The influence of crude oil-contaminated and remediated sites on agrifood production is not clearly understood. To address this knowledge gap, the research was divided into two stages involving: (1) assessment of the efficiency of two bioremediation strategies to support hydrocarbons degradation as well as agrifood production with the initial analysis of the experimental materials, and (2) evaluation of the effect of different crude oil remediation intervention values (CRIV) on selected vegetables (Brassica juncea, Brassica oleracea, Lactuca sativa and two different cultivars of Solanum lycopersicum). Results from the first stage showed that the crude oil used had a pristane/phytane ratio of 0.98 (within the 0.8 – 3.0 range of most crude oils), higher concentrations of C10 – C14, C15 – C20 and C21 – C27 alkanes than the C28 – C36 alkanes including higher concentrations of two of the US EPA priority pollutant polycyclic aromatic hydrocarbons (PAHs) - phenanthrene and anthracene. Four treatments were prepared in which weekly tillage enhanced the degradation of C15 – C20 and C21 - C27 alkanes in the Remediation by Enhanced Natural Attenuation (RENA) treatment. The two bioremediation strategies (RENA and bioaugmentation) enhanced PAHs degradation compared with the remediation-study control treatment while only RENA application among the two approaches supported the growth of B. juncea. Although there was no statistical significant difference (p > 0.05) between the major dietary mineral contents of samples from the various treatments compared with the control treatment samples, RENA application affected the Cr, Zn and Pb contents. Meanwhile, the Ca/P (> 1.0) and Na/K (< 0.60) ratios of all the harvested samples imply that they provide a good source of these minerals for bone formation and would not contribute to high blood pressure. The crude oil used also deterred the attack of juvenile caterpillars of cabbage white butterfly. Findings from the second stage revealed that the yield of the green leafy vegetables including one of the selected tomato cultivars (Micro-Tom), was in most cases impaired at CRIV ≥ 3,000 mg/kg total petroleum hydrocarbon (TPH). Compared with the control treatment samples’ composition, crude oil stress at 10,000 mg/kg TPH enhanced the concentration of K, Mn and crude protein of B. oleracea and L. sativa as well as the sucrose, total sugars, total phenolics and total flavonoids contents of the latter vegetable. Sucrose was also only detected in M82 tomato cultivar samples from the crude oil-containing treatments. The Cd content of B. oleracea, Pb contents of: L. sativa and M82 tomato harvested samples were all below the FAO/WHO Codex Alimentarius Commission 2015 recommended maximum levels. However, tartaric acid was only detected in B. oleracea and L. sativa samples from the 10,000 mg/kg TPH treatment as well as in M82 tomato cultivar samples from the treatment involving CRIV of 5,000 mg/kg TPH. Generally, the yield of these crops in response to crude oil contamination varied in which B. juncea had the least tolerance to crude oil stress among the green leafy vegetables tested. Most of the quality parameters in the two tomato cultivars were not affected by CRIV between 750 - 5,000 mg/kg TPH with p-xylene having the greatest toxic potential among the VOCs emitted from the 5,000 mg/kg TPH treatment. The research findings, under the experimental conditions, indicated the effectiveness of RENA for the degradation of low molecular weight PAHs and its agricultural benefits. They also suggest that crude oil-contaminated sites at ≤ 3,000 mg/kg TPH present a similar growing environment to a clean site for agrifood production and the possibility that crude oil stress at 10,000 mg/kg TPH could enhance crop quality. Nonetheless, the contribution of bio- accumulated PAHs in these crops to the food chain demands further investigation.

