuations within the base level concentration range. Precipitation appeared to influence large TSS concentration fluctuations; however, due to limited data collection during storm events, more data is required to conclusively state this. Sediment cores throughout the lower Apalachicola River revealed that coarse particles settled out in upstream areas while fine particles tended to stay in suspension until low energy areas in the lower portions of the river or marsh system were reached. Finally, biomass samples were used to develop regression models utilizing remotely sensed data to predict biomass density in marsh areas with unprecedented accuracy. The documented patterns of this system are to be used as inputs and validation points to update an existing hydrodynamic model and to aid in the coupling and development of sediment transport and marsh equilibrium models. The field campaign developed and implemented here provides a foundation for this novel coupled modeling effort of estuarine systems. From the 2011 and 2012 sampling conducted, it is apparent that Apalachicola can be modeled as a closed system with river inflow and sediment influx as boundary conditions. Forcing local conditions should accurately represent the system. Ultimately, these models will be used to simulate future sea level rise scenarios and will provide useful decision making tools to coastal managers. Future work will include replicating water sampling in subsequent wet and dry seasons in Apalachicola, FL to confirm observed trends, in addition to implementing this sampling in Grand Bay, MS and Weeks Bay, AL. Additional biomass samples will be taken to validate the strong correlations found between remotely sensed data and in situ samples. In similar studies, it is recommended that water samples be taken to adequately represent influences from tidal cycles and riverine inflow. It is also recommended that spatially distributed biomass samples be taken to validate regression models.
M.S.
Masters
Civil, Environmental, and Construction Engineering
Engineering and Computer Science
Civil Engineering; Water Resources Engineering

O presente trabalho tem, como objetivo, analisar o processo de sedimentação atual no Canal do Ararapira, Sistema Estuarino Lagunar de Cananéia-Iguape (SP), através das características composicionais e granulométricas dos sedimentos de fundo e distribuição da matéria orgânica sedimentar e carbonatos, relacionando estes parâmetros à configuração geral do canal e aos processos oceanográficos que ali atuam. Foram realizadas análises granulométricas, conteúdo de carbonato e matéria orgânica sedimentar (C, N, S) em 60 amostras de sedimentos coletadas em um cruzeiro oceanográfico realizado no mês de julho de 2004. Dentre o total de 60 amostras, foram selecionadas 16 para realização da análise da fração arenosa. A análise espacial da distribuição dos sedimentos e da matéria orgânica sedimentar, apontou para a predominância de sedimentos arenosos com baixos teores orgânicos ao longo de praticamente toda extensão do canal exceto em determinados pontos localizados no centro-norte do canal onde há presença de sedimentos finos associados a baixios e desembocaduras de gamboas e pequenos cursos d\'água continentais e insulares. Constatou-se a predominância da influência continental ao longo de todo o canal com pequenas concentrações de carbonatos. Os teores elementares da matéria orgânica sedimentar possuem, normalmente, comportamento e distribuição que estão diretamente relacionados aos tipos de sedimentos e à topografia de fundo, bem como à circulação. Observou-se uma relação direta entre os sedimentos mais finos e um maior conteúdo de matéria orgânica.
The aim of this study is the analysis of modern sedimentary process taking place in the Ararapira Channel, at Cananéia-Iguape lagoonal estuarine system (SP). The employed parameters for this were the composition and grain size characteristics of the bottom sediments , the distribution of the carbonates , organic matter, and relates these parameters to the general configuration of the channel and to the oceanographic process that takes place over there. The grain size analysis, the carbonate content, and the sediment organic matter (C, N, S) were conducted over 60 sediment samples collected during an oceanographic cruise that took place in July 2004. Among the total of the 60 samples, 16 were selected for the coarse fraction analysis. The spatial analysis of the distribution of sediments and sedimentary organic matter showed that sandy sediments, with low organic content, are predominant practically all along the whole of the channel extension, except in points located in the central-northern portion of the channel, where there are thin sediment associated to shoals or small continental and insular river courses. The C, N, S and carbonates contents observed with the coarse fraction analysis, allow identifying the predominance of continental influence all along the channel, with lower carbonate concentrations. The sediment organic matter contents have, usually, behavior and distribution which are directly related to the type of sediment ,to the bottom topography, as well as to the circulation. It was possible to observe a direct relationship between the thin sediment and a larger content of the organic matter.

