Abstract: The use of earth observing satellites can be an effective supplement or alternative to traditional field sampling. The Landsat series of satellites have been particularity useful in assessing water quality in lakes, oceans, and reservoirs. This study utilized Landsat 5 and 7 imagery to model Secchi disk depth (SDD) and chlorophyll-a concentrations (Chl-a) at Lake Diefenbaker, Saskatchewan. I used data from these Landsat satellites to answer the following questions: First, can models that predict water quality (SDD and Chl-a concentration) be developed for Lake Diefenbaker using Landsat imagery? Second, can these models identify trends that have taken place at the reservoir from 1984-2012? Third, can I determine if ephemeral events like algal blooms or flooding have an effect on the reservoir? Novel models were developed from data collected in 2011 and 2012 that could predict SDD and Chl-a concentrations in the reservoir (linear regression, model I). These models explain less variation than comparable studies, but the loss in explanatory power is made up by their ability to predict data from any Landsat image of the reservoir. My study showed that predicted SDD and Chl-a concentration were positively related, an atypical relationship in freshwater systems. During the archive study period (1984-2012), both mean seasonal SDD and mean seasonal Chl-a have significantly decreased throughout the reservoir (p<0.05, regime-shift analysis). Spatially, the greatest decrease in SDD was closest to the major inflow the SSR, while downstream areas in the reservoir have decreased minimally. There was a decline in Chl-a concentrations that was spatially consistent throughout the reservoir. There was a significant negative relationship between flow rate and both water clarity and Chl-a concentrations (P<0.05, model II linear regression). Algal blooms occurred sporadically throughout the study period. There were blooms in 9% of images analyzed. Blooms typically occurred in the Qu’Appelle arm of the reservoir in the late summer and fall. The water quality data extracted by this study can be useful to many future studies, as historical data is absent for much of the reservoir’s history.

Dissolved organic matter (DOM) in surface waters affect many important ecological functions. For instance, transporting metals, nutrients, carbon, affecting pH and water colour. In large parts of the Northen hemisphere, surface waters have become browner as a consequense of increasing DOM concentrations and, to some extent, iron. Therfore, altering ecological functions in waters. As such, knowing the causes and extent of the increase is of great importance. This paper used monthly data from the national Swedish monitoring program to investigate trends in DOM-concentrations in the Rickleå river, Västerbotten, Sweden. Results showed a large increase in concentrations of DOM from 1970-2019. However, the increase was most pronounced between 1970-1990, showing no trend after 2003 and indications of a decrease from 2009. DOM-quality changed as well to larger and more colored molecules during 1987-2002 and less coloured, smaller molecules after 2003. Changes in water flow could be an explanation for short-term fluctuations in DOM-concentration, but did not correlate well to increasing trends. However, a large lake at the river inlet as well as hydroelectric dams along the watershead complicates the interpretation between flow and DOM correlation. Climate change did not seem to be an important driver of long term increases in DOM. Further investigations should be carried out to test this hypothesis as well to investigate the cause for the increase.

Ce travail a pour objectif d’étudier les conditions physicochimiques qui causent dans la Loire des développements excessifs de phytoplancton, et de mettre en évidence les modifications des équilibres biogéochimiques qui en résultent. L’analyse des variables de l’eutrophisation a été conduite sur plusieurs niveaux d’échelle temporelle et spatiale, sur la base de longues chroniques de qualité de l’eau (1980- 2012), de données acquises à l’échelle journalière pendant la thèse (2012-2014), et d’un modèle numérique biogéochimique à résolution horaire. Depuis les conditions hypereutrophes des années 1980, la biomasse phytoplanctonique qui se développe en période estivale a été réduite d’un facteur 2,5 dans la Loire et dans ses affluents, de manière concomitante avec la baisse généralisée d’un facteur 3 des teneurs en phosphore biodisponible, liée au contrôle des rejets ponctuels urbains et industriels. Le fleuve de la Loire (France) reste cependant sensible à l’eutrophisation, du fait d’une forte pression agricole et urbaine, des étiages prononcés, et une morphologie fluviale à chenaux multiples qui ralentit l’écoulement, laissant pleinement au phytoplancton le temps de se développer. Lorsque les conditions hydrologiques le permettent, le développement du phytoplancton impacte fortement le fonctionnement de l’écosystème, en agissant significativement sur les cycles biogéochimiques des nutriments, du carbone et de l’oxygène. / This thesis aims at studying the physical and chemical causes and consequences that result from excessive phytoplankton growth in the Loire River. The analysis identified some parameters characterizing river eutrophication and was conducted on several spatial and temporal scales. This was based on long-term water quality time-series (1980-2012), a daily survey carried out during this work (2012-2014), and the numerical modeling of the river biogeochemical functioning with an hourly resolution. Phytoplankton development in summer was reduced 2.5-fold in the Loire River and in the main tributaries, synchronously with the generalized reduction 3-fold of bioavailable phosphorus as a result of controlling and limiting phosphorus point sources. However, the Loire River remains sensitive to eutrophication, with a significant urban and agricultural pressure, low water levels in summer, and its multiple channels morphology slowing down the water velocity. All these factors combined favor phytoplankton development. When hydrological conditions are favorable, phytoplankton grows and significantly affects the ecosystem functioning, with an impact on nutrients, carbon and oxygen biogeochemical cycles.

