Rozprawy doktorskie na temat „Biogeochemical modelling”

The length of a planet's `habitable period' is an important controlling factor on the evolution of life and of intelligent observers. This can be defined as the amount of time the surface temperature on the planet remains within defined `habitable' limits. Complex states of habitability derived from complex interactions between multiple factors may arise over the course of the evolution of an individual terrestrial planet with implications for long-term habitability and biosignature detection. The duration of these habitable conditions are controlled by multiple factors, including the orbital distance of the planet, its mass, the evolution of the host star, and the operation of any (bio)geochemical cycles that may serve to regulate planetary climate. A stellar evolution model was developed to investigate the control of increasing main-sequence stellar luminosity on the boundaries of the radiative habitable zone, which was then coupled with a zero-D biogeochemical carbon cycle model to investigate the operation of the carbonate-silicate cycle under conditions of varying incident stellar flux and planet size. The Earth will remain within habitable temperature limits for 6.34 Gyr (1.8 Gyr from present), but photosynthetic primary producers will experience carbon-starvation due to greatly increased terrestrial weathering from 5.38 Gyr (0.84 Gyr from present) onwards, with significant implications for planetary habitability. Planet mass was discovered to have a significant control on the length of the habitable period of Earth-like planets, but more data on the bulk density and atmospheric composition of newly-discovered exoplanets is required before definitive estimates of their long-term habitability can be made. Exoplanet case studies reveal habitable periods significantly longer than that of the Earth, possibly up to 80 Gyr in the case of planets in the orbit of M-dwarfs. Contemporary measures of habitability that rely strongly on surface temperatures are becoming obsolete, and a move towards the inclusion of integrated biogeochemical cycle models and the development of multiparameter habitability indices will strengthen contemporary understanding of the distribution and evolution of potentially habitable terrestrial worlds.

Mestrado em Meteorologia e Oceanografia Física
A capacidade de fornecer dados oceanográficos sobre variáveis biológicas e químicas tem-se tornado num tema de relevância científica nos últimos anos. A procura por este tipo de informação provém de áreas e aplicações tão diversas como a investigação em ecossistemas marinhos, a monitorização da qualidade da água e o suporte à gestão do ambiente marinho e costeiro. Este trabalho consiste numa visão geral sobre a incorporação de um módulo biogeoquímico baseado em fluxos de azoto (NPZD) num modelo de circulação oceânica regional (ROMS) para a Margem NW Ibérica e para o período de 2007 a 2010. O estudo foca-se especialmente na validação do modelo, tanto empírica como objectiva, através da comparação entre os valores de clorofila-a simulados e os que constam numa extensa base de dados produzida pelo Ifremer/CERSAT, assim como na verificação da capacidade de reprodução de alguns fenómenos teoricamente expectáveis. A validação do modelo mostra que, embora existam algumas falhas, como uma subestimação geral dos valores superficiais de clorofila-a ou a antecipação ao início dos blooms primaveris, a resposta deste é satisfatória. Embora ainda exista muito a melhorar, é possível afirmar que está criado um modelo com acoplamento biogeoquímica-hidrodinâmica, completamente funcional e credível, com capacidade de simulação a uma escala inter-anual para a Margem NW Ibérica.
Providing oceanographic data on biological and chemical variables has become an issue of scientific concern over the last years. The demand for this kind of information arises from a range of fields and applications such as scientific research on marine ecosystems, monitoring of seawater quality and decision-making support for marine and coastal management. This work consists of an overview on the incorporation of a nitrogen-based (NPZD) biogeochemical module into a regional oceanic circulation model (ROMS) for the NW Iberian Margin for the 2007 to 2010 period. The study focuses especially in both empirical and objective model performance assessments through comparison of chlorophyll-a model outputs with an extensive satellite dataset produced by Ifremer/CERSAT and in the verification of the model ability to reproduce theoretically expected phenomena. The model validation shows that despite some flaws, as a general underestimation of chlorophyll-a surface values and an anticipation in the starting of the spring bloom, the model response is satisfactory. With still much to improve, its however possible to state that a fully-functional and reliable coupled biogeochemicalocean circulation model is available for the NW Iberian Margin, running at the inter-annual scale.

The last decades have seen a large effort of the scientific community to study and understand the physics of sea ice. We currently have a wide - even though still not exhaustive - knowledge of the sea ice dynamics and thermodynamics and of their temporal and spatial variability. Sea ice biogeochemistry is instead largely unknown. Sea ice algae production may account for up to 25% of overall primary production in ice-covered waters of the Southern Ocean. However, the influence of physical factors, such as the location of ice formation, the role of snow cover and light availability on sea ice primary production is poorly understood. There are only sparse localized observations and little knowledge of the functioning of sea ice biogeochemistry at larger scales. Modelling becomes then an auxiliary tool to help qualifying and quantifying the role of sea ice biogeochemistry in the ocean dynamics. In this thesis, a novel approach is used for the modelling and coupling of sea ice biogeochemistry - and in particular its primary production - to sea ice physics. Previous attempts were based on the coupling of rather complex sea ice physical models to empirical or relatively simple biological or biogeochemical models. The focus is moved here to a more biologically-oriented point of view. A simple, however comprehensive, physical model of the sea ice thermodynamics (ESIM) was developed and coupled to a novel sea ice implementation (BFM-SI) of the Biogeochemical Flux Model (BFM). The BFM is a comprehensive model, largely used and validated in the open ocean environment and in regional seas. The physical model has been developed having in mind the biogeochemical properties of sea ice and the physical inputs required to model sea ice biogeochemistry. The central concept of the coupling is the modelling of the Biologically-Active-Layer (BAL), which is the time-varying fraction of sea ice that is continuously connected to the ocean via brines pockets and channels and it acts as rich habitat for many microorganisms. The physical model provides the key physical properties of the BAL (e.g., brines volume, temperature and salinity), and the BFM-SI simulates the physiological and ecological response of the biological community to the physical enviroment. The new biogeochemical model is also coupled to the pelagic BFM through the exchange of organic and inorganic matter at the boundaries between the two systems . This is done by computing the entrapment of matter and gases when sea ice grows and release to the ocean when sea ice melts to ensure mass conservation. The model was tested in different ice-covered regions of the world ocean to test the generality of the parameterizations. The focus was particularly on the regions of landfast ice, where primary production is generally large. The implementation of the BFM in sea ice and the coupling structure in General Circulation Models will add a new component to the latters (and in general to Earth System Models), which will be able to provide adequate estimate of the role and importance of sea ice biogeochemistry in the global carbon cycle.

The last decades have seen a large effort of the scientific community to study and understand the physics of sea ice. We currently have a wide - even though still not exhaustive - knowledge of the sea ice dynamics and thermodynamics and of their temporal and spatial variability. Sea ice biogeochemistry is instead largely unknown. Sea ice algae production may account for up to 25% of overall primary production in ice-covered waters of the Southern Ocean. However, the influence of physical factors, such as the location of ice formation, the role of snow cover and light availability on sea ice primary production is poorly understood. There are only sparse localized observations and little knowledge of the functioning of sea ice biogeochemistry at larger scales. Modelling becomes then an auxiliary tool to help qualifying and quantifying the role of sea ice biogeochemistry in the ocean dynamics. In this thesis, a novel approach is used for the modelling and coupling of sea ice biogeochemistry - and in particular its primary production - to sea ice physics. Previous attempts were based on the coupling of rather complex sea ice physical models to empirical or relatively simple biological or biogeochemical models. The focus is moved here to a more biologically-oriented point of view. A simple, however comprehensive, physical model of the sea ice thermodynamics (ESIM) was developed and coupled to a novel sea ice implementation (BFM-SI) of the Biogeochemical Flux Model (BFM). The BFM is a comprehensive model, largely used and validated in the open ocean environment and in regional seas. The physical model has been developed having in mind the biogeochemical properties of sea ice and the physical inputs required to model sea ice biogeochemistry. The central concept of the coupling is the modelling of the Biologically-Active-Layer (BAL), which is the time-varying fraction of sea ice that is continuously connected to the ocean via brines pockets and channels and it acts as rich habitat for many microorganisms. The physical model provides the key physical properties of the BAL (e.g., brines volume, temperature and salinity), and the BFM-SI simulates the physiological and ecological response of the biological community to the physical enviroment. The new biogeochemical model is also coupled to the pelagic BFM through the exchange of organic and inorganic matter at the boundaries between the two systems . This is done by computing the entrapment of matter and gases when sea ice grows and release to the ocean when sea ice melts to ensure mass conservation. The model was tested in different ice-covered regions of the world ocean to test the generality of the parameterizations. The focus was particularly on the regions of landfast ice, where primary production is generally large. The implementation of the BFM in sea ice and the coupling structure in General Circulation Models will add a new component to the latters (and in general to Earth System Models), which will be able to provide adequate estimate of the role and importance of sea ice biogeochemistry in the global carbon cycle.