The aim of this project was to investigate the biogeochemistry and transport of metals in a river/estuarine system contaminated by acid mine drainage. The Rio Tinto and Rio Odiel drain a metalliferous mining area in the Iberian Pyrite Belt in the south-west of Spain. The pH values in the rivers were low (< 3) and dissolved metal concentrations were . extremely high, up to 2.6 mM Zn, 860 \M Cu, 6.0 jaM Cd and 72 nM U . The seasonal cycle of low precipitation and flash floods was identified as an important factor in generating the more severe contamination of the rivers with Fe, A l , Mn, Zn, Cu, N i , Co and Cd observed during autumn and winter, compared to spring and summer. The estuarine behaviour of dissolved Fe, Mn, Zn, Cu, N i , Co and Cd was primarily = controlled by pH. Apart from an addition of these metals from the sediment in the upper Tinto estuary, conservative mixing was observed up to pH ~ 5 (at S ~ 30), above which Fe, Mn, Zn, Cu, N i and Co were removed from solution. Voltammetric speciation studies showed that Cu complexing organic ligands (logK'cuL ~ 11-5, CL = 32 - 199 nM) in the estuary were saturated, and thermodynamic calculations indicated that the concentration of Cu^"^ reached values (pCu^"^ < 9) that are toxic to some marine and estuarine organisms. The estimation of fluxes indicated that the dissolved metal export from this system to thecoastal zone averages 101 d'^ Zn, 2.3 t d"' Cu, 180 kg d"^ N i and 236 kg d"^ Co, with higher contributions during wet, compared to the dry seasons. On-line measurements of Zn, Cu and N i in the Gulf of Cadiz revealed metal plumes associated with the Tinto/Odiel system and the Guadiana and Guadalquivir rivers. As a result of entrainment by the Atlantic Ocean surface current flowing into the Mediterranean Sea, the metal contamination in waters of the Gulf of Cadiz is transported south and eastward.

This contribution focuses on the medium-term (months to years) morphodynamic modelling of natural estuaries. A 2D morphodynamic model based on the Telemac system was calibrated and validated using extensive field measurements' at Teignmouth (UK). Statistical tools indicate that the model is capable of predicting the observed hydrodynamics with 'good' accuracy, given that measurement noise is removed. Despite some qualitative agreement, morphological predictions show a more limited skill; consistent with the current 'state of the art' in this area of scientific research. The typical long simulation times associated with process-based morphodynamic models are optimised through the successful implementation of an input reduction approach, adapted from Latteux (1995). The technique is shown to reduce the model run times by up to 85% without a significant loss in accuracy. Bathymetric surveys spanning 2 years (December 2002 to November 2004) at Teignmouth have clearly demonstrated a seasonal variability in the sediment volumes within the estuary, with accretion in the relatively energetic winter periods and erosion during the quiescent summer months. The net longer-term trend over this period is accretionary with average seabed accumulation rates of 20 cm.year"'. It is demonstrated that i f the wave stirring effect is neglected, the predictions carried out with a single grain size do not replicate the observed sediment import to the estuary from the neighbouring coastal region, due to the ebb dominated tidal regime found at Teignmouth. The importance of the combined effects of wave stirring and mixed grain sizes on reproducing the sediment import processes is confirmed by the Brier skill scores. Model predictions show a high influx of suspended sediment into the estuary in the presence of wave stirring effects at the coastal region. These sediments are advected into the estuary during the flood phase and are rapidly deposited at the outer estuary, since lag effects are neglected. The sediment input is predicted to be dominated by the finer sediment fractions (primarily silts and clays) although in very energetic conditions even granule-sized sediments can enter the estuary. Starting from an isotropic sediment distribution, a realistic spatial redistribution of sediment grain sizes is predicted, with sediments generally fining towards the shallower and upper regions of the estuary, whilst coarser grains were concentrated seawards.

This study examines the geochemistry of salt marshes and intertidal sediments from the Solent estuarine system, southern England. Micro-, meso- and macro-scale studies have been carried out to assess the geochemical processes operating in these intertidal sediments and the use of radionuclides as tracers of sedimentary processes in the Solent area. Measurement of 210Pbxs, 137Cs and 60Co provides valuable information on sedimentary processes occurring in the Solent estuarine system. Subsurface maxima in activity are observed for 137Cs and 60Co (after normalisation to Al) which can be related to historical input, providing dated sediment horizons. This has enabled determination of Recent sediment accumulation rates and reconstruction of historical pollution records. Sediment accumulation rates obtained using 210PbXS/ l37Cs and 60Co in salt marsh environments provide an indication of the rate of Recent sea level rise, estimated as 4 mm y-1. This is in broad agreement with tide gauge data and when compared with longer term archaeological and radiochronological data may indicate an increase in the rate of mean sea level rise over the last 1000 years. Salt marsh areas with accumulation rates lower than 4 mm y 1 (from 137Cs and 60Co dating) are degenerating (undergoing die-back) indicating that they are failing to keep pace with the rising sea level. While local (intra-estuary) effects influence rates of sediment accumulation on a particular salt marsh the main control of sediment accretion over the whole Solent area is a rise in mean sea level. Dating of salt marsh sediment cores has allowed assessment of the historical record of anthropogenic pollutant input to the Solent (in particular for Pb and Cu). Pb isotope studies of salt marsh sediments from Southampton Water indicate increasing importance of anthropogenic Pb (from Precambrian ores) since the beginning of this century. A very prominent transient spike due to an anthropogenic Pb input is found in salt marsh sediments from the relatively unpolluted Beaulieu estuary. This may be related to military marshalling in the Beaulieu river before the Allied D-Day landings in 1944. Anthropogenic Cu is present in the Solent region mainly due to discharge from the Esso refinery at Fawley, Southampton Water. Analysis of Cu fluxes has shown that discharges peaked in ca.1970 and have significantly reduced since 1971 (due to effluent clean-up by the refinery). The reliable use of radionuclides as indicators of sediment accumulation depends on their chemical immobility (lack of redox migration). 60Co shows evidence for early diagenetic remobilisation at two salt marsh sites, and 2iopb m a v a i s o be mobile in some salt marsh areas. Remobilisation of 210Pb is apparently localised and may be aided by flooding/drainage cycles in the marsh. The use of these radionuclides as tracers of sediment accumulation in areas where significant early diagenetic remobilisation occurs is problematic. Where possible a number of chemically different radionuclides should be used to eliminate bias in calculated sediment accumulation rates due to redox mobilisation or diffusive processes. Detailed geochemical studies can assist in determining whether redox movement of radionuclides is occurring. A critical examination of the geochemical behaviour of both the stable counterparts of radionuclides and redox-sensitive elements is required if realistic sediment accumulation rates are to be obtained.