Xestospongia muta, the giant barrel sponge, is a key component of coral reef benthic communities in Southeast Florida and the Caribbean. Xestospongia muta increases habitat complexity and stability, and filters large volumes of water, enhancing water quality and facilitating nutrient cycling. Therefore, it is important to investigate trends in the X. muta population on Southeast Florida reefs in response to anthropogenic stressors, changing environmental conditions and acute disturbances and how these events affect its ecological role in the benthic community. This study identified trends in X. muta population density, volume, and size class distribution over time and across reef habitats on the Southeast Florida Reef Tract (SEFRT). Density and volume changes were also investigated following acute physical disturbance caused by Hurricane Irma in September of 2017. Images and demographic data collected at 41 permanent sites from two long-term monitoring projects, The Southeast Florida Coral Reef Evaluation and Monitoring Project (SECREMP) and the Broward County Biological Monitoring Project (BC BIO), were used to evaluate the X. muta population trends. My analysis of the data from 2003 to 2018 shows that Xestospongia muta densities and volume increased over time regionally on the SEFRT and increased on the nearshore, middle, and outer reefs of the SEFRT. Xestospongia muta was found to be more abundant on the SEFRT compared to other locations including the Bahamas, the Florida Keys, Colombia, Belize and Saba. Highest mean density on the SEFRT was 0.35 individuals m-2 ±0.04 SEM, which was higher than the mean densities between 0.21 and 0.29 individuals m-2 at the Caribbean sites previously mentioned. Xestospongia muta individuals were categorized into size classes by volume to investigate density distribution of size classes on the SEFRT. Greater abundances in the smallest of five size classes (≤143.13 cm3) drove the increasing density trends. Despite the increasing trends from 2003 to 2017 with a peak in density and volume in 2017, Hurricane Irma caused a region-wide decline in population density and volume as well as a loss of individuals within the largest size class by volume (>17383.97 cm3). These results indicate that the X. muta population is exhibiting increasing long-term trends on the SEFRT, but also demonstrate that acute physical disturbances have a significant impact on the demographics of the population. Because of this sponge’s multiple roles in the reef communities, these trends have implications for structural complexity, nutrient cycling, water filtration, as well as carbon sequestration on the SEFRT.

Les effets du changement climatique sur la biodiversité à l’échelle du globe sont maintenant sans équivoque. Parmi les écosystèmes affectés, les cours d’eau sont particulièrement vulnérables aux fluctuations du climat. Les modifications de structure et de composition des communautés aquatiques constituent alors un signal intégrateur des réponses écologiques à ces changements climatiques. Dans certaines circonstances, ce signal peut également être exacerbé, modéré ou potentiellement masqué par d’autres variations abiotiques.L’objectif de ce travail de thèse était donc d’évaluer l’effet relatif de différents facteurs de forçage sur les tendances d’évolution à long-terme des communautés de macroinvertébrés benthiques de grands cours d’eau, dans un contexte de changement climatique global. Nos investigations ont ciblé plus spécifiquement la Loire moyenne car, en tant que grande rivière de plaine, elle est particulièrement concernée par les problèmes liés aux stress multiples. En ce qui concerne le choix du compartiment biologique, la faune benthique a été sélectionnée pour son intérêt reconnu en bioévaluation des cours d’eau, notamment grâce à une grande diversité de réponses potentielles aux perturbations environnementales et à un certain nombre d’avantages méthodologiques.Dans un premier temps, nous nous sommes appliqués à caractériser les modifications temporelles de dix paramètres abiotiques majeurs sur trois décennies (1977-2008). Nous avons notamment mis en évidence le réchauffement graduel de la Loire (c. +1,2°C en moyenne annuelle sur les trois décades), couplé à une réduction significative du débit moyen (c. -25%), les deux tendances étant exacerbées en période chaude (mai-août). Dans le même temps, alors que ces modifications étaient susceptibles de provoquer une augmentation du niveau trophique du fleuve, nous avons souligné l’existence d’un effet confondant de l’amélioration des traitements d’épuration (i.e. réduction des apports en phosphore), se traduisant principalement par la baisse des concentrations en phosphates et la limitation des organismes phytoplanctoniques.Dans un second temps, nous nous sommes intéressés aux réponses structurelles et fonctionnelles long-terme (i.e. 30 ans) des invertébrés de la Loire à ces deux évolutions