Forest models are tools for explaining and predicting the dynamics of forest ecosystems. They simulate forest behavior by integrating information on the underlying processes in trees, soil and atmosphere. Bayesian calibration is the application of probability theory to parameter estimation. It is a method, applicable to all models, that quantifies output uncertainty and identifies key parameters and variables. This study aims at testing the Bayesian procedure for calibration to different types of forest models, to evaluate their performances and the uncertainties associated with them. In particular,we aimed at 1) applying a Bayesian framework to calibrate forest models and test their performances in different biomes and different environmental conditions, 2) identifying and solve structure-related issues in simple models, and 3) identifying the advantages of additional information made available when calibrating forest models with a Bayesian approach. We applied the Bayesian framework to calibrate the Prelued model on eight Italian eddy-covariance sites in Chapter 2. The ability of Prelued to reproduce the estimated Gross Primary Productivity (GPP) was tested over contrasting natural vegetation types that represented a wide range of climatic and environmental conditions. The issues related to Prelued's multiplicative structure were the main topic of Chapter 3: several different MCMC-based procedures were applied within a Bayesian framework to calibrate the model, and their performances were compared. A more complex model was applied in Chapter 4, focusing on the application of the physiology-based model HYDRALL to the forest ecosystem of Lavarone (IT) to evaluate the importance of additional information in the calibration procedure and their impact on model performances, model uncertainties, and parameter estimation. Overall, the Bayesian technique proved to be an excellent and versatile tool to successfully calibrate forest models of different structure and complexity, on different kind and number of variables and with a different number of parameters involved.

Forest models are tools for explaining and predicting the dynamics of forest ecosystems. They simulate forest behavior by integrating information on the underlying processes in trees, soil and atmosphere. Bayesian calibration is the application of probability theory to parameter estimation. It is a method, applicable to all models, that quantifies output uncertainty and identifies key parameters and variables. This study aims at testing the Bayesian procedure for calibration to different types of forest models, to evaluate their performances and the uncertainties associated with them. In particular,we aimed at 1) applying a Bayesian framework to calibrate forest models and test their performances in different biomes and different environmental conditions, 2) identifying and solve structure-related issues in simple models, and 3) identifying the advantages of additional information made available when calibrating forest models with a Bayesian approach. We applied the Bayesian framework to calibrate the Prelued model on eight Italian eddy-covariance sites in Chapter 2. The ability of Prelued to reproduce the estimated Gross Primary Productivity (GPP) was tested over contrasting natural vegetation types that represented a wide range of climatic and environmental conditions. The issues related to Prelued's multiplicative structure were the main topic of Chapter 3: several different MCMC-based procedures were applied within a Bayesian framework to calibrate the model, and their performances were compared. A more complex model was applied in Chapter 4, focusing on the application of the physiology-based model HYDRALL to the forest ecosystem of Lavarone (IT) to evaluate the importance of additional information in the calibration procedure and their impact on model performances, model uncertainties, and parameter estimation. Overall, the Bayesian technique proved to be an excellent and versatile tool to successfully calibrate forest models of different structure and complexity, on different kind and number of variables and with a different number of parameters involved.

Mestrado em Ciências do Mar e das Zonas Costeiras
Estuaries are highly dynamic systems which may be modified in a climate change context. These changes can affect the biogeochemical cycles. Among the major impacts of climate change, the increasing rainfall events and sea level rise can be considered. This study aims to research the impact of those events in biogeochemical dynamics in the Tagus Estuary, which is the largest and most important estuary along the Portuguese coast. In this context a 2D biophysical model (MOHID) was implemented, validated and explored, through comparison with in-situ data. In order to study the impact of extreme rainfall events, which can be characterized by an high increase in freshwater inflow, three scenarios were set by changing the inputs from the main tributaries, Tagus and Sorraia Rivers. A realistic scenario considering one day of Tagus and Sorraia River extreme discharge, a scenario considering one day of single extreme discharge of the Tagus River and finally one considering the extreme runoff just from Sorraia River. For the mean sea level rise, two scenarios were also established. The first with the actual mean sea level value and the second considering an increase of 0.42 m. For the extreme rainfall events simulations, the results suggest that the biogeochemical characteristics of the Tagus Estuary are mainly influenced by Tagus River discharge. For sea level rise scenario, the results suggest a dilution in nutrient concentrations and an increase in Chl-a in specific areas.For both scenarios, the suggested increase in Chl-a concentration for specific estuarine areas, under the tested scenarios, can lead to events that promote an abnormal growth of phytoplankton (blooms) causing the water quality to drop and the estuary to face severe quality issues risking all the activities that depend on it.
Os estuários são sistemas altamente dinâmicos que se encontram em risco devido a eventos relacionados com as alterações climáticas. Estas alterações podem ter impactos nos ciclos biogeoquímicos. Entre esses efeitos podem considerar-se o aumento de períodos de chuvas torrenciais e o aumento do nível médio do mar. Assim, o objetivo deste trabalho é o estudo do impacto destes eventos na dinâmica biogeoquímica do Estuário do Tejo, que se trata do maior sistema estuarino da Península Ibérica. Neste contexto, foi implementado, validado e explorado através de comparação com dados in-situ, um modelo biofísico 2D (MOHID). De forma a avaliar a resposta biogeoquímica do estuário a períodos de chuvas torrenciais, caracterizadas por variações abruptas nas descargas fluviais dos principais tributários, Tejo e Sorraia, foram considerados três cenários. O primeiro considerando um dia de descarga extrema para os rios Tejo e Sorraia. O segundo, considerando uma descarga extrema apenas para o Rio Tejo e por último, considerando uma descarga apenas para o Rio Sorraia. Relativamente ao aumento do nível médio do mar, foram estabelecidos dois cenários, o primeiro com o nível médio do mar atual e o segundo considerando um aumento de 0.42 m, conforme estimado em estudos anteriores. Os resultados para a simulação das chuvas torrenciais indicam que as modificações previstas para os padrões biogeoquímicos dependem essencialmente da descarga do Rio Tejo. Para o cenário de aumento do nível médio do mar os resultados sugerem uma diminuição da concentração de nutrientes e um aumento de clorofila em áreas específicas. Em ambos os cenários, o aumento de clorofila em determinadas zonas do estuário, sugerido pelos resultados, pode levar a eventos que promovam um crescimento anormal de fitoplâncton fazendo com que a qualidade da água diminua e colocando em risco todas as atividades que dependem no Estuário do Tejo.

This thesis presents a combined modelling and observational study of an intermittently open and closed lake or lagoon (ICOLL) in south-eastern Australia. ICOLLs are a common, yet vulnerable type of estuary characterised by low freshwater inflow leading to a sand berm being formed across the entrance preventing oceanic flushing. The accumulation of nutrients during the closed phase, and the increased water residence time, can have detrimental effects on the estuary if the nutrient load cannot be assimilated. The general aim of this study was to develop a quantitative understanding of ecological processes in Intermittently Closed and Open Lakes or Lagoons (ICOLLs) through a combination of field work and ecological modelling. The field-based component of the studied was completed in Smiths Lake, NSW Australia. The field data shows that concentrations of NH3, NOx and Chlorophyll a in Smiths Lake gradually increases over time between the two studied opening events, before declining while the lake is open to the ocean. Phosphorus concentration is relatively low throughout both cycles. Of the 2 opening events, one was long (~ 3.5 months) and one was short (~3 weeks). Initially ammonia concentrations following this short open period were 2-4 times higher than the initial values from the previous 2 closures. The reduced open phase also resulted in more persistent stratification. The observations show that the duration of the open/closed phases will influence the physiochemical characteristics of the water column. A spatially resolved, eleven-box ecological model was developed for Smiths Lake. The process descriptions in the ecological model are based on a combination of physical and physiological limits to the processes of nutrient uptake, light capture by phytoplankton and predator/prey interactions. An inverse model is used to calculate mixing coefficients from salinity observations. When compared to field data, the ecological model obtains fits for salinity, nitrogen, phosphorus, chlorophyll a and zooplankton that are within 1.5 standard deviations of the mean of the field data. Simulations show that nutrient limitation (nitrogen and phosphorus) is the dominant factor limiting growth of the autotrophs during both the open and closed phases of the lake. The model is characterised by strong oscillations in phytoplankton and zooplankton abundance,typical of predator-prey cycles. A sensitivity analysis was completed using a simplified 1-box configuration, coupled with the existing ecological model. When small perturbations in the initial conditions of DIN, phytoplankton and zooplankton are implemented, the standard deviations of the state variables strongly attract to a declining oscillation, showing the variation between runs decreasing with time. The most sensitive parameters in the model were the feeding efficiency of small and large zooplankton, and the mortality of epiphytes and small zooplankton which all had normalised sensitivities of 1.28, 1.11, 1.01 and 1.05 respectively for a 10% change in parameter value. The non-linearity of the model is illustrated by increasing the percentage change of the parameter. For a 25% change in feeding efficiency of small and large zooplankton, the normalised sensitivity increased to 1.28 and 1.15 respectively, and for a 50% change, they increased further to 1.78 and 1.35 respectively. The ecological state variables were also sensitive to increased catchment loads and depths. The modelled system switches from seagrass dominated to algal dominated at loads over 10?? the current loads, with increased plankton biomass and suspended solids shading the seagrass. The spatially resolved ecological model is run for a variety of open/closed cycles to assess the impact of various opening regimes on the model state variables. The results indicate that Smiths Lake is capable of assimilating its current nutrient loads without persistent phytoplankton blooms or a decrease in seagrass biomass. When catchment loads are increased by 10?? or the duration of the lake open/closed cycle is increased there is a corresponding increase in seagrass biomass. In contrast, small and large phytoplankton both increase in biomass as the duration of the open phase increases. Small and large phytoplankton growth is generally limited by phosphorus, and seagrass growth is limited by nitrogen under normal catchment loads. Due to the shallow depths and low phytoplankton biomass, seagrass only becomes light limited when the nutrient and suspended solids loads are increased 10??. This switch to light limitation only decreases the biomass for short periods.

