The overarching goal of this thesis is to develop a diagnostic and predictive model to quantify the estuarine CO2 dynamics across scales – from catchment to the globe – using an approach that explicitly resolves the strong physical and biogeochemical gradients typically observed in these systems.Chapter 1 provides fundamental definitions and descriptions of estuaries, as well as an assessment of their role in the global carbon cycle. It also raises the specific objectives and research questions tackled in the present study. Chapter 2 presents the rationale behind the novel modelling approach (C-GEM, Carbon-Generic Estuary Model) developed in the framework of this thesis. First, the dominant processes that control the estuarine biogeochemistry in estuaries are discussed in detail. Then, the power of reactive-transport models (RTMs) in understanding and quantifying the estuarine biogeochemical functioning is illustrated on the basis of local modelling studies. Finally, trends in estuarine biogeochemical dynamics across different geometries and environmental scenarios are briefly explored with C-GEM and results are discussed in the context of improving the modelling of estuarine carbon dynamics at regional and global scales. In Chapter 3, a detailed description of C-GEM, both in terms of structure and set-up, is provided and model’s performance is successfully evaluated through comprehensive model-data and model-model comparisons in the macro-tidal Scheldt estuary (BE/NL). In Chapter 4, C-GEM is combined with a generic set of forcing conditions and parameter values to quantify the carbon dynamics (net ecosystem metabolism, CO2 exchange at the air-water interface, carbon filtering capacity) in three idealized estuaries subject to temperate climatic conditions. Their hydro-geometrical characteristics span the wide diversity of estuarine morphological characteristics. Model results are used to upscale the estuarine CO2 dynamics under present-day conditions and to quantify the response of the estuarine filter to future atmospheric CO2, land use and climate change scenarios. In Chapter 5, C-GEM is applied to derive estimations of carbon export and CO2 outgassing from all tidal estuaries discharging in the North Sea. Overall, our results suggest that the estuarine carbon filtering capacity and the contribution of these land-ocean transition systems to the atmospheric CO2 budget might not be as high as previously thought. Finally, a conclusive chapter (Chapter 6) provides a synthesis of the key findings and arguments projected by the present research work. Moreover, recommendations are given in the light of further applications of the modelling approach developed during this thesis. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The distribution and geologic history of nitrogen on Earth is poorly known. Traditionally thought to be an inert gas, with only a small but important biologic cycle, geochemical investigation highlights that it can also be present in rocks and minerals. Even at low concentrations, the great mass of the solid Earth allows for the possibility of substantial N mass and cycling in the geosphere over Earth history. Thus, the assumption that N on the surface of the Earth has remained in steady state over Earth history can be questioned. The research goals of this thesis are to investigate the Earth System N cycle using both large- and small-scale approaches. I present a comprehensive literature compilation to ascertain the N budget of Earth. Determining the total abundance of N in all reservoirs of the Earth, including the atmosphere, oceans, crust, mantle, and core is crucial to a discussion of its cycling in the past. This budget study suggests that the majority of planetary N is likely in the core, with the Bulk Silicate Earth a more massive reservoir than the atmosphere. I also present experimental data and data from lunar samples as added context. As quantification of geologic N is difficult, I present research detailing the adaptation of a fluorometric technique common in aquatic geochemistry for use on geologic samples. I compare fluorometry analysis of geochemical standards to several other techniques: colourimetry, elemental analyzer mass spectrometry, and neutron activation analysis. Fluorometry generally behaves well for crystalline samples, and is a relatively quick and easy alternative to more expensive or intensive techniques. As a preliminary application, I have determined a N budget estimate for the continental crust based on analysis of crystalline crustal rocks and glacial tills from North America. This budget is consistent with published work, suggesting about 2 × 1018 kg N, or half a present atmospheric mass of N, is in the continental crust. I also present a geochemical study measuring N-isotopes and redox sensitive trace elements from a syn-glacial unit deposited during the the Marinoan Snowball Earth. Snowball Earth events were the most extreme glaciations in Earth history. The measurements presented herein are the first to quantify biologic activity via N-isotopes as well as the redox state of the atmosphere and ocean using trace elements from this intriguing time period in Earth history. The data suggests that there was active N- fixing in the biosphere, persistent but limited O2, nitrification, and nearly quantitative denitrification during the glaciation. After the glacial interval, O2 levels increased and denitrification levels dropped, indicated by near-modern δ15N values. The combined use of N-isotope with redox sensitive trace elements provides a more nuanced and comprehensive view in reconstructing past ocean and biologic conditions. Lastly, I present an Earth-system N cycle model with nominal results. Previous modelling efforts have agreed with the traditional notion that atmospheric N-levels have remained constant over geologic time. This is in contrast with modern geochemical evidence suggesting net transport of N from the surface into the mantle. The