L'imagerie simultanée IRM-TEP ouvre de nouvelles perspectives pour l'exploration in vivo des fonctions cérébrales. Pour une quantification du signal de tomographie par émission de positons, il est indispensable de corriger l'atténuation tissulaire des photons. En l'absence de mesure tomodensitométrique en IRM-TEP, les cartes de radiodensité ne sont pas disponibles. Il est nécessaire de trouver une méthode fiable et exacte pour générer une carte d'atténuation du sujet à partir des données disponibles TEP ou IRM. Nous avons développé une technique qui génère une carte d'atténuation propre à un sujet par une approche multi-atlas (MaxProb). Cette approche utilise uniquement l'image IRM T1 du sujet, couramment acquise dans les protocoles cliniques et de recherche, ainsi qu'une base de données d'atlas.L'évaluation de MaxProb montre de très bonnes performances, le biais de quantification de l'image TEP étant réduit à moins de 2%. Cette évaluation pratiquée sur une acquisition dynamique TEP a en outre montré qu'une carte d'atténuation imparfaite , combinée à une distribution spatiale inhomogène du traceur au cours du temps, peut produire un biais non-constant des cinétiques TEP. Cela impacte les paramètres biologiques estimés par modélisation sur les cinétiques TEP. La méthode MaxProb n'est cependant pas affectée par ce phénomène. MaxProb fournit une quantification fiable des paramètres physiologiques estimés par modélisation même lorsque le cervelet est utilisé comme région de référence. Notre évaluation a aussi porté sur la reproduction par simulation d'une étude réaliste d'imagerie TEP d'une décharge dynamique d'un neurotransmetteur. Par rapport à la méthode de correction d'atténuation standard (UTE), MaxProb améliore la sensibilité de détection des variations physiologiques, même faibles. Ceci ouvre la voie à de nouveaux protocoles d'imagerie dynamique et simultanée en IRM-TEP, augmentant la puissance de détection, et réduisant les nombres de sujets nécessaires à la mise en évidence d'un phénomène neurophysiologique ou d'un dysfonctionnement physiopathologique / Simultaneous PET-MR imaging brings new perspectives for understanding many aspects of brain function. To achieve PET-MR’s full potential, accurate brain attenuation correction (AC) is required for absolute PET quantification. In PET-MR scanners, radiodensity maps are not directly available unlike in PET/CT, and the attenuation map has to be derived from the MR data (MRAC methods). In this thesis, I have developed a multi-atlas procedure that produces a subject-specific µ-map for brain imaging (MaxProb) via multiple registrations of CT-MR atlas pairs to an MR target. The solution proposed only requires a T1-weighted MRI of the subject, commonly acquired in clinical and research protocols, and a CT-MR atlas database. The MaxProb method permits generating pseudo-CT images for brain MRAC with high accuracy. Results obtained show very good performance of the method and a bias in reconstructed PET of less than 2%. I have also demonstrated for the first time that an inaccurate attenuation correction map, combined with inhomogeneous spatial tracer distribution as is regularly encountered in dynamic brain PET, can lead to a non-constant bias of the activity measure across time, and this can distort kinetic parameter estimation. MaxProb AC is not affected by this phenomenon. Accurate quantification is also achieved with MaxProb on physiological parameters estimated from kinetic modelling, even when cerebellum (surrounded by bone) is used as reference region: In a simulation study, I have shown that compared to a standard approach (UTE), MaxProb multi-atlas MRAC enhances sensitivity to detect physiological variations in binding parameters, opening the way for new dynamic PET studies on simultaneous PET-MR systems

L'atténuation est un paramètre clé dans l'évaluation de l'aléa sismique car elle contrôle l'amplitude et la durée du mouvement du sol. Deux mécanismes contribuent à l'atténuation des ondes sismiques courte-période (f>1Hz, avec f la fréquence) : (1) l'absorption, quantifiée par son facteur de qualité Qi(f); et (2) le scattering, quantifié par Qsc(f). L'objectif principal de cette thèse est de cartographier l'atténuation sismique en France Métropolitaine en déterminant l'importance relative de ces deux processus. Pour mener à bien cette tâche, nous avons modélisé le transport de l'énergie sismique multi-diffusée - aussi appelée coda sismique - à l'aide de l'équation de transfert radiatif dans un milieu présentant des variations latérales des propriétés de diffusion et d'absorption. En utilisant une approche perturbative, nous avons calculé les noyaux de sensibilité de l'intensité de la coda sismique à des variations spatiales de Qi(f) et Qsc(f) à 2-D, dans le cas où la diffusion est isotrope. Dans un deuxième temps, nous avons mesuré la vitesse de décroissance énergétique de la coda sismique, quantifiée par le facteur de qualité de la coda Qc(f), sur plus de 120000 formes d'onde collectées en France, en Belgique et sur l'ensemble de l'arc alpin. L'approche théorique développée dans cette thèse