A method is presented, using calculations of the underwater light field, to examine viability of phytoplankton at depth. For this study, viability is defined as the ability of phytoplankton to harvest, and efficiently convert enough photons into primary production to overcome metabolic demands. How the available light field influences the production environment is examined. Changes in water column constituents, such as chlorophyll and colored dissolved organic matter (CDOM) concentration, alter the spectral quality and quantity of the light field at depth. Certain species with specialized survival strategies, such as assemblages of photoprotective and light-harvesting accessory pigments, may be better-suited to 'making a living' at depth in response to the spectral quality of the underwater light field. Stations for study were identified from various cruises off the West Florida Shelf that exhibited variations in chlorophyll and/or CDOM concentration, including an optically complex, red-tide station. Optical and water column constituent measurements from these stations were used to develop input parameters to Hydrolight 4.1, a radiative transfer theory model, to simulate the underwater light field and to calculate absorbed radiation by phytoplankton (ARP). Values for respiration and quantum yield from the literature were used to calculate comparative values of net photosynthesis at these stations. The effect of differences in spectral light harvesting (pigmentation), photosynthetic efficiency rates, and respiration, on viability through the water column was examined.

Colored dissolved organic matter (CDOM) is a part of total dissolved organic matter (DOM) and plays an important role in marine carbon cycling. Thus, a better description of the fates of CDOM may increase our understanding of DOM sources and sinks in marginal seas. This study aims to explore the distributions and possible controlling factors of DOM in the Taiwan Strait (TS) and the East China Sea (ECS) in the summer season. The TS is a marginal sea of interest as it receives freshwater from both Taiwan Island and Mainland China and it also connects water transports between ECS, South China Sea (SCS) and Kuroshio water (KW). The concentration of DOM is slightly higher in the western side (China coast) than in the eastern side (Taiwan coast), and the highest concentration is always found in the Minjiang plume, revealing a significant impact of river discharge. The absorption and fluorescence properties of CDOM varied to a large degree with space arisen from the mixing of source waters including freshwater (from Taiwan and Mainland China), Changjiang diluted water (CDW), SCS water and KW. The KW and river-plume waters (Changjiang, Minjiang) have the lowest and highest values for absorption coefficient (a(325)) and fluorescence intensity of terrestrial humic-like CDOM (Ft: Ex/Em= 320-360/420-460), respectively. Both a (325) and Ft correlated inversely with salinity. Although the spectral slope (S) varied only within a small range, it still can be used to differentiate water masses in TS, as the S value is generally lower in coastal waters than in SCS and KW. Meanwhile, Ft is highly correlated with surface DIN and Si in TS, showing that these parameters are strongly influenced by terrestrial inputs. There are six types of water masses mixing in the ECS in summer named CDW, Yellow Sea water (YSW), China coastal upwelling water, KW, Taiwan Strait Warm Current (TSWC) and Kuroshio upwelling water. Generally, the concentrations of DOC, DON and DOP are the highest in the surface water and decrease with depth due to strong degradation below the surface. The DOC/DOP and DOC/DON ratios of the most stations are higher than the Redfield ratio, showing a carbon enrichment of DOM in the ECS. The optical properties of CDOM show particular DOM characteristics in different water masses and reveal clearly the sources of DOM over various zones. After the operation of Tree-Gorges Dam, the CDW covering zone is likely reduced as reflected from the spatial patterns of salinity and absorption coefficient. The factor analysis implies that the terrestrial inputs and influence may be the dominant factor in constraining DOM and CDOM distributions in the TS and ECS.

