The goal of this research was to improve ocean colour chlorophyll a (Chla) retrievals in the coastal Case 2 waters of the Salish Sea by characterizing the main drivers of optical variability and using this information to parameterize empirical algorithms based on an optical classification. This was addressed with three specific objectives: (1) build a comprehensive spatio-temporal data set of in situ optical and biogeochemical parameters, (2) apply a hierarchical clustering analysis to classify above-water remote sensing reflectance (Rrs) and associated bio-optical regimes, (3) optimize and validate class-specific empirical algorithms for improved Chla retrievals. Biogeochemical and optical measurements, acquired at 145 sites, showed considerable variation; Chla (mean=1.64, range: 0.10 – 7.20 µg l-1), total suspended matter (TSM) (3.09, 0.82 – 20.69 mg l-1), and absorption by chromophoric dissolved organic matter (a_cdom (443)) (0.525, 0.007 – 3.072 m-1), thus representing the spatial and temporal variability of the Salish Sea. A comparable range was found in the measured optical properties; particulate scattering (b_p (650)) (1.316, 0.250 – 7.450 m-1), particulate backscattering (b_bp (650)) (0.022, 0.005 – 0.097 m-1), total beam attenuation coefficient (c_t (650)) (1.675, 0.371 – 9.537 m-1), and particulate absorption coefficient (a_p (650)) (0.345, 0.048 – 2.020 m-1). Empirical orthogonal function (EOF) analysis revealed 95% of the Rrs variance was highly correlated to b_p (r = 0.90), b_bp (r = 0.82), and TSM concentration (r = 0.80), suggesting a strong influence from riverine systems in this region. Hierarchical clustering on the normalized Rrs revealed four spectral classes. Class 1 is defined by high overall Rrs magnitudes in the red, indicating more turbid waters, Class 2 showed high Rrs values in the red and well defined fluorescence and absorption features, indicated by a high Chla and TSM presence, Class 3 showed low TSM influence and more defined Chla signatures, and Class 4 is characterized by overall low Rrs values, suggesting more optically clear oceanic waters. Spectral similarities justified a simplification of this classification into two dominant water classes – (1) estuarine class (Classes 1 and 2) and (2) oceanic class (Classes 3 and 4) – representing the dominant influences seen here. In situ Chla and above-water remote sensing reflectance measurements, used to validate and parameterize the OC3M/OC3S3, two-band ratio, FLH and, modified FLH (ModFLH) empirical algorithms, showed a systematic overestimation of low Chla concentrations and underestimation of higher Chla values for all four algorithms when tuned to regional data. FLH and ModFLH algorithms performed best for these data (R2 ~ 0.40; RMSE ~ 0.32). Algorithm accuracy was significantly improved for the class-specific parametrizations with the two-band ratio showing a strong correlation to the Chla concentrations in the estuarine class (R2 ~ 0.71; RMSE ~ 0.33) and the ModFLH algorithm in the oceanic class (R2 ~ 0.70; RMSE ~ 0.26). These results demonstrated the benefit of applying an optical classification as a necessary first step into improving Chla retrievals from remotely sensed data in the contrasted coastal waters of the Salish Sea. With accurate Chla information, the health of the Salish Sea can be viably monitored at spatial and temporal scales suitable for ecosystem management. / Graduate / 0416 / stephen.uvic@gmail.com

Em ambientes costeiros, a variabilidade da biomassa de fitoplâncton é dirigida por forçantes físicas locais que apresentam distintas escalas temporais em ocorrência, intensidade e durabilidade. No canal de São Sebastião, ambiente advectivo, parte-se do pressuposto de que qualquer adição da biomassa de fitoplâncton não se deve ao crescimento local, mas ao transporte de células fitoplanctônicas movidas pelas correntes guiadas a ventos e marés. Dessa maneira, o objetivo central deste trabalho é analisar a variabilidade em alta frequência das variações da biomassa fitoplanctônica e investigar suas relações temporais com a intensidade e direção dos ventos e a amplitude das marés. Em média, o acúmulo de clorofila é estável no tempo, com curtos episódios de lento aumento e diminuições bruscas da biomassa fitoplanctônica, sendo os valores encontrados relativamente baixos, característicos de ambientes oligomesotróficos. Análises espectrais da série temporal da concentração de clorofila-a e da altura da maré revelaram alta correlação entre as duas séries durante as marés de sizígia, com periodicidades de aproximadamente 12 e 24 horas. Em relação à direção e intensidade do vento, o espectro