nous a permis d'établir une relation approximative entre Qc et Qi. Cette relation prend la forme d'une intégrale de Qi sur le rai direct reliant la source à la station. Cette approximation a été utilisée afin de cartographier pour la première fois les variations régionales de l'absorption entre 1 et 32 Hz dans les Alpes et en France Métropolitaine. Nos résultats mettent en évidence de très fortes variations latérales (±30%) de l'absorption. À basse fréquence (f~1Hz), une corrélation claire apparaît entre la géologie de surface et les structures d'absorption : les zones de forte absorption se localisent sur les séries sédimentaires peu consolidées tandis que les régions de faible absorption correspondent au socle affleurant dans le Massif Armoricain, le Massif Central et dans les chaînes de montagne comme les Pyrénées et les Alpes. À haute fréquence (f~24Hz), la corrélation entre géologie de surface et atténuation disparaît. Nous avons formulé l'hypothèse que la dépendance fréquentielle de la structure en atténuation est due à un changement du contenu ondulatoire de la coda sismique avec la fréquence. Ainsi la sensibilité de la coda aux structures profondes de la croûte augmenterait avec la fréquence. Enfin, nous avons initié la mise en oeuvre des noyaux de sensibilité isotrope exacts à 2-D afin d'obtenir une tomographie d'absorption. L'inversion des mesures de Qc par décomposition en valeurs singulières nous a permis de construire la première tomographie d'absorption qui tienne compte de toute la sensibilité des trajets des ondes multi-diffusées. La carte préliminaire d'absorption obtenue pour les Pyrénées est prometteuse. Nos résultats fournissent des bases théoriques solides pour l'inversion linéarisée de Qsc et Qi à partir de la coda sismique. Ils offrent également des informations complémentaires aux tomographies de vitesse et des perspectives d'amélioration de la régionalisation des calculs de l'aléa sismique en France Métropolitaine. / Attenuation is a key parameter for seismic hazard assessment. It plays an important role in the observed variability of ground motion amplitude and duration. There are two main causes for attenuation of short period seismic waves (f>1Hz, with f the frequency) : (1) absorption, quantified by the quality factor Qi ; and (2) scattering, quantified by Qsc. The main objective of this thesis is to map the seismic attenuation in Metropolitan France and to determine the relative importance of these two processes. To model the transport of multiply-scattered seismic waves - also known as the seismic coda - we employ a scalar version of the radiative transfer equation with spatially dependent absorption and scattering properties. The sensitivity kernels of the coda intensity to spatial variations of Qi and Qsc are computed in 2-D isotropically and anisotropically scattering media. The coda quality factor Qc (f) - quantifying the decay rate of the seismic coda energy - have been estimated on a collection of 120000 waveforms recorded in France, Belgium and in the Alpine range. According to the theory developed in this thesis, we establish a linearized approximate relation between the coda quality factor Qc (f) and the absorption quality factor Qi. This relation is expressed as an integral along the direct ray path connecting the source to the station. This approximation is used to map regional variations of absorption in the Alps and in Metropolitan France between 1 and 32Hz. Our maps reveal strong lateral variations (±30%) of absorption in the crust. At low frequency (f~1Hz), the correlation between sedimentary deposits and high absorption regions is clear : strong absorption zones are localized on the poorly consolidated sedimentary series while low absorption regions correspond to the basement which outcrops in the Massif Armoricain, the Massif Central and in the mountain ranges as the Pyrenees or the Alps. At high frequency (f~24Hz), the correlation between surface geology and absorption structures tends to disappear. We hypothesize that the frequency dependence of the attenuation structure is caused by a change of the wavefield composition which accentuates the sensitivity of the coda to the deeper parts of the medium as the frequency increases. Finally, we initiate the implementation of the exact 2D isotropic sensitivity kernels to retrieve the crustal absorption structures. Using the linear relation between Qc and Qi, we obtain the first absorption map which takes into account the precise spatio-temporal sensitivity of coda waves. The inverse problem is solved with a singular value decomposition approach. The preliminary map of Qi for the Pyrenees is promising. Our results constitute a solid theoretical basis to develop linearized inversions of Qsc and Qi from the analysis of the seismic coda. They also significantly improve the knowledge of the regional variations of seismic attenuation in Metropolitan France. Our maps provide new insights on the crustal structure of the Alpine Range in complement to seismic velocity images. These attenuation maps have direct implication for the design of future seismic hazard maps.