We develop three models for the flow in an estuary. The first being a 2 1-dimensional time-periodic model of a flow in the vertical cross section. The second model adds a third un-coupled velocity field U, in the along-estuary direction. The final model is a 3 + 1-dimensional, fully-coupled, time-periodic flow. We study the transport of material in each model using what are called lobe diagrams. Such diagrams allow us to separate the flow into different regions and then calculate the transport of material between adjacent regions. We also study the presence and bifurcations of curves which form partial barriers (ie. cantori and barriers formed from segments of unstable and stable manifolds of hyperbolic periodic points) or complete barriers (ie. KAM curves and other invariant circles) to transport. We use these models to develop an understanding of both the mixing within the flow and the formation and leakage of patches of higher concentration within a cloud of pollution released into the estuary. We also study the time taken for particles to exit the bounds of the estuary. As a result we get an understanding of which regions of the flow flush pollution out of the estuary in the least time and out of which end of the estuary they flush the pollution. We apply this understanding, and that gained from studying the mixing and formation of patches, to the problem of the optimal discharge of effluent into an estuary.

Understanding the effect of physical forcing on estuarine functioning is of major importance to determine the rate of exchange of water, sediments, pollutants and nutrients between the continent and the ocean. The combination of numerical models and discrete datasets is used to describe and investigate processes of natural variability in the partially-mixed, non-turbid, macrotidal Solent-Southampton Water estuarine system (UK). The estuarine circulation and the response of wind forcing is examined using a three dimensional, free surface, finite volume and finite element grid model. Results from short-term (three months) simulations have been compared against data (ADCP measurements, tidal elevations and salinity distributions) collected in spring 2001 in Southampton Water and the Solent. The model reproduces the unique tidal curve of Southampton Water and the partially-mixed conditions prevailing in the upper estuary. The contribution of the local wind forcing (wind intensity · 12 m s−1) to changes in water level is estimated to be up to 6 cm in Southampton Water in the model. The modelled salinity stratification varies over a semi-diurnal cycle with the highest stratification occuring at mid-ebb. Wind forcing is more efficient in altering stratification at ebb than flood. The temporal and spatial variability of light attenuation is also investigated. Turbidity is demonstrated to be the major contribution to light attenuation using a time-series of discrete data collected in 2001, 2002 and 2003. A typical seasonal cycle of the coefficient of light attenuation is revealed, with a minimum in May-June and a maximum occuring in September-October. A second dataset of continuous measurements (10-minute interval) demonstrates the spring-neap modulation of the turbidity. The mouth of Southampton Water is more exposed to tidal mixing and therefore more turbid than the mid-estuary. A five-compartment zero-dimensional pelagic ecosystem model including a sediment compartment has been developed to assess the impact of the variability of the light attenuation on the timing and the magnitude of the spring phytoplankton bloom. Using high resolution irradiance forcing and a constant coefficient of attenuation k set to the minimum May-June value, simulations compare well with discrete data of chlorophyll a, and less successfully with zooplankton and Dissolved Inorganic Nitrogen. A sensitivity analysis indicates that interranual variability in the phytoplankton spring bloom originates in order of importance from 1) parameterization of k 2) the variation of the seasonal cycle of surface irradiance 3) the intrinsic dynamics determined by the combination of fixed parameters of the ecosystem model.