cruzado de ondaletas apresentou áreas de forte correlação com a clorofila-a e periodicidades dominantes de três dias. Além disso, observou-se que ventos vindos do quadrante norte/nordeste carregam águas com maiores concentrações de materiais particulados ou detritos. / In coastal environments, the dynamics of phytoplankton biomass is driven by local physical forcings that have different time scales in occurrence, intensity and durability. For being an advective environment, it is normally assumed that any positive change in phytoplankton biomass in the São Sebastião Channel is not due to local growth, but to the transport of phytoplankton cells moved by currents associated with winds and tides. Thus, the main objective of this project is to analyze the variability in high-frequency variations of the phytoplankton biomass and investigate their temporal relationships with intensity and direction of winds and high tides. On average, the chlorophyll accumulation is stable over time, with short episodes of slow rise and sudden decreases of phytoplankton biomass and relatively low values, characteristic of oligo-mesotrophic environments. Spectral analysis of the time series of chlorophyll a concentration and tide height showed a high correlation between the two series during the spring tides, and dominant periodicities of about 12 to 24 hours. Regarding direction and intensity of the wind, the cross wavelet spectrum presented strong correlation areas with chlorophyll a and dominant periodicities of 3 days. In addition, it was observed that winds from the north/northeast quadrant carry water with higher concentrations of particulate matter or debris.

L'acquisition de paramètres marins à partir des données spatiales de la couleur de l'eau nécessite l'élimination de la contribution de l'atmosphère au signal mesuré par le capteur. En effet, la majorité du rayonnement solaire mesuré par les instruments optiques dans les longueurs d'ondes qui intéressent la couleur de l'eau provient de la diffusion par les molécules de l'air et les aérosols atmosphériques. L'élimination de la contribution de l'atmosphère est appelée correction atmosphérique (CA). Pour les eaux claires, les méthodes de CA supposent une réflectance marine nulle dans le proche infra-rouge (PIR). Ceci permet d'estimer la réflectane de l'atmosphère et de l'extrapoler vers les bandes du visible, et donc de déterminer le signal marin qui contient les informations sur les propriétés optiques des eaux marines. Cette hypothèse n'est cependant pas vérifiée pour les eaux turbides, qui représentent la quasi totalité des eaux côtières. Par conséquent, de nombreux algorithmes de CA ont été développés pour les eaux côtières incluant des hypothèses alternatives. L'objectif de ce travail de thèse est de valider et d'améliorer ces méthodes de CA pour les images MODIS Aqua. Pour cela, diverses approches de CA développées pour les eaux cotières ont été comparées et validées : (1) l'algorithme standard de la NASA, (2) le "NIR Similary spectrum algorithm" qui inclut des hypothèes d'homogénéité spatiale des réflectances marines et atmosphériques, (3) l'algorithme qui utilise les bandes dans l'infrarouge moyen pour la CA dans les eaux très turbides, et (4) un algorithme utilisant un réseau de neurones artificiels. L'exercice de validation à partir de données in situ, et en fonction des types d'eaux, a permis d'identifier différentes pistes d'amélioration pour l'estimation du signal marin. L'un d'entre elles comprend l'utilisation de relations spectrales pour forcer les modèles de réflectances marines utilisés par les algorithmes CA pour estimer le signal marin dans le PIR. Des modifications ont été apportées aux modèles de réflectances marines de l'algorithme standard de la NASA et du "NIR Similarity spectrum algorithm". Chacun des modèles a été forcé avec des relations spectrales préalablement validées grâce à des données globales. Une étude de sensibilité et une validation de ces algorithmes modifiés à partir de données MODIS-Aqua dans la Manhe Orientale/Mer du Nord et la Guyane Française ont démontré que les modifications suggérées amélioraient les estimations du signal marin dans les eaux côtières optiquement complexes. / To acquire marine parameters from remote sensing ocean color data, the sensor-measured signal needs to be corrected for the atmospheric contribution. Indeed, the solar radiation reflected by air molecules and atmospheric aerosols is significant in the sensor bands of interest for ocean color applications. The removal of the atmospheric contribution is called the atmospheric correction (AC). In open ocean waters, the AC relies on the