Le 7 août 2009, un pipeline transportant du pétrole brut s'est rompu, provoquant le déversement de 5100 m3 de brut sur 5 hectares de la Réserve Naturelle des Coussouls de Crau. Le pétrole a atteint l'aquifère et a formé un LNAPL qui alimente un panache de polluants dissous, dont le benzène, composé cible car toxique. Cette étude vise à montrer que la biodégradation du pétrole (biostimulation ou atténuation naturelle), en particulier des composés dissous, est une mesure efficace de gestion à long terme des risques pour la ressource en eau. Une première étude en microcosmes a montré la biodégradation, même dans les conditions les plus réductrices, des composés cibles dont le benzène. Cette étude a confirmé que la disponibilité en oxydant est un facteur limitant et que le phosphate est un levier puissant pour stimuler la croissance bactérienne. Une seconde étude sur site a prouvé la faisabilité de la biostimulation par injection de nitrate et de phosphate dans la nappe et son efficacité pour l'abattement des concentrations en polluants dissous. L'utilisation du radon comme traceur pour estimer la saturation en pétrole dans l'aquifère a été évaluée dans une troisième étude. La facilité de mise en oeuvre de la méthode ainsi que les résultats offrent des perspectives intéressantes pour l'optimisation des systèmes de pompage-écrémage sur des sites ayant un NAPL. Une dernière étude portant sur la mise en place des processus d'oxydoréduction et de dégradation sur site a montré une évolution rapide des conditions après l'accident, traduisant un environnement favorable à l'atténuation naturelle. La dégradation in situ du benzène a été mise en évidence via des mesures isotopiques. / On August 7, 2009 a pipeline transporting crude oil broke in the heart of the Nature Reserve of Coussouls de Crau, and 5,100 m3 of oil were spilled over 5 hectares. Oil infiltrated through the subsurface and reached the most important regional aquifer where it formed a LNAPL that created a plume of dissolved compounds. Among these compounds, benzene is of particular concern because of its toxicity and high solubility. This thesis aims at showing that biodegradation of crude oil, especially of dissolved compounds, is a good option for long-term management of risks for the water resource. A first study in microcosms demonstrated biodegradation of targeted compounds, including benzene, even under the most reducing conditions. This study also revealed that the availability of electrons acceptors was a limiting factor and that phosphate was a powerful lever to stimulate bacterial growth. An on-site study proved the feasibility of biostimulation by nitrate and phosphate injection in the aquifer and showed that biostimulation was efficient to reduce concentrations of dissolved compounds. Naturally occurring radon was used as a tracer to estimate oil saturation in the saturated zone in a third study. The ease of implementation of this method and the results offer interesting perspectives to optimize the yield of pump-and-skim systems in LNAPL-contaminated sites. The last study focused on the implementation of redox processes and degradation in the saturated zone after the spill. This study showed that processes quickly evolved and that conditions were favorable to natural attenuation. In situ benzene degradation was proven by the measurements of stable isotopes of carbon.