Oyster reefs in the western Mississippi Sound (WMS) are dependent on the salinity moderation by freshwater input. However, freshwater brings in high amount of pollutants, which affect the oysters negatively. Oyster diebacks happened as a result of hypoxia caused by excessive organic matter input to WMS in summer 2017. Colored dissolved organic matter (CDOM) is widely used as a proxy for determining organic matter distribution. In this study, hyperspectral and multispectral remote sensing data collected using unmanned aerial systems and in situ CDOM data were used to develop algorithms in order to retrieve CDOM remotely. Collected physical and biogeochemical parameters were used to understand the carbon fluxes regulating the quality and quantity of CDOM. Developed algorithms showed high accuracy after accounting for seasonal variations of CDOM. Further, seasonal induced photodegradation, photosynthesis, calcification, and exchange of CO2 were identified as possible factors that affect the carbon dynamics in the study area.

Two oceanographic cruises were conducted during September 2003 and March 2004 in the eastern half of the Cariaco Basin. Specific objectives were to examine the hydrography of the seasonal upwelling plume characteristic of this region, the spatial distribution of particles in the area, and to help determine the source and relative importance of in situ particle production vs. terrigenous particles delivered laterally from the coast. During September 2003, average surface salinities within the basin were higher (36.6) relative to Caribbean Sea waters outside the basin (35.6). Salinity patterns indicated that the Orinoco and Amazon River plumes did not enter or influenced the basin directly. The upwelling plume in March 2004 stimulated primary productivity. Beam attenuation and CDOM fluorescence profiles showed marked vertical structure in biomass of microbial populations, particularly near the oxic-anoxic interface typically located between about 250 and 300 m. There is an increasing difference in temperature and salinity between the Cariaco Basin and the adjacent Caribbean Sea below 200 m. Inside the Basin temperatures and salinities were higher by 4oC and 0.5. The influence of local rivers on the Cariaco Basin was evident during September 2003. Low salinity plumes with high beam attenuation (1m-1) lined the southern margin of the Basin. The primary rivers that affected the basin were the Unare and Neverí Their sediment input affected the shelf near the river mouths, and a surrounding radius of up to 40 Km. Their low salinity plumes were carried northwestward toward the CARIACO time series station. In March 2004, there was minimal or no terrigenous input from local rivers. Near the Manzanares River, off the city of Cumaná and near Cubagua Island, located south of Margarita Island, attenuation due to suspended particles (0.09 m-1) was observed at depth (70-150 m) during both cruises (0.09-0.15 m-1). Therefore, sediment transport from the shelf into the basin seems to occur year-round. More observations are necessary to determine the nature and origin of these particles. In March 2004, there was minimal or no terrigenous input

Submitted by STELA ROSA AMARAL GONÇALVES (stelinhaamaral@hotmail.com) on 2016-08-12T03:20:24Z No. of bitstreams: 1 Dissertação_final_imai_v3.pdf: 3555316 bytes, checksum: b4386413378a1a29e513286831a880a2 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-08-15T14:30:47Z (GMT) No. of bitstreams: 1 goncalves_sra_me_prud.pdf: 3555316 bytes, checksum: b4386413378a1a29e513286831a880a2 (MD5) / Made available in DSpace on 2016-08-15T14:30:47Z (GMT). No. of bitstreams: 1 goncalves_sra_me_prud.pdf: 3555316 bytes, checksum: b4386413378a1a29e513286831a880a2 (MD5) Previous issue date: 2016-07-08 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Informações quantitativas e qualitativas de sistemas aquáticos podem ser obtidas por meio de dados de sensoriamento remoto. Nesses sistemas, a porção fotoativa do carbono orgânico dissolvido (COD), pode apresentar correlação com o Carbono Orgânico Dissolvido Colorido (CDOM) que é responsável pela alteração da cor da água e consequentemente pode alterar processos de fotossíntese e fotodegradação. Sendo assim o presente trabalho teve como objetivo avaliar a variabilidade espacial das concentrações de CDOM de uma série temporal, de imagens do sensor Operational