assumption that the water is totally absorbent in the near infrared (NIR) part of the spectral region, allowing to retrieve the atmospheric contribution and to extrapolate it to the visible spectral range, and thus to determine the marine signal that contains the information on the optical properties of seawaters. However, this assumption is not valid in highly productive and turbid coastal waters. Hence, AC approaches for coastal waters need to rely on alternative assumptions. This Ph. D. thesis has as main objective to validate and improve these AC methods developed for contrasted coastal waters, with a focus on MODIS Aqua images. First, a validation and comparison of existing AC methods, relying on diverse assumptions and methods, is performed. Therefore, four commonly used AC methods are selected, (1) the standard NIR AC approach of NASA, (2) the NIR similarity spectrum AC approach including assumptions of spatial homogeneity in the water and aerosol reflectance, (3) the switching algorithm using the short wave infrared bands for AC in highly turbid waters, (4) an Artificial Neural Network algorithm. With the help of a validation exercise based on in situ data and as a function of the water type, several areas of improvement are delineated, including the use of spectral relationships to constrain NIR-modelling schemes. Modified NIR-modelling schemes are suggested for the standard NASA and NIR similarity spectrum AC methods. Both are forced with globally valid spectral relationships. Sensitivity studies and validation exercises, using MODIS-Aqua images in the Eastern English Channel/North Sea and French Guiana waters, are conducted showing that the suggested modified NIR-modelling schemes improve the estimations of the marine signal in contrasted coastal waters.

Em ambientes costeiros, a variabilidade da biomassa de fitoplâncton é dirigida por forçantes físicas locais que apresentam distintas escalas temporais em ocorrência, intensidade e durabilidade. No canal de São Sebastião, ambiente advectivo, parte-se do pressuposto de que qualquer adição da biomassa de fitoplâncton não se deve ao crescimento local, mas ao transporte de células fitoplanctônicas movidas pelas correntes guiadas a ventos e marés. Dessa maneira, o objetivo central deste trabalho é analisar a variabilidade em alta frequência das variações da biomassa fitoplanctônica e investigar suas relações temporais com a intensidade e direção dos ventos e a amplitude das marés. Em média, o acúmulo de clorofila é estável no tempo, com curtos episódios de lento aumento e diminuições bruscas da biomassa fitoplanctônica, sendo os valores encontrados relativamente baixos, característicos de ambientes oligomesotróficos. Análises espectrais da série temporal da concentração de clorofila-a e da altura da maré revelaram alta correlação entre as duas séries durante as marés de sizígia, com periodicidades de aproximadamente 12 e 24 horas. Em relação à direção e intensidade do vento, o espectro cruzado de ondaletas apresentou áreas de forte correlação com a clorofila-a e periodicidades dominantes de três dias. Além disso, observou-se que ventos vindos do quadrante norte/nordeste carregam águas com maiores concentrações de materiais particulados ou detritos. / In coastal environments, the dynamics of phytoplankton biomass is driven by local physical forcings that have different time scales in occurrence, intensity and durability. For being an advective environment, it is normally assumed that any positive change in phytoplankton biomass in the São Sebastião Channel is not due to local growth, but to the transport of phytoplankton cells moved by currents associated with winds and tides. Thus, the main objective of this project is to analyze the variability in high-frequency variations of the phytoplankton biomass and investigate their temporal relationships with intensity and direction of winds and high tides. On average, the chlorophyll accumulation is stable over time, with short episodes of slow rise and sudden decreases of phytoplankton biomass and relatively low values, characteristic of oligo-mesotrophic environments. Spectral analysis of the time series of chlorophyll a concentration and tide height showed a high correlation between the two series during the spring tides, and dominant periodicities of about 12 to 24 hours. Regarding direction and intensity of the wind, the cross wavelet spectrum presented strong correlation areas with chlorophyll a and dominant periodicities of 3 days. In addition, it was observed that winds from the north/northeast quadrant carry water with higher concentrations of particulate matter or debris.