Orientador: Marcelo Brocchi / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T16:38:13Z (GMT). No. of bitstreams: 1 Neves_MeirieledaSilvadas_M.pdf: 2620199 bytes, checksum: 70b2df72cfdb93196c91a87c813e12e9 (MD5) Previous issue date: 2015 / Resumo: O gênero Salmonella pertence à família Enterobacteriaceae que agrupa bacilos Gram-negativos, anaeróbios facultativos, fermentadores e geralmente flagelados. S. enterica é um dos patógenos de origem alimentar mais prevalente, sendo que infecções causadas por essa bactéria podem estar relacionadas a praticamente todos os tipos de alimentos. O trabalho foi proposto com o intuito de realizar a caracterização fenotípica e molecular de linhagens atenuadas de Salmonella enterica Typhimurium para genes codificadores de proteínas associadas ao nucleóide (NAPs Nucleoid associated Proteins). As características fenótipicas dos mutantes nulos de Salmonella enterica para os genes ihfA ou ihfB, codificadores das subunidades A e B de IHF, foram avaliadas através de crescimento in vitro, motilidade, sobrevivência frente ao estresse nutricional (sobrevivência em fase estacionária), sob condições ácidas, na presença de sais biliares e quanto à capacidade de invasão e sobrevivência em macrófagos (linhagem J774A.1). Testes de confirmação da atenuação e avaliação da capacidade de induzir proteção em caso de infecção por S. enterica foram realizados utilizando o modelo murino. Os mutantes não apresentaram diferença no crescimento in vitro e na capacidade de sobreviver na presença de sais biliares em comparação com a linhagem selvagem. As linhagens mutantes para os genes ihfA ou ihf ihf ihfB) apresentaram uma menor capacidade de sobrevivência sob condições ácidas quando comparadas com a linhagem selvagem. A motilidade dos mutantes simples também foi reduzida. Os mutantes simples e duplo apresentaram maior capacidade de sobreviver sob estresse nutricional quando comparados com a linhagem selvagem. O mutante para o gene ihfA e o duplo mutante apresentaram um aumento na capacidade de invadir macrófagos. ihf ihfB mostraram uma capacidade aumentada em sobreviver no interior de macrófagos quando comparadas com a linhagem selvagem. Os mutantes nulos viii de Salmonella enterica para os genes ihfA ou ihfB apresentam atenuação, em diferentes graus, quanto à virulência e apresentaram capacidade de induzir proteção no modelo murino de infecção por S. enterica. Esses resultados demonstram que essa proteína apresenta função relacionada com a virulência bacteriana, sendo um importante alvo de estudo na busca de linhagens atenuadas / Abstract: The genus Salmonella belongs to the Enterobacteriaceae family that comprises Gram-negative bacillus, facultative anaerobe, fermenting and generally flagellate. S. enterica is one of the most prevalent food-borne pathogen, and infections caused by this bacterium can be associated to almost all types of food. The work was proposed with the purpose of performing phenotypic and molecular characterization of attenuated strains of Salmonella enterica Typhimurium for genes encoding proteins associated with the nucleoid (NAPs - Nucleoid associated Proteins). The phenotypic characteristics of the null mutants of Salmonella enterica for genes ihfA or ihfB, encoding the A and B subunits of IHF, were evaluated by in vitro growth, motility, survival under nutritional stress (survival in the stationary phase), under acidic conditions, in the presence of bile salts and for the ability of invasion and survival in macrophages (J774A.1 strain). Attenuation tests and evaluation of the capacity to induce protection in case of infection by S. enterica were performed using the murine model. The mutants showed no difference in the in vitro growth and the ability to survive in the presence of bile salts in comparison with the wild type strain. The single mutant for ihfA or ihf ihf ihfB) showed decreased survival under acidic conditions when compared to the wild type strain. Motility of single mutants was also reduced. Single and double mutants showed higher ability to survive under nutritional stress when compared with the wild type strain. The mutant gene for ihfA and the double mutant showed an increased ability to invade ihf ihfB mutants showed an increased ability to survive within macrophages when compared with the wild type strain. Null mutants of Salmonella enterica for ihfA or ihfB genes exhibited attenuation, to varying degrees, for virulence and showed ability to induce protection in a murine model of infection by S. enterica. x These results demonstrate that this protein has function associated to bacterial virulence and is an important subject of study in search for attenuated strains / Mestrado / Genetica de Microorganismos / Mestra em Genética e Biologia Molecular