aim, in turn, of this model is to model N cycling over Earth history by explicitly incorporating both biologic and geologic fluxes. The model is driven by a mantle cooling history and calculated plate tectonic speed, as well as a prescribed atmospheric O2 evolution history. This approach is the first of its kind, to my knowledge, and produces stable model runs over Earth history. While tuning and sensitivity studies may be required for publishable results, nominal runs are compelling. In model output, atmospheric N varies by an factor of 2 − 3 over Earth history, and the availability of nutrients (i.e., PO4) exerts a strong control on biologic activity and movement of N throughout the Earth system. Such a planetary perspective on N serves as an entry point into discussions of planetary evolution as a whole. With the great increase in the number of discovered exoplanets, the scientific community is charged with developing models of planetary evolution and factors that promote habitability. Comparison of Earth to its solar system neighbours and future data on exoplanets will allow a system of evolution pathways to be explored, with the role of N expected to be prominent in discussions of habitability and planetary evolution. / Graduate / 0996 / 0425 / bwjohnso@uvic.ca

“Whiting” is a term used to describe a sharply defined patch of water that contains high levels of suspended, fine-grained calcium carbonate (CaCO3). These features are named for their bright (at times white) appearance when compared to surrounding waters, and have been found to occur globally, persisting for multiple consecutive days. Although whitings have been widely studied using chemical, biological, geological, and physical techniques, there has been little effort to document their spatio-temporal distributions in a systematic way, not to mention the lack of consensus on what generates whitings and allows them to persist for days to weeks at a time. In particular, although fishermen and aircraft pilots have reported whiting-like features off southwest Florida (e.g., a sighting off the Ten Thousand Islands was reported on October 29, 2013), there has been no targeted study on these features in this area. Therefore, the objective of this study is two fold: 1) to document the spatial-temporal distributions of whitings in southwest Florida (SWFL) coastal waters from 2003 through 2015 using satellite imagery to study how their occurrence is related to several environmental variables and 2) to conduct field and laboratory measurements to determine the particle composition and water characteristics in and outside the whiting features. To achieve objective one, a multi-year time series from 2003 through 2015 was developed over SWFL using Moderate Resolution Imaging Spectroradiometer (MODIS) observations. Customized processing was used in order to removed clouds and other artifacts and to delineate the surface whiting features. From this, statistics and distribution maps of whiting occurrence were generated. Annual mean whiting coverage peaked in 2011 (11 km2), when whiting reached a maximum daily visible coverage of 92 km2 on February 23. For the entire time series, the highest daily coverage observed was 126 km2 on December 6, 2008. Over all, whitings had higher spatial coverage during the spring and autumn, with 88% of all whiting coverage occurring within 40 km of the coastline. Images of average seasonal spatial distributions showed that over 90% of whitings located between 40 and 70 km of shore occurred specifically during the winter and autumn. A multivariate linear regression was performed, which found little to no correlation between annual whiting coverage and environmental factors such as sea surface temperature (SST), wind, and river discharge. This analysis was also applied to spatial distributions of whiting events within and outside of 20 km and 40 km from shore. The only statistically significant result was that of SST, as well as SST with river discharge and whiting events distributed more than 20 km from shore. In order to accomplish objective two, several field campaigns were conducted to collect in-situ data and water samples of pre-, post-, and occurring whiting event conditions to provide information on composition, driving forces, and variables that cannot be derived via satellites. Samples were collected for taxonomic identification, chemical analysis, bottom sediment grain size fractionation, in-situ remote sensing reflectance (Rrs), particle backscattering (bbp), chlorophyll-a concentration ([chl-a]), particulate absorption (ap), and gelbstoff (otherwise known as color dissolved organic matter, or CDOM) absorption (ag). Taxonomic identification of marine phytoplankton within whiting water revealed the presence of a dominant, small (<5 >μm), centric diatom species during a sampled whiting event. Through the use of scanning electron microscopy (SEM), these were identified as Thalassiosira sp. Amorphous to fully formed crystals of calcium carbonate were present, attached to cells of Thalassiosira sp., localized to the girdle bands. All other diatom species were devoid of similar growths. In comparing the waters within a whiting area to outside waters, no significant differences were found in ap, ag, nor [chl-a]. The carbonate parameters of whiting water differed from outside water, however due to low sample numbers these results are inconclusive. Average backscattering was twice as high within whiting waters compared to non-whiting water, and measured in-situ Rrs was higher at all wavelengths (400 – 700 nm) within whiting water, with a spectral shape similar to outside waters. Overall, this is the first time that SWFL whiting events have been characterized systematically using satellite imagery, field and laboratory as well as meteorological data to diagnose whiting causes and maintenance mechanisms. Although these results are inconclusive, they add new information to the existing literature on this phenomenon.