The potential for life to control its environment was first suggested by Lovelock (1972). Charlson et al (1987) proposed a role for marine planktonic ecosystems in global climate regulation via the production and ventilation to the atmosphere of dimethylsulphide (DMS), a by-product of phytoplankton metabolism. Once in the atmosphere DMS contributes to the formation of cloud condensation nuclei, and increases the amount and brightness of cloud. This affects the albedo of the planet, reflecting more incident sunlight back into space, and cooling the earth. In common with many other 'hypotheses' regarding complex adaptive systems, the hypothesis proposed by Charlson et al (1987) is not experimentally testable. The production and ventilation to the atmosphere of DMS is the result of complex interactions between biological, chemical and physical processes. Consequently, increasing use is being made of mathematical models that simulate these processes to advance understanding of it (Archer et al. 2002). This study examines one of the fundamental mechanisms proposed by the Charlson et al (1987) hypothesis, that increasing global temperatures will lead to increased ventilation of DMS from the ocean to the atmosphere. The study develops one-dimensional biogeochemical models of DMS production by upper ocean ecosystems, based on the model proposed by Gabric et al. (1993b). The models are examined to elucidate their fundamental mathematical properties, and are subjected to sensitivity analysis to identify important processes and parameters. These investigations identify a simpler model that can reproduce the predictions of the Gabric et al. (1993b) model. Predictions derived from model simulations forced by climatologies of measured physical data are compared to a global database of measurements of sea surface DMS concentrations, and to observed depth profiles of DMS in the upper ocean. These comparisons confirm that all models are in good qualitative agreement with measured data. The fifteen global climate prediction models currently in use around the globe all predict substantial warming effects from the ventilation of anthropogenic carbon dioxide to the atmosphere. A simplified DMS model is calibrated to climatologies of Antarctic chlorophyll and DMS data and reproduces the data with great precision. The calibrated model is applied in global warming scenarios to 'test' the efficacy of the mechanism proposed by the Charlson et al (1987) hypothesis. This simulation provides evidence that the response predicted by the hypothesis is indeed feasible, and that substantial increases (up to 45%) in the ventilation of DMS to the atmosphere could be possible in some circumstances. The results of the modelling study provide impetus for further examination of field data. If couplings between marine biota and atmosphere are feasible, then they may be operating contemporarily, and may be detectable. Atmospheric DMS is oxidised to form aerosols (Miller et al. 2002) that influence the aerosol optical depth of the atmosphere. Archives of remote sensed ocean chlorophyll a concentration and aerosol optical depth are examined for evidence of the biologically mediated couplings. A clear coupling between aeolian dust and marine phytoplankton is evident from this analysis, suggesting that the deposition of dust from the atmosphere is a major factor controlling phytoplankton growth in many parts of the ocean. A second coupling between marine phytoplankton and atmospheric aerosols is also detected. This coupling is apparently not related to dust and is symmetrical about the equator, despite the substantial differences in the atmospheres and oceans of each hemisphere. It is speculated that this coupling may reflect the influence of the ventilation of DMS produced by marine phytoplankton on the atmosphere. This thesis provides new evidence supporting the important role of marine ecosystems in global climate regulation by the production of DMS. This evidence is principally obtained from a biogeochemical modelling approach, but is supported by analyses of empirical data. The concordance of results obtained from different approaches suggests that the contribution of marine ecosystems to global climate regulation is real, important and currently active.

The potential for life to control its environment was first suggested by Lovelock (1972). Charlson et al (1987) proposed a role for marine planktonic ecosystems in global climate regulation via the production and ventilation to the atmosphere of dimethylsulphide (DMS), a by-product of phytoplankton metabolism. Once in the atmosphere DMS contributes to the formation of cloud condensation nuclei, and increases the amount and brightness of cloud. This affects the albedo of the planet, reflecting more incident sunlight back into space, and cooling the earth. In common with many other 'hypotheses' regarding complex adaptive systems, the hypothesis proposed by Charlson et al (1987) is not experimentally testable. The production and ventilation to the atmosphere of DMS is the result of complex interactions between biological, chemical and physical processes. Consequently, increasing use is being made of mathematical models that simulate these processes to advance understanding of it (Archer et al. 2002). This study examines one of the fundamental mechanisms proposed by the Charlson et al (1987) hypothesis, that increasing global temperatures will lead to increased ventilation of DMS from the ocean to the atmosphere. The study develops one-dimensional biogeochemical models of DMS production by upper ocean ecosystems, based on the model proposed by Gabric et al. (1993b). The models are examined to elucidate their fundamental mathematical properties, and are subjected to sensitivity analysis to identify important processes and parameters. These investigations identify a simpler model that can reproduce the predictions of the Gabric et al. (1993b) model. Predictions derived from model simulations forced by climatologies of measured physical data are compared to a global database of measurements of sea surface DMS concentrations, and to observed depth profiles of DMS in the upper ocean. These comparisons confirm that all models are in good qualitative agreement with measured data. The fifteen global climate prediction models currently in use around the globe all predict substantial warming effects from the ventilation of anthropogenic carbon dioxide to the atmosphere. A simplified DMS model is calibrated to climatologies of Antarctic chlorophyll and DMS data and reproduces the data with great precision. The calibrated model is applied in global warming scenarios to 'test' the efficacy of the mechanism proposed by the Charlson et al (1987) hypothesis. This simulation provides evidence that the response predicted by the hypothesis is indeed feasible, and that substantial increases (up to 45%) in the ventilation of DMS to the atmosphere could be possible in some circumstances. The results of the modelling study provide impetus for further examination of field data. If couplings between marine biota and atmosphere are feasible, then they may be operating contemporarily, and may be detectable. Atmospheric DMS is oxidised to form aerosols (Miller et al. 2002) that influence the aerosol optical depth of the atmosphere. Archives of remote sensed ocean chlorophyll a concentration and aerosol optical depth are examined for evidence of the biologically mediated couplings. A clear coupling between aeolian dust and marine phytoplankton is evident from this analysis, suggesting that the deposition of dust from the atmosphere is a major factor controlling phytoplankton growth in many parts of the ocean. A second coupling between marine phytoplankton and atmospheric aerosols is also detected. This coupling is apparently not related to dust and is symmetrical about the equator, despite the substantial differences in the atmospheres and oceans of each hemisphere. It is speculated that this coupling may reflect the influence of the ventilation of DMS produced by marine phytoplankton on the atmosphere. This thesis provides new evidence supporting the important role of marine ecosystems in global climate regulation by the production of DMS. This evidence is principally obtained from a biogeochemical modelling approach, but is supported by analyses of empirical data. The concordance of results obtained from different approaches suggests that the contribution of marine ecosystems to global climate regulation is real, important and currently active.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
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This research has utilised the Massachusetts Institute of Technology gen- eral circulation model (MITgcm) along with observations taken as part of the River In uences on Shelf Ecosystems (RISE) study to investigate the dynamic processes associated with the Columbia River plume at different temporal and spatial scales. Firstly, a high resolution ( x= y=25 m) investigation of the near-field plume was undertaken using the fully non-hydrostatic mode of the MITgcm. This resulted in the reproduction of a detailed inner plume as well as a series of radiated internal waves. In addition to first mode internal waves, second order waves were radiated from the plume boundary when propagation ve- locity becomes sub-critical. Third mode internal waves were also observed, trapped at the plume head. The fine plume structure produced revealed sec- ondary fronts within the plume that also generated internal waves. These features increase the mixing occurring inside the plume, resulting in greater entrainment of underlying waters into the plume. The use of Lagrangian drifters within the model produced detailed results of the recirculation tak- ing place within the emerging plume and how this recirculation changes with depth. This has implications for the near-field recirculation of biologically important solutes present in the plume waters. A second coarser resolution horizontal grid ( x= y=500 m) was imple- mented to investigate the processes of the large-scale plume with the addi- tion of wind forcing. Experiments with both simplified and realistic wind scenarios were carried out and comparisons with in-situ data were made. This revealed the dominance of wind effects on the outer plume and tidal effects on the inner plume. In the simplified wind cases, the classical the- ory of plume propagation under the action of upwelling and downwelling favourable winds was recreated. For the case of realistic winds, there was some success in reproducing a hindcast of the plume location. Tracer fields were used to represent nutrient concentrations based on observed data. Whilst these results showed variations from observations, they did allow a spatially and temporally complete view to be taken of nutrient distribu- tion in the region.