concomitantes majeures. En premier lieu, nous avons constaté que le réchauffement et, dans une moindre mesure, la réduction du débit sont impliqués dans la disparition ou le déclin progressif de taxons rhéophiles et psychrophiles (e.g. Chloroperlidae). En parallèle, ces modifications hydroclimatiques expliquent une majeure partie de l’apparition et de la colonisation de taxons limnophiles et thermophiles, comprenant certaines espèces invasives (e.g. Corbicula sp.). En termes de réponses fonctionnelles, ces changements s’illustrent par une évolution adaptative des profils de traits biologiques cohérente avec les prédictions a priori qu’il est possible de faire dans un cadre théorique. Toutefois, cette dérive progressive vers un assemblage généraliste et polluotolérant est partiellement confondue par l’amélioration de la qualité d’eau, qui explique l’apparition de nouveaux taxons polluo-sensibles lors des dernières années (e.g. Philopotamidae). Bien qu’aucune résilience taxonomique ou fonctionnelle ne soit constatée, cette tendance se manifeste, via les traits biologiques, par un transfert probable des ressources trophiques depuis les organismes phytoplanctoniques vers des biofilms épibenthiques et des macrophytes.Pour finir, nous avons exploré la variabilité spatiale multi-sites de ces tendances biotiques et abiotiques et montré que l’ensemble de ces résultats, qui corrobore déjà un certain nombre d’observations en Europe, constitue également un patron homogène le long de la Loire moyenne (sur près de 300 km) et entre différents hydrosystèmes (e.g. Loire, Seine, Meuse). / Evidence for climate change effects on biodiversity at global scale is now unequivocal. Among impaired ecosystems, running waters are particularly vulnerable to climate fluctuations. Changes in aquatic community structure and composition are then considered as integrative signals of the ecological responses to these climate changes. Under certain circumstances, these signals can be also exacerbated, confounded or potentially obscured by other abiotic variations.Therefore, the aim of this PhD was to assess the relative effect of different drivers on longterm trends in benthic macroinvertebrate communities, in the context of global climate change. Our investigations were focused more precisely on the Middle Loire River since, as lowland large river, it is particularly concerned by the potential impact of multiple stressors. Regarding the choice of the biological model, benthic fauna has been selected according to its acknowledged interest in bioassessment of running waters, especially thanks to a great diversity of potential responses to environmental disturbances and a number of methodological advantages.First, we investigated the temporal changes of ten major abiotic parameters over three decades (1977-2008). We highlighted the gradual warming of the Loire River (c. +1.2°C in the mean annual temperature over the three decades), coupled with a significant drop in mean discharge (c. -25%), both trends being exacerbated during the warm period (May-August). In the same time, although these changes were expected to induce a rise in the trophic level of the river, we emphasized a confounding effect of the wastewater treatment improvement (i.e. phosphorus input reduction), leading mainly to a drop in phosphate concentrations and a phytoplankton limitation.Second, we assessed the long-term structural and functional responses (i.e. over a 30-year period) of invertebrates of the Loire River to both major concomitant trends. On the one hand, we highlighted that water warming and to a lesser extent discharge reduction were significantly involved in the disappearance or decrease in rheophilic and psychrophilic taxa (e.g. Chloroperlidae). On the other hand, they explained also a major part of the appearance and increase of limnophilic and thermophilic taxa, including invasive species (e.g. Corbicula sp.). In terms of functional responses, these changes were illustrated by an adaptive evolution of the biological trait profiles in agreement with a priori predictions that is possible to make in a theoretical framework. However, this shift towards a generalist and pollution tolerant assemblage was partially confounded by improvement in water quality, explaining the settlement of new pollution-sensitive taxa during the last years (e.g. Philopotamidae). Although no taxonomic or functional resilience was observed, this trend was translated, via biological traits, into a probable transfer of trophic resources from phytoplankton to periphytic biofilms and macrophytes.Finally, we explored the multi-site spatial variability of these biotic and abiotic trends and we showed that our results as a whole, which supported already a number of observations in Europe, exhibited also a strong homogeneous pattern along the Middle Loire River (on nearly 300 km) and among different hydrosystems (e.g. Loire, Seine, Meuse).