Tesis por compendio / [ES] El nitrógeno (N) es uno de los elementos más importantes para la vida, pero el desequilibrio provocado sobre el ciclo del N está causando daños importantes a muchos ecosistemas en todo el mundo. En aguas costeras, los procesos del N se ven alterados por fertilizantes, la urbanización o la producción de energía. El objetivo principal de esta tesis es contribuir a la evaluación de cómo la actividad antropogénica y el cambio climático modifican la dinámica del N en aguas costeras. Con este propósito se seleccionaron dos lugares de estudio: la demarcación hidrográfica del Júcar (JRBD) en el Noroeste del Mar Mediterráneo y la Región Hidrológica del Golfo Central (CGHR) al Sur del Golfo de México. La tesis se presenta como una colección de cuatro artículos. El primer artículo evalúa cómo la nitrificación en aguas costeras es alterada por las presiones antropogénicas y en asentamientos urbanos en el JRBD. Mediante la aplicación de un modelo biogeoquímico simple que simula la dinámica del nitrito en nueve áreas costeras, se evaluó el desacoplamiento de los dos pasos de la nitrificación. Las conclusiones indican que las presiones antropogénicas modifican los picos de nitrito en invierno debido a las bajas temperaturas y que el segundo paso de la nitrificación es más sensible a la temperatura, lo que implica que el cambio climático puede contribuir al desacoplamiento. El segundo artículo evalúa las tendencias del nitrógeno inorgánico disuelto (NID) por el cambio climático en el JRBD. El efecto de las variables meteorológicas en las concentraciones de NID se estudió mediante la aplicación de redes neuronales artificiales simples entrenadas con datos de campo. Se observaron tendencias decrecientes de nitrito y nitrato a lo largo del siglo XXI bajo los escenarios climático RCP 4.5 y RCP 8.5, debido al aumento de las temperaturas y a la disminución de las precipitaciones, con cambios más significativos en invierno. El amonio no mostró ninguna tendencia anual significativa, pero se observaron aumentos o disminuciones durante algunos meses. En el tercer artículo se desarrolla un nuevo método basado en teoría de sistemas grises y entropía de Shannon para obtener información útil sobre la contaminación por N en áreas donde los datos disponibles son limitados. El método se aplicó a ocho estuarios del CGHR asociados a manglares. Se desarrollaron dos índices: el índice gris de prioridad de gestión de nitrógeno (GNMP) y el índice gris de presión de uso del suelo (GLUP). Ambos fueron comparados para validar la metodología y los resultados indican que la urbanización sobre playas y manglares es la principal causa de la contaminación de N. El cuarto artículo es un análisis espaciotemporal de la contaminación de N a lo largo de dos ríos que desembocan en una zona turística del CGHR asociada a manglares. Mediante técnicas estadísticas como el análisis de cluster, la prueba de MannKendall y la prueba W de MannWhitney, se realizó una evaluación del origen de la contaminación de N y las variaciones temporales de los compuestos de N. Los resultados concluyen que las concentraciones de N orgánico están aumentando a lo largo de la costa, y la principal fuente identificada fue la descomposición de la especie invasora de jacintos de agua en aguas salinas, que ha cubierto completamente las playas y manglares circundantes potenciado por la contaminación de N. El conjunto de la investigación concluye que tanto la contaminación como el cambio climático alteran el ciclo del N en aguas costeras al modificar elementos importantes del N como la nitrificación, las variaciones interanuales de las concentraciones de N o los ecosistemas costeros. Las diferencias en las características ecológicas y socioeconómicas de las dos zonas de estudio desempeñaron un papel decisivo en las presiones e impactos de las actividades antropogénicas. Además, los métodos desarrollados pueden aplicar / [CAT] El nitrogen (N) és un dels elements més importants per a la vida, però el desequilibri provocat sobre el cicle del N està causant danys importants a molts ecosistemes. En aigües costaneres els processos del N es veuen alterats per fertilitzants, el