The shallow water configuration of the gulf of Trieste allows the propagation of the stress due to wind and waves along the whole water column down to the bottom. When the stress overcomes a particular threshold it produces resuspension processes of the benthic detritus. The benthic sediments in the North Adriatic are rich of organic matter, transported here by many rivers. This biological active particulate, when remaining in the water, can be transported in all the Adriatic basin by the basin-wide circulation. In this work is presented a first implementation of a resuspension/deposition submodel in the oceanographic coupled physical-biogeochemical 1-dimensional numerical model POM-BFM. At first has been considered the only climatological wind stress forcing, next has been introduced, on the surface, an annual cycle of wave motion and finally have been imposed some exceptional wave event in different periods of the year. The results show a strong relationship between the efficiency of the resuspension process and the stratification of the water column. During summer the strong stratification can contained a great quantity of suspended matter near to the bottom, while during winter even a low concentration of particulate can reach the surface and remains into the water for several months without settling and influencing the biogeochemical system. Looking at the biologic effects, the organic particulate, injected in the water column, allow a sudden growth of the pelagic bacteria which competes with the phytoplankton for nutrients strongly inhibiting its growth. This happen especially during summer when the suspended benthic detritus concentration is greater.

Located in the south-west region of Spencer Gulf, South Australia, a multi-million dollar aquaculture industry based on the ranching of southern bluefin tuna (Thunnus maccoyii) contributes significantly to the regional economy. The interaction between aquaculture activities and the environment is of significant interest to industry stakeholders, management authorities and the broader science community. No studies, to the best of my knowledge, have investigated the relationships between the hydrodynamics and biogeochemistry of the system and the ability of the benthic ecosystem to deal with the increased loads of organic material from aquaculture activities. This thesis uses a multi-disciplinary approach combined with modern statistical techniques to explore the linkages between hydrodynamics, sediment geochemistry, sedimentary nutrient cycling and the aquaculture industry. Modelling results have identified that swell entering the mouth of Spencer Gulf from directly south causes the greatest swell heights in the central tuna farming zone. Winds from the north-east through to south-east generate the greatest wind-wave heights in the central tuna farming zone. This is directly related to the available fetch. The energy contained in the locally generated wind waves was the same order of magnitude as that of the dissipated oceanic swells. Yet the incoming swell poses the greatest risk to aquaculture activities as the increased wave length causes swell energy to penetrate to the seafloor. The results of this work suggest that the sediment geochemistry is tightly coupled to both the hydrodynamic regime and the buildup of silt originating from aquaculture activities. In the more exposed regions of the tuna farming zone, periodic resuspension events caused by swell propagating into the area from the Southern Ocean, resuspend fine unconsolidated sediments into the lower 10 m of the water column. This material is then advected through the region by the residual (low-frequency) currents until it settles out in areas of lower energy. This process has created two distinct provinces within the region that can either be classified as depositional or erosional. The combined effect of wave action and tidal currents have generated a heterogeneous distribution of biogeochemical properties within the sediments. Denitrification rates were measured in these heterogeneous sediments using a novel technique based on Bayesian statistics to explicitly account for the spatial variability of the sediment biogeochemistry. The denitrification rates were found to be generally low, largely due to the lack of organic matter entering the sediments. However, adjacent to aquaculture activities, the high organic loads stimulate sedimentary denitrification, with rates reaching values of up to three orders of magnitude greater than the control sites. Denitrification efficiencies were high adjacent to the aquaculture activities, with up to 95% of the dissolved inorganic nitrogen produced from the breakdown of organic matter in the sediments being removed. Variability in the denitrification efficiencies was related to the textural characteristics of the sediments, with high efficiencies in finer sediments. It is proposed that this is due to the lower permeability of these sediments restricting the advective exchange of porewater nutrients.

Continental shelves are characterised by an active benthic system which is closely coupled to the pelagic: hence, the distinction between new and recycled production is not clear since the short and long-term processes are effectively coincident in space. In shelf ecosystems up to 40% of phytoplankton production can settle to the seabed and a large proportion of organic matter remineralisation occurs in the benthic compartment. However the benthic response of phytoplankton sedimentation is not unique and the receiving sediment type is a key factor determining the organic matter remineralisation rates. The aim of this project was to determine the relative importance of benthic regeneration processes at the Stonehaven monitoring site, Scotland, UK. Single and multi-beam acoustic and ground truthing surveys were carried out in the study area and the seabed landscape was described by sediment classes ranging from muddy sand to boulders and rock. General additive models were developed to link full coverage acoustic properties with sediment chemical concentrations developing full coverage maps of organic matter sources identifying the factors that can influence them. Direct measurements of sediment-water fluxes were carried out at monthly intervals throughout the year at a selected number of sampling stations identified by the acoustic analysis. The results revealed that water temperature, turbidity, sediment chlorophyll-a content and permeability were the main drivers of sediment biogeochemistry. Sediment nutrient regeneration rates contributed to the water annual budget of 25% and 89% for nitrogen and silicate respectively. Contrarily the sediment was a net sink for phosphate suggesting the importance of external supplying sources for this element. Finally, using a combined statistical modelling, we up-scaled results from a limited number of stations developing full coverage biogeochemical maps in the study area identifying 'hot spot' of sediment activity in a depositional area characterised by fine-grained sediment.

This work aims to increase our understanding of the nature of large scale features of sea ice from a dynamics point of view.Sea ice plays an important part in the exchange of heat and humidity between sea and air and thus is an important component of the climate system. Its physical presence also directly impacts the various forms of life such as diatoms, polar bears and humans alike.The dynamics of sea ice affect both weather and climate, through the large scale drift in the Arctic from the Siberian coast towards Fram Strait, through creation of cracks in the ice called leads or polynyas, and through ridging and other mechanical deformations of ice floes.In this work, we have focused on modelling of ridged ice for a number of reasons. Direct observations of the internal ice state is very difficult to perform and in general, observations of sea ice are either sparse or of limited information density. Ridged ice can be seen as the memory of high ice stress events, giving us a view on these highly dynamic events. Ridging is of major importance for the ice thickness distribution, as the thickest ice can only be formed through mechanical processes. Further, ridged ice is of direct interest for anyone conducting shipping through seasonal or perennial ice covered seas as it can form impenetrable barriers or in extreme even cases crush a ship caught within the ice pack. To this end, a multi-category sea ice model, the HELsinki Multi category Ice model (HELMI), was implemented into the Rossby Centre Ocean model (RCO). HELMI has explicit formulations for ridged and rafted ice, as well as sub-grid scale ice thickness distribution (a feature shared with other multi category models) and an ice strength based on energetics. These features give RCO better representation of sub-grid scale physics and gives us the possibility to study the deformed ice in detail. In paper I we look at the change in behaviour in the Arctic as the ice becomes more mobile, leading to a slight increase in modelled ridged ice volume in the central Arctic, despite a general trend of a decreasing ice cover.Paper II takes us to the Baltic Sea and the possibilities of modelling ridge ice concentration with a statistical model.In Paper III we investigate how the diminishing ice cover in future scenarios affects the biological activity in the Baltic Sea.Finally Paper IV investigates how the ice stress and the internal ice force can be interpreted in terms of ice compression on the ship scale.

At the time of the doctoral defence the following paper was unpublished and had a status as follows: Paper 4: Manuscript

For decades the Baltic Sea has been subject to eutrophication due to heavy anthropogenic nutrient loads on the aquatic ecosystem. Quantitative projections of its effects require an understanding of its driving mechanisms, i.e., the hydrodynamics that are responsible for the physical transport and mixing and the biogeochemical nutrients pathways within the algal ecosystem and between the particulate and dissolved phases in the water and in the sediments. A simple basin-scale hydrodynamic framework is set for the Gulf of Finland to test different descriptions of the biogeochemical transformations and determine the most robust modelling strategy. A recently developed criterion to determine the occurrence of anoxic events, based on the amount of fresh carbon detritus in the sediments is implemented in comparison with the classical criterion based on the oxygen concentration in the bottom water. Time-averaging of the hydrodynamics over larger than daily intervals is proved to hinder the capture of rapid mixing events jeopardizing irremediably the water quality simulation. The new carbon based criterion for anoxia shows a better dynamic response and is less sensitive to the model’s internal parameters. An internal source in the sediments correlated to the amount of fresh detritus, to represent the release of iron-bound phosphorus is confirmed as a versatile modelling assumption.

The focus of this thesis is on biogeochemical cycling in terrestrial ecosystems, and the effects on soil and surface water quality at a range of spatial scales throughout Scotland. The fundamental challenge of this research was to integrate the dynamic Model of Acidification of Groundwater In Catchments (MAGIC), within a spatial framework, by extrapolating knowledge of biogeochemical processes at the catchment scale to larger (i.e. regional and national) spatial units. The MAGIC model was applied to 9 Scottish sites in the U.K. Acid Waters Monitoring Network (UKAWMN), 59 sites in the region of Galloway and 733 sites throughout Scotland. Reduction in sulphur (S) emissions associated with the Second S Protocol and different forestry (land use) scenarios were modelled at these different scales to predict the existing and likely future extent of soil and surface water acidification in Scotland. The sensitivity of MAGIC to soil input data derived from two different methodologies was tested at the national scale. Anticipated reductions in S emissions are predicted to have a marginal beneficial effect on the reversibility of soil acidification at all spatial scales throughout Scotland, irrespective of the methodology used to determine the soil input parameters. With the exception of the most acid sensitive parts of Scotland, surface water Acid Neutralising Capacity (ANC) modelled at a national scale presents a picture of improving ANC in response to the Second S Protocol. From a policy perspective however, these results are potentially misleading. It is important that European legislation targets the most acid sensitive soils and surface waters as it is these ecosystems that require protection.