Estuaries are of immense importance to many communities. It has been estimated that 60 to 80 % of commercial marine fishery resources depend on estuaries for part, or all of, their life cycle. The characteristics of estuarine flow, water quality and sediment conditions are important as they play a critical role in the functionality and health of these systems. This study utilised both field data and numerical modelling technique to help enhance our understanding of the physical processes of a very shallow subtropical estuarine system. This study first quantified various salt flux components within the shallow subtropical estuarine system Coombabah Lake in Gold Coast, Queensland, Australia to better understand the system’s physical processes for assisting future management decisions in this ecologically and economically significant region. Residual water transport was identified as the dominant factor influencing residual salt transport, which alternates direction frequently. This study then developed a new simple and robust traversing system to measure flow properties within estuarine bottom boundary layers to estimate two important parameters used in numerical modelling of aquatic systems: bed shear stress and bed roughness height. Four commonly-employed techniques: (1) Log-Profile; (2) Reynolds stress; (3) Turbulent Kinetic Energy; and (4) Inertial Dissipation used to estimate bed shear stresses from velocity measurements were also compared. Bed shear stresses estimated with these four methods agreed reasonably well; of these, the Log Profile method was found to be most useful and reliable for the unstratified conditions studied. A three-dimensional hydrodynamic model with unstructured meshes utilising the MIKE3 FM modelling system and simulated the hydrodynamic regime was set up for Coombabah Lake to assist with enhancing our understanding of the hydraulic properties within this shallow sub-tropical estuarine system. The sensitivity of calibration parameters of a very shallow estuarine model was also investigated. The model utilised the hydraulic data collected by the newly developed traversing system and that collected during the first part of the study used to examine salt flux dynamics. The hydrodynamic regime of the lake was found to be favourable for settlement of suspended sediments. The results also revealed that the correct bathymetry is the most important parameter for accurate modelling, followed by appropriate bed roughness in the numerical scheme for very shallow environments. This study finally provided an understanding of the sediment dynamics within Coombabah Lake and the surrounding waters. It utilised ten days of observed hydrodynamic and sediment data and employed the three-dimensional model with unstructured meshes utilising the MIKE3 FM modelling system. Sediment dynamics of the lake were found to be dominated by advection process driven by tides with wave and wind playing minor roles – even though the system was shallow. Simulation results agreed well with field data and supported the aforementioned findings. Correlation between TSS and turbidity was very poor; therefore, the employed automatic data logging system (turbidity meters) was determined inappropriate for the estimation of TSS concentration in the very shallow subtropical estuarine system.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Engineering
Science, Environment, Engineering and Technology
Full Text

Estuaries are often challenging to manage, as management must strike a balance between the needs of the users and the ecological and economic values within the context of multiple legislative drivers. To help facilitate integrated management, a novel Estuarine Planning Support System (EPSS) framework, using the Humber Estuary in Eastern England as a case study, has been developed. This integrated EPSS framework goes beyond previous approaches as it brings together the legislative drivers, management tools and other mechanisms for controlling plans (formal/legal management, action or work plans (e.g. shoreline management plans) and projects (a new structure or activity such as extending a port). It thereby enables managers and users to assess and address both the current environmental state, and the way in which the new project could impact an estuary in an accessible and understandable tool. This study has been primarily completed by desk based research using peer reviewed literature, technical and research reports, marine licence applications and legislation, with correspondence to several sources to determine the baseline information and existing knowledge gaps. Further to the framework, an EPSS tool was developed to provide a practical application of these requirements. The GIS-based tool ensures that the information is accessible for regulators, managers, the scientific community, developers and the public. Whilst the tool is adaptable for regions within and outside the United Kingdom (UK), the research presented in this thesis focussed on the Humber Estuary. The successful application of the tool for a complex socio-economic and environmental system such as the Humber Estuary shows that the tool can efficiently guide users through the complex administrative requirements needed to implement a management plan, and therefore support sustainable development. In addition, the tool can be used as a scoping mechanism to identify potential stressors which are to be addressed in an environmental impact assessment (EIA). The tool was validated against four case studies and was also tested by a number of stakeholders to determine the utility and accuracy of the tool. The tool was subsequently updated to reflect feedback from the stakeholders. This project should be viewed as a ‘proof of concept’ in that its primary purpose is to demonstrate the potential for developing and operationalizing an approach in the field. The method has the potential to integrate highly technical knowledge from scientists, and the views of non-scientists, to make better-informed management and planning decisions and to provide reasonable assurance to justify those decisions. The tool can be used to prevent conflicts among stakeholders and/or between uses and users and the environment, and makes it possible to integrate all the existing background data in thematic maps and identifies the human activities that use the areas, resources and services. The EPSS tool can save time and resources, aid in the decision-making process and make the decision process more transparent and consistent. It has the potential to make the governance of the marine area more logical, simple, fast and therefore more cost effective. The tool has been developed to be flexible in its approach, this means that it can be easily adapted to be used internationally and to allow for it to be adaptable to future changes. It combines the many aspects required for a holistic approach to marine management, from the inclusion of governance and stakeholder views, to the need for, and use of, monitoring information. In marine management, there will always be a need for robust and scientifically and legally defendable science to inform management. The increasingly large spatial scales that are addressed by policy makers, and the reduction in funding, means that new methods are needed to provide the evidence base which this tool helps to provide, and can be applied worldwide. The developed toolbox is an important step towards such an integrated, holistic ecosystem based approach for marine management, demonstrating that a single tool can bring together the legislative, environmental and economic considerations. The tool is a method to undertake the assessments that are currently being carried out by separate organisations, to combine in a single process that is consistent and transparent and on a quicker timescale helping to reduce costs.