Land Imager OLI a bordo do satélite Landsat 8, ao longo de um ano no reservatório de Barra Bonita/SP, sendo este o primeiro de uma série de reservatórios em cascata do Rio Tietê, no estado de São Paulo. Foram encontradas correlações entre a concentração laboratorial do COD e o CDOM para o campo de maio o que motivou a modelagem. Foram ajustados modelos inversos, de banda simples e de razão de bandas, para predição de CDOM com dados de dois trabalhos de campo realizados no ano de 2014, sendo o primeiro no mês de maio e o segundo no mês de outubro. Além disso, foram testados modelos encontrados na literatura, também com os dados levantados em campo, para estimativa de CDOM. Os resultados obtidos mostraram que, para os modelos bio-ópticos, de banda simples e razão de bandas, não há diferenças estatistica. O melhor modelo foi selecionado baseado em análise de erro, depois da aplicação dos modelos na imagem OLI coincidente com o trabalho de campo. Uma série de imagens do sensor OLI no período de um ano foi adotada tendo em vista da disponibilidade dos dados gratuitos e resolução radiométrica de 12 bits. A série temporal de imagens do sensor OLI, após ser processada para minimizar os efeitos atmosféricos, permitiu mostrar a dinâmica de CDOM no reservatório em conjunto com dados de precipitação e temperatura do Instituto Nacional de Meteorologia (INMET). Foi possível observar que o reservatório apresenta uma tendência de valores maiores de CDOM após aportes de nutrientes causados por eventos de precipitação. A temperatura apesar de influenciar na velocidade da reação de degradação não foi o fator principal para a variação da concentração de CDOM. O ajuste e avaliação de modelos foi essencial para escolha do modelo mais adequado a realidade local e sazonal do escopo do trabalho. Além disso o modelo aplicado pode contribuir para o cálculo do balanço de carbono, como também em outros estudos que necessitem dessa informação. / Quantitative and qualitative information about aquatic systems can be obtained by using the Remote Sensing techniques. In these aquatic systems, the photoactive portion of Dissolved Organic Carbon (DOC) can be correlated with the Colored Dissolved Organic Matter (CDOM), responsible for the water color alteration and can modify the photosynthesis and photodegradation process. In this sense, this project aimed to evaluate the spatial variability of CDOM concentrations in a one-year temporal analysis from images acquired by the Operational Land Imager OLI sensor onboard the satellite Landsat 8. The study site is the reservoir located in Barra Bonita, State of São Paulo, which is the first in a series of cascading reservoirs from Tietê River in State of São Paulo. The results showed correlations between the COD and CDOM concentrations for the data acquired in May 2014, motivating the CDOM modeling. Inverse models were adjusted, by using simple spectral band and band ratio, for CDOM prediction using data acquired from two field works carried out in 2014, the first in May and the second in October. Moreover, the models found in related literature were tested, also with the data collected in field, for the CDOM estimative. The obtained results showed that for the bio-optical models, from simple spectral band and band ratio, there is no statistic differences. The model who best fitted to the CDOM estimation was selected based on error analysis after their application in OLI images, which coincided with the field work. One year OLI images were used considering their availability, without fees, and their radiometric resolution of 12 bits. This temporal series, after being processed to attenuate the atmospheric effects, allowed showing the CDOM dynamics in the Barra Bonita reservoir combined with temperature and precipitation data from the Instituto Nacional de Metereologia (INMET). It was possible observe that the reservoir shows a bias of higher values of CDOM after nutrients intakes caused by precipitation. The temperature, despite of its influence on degradation reaction velocity, was not the principal factor for the CDOM concentration variation. Finally, the adjustment and models validation was essential for the correct choice of the model which better represents the local and season reality. In addition, the applied model can contribute for the carbon balance calculation, as well for other researches, which use this information.