La mer Méditerranée est considérée comme un point chaud du changement climatique. Cette région très peuplée au climat aride devrait voir son climat devenir plus chaud et plus aride encore, tout en subissant une pression anthropique toujours plus forte. Dans ce contexte, de nombreuses données physiques et biogéochimiques sont actuellement relevées en mer Méditerranée, dans le cadre du projet MERMEX, afin de mieux étudier et comprendre les cycles biogéochimiques en mer Méditerranée. Complémentaire aux mesures, la modélisation est un outil unique pour aider à comprendre et quantifier les processus contrôlant la biogéochimie marine de la Méditerranée, ses spécificités et son évolution future. Dans cette étude, nous proposons la mise en place, et l’évaluation d’un modèle régional couplé dynamique - biogéochimie marine (NEMO-PISCES), à haute résolution, qui sera le premier modèle couvrant l’intégralité de la mer Méditerranée disponible pour la communauté MERMEX. Ainsi, après avoir évalué la dynamique du modèle NEMO-MED12, utilisée comme forçage, grâce à une simulation de traceurs passifs (CFC), nous effectuons les premières utilisations de cet outil, avec lequel (i) nous évaluons la quantité de carbone anthropique en mer Méditerranée grâce à une approche par perturbation, ainsi que l’acidification associée des masses d’eau ; (ii) nous effectuons une étude des régimes trophiques en mer Méditerranée, tels que perçus par le modèle, sur différentes couches de la zone euphotique
The Mediterranean Sea is considered as a hot spot of climate change. This arid region, already under high anthropogenic influence, is said to become even warmer and drier, with still an increasing anthropogenic pressure. In this context, numerous physical and biogeochemical data are currently collected in the Mediterranean Sea, within the MERMEX project, enabling to better study and understand the Mediterranean biogeochemical cycles. Complementary to in-situ observations, modelling is an unique tool that helps to understand and quantify biogeochemical controling processes in the Mediterranean Sea, its specificity, and its evolution. In this study, we propose the setting and evaluation of a regional, high resolution, marine dynamicalbiogeochemical coupled model (NEMO-PISCES). It will be the first model available for the MERMEX community, that covers the whole Mediterranean Sea. Therefor, after the evaluation of NEMO-MED12 dynamical forcing fields, within passive tracers simulation (CFC), firsts use of this tool have been made : (i) we have evaluated anthropogenic carbon uptake and induced acidification of the Mediterranean Sea, within a perturbation approach ; (ii) we have analysed Mediterranean Sea trophic regimes, as represented by the model, for different layers of the photic zone

[Tuncated abstract] Soil is a relatively low cost and robust geochemical sampling medium and is an essential part of most mineral exploration programs. In areas of covered terrain, however, soils are less reliable as a sampling medium because they do not always develop the geochemical signature of the buried mineralisation; possibly a result of limited upward transport of ore related elements into the surficial overburden. As economic demands on the resources industry grow, mineral exploration continues to expand further into areas of covered terrain where the rewards of finding a new deposit relative to the risks of finding it may be comparatively low. Thus, improving the costeffectiveness of a geochemical exploration program requires a sound understanding of the mechanisms by which soil geochemical anomalies form in transported overburden. This thesis examines the deep biotic uplift of ore related elements by deep rooting vegetation as a mechanism for the development of soil geochemical anomalies within transported overburdens, in semi-arid and arid regions. '...' Vegetation and soils were analysed at two Au prospects in Western Australia: Berkley, Coolgardie and Torquata, 210 km south-east of Kambalda, in semi-arid Western Australia to complement both the mass balance and the differential modelling. At Berkley, both the vegetation and soils located directly over the mineralisation showed high concentrations of Au. There may be indirect evidence for the operation of the deep plant uptake flux taking effect from the field evidence at Berkley. Firstly, anomalous concentrations of Au were found in the surface soils, with no detectable Au in the transported overburden. Secondly, the trace element concentrations in vegetation showed correlation to the buried lithology, which to our knowledge has not been reported elsewhere. The results from the samples at Torquata, in contrast, were less conclusive because the Au is almost exclusively associated with a surficial calcrete horizon (at <5 m soil depth). Strong correlations of Ca and Au in leaf samples however, suggest that the vegetation may be involved in the formation of calcrete and the subsequent association of Au with the calcrete. Among the vegetation components, the litter and leaf samples gave the greatest anomaly contrast at both prospects. Finally, three main drivers for the deep biotic uplift of elements were identified based on the results from the mechanistic numerical modelling exercise: i) the deep uptake flux; ii) the maximum plant concentration and; iii) the erosional flux. The relative sizes of these three factors control the rates of formation and decay, and trace element concentrations, of the soil anomaly. The main implication for the use of soils as exploration media in covered terranes is that soil geochemical anomalies may only be transient geological features, forming and dispersing as a result of the relative sizes of the accumulative and loss fluxes. The thesis culminates in the development of the first quantitative, mechanistic model of trace element accumulation in soils by deep biotic uplift.

En aquesta tesi s’ha desenvolupat un model de transport reactiu que integra tots els processos principals i secundaris que afecten la desnitrificació in situ induïda a diferents escales de treball. Així, l’eina obtinguda relaciona els processos biològics induïts quan s’afegeix un donador d’electrons a l’aqüífer amb els processos geoquímics (interacció aigua-roca) i la geoquímica dels isòtops. A la primera part de la tesi (Capítol 2) és on s’ha desenvolupat el model conceptual i on s’han establert les relacions que existeixen entre la microbiologia i la geoquímica prèvia de l’aqüífer a escala de batch. D’altra banda, també s’ha desenvolupat el model conceptual de tota la geoquímica isotòpica associada al procés (δ15N-NO3-; δ18O-NO3- i δ13C-DIC incorporant tota la geoquímica del δ13C). En aquest sentit, s’ha desenvolupat un dels models biogeoquímics més complets de la literatura relacionats amb la desnitrificació in situ induïda. El model s’ha calibrat emprant dos experiments a escala de batch realitzats amb etanol i glucosa com a fonts de carboni externa. En tots dos casos, s’han obtingut molt bons ajustos amb les dades experimentals. A més, el model també incorpora l’acumulació de nitrit en el cas de l’experiment de la glucosa. L’avaluació dels processos geoquímics induïts per l’EIB ha posat de manifest que en funció de la font de carboni s’indueixen processos de precipitació (en el cas de l’etanol) i processos de dissolució de carbonats (en el cas de la glucosa). Aquests dos processos poden alterar la velocitat de l’aigua i crear importants problemes operacionals durant l’EIB. També s’han incorporat els processos de fraccionament isotòpic del nitrat millorant l’avaluació de l’abast de la desnitrificació en els models a escala de camp. Un cop elaborat el model biogeoquímic que estableix el model conceptual que quantifica les interaccions entre els diferents processos que hi intervenen, el model s’ha escalat a un cas de desnitrificació induïda a escala de camp en un aqüífer fracturat (Roda de Ter (Osona, Espanya)). En aquest apartat de la tesi (Capítol 3), s’ha perseguit avaluar quin era l’impacte del canvi d’escala en els paràmetres biogeoquímics. A més a més, també s’ha determinat el canvi de porositat induïda per la precipitació de calcita. Finalment, la incorporació dels isòtops al RTM ha permès comparar qualitativament i quantitativament l’extensió dels processos de desnitrificació calculats pel RTM i per l’equació de Rayleigh. Els resultats demostren que l’equació de Rayleigh descriu bé, en termes qualitatius, l’extensió de la desnitrificació, però en general la subestima entre un 60 i un 80%. Finalment, un cop avaluada l’aplicabilitat del model tant a escala de batch com a l’escala de camp, s’ha desenvolupat un model que reprodueix diferents escenaris d’injeccions de carboni orgànic en un experiment de columna de llarga durada considerant els canvis sobre les propietats hidràuliques produïts pel creixement microbià. Així, s’ha determinat que el creixement del biofilm va augmentar set cops la dispersivitat, augmentant, per tant, la heterogeneïtat del sistema i, conseqüentment, es va produir un canvi del model conceptual del flux i del transport del transport normal al transport no-Fickià. Aquesta transició es va caracteritzar emprant un model de transferència simple de massa. A més a més, el model de llarga durada ha permès determinar que freqüències d’injecció més espaiades en el temps produeixen un impacte menor en les propietats hidràuliques del medi. A més a més, les estratègies d’injecció amb la relació Carboni:Nitrogen per sota de l’estequiomètrica es poden emprar per a minimitzar el risc de bioclogging mantenint les taxes de degradació, sempre i quan hi hagi una població important de microorganismes.
In this thesis, an integrated reactive transport model has been developed that takes into account microbiology, geochemistry, and isotope geochemistry. The first section of the thesis (Chapter 2) addresses the development of a biogeochemical model with isotope geochemistry. The goal of this chapter is the setup of the conceptual relationships among microbiology, geochemistry, and isotope geochemistry (δ15N-NO3-, δ18O-NO3-, δ13C-DIC, and all geochemistry of δ13C) during Enhanced in situ Biodenitrification. Thus, one of the most complete biogeochemical models in the literature of EIB has been developed. The model was validated with a batch-scale biodenitrification experiment using groundwater and sediment from a Roda de Ter (Osona, Spain) site and two different external organic carbon sources, i.e., ethanol and glucose. In both cases, the model fit notably well with the experimental data. Moreover, the developed model also incorporated the nitrite accumulation observed in the glucose experiment. Consideration of the water-rock interaction in the model determined that if ethanol is used as an organic carbon source, carbonate mineral precipitation is induced, whereas if glucose is used, carbonate mineral dissolution is observed. Moreover, nitrate isotope incorporation facilitated the determination of the extent of denitrification at the field scale. Finally, the incorporation of a carbon isotope flow in the model was another tool used to verify the full consistence of the model due to the central role of inorganic carbon in biodenitrification and water-rock interactions. Moreover, modeling of carbon isotope flow showed that both ethanol and glucose were inversely fractionated. After the conceptual model was carried out, it was applied to an Enhanced in situ Biodenitrification application in fractured media (also Roda de Ter (Spain)). The main goal of this chapter is to incorporate the groundwater flow equations into a previously develop biogeochemical model and to validate it in media with a complex hydrogeology. It was observed that certain batch parameters can be used directly in the field (maximum consumption rate of electron donor (kmax) and stoichiometric relationships) and that the other parameters (saturation constants (Ks) and decay (b)) should be adapted, but the modifications involved less than one order of magnitude. Moreover, the induced calcite precipitation caused a change of porosity of less than 3%. As a secondary goal, the use of the Rayleigh equation to determine the extent of EIB was also verified from a practical perspective. The model demonstrated that the Rayleigh equation underestimated the percentage of degradation by approximately 60-80% and increasingly at the fringes of the plume. Chapter 4 focuses on a model that reproduces the system under different injection conditions and with the presence of important biofilm growth. This chapter evaluates how different feeding strategies modify the hydraulic properties of the media. It was observed that a weekly feeding strategy did not modify the hydraulic properties of the media, whereas daily feeding significantly modified the dispersivity. These changes in dispersivity implied an increase in heterogeneity and a consequent change in the conceptual model of flow transport along the column from normal to non-Fickian. This transition was well characterized using a single-rate mass transfer model. Moreover, the long-term model demonstrated that use of a feeding strategy with less carbon than predicted by stoichiometry implied a reduction of biomass without a reduction in nitrate degradation rates (because of the presence of an important biomass population). Overall, the elaboration of this thesis has contributed to the knowledge of all processes involved in Enhanced in situ Biodenitrification and their quantification using numerical models. The developed model will allow improvement in the design, planning, monitoring and optimization of this technology at the field scale.