Mercury (Hg) is a toxic heavy metal that poses significant human and environmental health risks. Mineral-associated Hg is the largest reservoir of Hg in the environment where it can account for nearly 60% of the global Hg mass inventory. A large fraction of this pool is comprised of mercury sulfide (HgS) minerals, including metacinnabar (beta-HgS). HgS minerals have long been considered insignificant sources of Hg to aqueous or atmospheric pools in all but severely acidic environments due to their low solubility and slow abiotic dissolution kinetics. Little previous work has been conducted investigating the bacterial colonization of HgS minerals and the potential role of these mineral-associated communities in impacting the mobility of mineral-hosted Hg. To address this gap in knowledge, the studies within this dissertation employed a combination of field- and laboratory-based methods. Using culture-independent techniques, this work revealed that sulfur-oxidizing bacteria can extensively colonize metacinnabar within aerobic, near neutral pH, creek sediments, suggesting a potential role for chemolithotrophic bacteria in metacinnabar weathering. Within laboratory incubations, the dominant bacterial colonizer (Thiobacillus thioparus), induced extensive release and volatilization of metacinnabar-hosted Hg. These findings expose a new pathway for metacinnabar dissolution and point to mineral-hosted Hg as an underappreciated source of elemental Hg that may contribute to global atmospheric Hg budgets. In addition, this work elucidates the importance of thiosulfate, a major intermediate sulfur species in the environment, in stimulating metacinnabar dissolution. Therefore, the work within this dissertation shows that authigenic HgS minerals are not merely a sink for Hg within non-acidic natural environments and instead are a source of dissolved and gaseous Hg. This work provides critical information for predicting the transport of Hg in the environment and for developing appropriate management and remediation strategies for Hg-contaminated systems. / Engineering and Applied Sciences

Please read the abstract in the front section of this document / Dissertation (MSc (Microbiology))--University of Pretoria, 2005. / Microbiology and Plant Pathology / unrestricted

Recent studies have characterized coastal estuarine systems as important components of the global carbon cycle. This study investigated carbon cycling through the microbial loop of Florida Bay by use of bacterial growth efficiency calculations. Bacterial production, bacterial respiration, and other environmental parameters were measured at three sites located along a historic phosphorus-limitation gradient in Florida Bay and compared to a relatively nutrient enriched site in Biscayne Bay. A new method for measuring bacterial respiration in oligotrophic waters involving tracing respiration of 13C-glucose was developed. The results of the study indicate that 13C tracer assays may provide a better means of measuring bacterial respiration in low nutrient environments than traditional dissolved oxygen consumption-based methods due to strong correlations between incubation length and δ13C values. Results also suggest that overall bacterial growth efficiency may be lower at the most nutrient limited sites.