A l'heure actuelle le rôle des zones côtières dans le cycle global du carbone est encore relativement mal documenté. Ceci est lié à la forte hétérogénéité et au fort dynamisme de ces zones au sein desquelles de nombreux processus physiques et biologiques interagissent sur les stocks et les flux de carbone. Le carbone organique dissous (DOC) est un élément essentiel à la compréhension du cycle du carbone océanique, notamment dans les zones côtières où il peut représenter jusqu'à 90% du carbone organique total. Compte tenu des nombreuses incertitudes qui résident encore sur la dynamique de cette matière carbonée, l'objectif général de cette thèse visait à améliorer les connaissances sur la distribution du DOC au niveau de ces interfaces "continent/océan" en s'appuyant sur les propriétés optiques de la fraction colorée de ce DOC, la matière organique dissoute (CDOM). Pour cela, des échantillonnages ont été réalisés entre 2010 et 2015 dans trois sites côtiers fortement contrastés (Manche orientale, Guyane Française, Vietnam) et ont permis de : (i) caractériser la dynamique de la CDOM et du DOC et d'identifier une forte hétérogénéité de la relation entre ces deux paramètres au sein de ces sites côtiers aux caractéristiques contrastés, (ii) de proposer une relation novatrice applicable à la télédétection "couleur de l'eau" permettant de dériver les concentrations en DOC à partir des propriétés optiques de la CDOM potentiellement généralisable dans des sites côtiers dominés par les apports terrigènes. Dans un second temps, des études en milieu contrôle (45 jours) couplées à un suivi de terrain (2012-2014) ont été effectuées afin de caractériser spécifiquement la cinétique et l'impact d'une production biologique de matière organique dissoute sur les relations entre CDOM et DOC. Elles ont permis d'identifier un marquage optique (i.e. S320-412) de cette production autochtone de MOD lors de l'efflorescence printanière de Phaeocystis.globosa caractéristique des eaux côtières de la Manche et de proposer une approche pour estimer les contenus en DOC depuis les propriétés optiques du CDOM dans de telles situations de production marine de matière organique dissoute. / The coastal ocean represents an important component of the global carbon cycle however its participation to the overall carbon flux is currently not well constrained. Information on DOC stock and its variability in the coastel ocean is however still very scarce and its represents a strong limitation to our current understanding of the exact role of these ecosystems in the oceanic carbon cycle. In this context, the general aims of this study was to get more insights on dissolved organic carbon dynamics in the coastal ocean through the optical properties of dissolved organic matter (CDOM) that present the advantage to be easily measured from in situ or satellite observations. In practice, in situ data gathered during several sampling cruises conducted in three constrasted continental margins (Eastern Channel, French Guiana, Vietnam) have allowed : (i) the characterization of the strong regional discrepancies in the CDOM-DOC relationships between the three coastal sites investigated, (ii) the possible use of a generalized parameterization to retrieve DOC concentrations from CDOM optical properties (estimated in situ or from ocean color remote sensing)over a large range of coastal sites dominated by terrestrial imput of DOM. A further objective of this work was to investigate the impact on DOM dynamics of the phytoplankton bloom event of Phaeocystis.globosa known to affect the coastal waters of the eastern English Channel during the spring period. In practice, this DOM production was investigated during a 45 days mesocom experiment coupled to field survey data (2012-1014) leading to the identification of an optical marker of this marine CDOM production (i.e. S320-412). We further demonstrated that this optical parameter provides useful information to enhance our ability to retrieve DIC 1 from CDOM optical properties in a context of an algal bloom event.