L'étude de l'impact que les structures hydrodynamiques à mésoéchelle peuvent avoir sur la distribution spatiale des organismes planctoniques et le transport de matière entre la zone côtière et le large est essentielle à la compréhension du fonctionnement de l'écosystème planctonique dans l'océan côtier. L'influence des tourbillons anticycloniques et des processus physiques associés sur l'écosystème planctonique pélagique est examinée au moyen d'un modèle couplé physique-biogéochimie. Dans un premier temps, les sorties du modèle sont confrontées à des données in situ et satellitales afin de vérifier le réalisme du modèle. Pendant la majeure partie de la simulation, et plus particulièrement sur la partie ouest du golfe de Lion pendant la période estivale, l'erreur commise par le modèle sur l'estimation de la chlorophylle de surface (proxy du phytoplancton) est inférieure à celle donnée par le calcul issu de la télédétection. Ensuite, la distribution du plancton en présence d'un tourbillon a été étudiée. Dans les sorties du modèle, un filament avec une forte concentration en chlorophylle est systématiquement observé sur le bord nord/nord-est de la structure, est confirmé par des données satellitales. Enfin, grâce à une simulation longue sur la période 2011-2004, plusieurs tourbillons ont été comparés du point de vue de leur impacts sur les échanges entre la côte et le large de matière et plancton. L'intensité et la direction de ces échanges sont hétérogènes et dépendent des forçages physiques qui ont donné lieu à la génération de ces tourbillons
The role that mesoscale physical structures play in driving plankton community shifts and transporting matter is key to the understanding of food web dynamics at the regional scale

Cette thèse met en perspective un ensemble d’éléments des scénarios socio-économiques sous l’angle de la modélisation du climat. Ces éléments contribuent à améliorer la compréhension de l’état actuel des sciences du climat en ce qui concerne les scénarios. En parallèle, ces éléments montrent le potentiel du récent modèle compact du système Terre OSCAR v2.2.Le premier élément concerne l’incertitude des émissions. Bien que les inventaires d’émissions soient incertains, nous ignorons dans quelle mesure ces incertitudes affectent les projections climatiques. Nous quantifions cet impact pour les émissions des énergies fossiles, la principale cause du changement climatique. Nous montrons que ces incertitudes dans les émissions sont amenées à augmenter avec l’utilisation des énergies fossiles non-conventionnelles, mais qu’elles n’augmentent pas de manière significative l’incertitude dans les projections climatiques. Ceci est vrai pour la majeure partie des variables, comme l’augmentation de la température moyenne de surface, mais pas pour certaines qui sont d’intérêt pour la qualité de l’air.Le second élément est une analyse climatique des récents scénarios Shared Socio-Economic Pathways. Nous identifions des failles dans la base de données, que nous comblons. Sur cette base, nous calculons les projections climatiques des scénarios SSP. Nous montrons la présence d’incohérence dans l’utilisation des émissions CO2 dues à l’utilisation des terres (LUC) calculées par les modèles intégrés (IAMs) et des variables associées à l’utilisation des terres. Nous identifions des compromis dans les réductions d’émissions pour l’atténuation du changement climatique. Nous réévaluons de manière plus robuste les budgets carbone. Les incertitudes dans les élévations de températures sont examinées en détail.Le troisième élément concerne les émissions négatives. La plupart des scénarios qui limitent le changement climatique bien en dessous de 2°C par rapport au préindustriel, respectant ainsi l’Accord de Paris, utilisent des émissions négatives. A l’aide d’une version développée de OSCAR v2.2, nous calculons les implications pour le système Terre de plusieurs aspects des techniques d’absorption de dioxyde de carbone (CDR). Nous identifions les réversibilités des différentes parties du système terre, et évaluons le potentiel de refroidissement de ces techniques. Nous montrons aussi que la reforestation pourrait être moins apte à atténuer le changement climatique, du fait du changement dans l’albedo de surface. Par ailleurs, le potentiel d’alcalinisation des eaux de surfaces pour atténuer le changement climatique pourrait être inférieur à celui initialement estimé.Dans l’ensemble, cette thèse identifie des défauts dans le développement actuel des scénarios. Certains ne constituent pas un problème pour les projections climatiques, comme les incertitudes dans le calcul des émissions. D’autres nécessitent une attention particulière, comme le calcul des émissions CO2 dues au LUC par les IAMs ou l’éventuelle surestimation des capacités des techniques de CDR. Ce travail renforce l’urgence du besoin d’atténuation du changement climatique
This thesis puts into perspective different elements of socio-economic scenarios from a climate change modelling point of view. These elements contribute at improving the comprehension of the current state of climate sciences regarding the scenarios. In the meantime, these elements demonstrate the potential of the recent reduced-form Earth System Model OSCAR v2.2.The first element concerns the uncertainty of emissions. Although emission inventories are uncertain, we ignore what impact on climate change have these uncertainties. We quantify this impact for fossil-fuel emissions, the major contributor to climate change. We show that the uncertainties in emissions are expected to increase with the use of non-conventional fuels, but that they do not increase significantly the uncertainty from Earth system modelling in variables, such as the increase in global surface temperature.The second element is a climate assessment of the recent Shared Socio-economic Pathways (SSP) scenarios. We identify loopholes in the SSP database, and we complete it to calculate the climate projections under these scenarios. Our conclusions suggest inconsistencies in CO2 emissions from Land Use Change (LUC) calculated by the Integrated Assessment Models and in the associated land variables. We identify trade-offs between greenhouse gases in the mitigation of climate change. Using a robust assessment, new carbon budgets are proposed. The uncertainties in increases in global surface temperature are discussed.The third element concerns the negative emissions. Most climate scenarios limiting global warming well below 2°C above preindustrial levels, thus respecting the Paris Agreement, use negative emissions. Using a developed version of OSCAR v2.2, we evaluate the implications for the Earth system of different aspects of different Carbon Dioxide Removal (CDR) technologies. We identify the reversibility in the different components of the Earth system and calculate the cooling potential of carbon dioxide removal technologies. We also show that the potential of afforestation/reforestation techniques may be impeded by the change in albedo, and that the potential of oceanic enhanced weathering may be lower than expected.Overall, this thesis identifies loopholes in the current development of scenarios. Some do not hinder current conclusions regarding climate change, such as the uncertainties in emission inventories. Others call for further analysis, such as the inconsistencies in the use of CO2 emissions from LUC or the eventual overestimation of the potential of some CDR technologies. It emphasizes the need for an urgent mitigation of climate change