Quarante pour cent des réservoirs du monde souffrent d'eutrophisation. Ce problème mondial augmente la biomasse de phytoplancton dans les réservoirs et perturbé leurs utilisations. Comprendre les mécanismes et les processus qui contrôlent la prolifération de cyanobactéries sont de grande préoccupation. Les modèles d'écosystèmes nous permettent de simuler, d'analyser et de comprendre les processus écologiques dans les lacs et les réservoirs. La communauté de phytoplancton et de l'application du modèle écologique sont mal documentées dans le Moyen-Orient. Karaoun réservoir, le plus grand plan d'eau au Liban, a été construit pour l'irrigation et la production hydroélectrique. Il ya un grand intérêt dans la qualité de ce réservoir d'eau car il sera utilisé pour alimenter la capitale Beyrouth avec de l'eau potable. Les objectifs de la thèse sont de concevoir et mettre en œuvre des campagnes de terrain pour suivre et comprendre la dynamique du phytoplancton et des cyanobactéries dans le lac de barrage de Karaoun, de modéliser le fonctionnement physique et biogéochimique de cette retenue. Des campagnes d'échantillonnage ont été effectuées deux fois par mois entre mai 2012 et Août 2013 pour évaluer l'état trophique et la diversité biologique et la dynamique de la communauté de phytoplancton en réponse aux changements des conditions environnementales. Ces mesures de campagne ont été ensuite utilisées pour calibrer et valider un modèle hydrodynamique-écologique unidimensionnel sur Karaoun réservoir. Nos résultats ont montré que : la retenue de Karaoun, fortement stratifiée thermiquement entre mai et août, est eutrophe, et présente une faible biodiversité. Seulement 30 espèces de phytoplancton ont été recensées en 2012-2013. La stratification thermique qui apparaît au printemps réduit la croissance des diatomées et entraîne leur remplacement par des chlorophycées. Les cyanobactéries dominent en été : Aphanizomenon ovalisporum lorsque la température de surface de l'eau est inférieure à 25 °C, Microcystis aeruginosa lorsqu'elle est supérieure à 25°C. Le dinoflagellé Ceratium hirundinella constitue l'espèce dominante en fin d'automne lorsque la colonne d'eau est mélangée, l'intensité lumineuse est faible et la température de l'eau d'environ 19 °C. Contrairement aux températures de surface élevées, supérieures à 26 °C, auxquelles prolifère A. ovalisporum dans les autres lacs, une prolifération d'A. ovalisporum survient en octobre 2012 dans la retenue de Karaoun, à une température de l'eau de 22 °C et alors que la stratification thermique est faible. La cylindrospermopsine (CYN), une cyanotoxines, a été détectée dans la retenue de Karaoun, même en l'absence d'A. ovalisporum, seule espèce qui la produit identifiée dans la retenue. La CYN atteint une concentration de 1,7 µg/L, supérieure à la valeur guide pour l'eau potable de 1 µg/L (Organisation Mondiale de la Santé). Une configuration simple de Dyresm-Caedym a permis de simuler avec succès la croissance et la succession des cyanobactéries A. ovalisporum et M. aeruginosa. Le modèle réalise de bonnes performances pour la simulation du niveau de l'eau du réservoir (RMSE <1 m pour une variation annuelle de 25 m), des profils de température de la colonne d'eau (RMSE <1 °C pour des variations annuelles comprises entre 13 et 28 °C) et de la biomasse des cyanobactéries (RMSE <48 µg/L équivalent chlorophylle-a, concentration entre 0 et 206 µg/L). A l'échelle locale, cette thèse est importante pour les autorités de gestion des eaux libanaises qui visent à utiliser ce réservoir pour production d'eau potable. Il a également permis de mieux comprendre les processus et les mécanismes qui contrôlent la prolifération de cyanobactéries. L'application de configurations de modèles simples avec procédés principaux pourrait être transposée sur d'autres réservoirs eutrophies / AbstractMany reservoirs throughout the world suffer from eutrophication. This worldwide problem increases phytoplankton biomass in reservoirs and impairs their uses. Understanding the mechanisms and processes that control cyanobacterial blooms are of great concern. Ecosystem models enable us to simulate, analyze and understand ecological processes in lakes and reservoirs. Except for Lake Kinneret, the phytoplankton community and ecological model application are poorly documented in the Middle East. Karaoun Reservoir, the largest water body in Lebanon, was built for irrigation and hydropower production. There is a great interest in the water quality of this reservoir as it will be used to supply the capital Beirut with drinking water. The objectives of this thesis are to: 1) design and implement a physico-chemical and reinforced biological monitoring in Karaoun reservoir, 2) understand the physico-chemical determinants of cyanobacterial blooms in Karaoun reservoir, and 3) calibrate a deterministic model that can be used to predict cyanobacteria biomass. Sampling campaigns were conducted semi-monthly between May 2012 and August 2013 to assess the trophic state and the biodiversity and dynamics of its phytoplankton community in response to changes in