desenvolupament urbà o la producció d'energia. L'objectiu principal d'aquesta investigació és contribuir a l'avaluació de com l'activitat antropogénica i el canvi climàtic modifiquen la dinàmica del N en aigües costaneres. Amb aquest propòsit es van seleccionar dos llocs d'estudi: la demarcació hidrogràfica del Xúquer (JRBD) al Nord-oest de la Mar Mediterrània i la Regió Hidrològica del Golf Central (CGHR) al Sud del Golf de Mèxic. La tesi es presenta com una col·lecció de quatre articles. El primer article avalua com la nitrificació en aigües costaneres es veu alterada per les pressions antropogèniques i prop dels assentaments urbans en el JRBD. Mitjançant l'aplicació d'un model biogeoquímic que simula la dinàmica del nitrit a nou àrees costaneres, es va avaluar el desacoblament dels dos passos de la nitrificació. Les conclusions indiquen que les pressions antropogèniques modifiquen els pics de nitrit observats a l'hivern a causa de les baixes temperaturas i que el segon pas de la nitrificació és més sensible a la temperatura, la qual cosa implica que el canvi climàtic pot contribuir al desacoblament d'aquests dos passos. El segon article avalua les tendències futures de nitrogen inorgànic dissolt (NID) pel canvi climàtic en el JRBD. L'efecte de les variables meteorològiques en les concentracions de NID es va estudiar mitjançant l'aplicació de xarxes neuronals artificials simples entrenades amb dades de camp. Es van observar tendències decreixents de nitrits i nitrats al llarg del segle XXI sota els escenaris climàtics RCP 4.5 i RCP 8.5, a causa de l'augment de les temperatures i a la disminució de les precipitacions, amb canvis més significatius a l'hivern. L'amoni no va mostrar cap tendència anual significativa, però es van observar augments o disminucions durant alguns mesos. En el tercer article es desenvolupa un nou mètode basat en la teoria dels sistemes grisos i l'entropia de Shannon per a obtindre informació útil sobre la contaminació per N en àrees on les dades disponibles són limitats. El mètode es va aplicar a huit estuaris del CGHR associats a manglars. Es van desenvolupar dos índexs: l'índex gris de prioritat de gestió de nitrogen (GNMP) i l'índex gris de pressió d'ús de la terra (GLUP). Els dos van ser comparats per a validar la metodologia. Els resultats indiquen que el desenvolupament urbà sobre platges i manglars és la principal causa de la contaminació de N en l'àrea d'estudi. El quart article és una anàlisi espacio-temporal de la contaminació de N al llarg de dues rius que desemboquen en una zona turística costanera del CGHR associada a manglars. Mitjançant tècniques estadístiques com l'anàlisi de clúster, les proves MannKendall i W de MannWhitney, es va realitzar una avaluació de l'origen de la contaminació de N i les variacions temporals dels compostos de N. Els resultats conclouen que les concentracions de N orgànic estan augmentant al llarg de la costa, i la principal font identificada va ser la descomposició de l'espècie invasora de jacints d'aigua en aigües salines, que ha cobert completament les platges i manglars circumdants potenciat per la contaminació de N. El conjunt de la investigació conclou que tant la contaminació com el canvi climàtic alteren el cicle del N en aigües costaneres en modificar els processos del N com la nitrificació, les variacions interanuals de les concentracions de N i la destrucció dels ecosistemes costaners. Les diferències en les característiques ecològiques i socioeconòmiques de les dues zones d'estudi van exercir un paper decisiu en les pressions i impactes de les activitats antropogèniques. A més, els mètodes desenvolupats poden / [EN] Nitrogen (N) is one of the most important elements for life on Earth, but the unbalance caused to the N cylce is causing dramatic damage to many ecosystems around the world. In coastal waters, the N processes are altered by anthropogenic activities such as the excessive use of fertilizers, urban development or energy production. The main objective of this research is to contribute to the evaluation of how anthropogenic activities and climate change modify the N dynamics in coastal waters. For this purpose, two