A Confluência Brasil-Malvinas (CBM) é formada pelo encontro da Corrente do Brasil (CB) com a Corrente das Malvinas (CM) no Atlântico Sul. Esta é uma das áreas mais energéticas do oceano global e é demarcada por um intenso gradiente meridional de temperatura. Imagens de satélites e observações in situ mostram a presença de meandros e vórtices, tanto ciclônicos como anticiclônicos, na região da CBM. Com o conhecimento de campos de anomalia da altura da superfície do mar (AASM) e campos de temperatura da superfície do mar (TSM) para a região da Frente Brasil-Malvinas (FBM) é possível se estimar a variação da energia associada às ondas de Rossby anuais e bianuais existentes em seu entorno e detectar a posição da frente termal existente nesta região. Nesse contexto, foi realizado o estudo do deslocamento meridional da FBM numa escala de tempo interanual, da variação do espectro de ondas de Rossby na CBM e da variabilidade associada ao campo médio de velocidades geostróficas absolutas. A comparação do espectro de ondas de Rossby na CBM para o período de 2001-2008 apresentou aumento da energia associada aos períodos anual e bianual em relação aos valores obtidos da análise do período de 1993-2000. Essa alteração do espectro não teve relação com a alteração média da frente termal detectada porém, houve aumento significativo da variabilidade meridional da posição da frente média, possivelmente devido a um aumento do fluxo da CB. Maior variabilidade também foi observada nos mapas de velocidade geostrófica para o mesmo período de 2001-2008. Estes mapas exibiram ainda um possível posicionamento mais austral da CB, corroborando o aumento da variabilidade oriundo da maior instabilidade gerada por ondas planetárias na região da CBM. / The Brazil-Malvinas Confluence (BMC) is formed by the encounter of the Brazil Current (BC) with the Malvinas Current (MC) at the South Atlantic ocean. This is one of the most energetic regions of the world oceans and it is characterized by intense meridional sea surface temperature gradients. Satellite data and in situ observations often reveal the presence of cyclonic and anticyclonic meanders and vortices at the BMC region. The sea surface height anomaly (SSHA) and the sea surface temperature (SST) fields of the Brazil-Malvinas Frontal (BMF) region can be used to determine the energy variations associated with the annual and bi-annual Rossby waves that occur at its surroundings and to detect the position of the thermal front. Our study involved the determination of the BMF meridional displacement on an interannual scale, the spectral variations of the Rossby wave field at the BMC region, and the variability associated to the mean absolute geostrophic velocities. The Rossby wave spectra at the BMC for 2001-2008 show an increase of the energy associated with both the annual and bi--annual periods relative to the 1993-2000 interval. These spectral changes are not directly related to the mean changes in the thermal front region, however we detected a significant meridional variability of the mean position of the front most probably due to an increase in the BC flux. Large variations were also observed in the geostrophic velocity field for the 2001-2008 period. These maps exhibited a farther south location of the BC. This corroborates the variability increase due to a greater instability introduced by the planetary waves at the BMC region.

A Confluência Brasil-Malvinas (CBM) é formada pelo encontro da Corrente do Brasil (CB) com a Corrente das Malvinas (CM) no Atlântico Sul. Esta é uma das áreas mais energéticas do oceano global e é demarcada por um intenso gradiente meridional de temperatura. Imagens de satélites e observações in situ mostram a presença de meandros e vórtices, tanto ciclônicos como anticiclônicos, na região da CBM. Com o conhecimento de campos de anomalia da altura da superfície do mar (AASM) e campos de temperatura da superfície do mar (TSM) para a região da Frente Brasil-Malvinas (FBM) é possível se estimar a variação da energia associada às ondas de Rossby anuais e bianuais existentes em seu entorno e detectar a posição da frente termal existente nesta região. Nesse contexto, foi realizado o estudo do deslocamento meridional da FBM numa escala de tempo interanual, da variação do espectro de ondas de Rossby na CBM e da variabilidade associada ao campo médio de velocidades geostróficas absolutas. A comparação do espectro de ondas de Rossby na CBM para o período de 2001-2008 apresentou aumento da energia associada aos períodos anual e bianual em relação aos valores obtidos da análise do período de 1993-2000. Essa alteração do espectro não teve relação com a alteração média da frente termal detectada porém, houve aumento significativo da variabilidade meridional da posição da frente média, possivelmente devido a um aumento do fluxo da CB. Maior variabilidade também foi observada nos mapas de velocidade geostrófica para o mesmo período de 2001-2008. Estes mapas exibiram ainda um possível posicionamento mais austral da CB, corroborando o aumento da variabilidade oriundo da maior instabilidade gerada por ondas planetárias na região da CBM. / The Brazil-Malvinas Confluence (BMC) is formed by the encounter of the Brazil Current (BC) with the Malvinas Current (MC) at the South Atlantic ocean. This is one of the most energetic regions of the world oceans