O estudo da penetração da radiação solar no meio aquático foi desenvolvido em quatro partes. Na primeira delas, voltada para a atenuação da radiação solar na coluna d’água, foram discutidos fatores de interferência e suas inter-relações. Neste sentido, foi feita uma comparação da penetração da radiação solar em ecossistemas continentais naturais e artificiais, analisando as diferenças e similaridades. O estudo comparativo da atenuação da radiação solar subaquática em toda extensão de reservatórios constituiu a segunda parte deste trabalho. A comparação foi feita entre reservatórios que apresentam proximidades de localização, mas com diferenças marcantes nos usos e ocupações nas regiões em que os mesmos estão inseridos. Na terceira parte foram apresentados dois recursos de grande utilização na obtenção das respostas imediatas do ambiente aquático, do ponto de vista óptico, diante dos impactos sofridos. O primeiro recurso foi a determinação do espectrograma da radiação solar, indicando a atenuação da radiação solar subaquática na faixa fotossinteticamente ativa (400 nm - 700 nm). O outro recurso foi a obtenção do espectro de absorção da água superficial, que permitiu o estabelecimento do “Índice de Absorção Espectral da Água”, I.A.E.A., que facilmente possibilita a detecção de fontes pontuais de poluição e contaminação. Como quarta e última parte foi proposto o desenvolvimento de um aparelho a partir da reconstrução do hidrofotômetro (Modelo Nº 268 WA 310 GM MFG & Instrument Corp. Bronx. N.Y. 10 451), onde foi introduzido e adaptado o detector fotocondutivo (PIN - 250DP) em substituição às fotocélulas anteriormente danificadas. Durante o trabalho de campo, este aparelho foi testado e foi feita a comparação com os obtidos do Quanta-meter LI-COR (LI - 185A) também utilizado neste trabalho. / The study of solar radiation penetration in aquatic environment was developed in four parts. The first one, directed to solar radiation attenuation in the water column, interference factors and their inter-relations were discussed. In this sense, a penetration comparison of the solar radiation in natural and artificial continental ecosystems was carried out, analyzing differences and similarities. The second part of this work consisted of a comparative study of underwater solar radiation in the entire reservoir. The comparison was done between reservoirs that are near to one another, but with marked differences in use and occupation within the regions where they are located. In the third part, two resources of great utilization in obtaining immediate response from the aquatic environment, from an optical point of view of the impacts experienced, were presented. The first resort was the spectrogram determination of solar radiation, which indicated the underwater solar radiation attenuation in the active photosynthetic range (400 nm - 700 nm). The other resort was the superficial water absorption spectrum, which allowed establishing the “Water Spectral Absorption Index”, I.A.E.A. that easily makes possible detection of accurate sources of pollution and contamination. The fourth and last part proposed to develop an apparatus from the construction of an underwater hydrophotometer (Model 268 WA 310 GM MFG & Instrument Corp. Bronx N.Y. 10451), where the photoconductor detector was adapted and introduced (PIN - 250DP) substituting the previously damaged photocells. During field work, this apparatus was tested and comparison was performed with data obtained from Quanta-meter LI-COR (LI - 185A), also used in this work.

This thesis deals with the problem of shielding ionizing radiation which is a beam that has enough energy to ionize an atom or a molecule of an irradiated substance. This radiation can occur in nuclear facilities such as a nuclear power plant, a particle accelerator, or in X-rays in healthcare. Until now, standard shielding materials, most often lead or concrete, have been used to protect against ionizing radiation. New trends are therefore trying to replace these materials with lighter, more effective and harmless materials. The practical part is focused on measure the data to obtain the basic properties of shielding materials, such as the attenuation factor and the buildup factor. A measuring platform is described here, which can be used to measure the data needed to calculate the attenuation factor and the buildup factor. The measurement results are compared with tabular values to determine the accuracy of the measurements. Furthermore, the results of measurements of five concrete materials from the company MICo, spol. s r.o. To obtain theoretical values, the simulation program MCNP6 was used, in which it is possible to create a model of the measuring platform, which was used in practical measurements. Next the shielding material, source and detector are defined. The result lead again to the data needed to determine the attenuation factor. The results of measurement and simulation data in MCNP6 are evaluated and graphically processed into such a form that it is possible to compare the properties of shielding materials with each other.

The work describes the design and manufacturing of a test device for post-mortem measurements of electrodes of electrochemical cells using X-ray diffraction spectroscopy. The theoretical part describes the diffractometer Rigaku Miniflex 600, for which the product is intended. At the same time, an overview of solutions in various applications is processed here in the form of a recherche. The practical part documents the current development of a new cell, on which tests were performed. Here is an overview of the influence of gases and insulating materials on the resulting data, especially distortion and attenuation. Subsequently, a new design with improved hermetic insulation and sample displacement error correction is described. The principle of operation of the manufactured cell, including the control unit and software, is elaborated in the form of technical documentation. Finally, the functionality is verified by comparing the diffractograms of the powder standards and the graphite electrodes.