study sites were selected: the Jucar River Basin District (JRBD) in the Northwestern Mediterranean Sea (Spain) and the Central Gulf Hydrological Region (CGHR) in the Southern Gulf of Mexico (Mexico). The thesis is presented as a collection of four research articles. The first article evaluates how nitrification in coastal waters is altered by anthropogenic pressures and close to urban settlements in the JRBD. Through the application of a simple biogeochemical model that simulates nitrite dynamics to nine coastal areas, an evaluation of the decoupling of the two steps of nitrification was carried out. The main conclusions indicate that anthropogenic pressures modify the nitrite peaks observed in winter driven by low temperatures. The research also concludes that the second step of nitrification is more sensitive to temperature, which entails that climate change may contribute to the decoupling. The second article evaluates the future trends of dissolved inorganic nitrogen (DIN) concentrations under climate change in the JRBD. The effect of meteorological variables on DIN concentrations was studied through the application of simple artificial neural networks trained with field data. Decreasing trends of nitrite and nitrate concentrations were observed throughout the 21st century under both climatic scenarios RCP 4.5 and RCP 8.5, mainly due to rising temperatures and decreasing rainfall, with major changes expected in winter. On the other hand, ammonium did not show any significant annual trend but it either increased or decreased during some months. The third article develops a new method based on grey systems theory and Shannon entropy to derive useful information regarding N pollution in areas where only limited data is available. The method was applied to eight estuaries of the CGHR associated to mangroves. Two indexes were developed: the Grey Nitrogen Management Priority (GNMP) index and the Grey Land Use Pressure (GLUP) index. The two indexes were then confronted to validate the methodology. The results indicate that the urban development over beaches and mangroves is the leading cause of N pollution in the study area. The fourth article is a spatiotemporal analysis of N pollution along two rivers discharging into a touristic coastal area of the CGHR associated to mangroves. Through statistical techniques such as clustering analysis, the Mann-Kendall test and the Mann-Whitney W-test, an evaluation of the origine of N pollution and the temporal variations of the N compounds was performed. The results conclude than organic N concentrations are increasing along the coast, and the main potential source identified was the decomposition of the invasive species of water hyacinths in saline waters, which has completely covered the surrounding beaches and mangroves, enhanced by N pollution. Overall, the main conclusions are that both pollution and climate change alter the N cycle in coastal waters by modifying N processes such as nitrification, the interannual variations of N concentrations and by destroying the coastal ecosystems. The differences in ecological and socio-economic characteristics of the two study sites played a significant role in the pressures and impacts of anthropogenic activities. Moreover, the methods developed can be applied to other coastal regions to evaluate the anthropogenic alteration of the N cycle worldwide. / This thesis was carried out with an international cotutelle between the Polytechnic University of Valencia in Spain and the Veracruzan University in Mexico. This thesis has been financed by the following scholarships: - Erasmus Mundus - MAYANET Grant Agreement Number 2014-0872/001 - 001, funded with support from the European Commission. - Cotutelle PhD scholarship granted by the Universitat Politècnica de València. - Excellence Scholarship awarded by the Mexican Government through the Mexican Agency for International Development Cooperation (AMEXCID) / Temiño Boes, R. (2020). Anthropogenic alteration of the nitrogen cycle in coastal waters: Case studies from the Mediterranean Sea and the Gulf of Mexico [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/158560 / TESIS / Compendio