Freshwater lakes provide many important ecosystem functions and services to support biodiversity and human well-being. Proximal and remote sensing methods represent an efficient approach to derive water quality indicators such as optically active substances (OAS). Measurements of above-ground remote and in situ proximal sensors, however, are limited to observations of the uppermost water layer. We tested a hyperspectral imaging system, customized for underwater applications, with the aim to assess concentrations of chlorophyll a (CHLa) and colored dissolved organic matter (CDOM) in the water columns of four freshwater lakes with different trophic conditions in Central Germany. We established a measurement protocol that allowed consistent reflectance retrievals at multiple depths within the water column independent of ambient illumination conditions. Imaging information from the camera proved beneficial for an optimized extraction of spectral information since low signal areas in the sensor’s field of view, e.g., due to non-uniform illumination, and other interfering elements, could be removed from the measured reflectance signal for each layer. Predictive hyperspectral models, based on the 470 nm–850 nm reflectance signal, yielded estimates of both water quality parameters (R² = 0.94, RMSE = 8.9 µg L−1 for CHLa; R² = 0.75, RMSE = 0.22 m−1 for CDOM) that were more accurate than commonly applied waveband indices (R² = 0.83, RMSE = 13.2 µg L−1 for CHLa; R² = 0.66, RMSE = 0.25 m−1 for CDOM). Underwater hyperspectral imaging could thus facilitate future water monitoring efforts through the acquisition of consistent spectral reflectance measurements or derived water quality parameters along the water column, which has the potential to improve the link between above-surface proximal and remote sensing observations and in situ point-based water probe measurements for ground truthing or to resolve the vertical distribution of OAS.

Submitted by SARAH CRISTINA ARAUJO MARTINS null (sarahca.martins@gmail.com) on 2017-08-27T12:54:53Z No. of bitstreams: 1 Dissertacao_MartinsSarah.pdf: 3974138 bytes, checksum: 73a1c2c28d4a0cbbde72b9e8a49211ce (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-08-29T17:18:44Z (GMT) No. of bitstreams: 1 martins_sca_me_prud.pdf: 3974138 bytes, checksum: 73a1c2c28d4a0cbbde72b9e8a49211ce (MD5) / Made available in DSpace on 2017-08-29T17:18:44Z (GMT). No. of bitstreams: 1 martins_sca_me_prud.pdf: 3974138 bytes, checksum: 73a1c2c28d4a0cbbde72b9e8a49211ce (MD5) Previous issue date: 2017-08-03 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / A matéria orgânica dissolvida (DOM) é a componente da água que pode ser usada como indicativo de sua qualidade, pois possui duas fontes: uma alóctone, relacionada com descargas de material terrestre, estando vinculada aos ácidos húmicos, e outra autóctone, associada às descargas fluviais ou produção própria do corpo hídrico estudado, estando relacionada aos ácidos fúlvicos. A matéria orgânica dissolvida colorida (CDOM) é a fração colorida da DOM, que pode ser usada como proxy para a observação desta última em águas interiores. O reservatório hidrelétrico de Funil (FHR) foi o corpo hídrico escolhido como área de estudo deste trabalho. Neste contexto, o objetivo geral desta pesquisa foi identificar e avaliar as mudanças no coeficiente de absorção da CDOM (aCDOM) na superfície da água ao longo do tempo (1995 – 2010), bem como entender a sua relação com mudanças no uso e cobertura da terra (LULC) na bacia de contribuição do FHR. Para alcançar tal objetivo foram realizados: (i) o mapeamento histórico de LULC (1995 – 2010, com 5 anos de intervalo) para detecção de mudanças; (ii) o estudo de um conjunto de modelos bio-ópticos baseados na literatura, bem como de um novo modelo empírico desenvolvido para estimar aCDOM via reflectância simulada (Rrs_simulated) para o sensor Thematic Mapper (TM); (iii) a distribuição espaço-temporal do aCDOM por meio da aplicação de um modelo bio-óptico em imagens TM/Landsat-5 de 1995 a 2010, e (iv) a análise das fontes possíveis de CDOM/DOM , assim como do comportamento/distribuição do aCDOM no FHR ao longo do tempo. Assim, o primeiro estudo desenvolvido nesta pesquisa foi o da parametrização do algoritmo maquinas de vetores de suporte (SVM) de acordo com as características da área de estudo para classificação supervisionada de LULC na bacia de contribuição do FHR. A detecção de mudança da classificação obtida para LULC demonstrou que a parametrização proposta para o SVM tornou o algoritmo