The availability of light is a primary limiting factor for seagrass recovery and sustainability. Understanding not only the quantity but the quality of light reaching the bottom is an important component to successful seagrass management and the key focus of this study. This study explores the spectral properties of the sub-surface light field in four shallow Seagrass Management Areas (SMA) in Tampa Bay. Wavelength-specific photosynthetically active radiation (PAR(λ)) and the spectral light attenuation coefficient (Kd(λ)) are used to estimate the percent blue, green, and red light remaining at the bottom relative to the surface. LIDAR Bathymetry is combined with Kd(λ) to produce high-resolution maps of percent subsurface light along the seagrass deep edge. The absorptance spectra from two seagrass species together with PAR(λ) is used to calculate the photosynthetically useable radiation (PUR(λ)), a term describing the actual wavelengths of light being used by the seagrass. Based on the average annual Kd(λ) , 32% - 39% percent of PAR reached the bottom at the seagrass deep edge, while only 14% - 18% of blue light reached bottom, suggesting that seagrass may be blue-light limited. Analysis of PUR(λ) data further confirmed that seagrass are blue-light limited. Each SMA was characterized in terms of the inherent optical properties (IOP) of absorption and scatter. Tampa Bay is considered a chlorophyll-dominated estuary. However, in this study, colored dissolved organic matter (CDOM) was the major absorber of blue light, accounting for 60% of the total absorption. To infer past light conditions, the IOPs were related to parameters more commonly used in routine monitoring programs. To estimate Kd(λ) an empirically-derived model using only the total absorption and scatter coefficients was used and resulted in a good fit between measured Kd(480) and modeled Kd(480). A deck-mounted flow-through system was used to survey each SMA for CDOM and chlorophyll a fluorescence, among other properties. A series of SMA-specific predictor equations were empirically derived to relate raw fluorescence to the IOPs. The Kitchen SMA was used as a case study. Survey results show a strong connection between CDOM-rich waters and the mangrove-dominated shoreline.

Although mass coral bleaching events are generally triggered by high seawater temperatures, experiments have demonstrated that corals and reef-dwelling foraminifers bleach more readily when exposed to high energy, short wavelength solar radiation (blue, violet and ultraviolet [UVR]: Lambda ~ 280 - 490 nm). In seawater, colored dissolved organic matter (CDOM), also called gelbstoff, preferentially absorbs these shorter wavelengths, which consequently bleach and degrade the CDOM. Alteration of watersheds and destruction of coastal wetlands have reduced natural sources of CDOM to reefal waters. I tested the null hypothesis that CDOM does not differ between reefs that differ in coral health, and that water transparency to UVR is not a factor in reef health. I measured absorption of UVR and UV irradiance at various reefs in the Florida Keys that differ in distance from shore and degree of anthropogenic development of the adjacent shoreline. My results show that intact shoreline - associated reefs and inshore reefs tend to be exposed to lower intensities of UVR, and lower degrees of photic stress, than developed shoreline - associated reefs and offshore reefs. Absorption due to CDOM (ag320) was higher, and photic stress, as revealed by increased production of UV-absorbing compounds, Mycosporine - like Amino Acids (MAAs), was lower at the surface compared to the bottom. The following results support my conclusion: ag320 and UV attenuation coefficients (Kd 's) were higher at intact compared to developed shoreline - associated reefs, and at inshore compared to offshore reefs. Spectral slope, S, was higher at offshore compared to inshore reefs, indicating a higher degree of photobleaching of CDOM. Relative expression of MAAs was higher at developed compared to intact shoreline - associated reefs, at offshore reefs compared to inshore reefs, and at the surface compared to the bottom. Solar energy reaching the benthos at two inshore reefs of the same depth (6m) was approximately an order of magnitude higher at the reef near developed shoreline compared to the reef near intact shoreline, and may be due to greater degree of diffuseness of the underwater light field combined with lower ag at the developed shoreline-associated reef.