Thesis (Ph. D.)--University of Sydney, 1999.
Title from title screen (viewed Apr. 21, 2008). Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the Dept. of Chemical Engineering, Graduate School of Engineering. Includes bibliography. Also available in print form.

Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2009.
Title from electronic title page (viewed Oct. 5, 2009). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Marine Sciences." Discipline: Marine Sciences; Department/School: Marine Sciences.

ABSTRACT This work examined the role of micro-organisms in the biogeochemical cycling of selenium within the benthic ecosystem of Lake Macquarie, a coastal lake in New South Wales with a history of anthropogenic heavy metal contamination. Certain micro-organisms possess the ability to oxidise or reduce selenium (Fleming and Alexander, 1973; Doran and Alexander, 1977), and microbial volatilisation of selenium from contaminated sediments and soils utilising naturally-occurring microflora has been shown in overseas research (Thompson-Eagle and Frankenberger, 1992) to be a potentially effective remediation strategy. In examining the impact of micro-organisms upon the oxidation state of selenium in Lake Macquarie sediments, this work also investigated and characterised selenium (and heavy metal) concentrations, speciation and geochemical phase associations (an indicator of potential bioavailability) in the sediments. Seven distinct bacterial species indigenous to Lake Macquarie were identified in this work with the ability to reduce selenium as selenite to elemental selenium, and selenium as selenate to organic forms of selenium, including volatile methylated selenium compounds. Metabolic parameters calculated for these organisms compared favourably with those reported in the literature by other researchers. Mixed populations of sediment micro-organisms were also isolated and studied in this work for their selenite and selenate reduction abilities. Total reduction of added selenite at levels up to 100 mg/L was recorded for a number of the organisms studied in this work. A maximum specific uptake rate for selenite of 3040 mgSe(IV).(gcells)-1.(h)-1 for one isolate (Shewanella putrefaciens) was determined, exceeding rates reported in the literature by other authors. Use of the indigenous micro-organisms from Lake Macquarie for the bioremediation of selenium containing waste streams was also examined in this work and selenium reduction in an immobilised cell reactor was demonstrated with such organisms. Concentrations, speciation, sediment core profiles and geochemical phase associations for selenium were determined for sediment samples collected at a variety of sites throughout Lake Macquarie and from Wyee Creek, a selenium-impacted fluvial input to the lake. The maximum concentration of selenium obtained in this work for the lake proper was 4.04 mg/kg, considerably lower than values reported over a decade ago (Batley, 1987) but consistent with reported reductions of selenium input into the lake from the lead-zinc smelter. Selective extraction methodology (Tessier et al. and BCR methods) studied geochemical phase association of selenium in Lake Macquarie sediments and found up to 44% of selenium was in bioavailable forms. Of interest and environmental concern was levels of selenium found in sediments of Wyee Creek, which previously received overflows from the ash dam associated with the Vales Point Power Station. Sediment selenium levels of up to 300 mg/kg were determined for this creek. These were an order of magnitude or more greater than those recorded for the lake itself and are of concern as to the potential impact on benthic organisms and those animals, including humans, who consume them. While this work can only provide a 'snapshot' of conditions within Lake Macquarie at the time of the sampling events recorded herein, it does make several important contributions to the understanding of selenium biogeochemistry in Lake Macquarie. These include: presentation of the hypothesis that selenium levels in surficial sediments being deposited in the north of the lake have decreased in recent years as a result of selenium reduction measures undertaken by the lead-zinc smelter; determination that up to 44% of selenium in surficial sediments from the lake is associated with sediment phases in which selenium has the potential to become remobilized and hence possibly bioavailable; and documentation of selenium concentrations in Wyee Creek, identifying the area as having selenium concentrations an order of magnitude or more greater than the lake itself. Concerning the role played by microorganisms in the biogeochemical cycling of selenium in Lake Macquarie, this work has: identified individual isolated and mixed cultures of bacteria that can reduce selenium as selenite to lower oxidation states; identified individual isolated and mixed cultures of bacteria that can reduce selenium as selenate to lower oxidation states; identified volatile methylated selenium compounds in the headspace gases of microorganisms reducing selenate; determined Minimum Inhibitory Concentrations for selenate and selenite for organisms isolated from Lake Macquarie; identified casein hydrolysate as a preferred carbon source for selenium reducing microorganisms from Lake Macquarie; and demonstrated that bioremediation of selenium contaminated waste streams using indigenous organisms from Lake Macquarie is feasible on the laboratory scale. Further research areas suggested by this work include: additional investigations of elevated selenium levels in Wyee Creek sediments; determination of the role of microbes in in-situ selenium reduction; and optimisation of selenium biotreatment/bioremediation of selenium-containing waste streams and sediments. In summary, this work, in rejecting the null hypothesis that the oxidation states of selenium in sediments from Lake Macquarie, NSW, are independent of microbial activity and accepting the alternate hypothesis that these oxidation states are not independent of microbial activity, contributes to the understanding of the role of microorganisms in the biogeochemical cycling of selenium, having applicability to both the specific ecosystem of Lake Macquarie, NSW, and also to selenium cycling in the environment in general. In addition, this work has identified selenium contamination in Wyee Creek, one of the fluvial inputs to Lake Macquarie, which was previously been undocumented in the literature and which may pose significant potential risk to humans and the ecosystem due to sediment selenium levels one or more orders of magnitude higher than those recorded in the lake itself. Finally, this work has also identified a number of microorganisms indigenous to Lake Macquarie with the ability to reduce selenium from toxic, mobile forms to less toxic, immobile or volatile forms, and these organisms have been shown to have the potential for use in treatment of selenium contaminated waste streams and also in the bioremediation of selenium-contaminated sediments.