capaz de diferenciar classes grandes e contínuas, classes estreitas e alongadas, além de áreas não contínuas e pequenas localizadas dentro de outra classe maior. A classificação obtida para o SVM apresentou boa avaliação estatística, com acurácia geral entre 86% e 96% para toda a série temporal, acurácia do produtor de 90%, acurácia do usuário maior do que 86% e índice Kappa entre 86% e 91%. Ainda, foi observado que o LULC desenvolvido na área de estudo se manteve relativamente estável ao longo da série histórica analisada. O segundo estudo realizado proporcionou o desenvolvimento de um modelo empírico em um comprimento de onda (485 nm) e uma razão de bandas (B4/B1) alternativos para estimativa de aCDOM via Rra_simulated para o TM/Landsat-5 (RMSE = 7%, Nash = 0.91). Este modelo também pôde identificar mesmo pequenas variações nos valores de reflectância via dados orbitais, assim como pode diferenciar variações sutis no aCDOM. Ainda, foram identificados dois padrões de comportamento da CDOM para o FHR: um associado ao LULC e à ocorrência de chuva/lixiviação, bem como outro relacionado à Clorofila-a (Chl-a) em situações de floração de algas. Os referidos estudos que compõe esta pesquisa foram padronizados como artigos científicos para a confecção deste documento. O primeiro estudo, sobre a parametrização do SVM, foi publicado na revista Modelling Earth Systems Environment – Springer (DOI 10.1007/s40808-016-0190-y). O segundo estudo, sobre a distribuição histórica do aCDOM está na etapa de revisão para futura submissão. / The dissolved organic matter (DOM) is a water compound related to water quality, since it has two sources: one allochthonous, related to terrestrial discharges that can be linked to humic acids, and another autochthonous, associated with river input and itself production, so related to or fulvic acids. The colored dissolved organic carbon (CDOM) is the colored fraction of DOM that could be used as a proxy for its occurrence in inland waters. The Funil hydroelectric reservoir (FHR) was chosen as the study site for this work. In this context, the general aim of this research was to identify and to evaluate the changes in CDOM absorption coefficient (aCDOM) at the water surface over time (1995 – 2010), and to understand its relationship with land cover land use (LULC) changes in FHR watershed. For match this goal, (i) a LULC historical mapping (1995 – 2010, with 5 years of interval) was made to change detection, (ii) a bio-optical model set and a new model were studied in order to estimate aCDOM from simulated reflectance (Rrs_simulated) for Thematic Mapper (TM) sensor, (iii) a aCDOM spatial and temporal distribution was obtained by applying a bio-optical model in TM/Landsat-5 imagery from 1995 to 2010, and (iv) the possible CDOM/DOM sources in FHR were found, as well aCDOM historical behavior/distribution over time was analysed. Thus, the first study was the support vector machine algorithm (SVM) parameterization according to study area characteristics to LULC supervised classification in FHR watershed. The obtained LULC change detection analysis demonstrates that the proposed SVM parameterization made the algorithm able to differentiate large and continuous classes, lengthy and thin areas, and non-continuous small areas located inside wide classes. The obtained classification had great statistics with overall accuracy among 86% and 98% over the time series, the producer accuracy of 90%, the user accuracy higher than 86%, and the Kappa statistics ranged from 86% to 91%. In addition, no significant changes in LULC were identified in the study site over all time series. The second study provides a bio-optical model at alternatives wavelength (485 nm) and a band ratio (B4/B1) for aCDOM estimation using simulated Rrs for TM/Landsat-5 (RMSE = 7%, Nash = 0.91). This model could identify even small variations in reflectance values from orbital data, as well as differentiate even slight alterations in aCDOM. Two significantly different aCDOM behaviors were also identified for FHR: one associated with LULC and rainfall/runoff occurrence, and other correlated to Chlorophyll-a high concentrations (Chl-a) in algal blooms situations. The referred studies that compose this research ware standardized as academic articles in this document. The first study, about SVM parameterization, was published yet in Modeling Earth Systems Environment – Springer (DOI 10.1007/s40808-016-0190-y). The second study, about aCDOM historical distribution is in the revision step to future submission.