Dans cette thèse nous avons simulé la distribution d’éléments traces en Méditerranée, dans le but de mieux contraindre la circulation thermohaline et les cycles biogéochimiques. Pour cela, nous avons utilisé le modèle dynamique à haute résolution NEMO-MED12 couplé avec le modèle de biogéochimie marine PISCES.La Méditerranée offre un cadre particulièrement attrayant pour l’étude des traceurs géochimiques. Il s’agit d’une mer semi-fermée, ce qui permet de mieux contraindre les différentes sources et puits des éléments (poussières atmosphériques, fleuves …). Plus particulièrement, nous avons modélisé le tritium (3H), traceur transitoire couramment utilisé pour l’étude de la variabilité interannuelle de la circulation thermohaline. Nous avons aussi simulé les isotopes de l’hélium (3He, 4He), traceurs conservatifs injectés par l’activité volcanique sous-marine et les sédiments, pour contraindre la circulation profonde. Nous nous sommes intéressés également à la composition isotopique du Néodyme (Nd), traceur permettant d’étudier les échanges de matière avec les marges continentales, ainsi qu’à la modélisation du radiocarbone (14C), qui permet d’avoir des informations uniques sur les variations de la circulation thermohaline et des processus de mélange sur les périodes récentes et passées.Cette ensemble de simulations nouvelles et la confrontation avec des observations récentes d’éléments traces issues de différents programmes d’observation (GEOTRACES, METEOR, PALEOMEX), a apporté une expertise nouvelle et supplémentaire sur la dynamique et les cycles biogéochimique en mer Méditerranée. Ce travail contribue à améliorer le modèle régional NEMO/Med12/PISCES développé pour ce bassin, apporte une expertise essentielle pour développer notre aptitude à prévoir l’évolution future de ce bassin sous la pression du changement anthropique
Useful diagnostics of the ventilation of the ocean’s interior are derived from geochemical tracers characterized by simple boundary conditions at the ocean’s surface, and a conservative behavior in marine waters. In this thesis, we simulated explicitly some trace elements distribution in the Mediterranean to better constrain the thermohaline circulation and biogeochemical cycles. We used a high resolution physical/biogeochemical model NEMO-MED12-PISCES.The Mediterranean offers a particularly attractive setting for studying geochemical tracers. It’s a semi-enclosed basin, which makes it easier to quantify the various sources and sinks of the elements (atmospheric dust, rivers ...). In particular, we modeled tritium (3H), a transient tracer currently used for the study of the interannual variability of the thermohaline circulation. We also simulated helium isotopes (3He, 4He), useful tracers for investigating the deep ocean circulation.We have simulated the isotopic composition of neodymium (Nd), tracer adapted to investigate the exchanges between dissolved/particulate phases, with the continental margins, and to constrain the modern and paleo thermohaline circulation, as well as radiocarbon (14C), an ideal tracer for studying air-sea gas exchange and for assessing the ventilation rate of the deep water masses over very long timescales.This study is part of the work carried out to assess the robustness of the NEMO-MED12 model, which will be used to study the evolution of the climate and its effect on the biogeochemical cycles in the Mediterranean Sea, and to improve our ability to predict the future evolution of the Mediterranean Sea under the increasing anthropogenic pressure

Le concept de « service écosystémique », en plein essor depuis la publication du Millenium Ecosystem Assessment en 2005, a permis de souligner l'importance des performances non-marchandes des écosystèmes. En arboriculture, assurer une bonne productivité tout en préservant les ressources naturelles et la santé humaine est aujourd’hui un défi majeur, qui peut être analysé sous l’angle des services écosystémiques. Quels sont ces services au sein d’un verger de pommiers ? Comment les analyser ? Quels sont les liens - conflits et synergies - entre services écosystémiques multiples et comment les systèmes de culture modifient-ils les profils de services multiples? Ce travail de thèse vise à répondre à ces questions avec une démarche novatrice combinant mesures expérimentales, modélisation et analyse statistique. Suite à une analyse bibliographique des services écosystémiques pouvant être délivrés dans des vergers, cinq services ont été sélectionnés. Il s’agit de la production de fruits, de la disponibilité de l’azote dans le sol, de la régulation du climat reposant sur la prévention de la dénitrification de l’azote et sur la séquestration du carbone, de la maintenance et de la régulation du cycle de l’eau y compris de sa qualité, et de la régulation des bioagresseurs. Conjointement à ces services nous avons considéré les nuisances environnementales dues aux pesticides. Pour chaque service nous avons identifié les fonctions écosystémiques sous-jacentes ainsi que les pratiques agricoles et les conditions pédoclimatiques ayant un impact sur ces fonctions. Les services et fonctions ont été décrits par un ou plusieurs indicateurs et quantifiés à l’aide de modèles dans les cas suivants : (i) neuf systèmes de culture réels sur deux dispositifs expérimentaux dans le sud-est de la France et (ii) 150 systèmes de culture fictifs conçus à partir de la combinaison de cinq leviers de pratiques et de leurs modalités, dans des conditions pédoclimatiques identiques. Les deux modèles utilisés ont été STICS, un modèle générique de simulation du fonctionnement du sol et des cultures sous l’influence des pratiques, qui a nécessité une paramétrisation et une évaluation sur pommier à partir de mesures expérimentales, et IPSIM, une plateforme de modélisation simulant les effets des pratiques et des conditions du milieu sur les dégâts aux cultures causés par les bioagresseurs. IPSIM a été paramétré sur pommier, sur la base d’une importante étude bibliographique et à dires d’experts. Les simulations des modèles ont fait l’objet d’analyses statistiques simples dans le cas des systèmes de culture réels, et d’analyses multivariées à deux tableaux (analyse en composantes principales avec variables instrumentales) pour les systèmes de culture fictifs. Pour les neufs systèmes de culture réels, 14 liens importants entre services écosystémiques ont été identifiés, notamment des conflits comme celui entre la prévention de la dénitrification ou de la lixiviation de l’azote et la disponibilité de l’azote dans le sol à court terme, et des synergies, comme celle entre l’humidité du sol ou la séquestration du carbone et la disponibilité de l’azote dans le sol à court terme. Ces liens entre services sont expliqués par les fonctions écosystémiques sous-jacentes. La comparaison de profils de services entre systèmes a mis en évidence l’impact de pratiques agricoles sur certains services. Ainsi, sur un même site, une forte densité de plantation augmente la production de fruits et la séquestration du carbone. La fertilisation exclusivement sous une forme organique diminue la production de fruits via un stress azoté mais diminue également la lixiviation. Par ailleurs, les profils de services sont fortement influencés par les caractéristiques pédoclimatiques de chaque site. Ces résultats confortent la nécessité d’une prise en compte explicite de l’interdépendance ‘pratiques x conditions du milieu’ pour analyser les services
The concept of « ecosystem service », which has been used increasingly since the publication of the Millennium Ecosystem Assessment in 2005, has highlighted the importance of ecosystem’s non-marketed performances. In orchards, ensuring high productivity while preserving natural resources and human health has become a real challenge that could be analyzed with the concept of ecosystem service. Which ecosystem services are delivered in an apple orchard? How to analyze them? What are the relationships - conflicts or synergies – among multiple ecosystem services and how do cropping systems change multiple ecosystem service profiles? This PhD work aims at answering those questions with an innovative approach combining experimental measures, modeling and statistical analysis.Based on a literature review of ecosystem services in orchards, five services were selected: fruit production, nitrogen availability in soil, climate regulation based on the prevention of nitrogen denitrification and on carbon sequestration, maintenance and regulation of water cycle, including water quality, and pest control. We also considered the environmental disturbances caused by the use of pesticides. For each service, we identified the underlying ecosystem functions as well as the agricultural practices and soil and climate conditions affecting these functions. Services and functions were described by one or multiple indicators and quantified using models in the case of (i) nine existing cropping systems on two experimental sites in southeastern France differing in terms of soil and climate conditions, and (ii) 150 virtual cropping systems designed out of the combination of five major agricultural practice levers and their modalities, in identical soil and climate conditions. The two models used were STICS, a generic soil-crop simulation model under the influence of practices which required a parameterization and an evaluation on apple orchards based on experimental measures, and IPSIM, a generic modeling framework simulating the impacts of agricultural practices and local conditions on crop injuries caused by pests. IPSIM was parameterized on apple orchards, based on an important literature review and expert opinions. Model simulations were analyzed with simple statistics in the case of the nine existing cropping systems and with two-table multivariate analyses (principal component analysis with instrumental variables) for virtual cropping systems.Concerning the existing cropping systems, 14 important relationships were identified among ecosystem services, especially conflicts, like the one between nitrogen denitrification or leaching prevention and soil nitrogen availability on the short term, and synergies such as the one between soil humidity or carbon sequestration and nitrogen availability on the short term. These relationships are explained by the underlying ecosystem functions. Comparing service profiles among cropping systems highlighted the impacts of agricultural practices on some services. That way, on a same site, a high planting density increases fruit production and carbon sequestration. An exclusively organic fertilization decreases fruit production through nitrogen stress but also nitrogen leaching in drained water. Furthermore, service profiles are strongly influenced by the soil and climate conditions of each site. These results strengthen the need to explicitly consider the ‘agricultural practices x soil and climate conditions’ interdependence in order to analyze ecosystem services. The results obtained with the virtual cropping systems simulations confirmed those of the existing ones and gave precision on the impacts of fertilization, irrigation and pest control for codling moth, rosy apple aphid and apple scab on ecosystem functions and services