ABSTRACT This work examined the role of micro-organisms in the biogeochemical cycling of selenium within the benthic ecosystem of Lake Macquarie, a coastal lake in New South Wales with a history of anthropogenic heavy metal contamination. Certain micro-organisms possess the ability to oxidise or reduce selenium (Fleming and Alexander, 1973; Doran and Alexander, 1977), and microbial volatilisation of selenium from contaminated sediments and soils utilising naturally-occurring microflora has been shown in overseas research (Thompson-Eagle and Frankenberger, 1992) to be a potentially effective remediation strategy. In examining the impact of micro-organisms upon the oxidation state of selenium in Lake Macquarie sediments, this work also investigated and characterised selenium (and heavy metal) concentrations, speciation and geochemical phase associations (an indicator of potential bioavailability) in the sediments. Seven distinct bacterial species indigenous to Lake Macquarie were identified in this work with the ability to reduce selenium as selenite to elemental selenium, and selenium as selenate to organic forms of selenium, including volatile methylated selenium compounds. Metabolic parameters calculated for these organisms compared favourably with those reported in the literature by other researchers. Mixed populations of sediment micro-organisms were also isolated and studied in this work for their selenite and selenate reduction abilities. Total reduction of added selenite at levels up to 100 mg/L was recorded for a number of the organisms studied in this work. A maximum specific uptake rate for selenite of 3040 mgSe(IV).(gcells)-1.(h)-1 for one isolate (Shewanella putrefaciens) was determined, exceeding rates reported in the literature by other authors. Use of the indigenous micro-organisms from Lake Macquarie for the bioremediation of selenium containing waste streams was also examined in this work and selenium reduction in an immobilised cell reactor was demonstrated with such organisms. Concentrations, speciation, sediment core profiles and geochemical phase associations for selenium were determined for sediment samples collected at a variety of sites throughout Lake Macquarie and from Wyee Creek, a selenium-impacted fluvial input to the lake. The maximum concentration of selenium obtained in this work for the lake proper was 4.04 mg/kg, considerably lower than values reported over a decade ago (Batley, 1987) but consistent with reported reductions of selenium input into the lake from the lead-zinc smelter. Selective extraction methodology (Tessier et al. and BCR methods) studied geochemical phase association of selenium in Lake Macquarie sediments and found up to 44% of selenium was in bioavailable forms. Of interest and environmental concern was levels of selenium found in sediments of Wyee Creek, which previously received overflows from the ash dam associated with the Vales Point Power Station. Sediment selenium levels of up to 300 mg/kg were determined for this creek. These were an order of magnitude or more greater than those recorded for the lake itself and are of concern as to the potential impact on benthic organisms and those animals, including humans, who consume them. While this work can only provide a 'snapshot' of conditions within Lake Macquarie at the time of the sampling events recorded herein, it does make several important contributions to the understanding of selenium biogeochemistry in Lake Macquarie. These include: presentation of the hypothesis that selenium levels in surficial sediments being deposited in the north of the lake have decreased in recent years as a result of selenium reduction measures undertaken by the lead-zinc smelter; determination that up to 44% of selenium in surficial sediments from the lake is associated with sediment phases in which selenium has the potential to become remobilized and hence possibly bioavailable; and documentation of selenium concentrations in Wyee Creek, identifying the area as having selenium concentrations an order of magnitude or more greater than the lake itself. Concerning the role played by microorganisms in the biogeochemical cycling of selenium in Lake Macquarie, this work has: identified individual isolated and mixed cultures of bacteria that can reduce selenium as selenite to lower oxidation states; identified individual isolated and mixed cultures of bacteria that can reduce selenium as selenate to lower oxidation states; identified volatile methylated selenium compounds in the headspace gases of microorganisms reducing selenate; determined Minimum Inhibitory Concentrations for selenate and selenite for organisms isolated from Lake Macquarie; identified casein hydrolysate as a preferred carbon source for selenium reducing microorganisms from Lake Macquarie; and demonstrated that bioremediation of selenium contaminated waste streams using indigenous organisms from Lake Macquarie is feasible on the laboratory scale. Further research areas suggested by this work include: additional investigations of elevated selenium levels in Wyee Creek sediments; determination of the role of microbes in in-situ selenium reduction; and optimisation of selenium biotreatment/bioremediation of selenium-containing waste streams and sediments. In summary, this work, in rejecting the null hypothesis that the oxidation states of selenium in sediments from Lake Macquarie, NSW, are independent of microbial activity and accepting the alternate hypothesis that these oxidation states are not independent of microbial activity, contributes to the understanding of the role of microorganisms in the biogeochemical cycling of selenium, having applicability to both the specific ecosystem of Lake Macquarie, NSW, and also to selenium cycling in the environment in general. In addition, this work has identified selenium contamination in Wyee Creek, one of the fluvial inputs to Lake Macquarie, which was previously been undocumented in the literature and which may pose significant potential risk to humans and the ecosystem due to sediment selenium levels one or more orders of magnitude higher than those recorded in the lake itself. Finally, this work has also identified a number of microorganisms indigenous to Lake Macquarie with the ability to reduce selenium from toxic, mobile forms to less toxic, immobile or volatile forms, and these organisms have been shown to have the potential for use in treatment of selenium contaminated waste streams and also in the bioremediation of selenium-contaminated sediments.