environmental conditions. These campaign measurements were then used to calibrate (summer and autumn 2012) and validate (spring and summer 2013) a one dimensional hydrodynamic-ecological model on Karaoun Reservoir. Our results show that : Karaoun Reservoir strongly stratifies between May and August was found eutrophic with low biodiversity, only 30 phytoplankton species in 2012-2013 study period. Thermal stratification established in spring reduced the growth of diatoms and resulted in their replacement by mobile green algae species during high nutrients availability and water temperatures lower than 22 °C. Water temperature higher than 25 °C favours cyanobacterium Microcystis aeruginosa that displaces Aphanizomenon ovalisporum in summer. Dinoflagellate Ceratium hirundinella dominated in mixed conditions, at low light intensity in late autumn at 19 °C. Unlike the high temperatures, above 26 °C, which is associated with blooms of Aphanizomenon ovalisporum in Lakes Kinneret (Israel), Lisimachia and Trichonis (Greece) and Arcos Reservoir (Spain), Aphanizomenon ovalisporum in Karaoun Reservoir bloomed in October 2012 when water temperature was 22°C and the reservoir was weakly stratified. The field growth conditions of Aphanizomenon ovalisporum in this study revealed that it can bloom at subsurface water temperature 22 °C increasing the risk of its development and expansion in European lakes. Cylindrospermopsin, a fatal toxin, was detected in almost all samples even when Aphanizomenon ovalisporum was not detected. It reached a concentration of 1.7 µg/L, higher than the drinking water guideline value of 1 µg/L of the World Health Organization. The toxin vertical profiles suggest its possible degradation or sedimentation resulting in its disappearance from water column. A simple configuration of the one-dimensional hydrodynamic-ecological model Dyresm-Caedym successfully simulated the growth and succession of the cyanobacteria Aphanizomenon ovalisporum and Microcystis aeruginosa. The model showed a good performance in simulating the water level (RMSE < 1 m, annual variation of 25 m), water temperature profiles (RMSE < 1.1 °C, range 13-28 °C) and cyanobacteria biomass (RMSE < 57 µg L-1 equivalent chlorophyll a, range 0-206 µg L-1).On the local scale, this thesis provides important background data for the Lebanese water management authorities who aim to use this reservoir for drinking water production. It also increases the understanding of processes and mechanisms that control cyanobacterial blooms. The application of simple model configurations with few major processes can be transposed on other eutrophic lakes and reservoirs

An important episode of carbon sequestration, Oceanic Anoxic Event 1a (OAE-1a), characterizes the Lower Aptian worldwide, and is mostly known from deeper-water settings. The present work of two Lower Aptian deposits, Madotz (N Spain) and Curití Quarry (Colombia), is a multiproxy study that includes fossil assemblages, microfacies, X-ray diffraction bulk and clay mineralogy, elemental analyses (major, minor, trace elements), Rock-Eval pyrolysis, biomarkers, inorganic and organic carbon content, and stable carbon isotopes. The results provide baseline evidence of the local and global controlling environmental factors influencing OAE-1a in shallow-water settings. The data also improve our general understanding of the conditions under which organic-carbon-rich deposits accumulate. The sequence at Madotz includes four intervals (Unit 1; Subunits 2a, 2b and 2c) that overlap the times prior to, during and after the occurrence of OAE-1a. The Lower Unit 1(3m thick) is essentially siliciclastic, and Subunit 2a (20m) contains Urgonian carbonate facies that document abruptly changing platform conditions prior to OAE-1a. Subunit 2b (24.4 m) is a mixed carbonate-siliciclastic facies with orbitolinid-rich levels that coincides with OAE-1a δ13C stages C4-C6, and is coeval with the upper part of the Deshayesites forbesi ammonite zone. Levels with pyrite and the highest TOC values (0.4-0.97%), interpreted as accumulating under suboxic conditions, and are restricted to δ13C stages C4 and C5. The best development of the suboxic facies is at the level representing the peak of the transgression. Subunit 2c, within δ13C stage C7, shows a return of the Urgonian facies. The 23.35-m section at Curití includes a 6.3-m interval at the base of the Paja Formation dominated by organic-rich marlstones and shales lacking benthic fossils and bioturbation, with TOC values as high as 8.84%. The interval overlies a level containing reworked and phosphatized assemblages of middle Barremian to lowest Aptian ammonites. The range of values and the overall pattern of the δ13Corg (-22.05‰ to -20.47‰) in the 6.3m-interval is comparable with Lower Aptian δ13C stage C7. Thus, conditions of oxygen depletion at this site also occurred after Oceanic Anoxic Event-1a, which developed between carbon isotope stages C3 and C6. Both sites, Madotz and Curití, attest to the importance of terrigenous and nutrient fluxes in increasing OM productivity that led to episodic oxygen deficiency.