and it is characterized by intense meridional sea surface temperature gradients. Satellite data and in situ observations often reveal the presence of cyclonic and anticyclonic meanders and vortices at the BMC region. The sea surface height anomaly (SSHA) and the sea surface temperature (SST) fields of the Brazil-Malvinas Frontal (BMF) region can be used to determine the energy variations associated with the annual and bi-annual Rossby waves that occur at its surroundings and to detect the position of the thermal front. Our study involved the determination of the BMF meridional displacement on an interannual scale, the spectral variations of the Rossby wave field at the BMC region, and the variability associated to the mean absolute geostrophic velocities. The Rossby wave spectra at the BMC for 2001-2008 show an increase of the energy associated with both the annual and bi--annual periods relative to the 1993-2000 interval. These spectral changes are not directly related to the mean changes in the thermal front region, however we detected a significant meridional variability of the mean position of the front most probably due to an increase in the BC flux. Large variations were also observed in the geostrophic velocity field for the 2001-2008 period. These maps exhibited a farther south location of the BC. This corroborates the variability increase due to a greater instability introduced by the planetary waves at the BMC region.

Seafloor compliance is a non-intrusive geophysical method sensitive to the shear modulus of the sediments below the seafloor. A compliance analysis requires the computation of the frequency dependent transfer function between the vertical stress, produced at the seafloor by the ultra low frequency passive source-infra-gravity waves, and the resulting displacement, related to velocity through the frequency. The displacement of the ocean floor is dependent on the elastic structure of the sediments and the compliance function is tuned to different depths, i.e., a change in the elastic parameters at a given depth is sensed by the compliance function at a particular frequency. In a gas hydrate system, the magnitude of the stiffness is a measure of the quantity of gas hydrates present. Gas hydrates contain immense stores of greenhouse gases making them relevant to climate change science, and represent an important potential alternative source of energy. Bullseye Vent is a gas hydrate system located in an area that has been intensively studied for over 2 decades and research results suggest that this system is evolving over time. A partnership with NEPTUNE Canada allowed for the investigation of this possible evolution. This thesis describes a compliance experiment configured for NEPTUNE Canada’s seafloor observatory and its failure. It also describes the use of 203 days of simultaneously logged pressure and velocity time-series data, measured by a Scripps differential pressure gauge, and a Güralp CMG-1T broadband seismometer on NEPTUNE Canada’s seismic station, respectively, to evaluate variations in sediment stiffness near Bullseye. The evaluation resulted in a (- 4.49 x10-3± 3.52 x 10-3) % change of the transfer function of 3rd October, 2010 and represents a 2.88% decrease in the stiffness of the sediments over the period. This thesis also outlines a new algorithm for calculating the static compliance of isotropic layered sediments.

Seafloor compliance is a non-intrusive geophysical method sensitive to the shear modulus of the sediments below the seafloor. A compliance analysis requires the computation of the frequency dependent transfer function between the vertical stress, produced at the seafloor by the ultra low frequency passive source-infra-gravity waves, and the resulting displacement, related to velocity through the frequency. The displacement of the ocean floor is dependent on the elastic structure of the sediments and the compliance function is tuned to different depths, i.e., a change in the elastic parameters at a given depth is sensed by the compliance function at a particular frequency. In a gas hydrate system, the magnitude of the stiffness is a measure of the quantity of gas hydrates present. Gas hydrates contain immense stores of greenhouse gases making them relevant to climate change science, and represent an important potential alternative source of energy. Bullseye Vent is a gas hydrate system located in an area that has been intensively studied for over 2 decades and research results suggest that this system is evolving over time. A partnership with NEPTUNE Canada allowed for the investigation of this possible evolution. This thesis describes a compliance experiment configured for NEPTUNE Canada’s seafloor observatory and its failure. It also describes the use of 203 days of simultaneously logged pressure and velocity time-series data, measured by a Scripps differential pressure gauge, and a Güralp CMG-1T broadband seismometer on NEPTUNE Canada’s seismic station, respectively, to evaluate variations in sediment stiffness near Bullseye. The evaluation resulted in a (- 4.49 x10-3± 3.52 x 10-3) % change of the transfer function of 3rd October, 2010 and represents a 2.88% decrease in the stiffness of the sediments over the period. This thesis also outlines a new algorithm for calculating the static compliance of isotropic layered sediments.