An understanding of the reactivity of hydrophobic organic micropollutants (HOMs) is of paramount importance to water quality managers because of their toxicity, persistence, and liability to bioaccumulate. In this study, the role played by the main estuarine variables (organic matter, suspended particulate matter [SPM], particle type and salinity) on HOM behaviour was investigated by employing samples from estuaries with different geochemical signatures (Chupa, Russia, and the Dart, Plym, Beaulieu and Carnon, U K ) . A laboratory-based technique was developed for the determination of the solubility and sorptive behaviour of HOMs using 14C-labelled, beta-emitting organic compounds (2,2\5,5'-tetrachlorobiphenyl (2,2’5,5'-TCB), bis(2-ethylhexyl)phthalate ester (DEHP), and benzo[a]pyrene (BaP)) coupled with liquid scintillation counting. The results indicate that relative solubility is mainly dependent upon the type of dissolved organic carbon (DOC) present, not its concentration, and is reduced with increasing salinity. The uptake of 2,2’5,5'-TCB and BaP by particles is time dependent with a system response time (the time required to achieve 63% of the new equilibrium) of about 0.37 hours for 2,2',5,5’-TCB and 0.02 hours for BaP. The adsorption, expressed as particle-water partition coefficients, KDS, is to a varying extent dependent on DOC, salinity and particle characteristics (iron/manganese hydroxides, particulate carbon and specific surface area). Adsorption is best defined by a linear isotherm and is enhanced in sea water compared with river water owing to a reduction in charge on particle surfaces at high ionic strengths. This effect has been quantified using an adsorption salting constant, Gp, whose values are typically in the range 0.4-2 L mol-2 The inverse relationship between KD and SPM concentration, an effect well documented in the literature, has been defined by a simple power law (KD = a SPM-b where a and b are site and compound-specific constants). Typical values for a and b are approximately 4x10^ and 0.6 for 2,2',5,5'- TCB, 50x105 and 1.0 for DEHP, and 2x105 and 0.5 for BaP, respectively. Empirical parameterisation of these effects are extremely useful for encoding into numerical transport and distribution models, and their application is demonstrated in this thesis by calculating the retention of HOMs by estuaries.

Geochemical and geophysical approaches have been used to investigate the freshwater and saltwater dynamics in the coastal Biscayne Aquifer and Biscayne Bay. Stable isotopes of oxygen and hydrogen, and concentrations of Sr2+ and Ca2+ were combined in two geochemical mixing models to provide estimates of the various freshwater inputs (precipitation, canal water, and groundwater) to Biscayne Bay and the coastal canal system in South Florida. Shallow geophysical electromagnetic and direct current resistivity surveys were used to image the geometry and stratification of the saltwater mixing zone in the near coastal (less than 1km inland) Biscayne Aquifer. The combined stable isotope and trace metal models suggest a ratio of canal inputprecipitation- groundwater of 38% - 52% - 10% in the wet season and 37% - 58% - 5% in the dry season with an error of 25%, where most (20%) of the error was attributed to the isotope regression model, while the remaining 5% error was attributed to the Sr2+/Ca2+ mixing model. These models suggest rainfall is the dominate source of freshwater to Biscayne Bay. For a bay-wide water budget that includes saltwater and freshwater mixing, fresh groundwater accounts for less than 2% of the total input. A similar Sr2+/Ca2+ tracer model indicates precipitation is the dominate source in 9 out of 10 canals that discharge into Biscayne Bay. The two-component mixing model converged for 100% of the freshwater canal samples in this study with 63% of the water contributed to the canals coming from precipitation and 37% from groundwater inputs ± 4%. There was a seasonal shift from 63% precipitation input in the dry season to 55% precipitation input in the wet season. The three end-member mixing model converged for only 60% of the saline canal samples possibly due to non-conservative behavior of Sr2+ and Ca2+ in saline groundwater discharging into the canal system. Electromagnetic and Direct Current resistivity surveys were successful at locating and estimating the geometry and depth of the freshwater/saltwater interface in the Biscayne Aquifer at two near coastal sites. A saltwater interface that deepened as the survey moved inland was detected with a maximum interpreted depth to the interface of 15 meters, approximately 0.33 km inland from the shoreline.

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A contaminação por hidrocarbonetos (HCs) do petróleo em regiões costeiras marinhas, como os estuários, é considerada uma das mais importantes e impactantes, devido aos danos que esses elementos podem ocasionar aos organismos e ao homem. O objetivo do presente estudo foi investigas, pela primeira vez, os hidrocarbonetos nos sedimentos superficiais do sistema estuarino do Rio Formoso (SERF), litoral Sul do estado de Pernambuco – Brasil. Os compostos de hidrocarbonetos alifáticos (HAs) foram determinados em cromatógrafo a gás (GC) Agilent Tecnologies 7820A, acoplado a um detector de ionização de chamas (DIC) e os compostos de hidrocarbonetos policíclicos aromáticos (HPAs) foram determinados no mesmo cromatógrafo, porém acoplado a um espectrômetro de massas 5975 (MS) em modo de monitoramento de íons selecionados (SIM). A concentração de alifáticos totais (∑Alif) nos sedimentos do SERF variou entre 1,37 e 126,64 μg g-1 peso seco (ps), com as concentrações de n-alcanos totais (Σn-Alc) entre 0,51 e 27,5 μg g-1 ps, oriundos principalmente de fontes biogênicas, como vegetais superiores. A concentração de HPAs (Σ16HPAs) variou entre 3,80 e 500,3 ng g-1 ps, provenientes de fontes petrogências e pirogênicas As concentrações de hidrocarbonetos alifáticos e aromáticos detectados nos sedimentos do sistema estuarino do Rio Formoso foram consideradas baixas, quando comparadas com outras áreas estudadas ao redor do mundo e aos índices propostos por estudos e agências reguladoras nacionais e internacionais, sugerindo um ambiente com pouco impacto sobre a biota. Contudo, a presença de compostos como HPAs é um indicativo de ação antrópica sobre o sistema, sendo importante a implantação e manutenção de um programa de monitoramento na área, quanto aos hidrocarbonetos, para avaliar os possíveis impactos que a presença desses compostos possam ocasionar sobre o SERF e garantir a conservação continuada de um estuário de tamanha importância ecológica, econômica e social.
The contamination by hydrocarbons (HCs) of oil in marine coastal regions, such as estuaries, is considered one of the most important and impactful due to the damage that these elements may cause to the bodies and man. The aim of this study was investigas for the first time, the hydrocarbons in the surface sediments of the estuarine system of the Formoso river (SERF), South coast of the state of Pernambuco - Brazil. Aliphatic hydrocarbon compounds (HAs) were determined on a gas chromatograph (GC) Agilent Technologies 7820A coupled to a flame ionization detector (FID) and polycyclic aromatic hydrocarbon compounds (PAH) were determined in the same chromatograph, however coupled a mass spectrometer 5975 (MS) in selected ion monitoring mode (SIM). The concentration of total aliphatic (ΣAlif) in SERF sediments ranged between 1.37 and 126.64 μg g-1 dry weight (dw), with total n-alkanes concentrations (Σn-Alc) between 0.51 and 27.5 μg g-1 dw, mainly from biogenic sources such as higher plants. The concentration of PAHs (Σ16HPAs) ranged from 3.80 to 500.3 ng g-1 dw, from petrogências sources and pyrogenic Hydrocarbon concentrations aliphatic and aromatic detected in the sediments of the estuarine system of the Formoso river were considered low compared with other areas studied around the world and the indices proposed by studies and national and international regulatory agencies, suggesting an environment with little impact on the biota. However, the presence of compounds such as PAHs is indicative of human action on the system, it is important to establishing and maintaining a monitoring program in the area, as hydrocarbons, to assess the possible impact that the presence of these compounds can cause on SERF and ensure the continued conservation of an estuary of such ecological, economic and social.