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

Aquaculture is an increasingly expanding industry driven both by economic opportunity and necessity, as countries seek contemporary solutions to food security. However there are risks with unchecked or poorly managed expansion, including the potential to harm natural ecosystems in the vicinity of aquaculture farms. It is unknown exactly how sensitive estuarine biogeochemistry is to a major input of dissolved inorganic nitrogen (DIN) from finfish aquaculture. DIN is the limiting nutrient in autotrophic growth in temperate Australian estuaries, and increase in DIN loading has the potential to greatly increase primary phytoplankton production with possible consequences ranging from general decrease in water quality to harmful algal blooms and a trophic shift to eutrophication. The present work investigates the impact of salmon farming on the marine environment and key ecological processes in the D’Entrecasteaux Channel and Huon Estuary in Tasmania. This study uses purpose built ecosystem models to assess the increase of nutrients in the region due to the nutrient input from fish farms. The results indicate a need to develop strategies to deal with nutrient loading from salmon aquaculture, particularly if the industry were to increase production beyond current levels. One method gaining increasing interest worldwide is Integrated Multitrophic Aquaculture (IMTA) in which species that utilize the waste products from the primary species are farmed alongside the focus species. Here I construct an IMTA process model to identify the most suitable macroalgae, from a set of potential species for this region, and present a thorough uncertainty analysis of the model. The model is then used within larger estuary models to quantify the potential benefits of IMTA at the system level. The thesis comprises separate chapters for the General Introduction, General Conclusion and four standalone chapters that focus on quantifying the potential of using macroalgae as an agent for IMTA in conjunction with finfish aquaculture in southeast Tasmania. In Chapter 2 the aim was to identify a suitable species of macroalgae for IMTA in the D’Entrecasteaux Channel and Huon Estuary. To achieve this aim, a macroalgae growth model was developed and then applied in a simulation of IMTA in a near field experiment, whereby macroalgae are grown close to a point source of nutrients. The model was used to compare the capacity of three species of macroalgae (Macrocystis pyrifera, Ulva lactuca and Porphyra umbilicalis) to remove ‘waste’ DIN under a range of scenarios. The species were selected based on certain assumptions about their intrinsic worth; M. pyrifera is a species that has largely disappeared from the region and so has environmental and conservation value, P. umbilicalis has high economic value in the seafood industry, while U. lactuca has the highest absolute growth rate of these three rapidly-growing algae and so is an obvious candidate as a potential ‘nutrient pump’. The model distinguishes between the species based on parameters representing sub-processes that control growth. An allometric growth term was developed to allow M. pyrifera to vary its height and thus exploit its ability to occupy the water column. The results show that M. pyrifera vastly out-performs the other two species in terms of its ability to remove the DIN output from the finfish cages in the near field case, largely as a result of its size advantage over the other species. Quantifying the potential optimization of IMTA considering cultivation depth, site selection and harvesting, suggests that varying cultivation depth up to a maximum of 5m impacts M. pyrifera production but has no effect on the other two species; DIN removal varied with flow rate (for all 3 species) and the appropriate harvesting scheme can improve bioremediation by a factor of 15 compared to non-harvested crops. In Chapter 3 a thorough uncertainty analysis of the model was conducted and a method to incorporate empirical data to improve model performance was also developed. A Bayesian inference method was used to quantify uncertainty in the IMTA model with M. pyrifera used as the extractive species. The deterministic model was reformulated into a stochastic form through the representation of sub-processes (e.g. mortality and maximal growth rate) as time varying, using first order auto-regressive processes. Parameter uncertainty was accounted for using prior distributions. We used data from three empirical growth experiments to test the effect of seeding density on ropes supporting M. pyrifera grown around salmon pens. The data were assimilated into the model using a Sequential Monte Carlo method. Through conditioning the state variables on the parameter priors alone we obtained a comprehensive uncertainty analysis of the model, and were able to constrain the model output to observed values. The results showed learning in a subset of model parameters, and overall the data assimilation method resulted in a 90% reduction in model uncertainty in both the state and parameters. These results will assist in future applications of the model by providing a more realistic parameter set. We were also able to show that low to medium density as an initial seeding of M. pyrifera resulted in best uptake of DIN. This approach offers a method by which empirical data from IMTA experiments can be used to improve IMTA process models. The next two chapters incorporate the model into a three-dimensional coupled hydrodynamic, sediment and biogeochemical model. The 3D model, which was used in the original study that prompted this work, has been developed through numerous case studies to offer a realistic simulation of estuarine dynamics. In chapter 4 an idealized ‘test’ estuary was created as the setting of finfish aquaculture. Firstly, through incremental increases in DIN output from finfish aquaculture a relationship between nutrient loading rates and water quality as determined by chlorophyll concentration, was obtained. Through the simulation of IMTA farms adjacent to the finfish sites, the capacity of M. pyrifera to remediate the estuary was then established. The results showed that M. pyrifera could effectively bioremediate the output from the finfish aquaculture as loading increased. This ensured a classification of ‘good’ water quality based on chlorophyll concentrations, was retained within the estuary. The hydrodynamic conditions was determined to be the primary driver of both the distribution of chlorophyll and successful IMTA. Farms in the southern section of the estuary achieved the highest biomass of macroalgae, but had little impact on the reduction of primary production due to this area being well flushed from strong river flow; which limited phytoplankton growth in this area. A region of freshwater influence was responsible for the high productivity observed in the northern region of the estuary, and IMTA in this section was solely responsible for reducing chlorophyll concentration. The last phase of the study (Chapter 5) focused on a more realistic simulation of macroalgae-based IMTA by incorporating the stylized model into a model of the D’Entrecasteaux Channel and Huon Estuary - a region of intensive salmon aquaculture in southeast Tasmania. In this chapter the aim was to estimate phytoplankton production in this region stimulated from ‘waste’ DIN from finfish aquaculture, and investigate the effectiveness of IMTA in remediating any increase in production. We identify the spatial pattern and magnitude of phytoplankton production in the region under a range of outputs from finfish aquaculture. Scenario analysis showed that the most productive area to grow M. pyrifera is in the immediate vicinity of the salmon farms, and that growing giant kelp in this way can mitigate undesirable effects on chlorophyll concentration of DIN loading from the farms if activity expands beyond current levels. However, mitigation using IMTA is non-linear and there are limits to the magnitude of salmon aquaculture activity beyond which significant declines in water quality seem inevitable, even if M. pyrifera is grown extensively around farms. This study provides a thorough investigation of the potential of macroalgae-based IMTA to prevent the potentially damaging waste DIN output from finfish aquaculture from adversely affecting water quality (as assessed by chlorophyll concentration). It provides important baseline information that will help both management and future studies into IMTA by: (i) identifying vertical distribution as the most important feature for potential macroalgae culture species in near field IMTA; (ii) showing the impact of farm arrangement on DIN uptake by macroalgae for a range of potential IMTA species; (iii) describing a method for data assimilation to improve the validity of model results and reduce uncertainty, and (iv) providing a general guide to considerations for the successful implementation of macroalgae-based IMTA to mitigate reduction in water quality resulting from the addition of anthropogenic nutrification in estuaries.

Zinc (Zn) plays an essential role in metabolic and structural functions for marine phytoplankton, being required in nearly 300 enzymes and proteins including carbonic anhydrase and alkaline phosphatase. The concentration of total dissolved Zn in the open-ocean is typically in the nanomolar (0.1-10 nmol L\(^{-1}\)) range, 98 % of which is complexed by natural strong organic ligands. In January and February 2010, the Primary productivity Induced by Iron and Nitrogen in the Tasman Sea (PINTS) cruise covered a north to south transect from the oligotropic Tasman Sea to the productive waters of the subantarctic Southern Ocean. For this thesis, samples for chemical analyses and laboratory- based cultures were collected to assess the relationship between phytoplankton growth and zinc bioavailability and speciation in this region. The pennate diatom \(Nitzschia\) \(closterium\) and the coccolithophorid \(Emiliania\) \(huxleyi\) were cultured at low free Zn concentrations ([Zn\(^{2+}\)] = 1.5 x 10\(^{-12}\) M and [Zn2+] = 1.5 x 10\(^{-14}\) M) to mimic the range of free Zn encountered in marine systems. Both species were able to maintain their photosynthetic activity and growth at the low [Zn\(^{2+}\)] applied. However, while E. huxleyi grew at these low concentrations, \(N. closterium\) seemed to accelerate its uptake with specific and efficient transporters and access complexed Zn. In the Tasman Sea, total dissolved Zn was observed at 0.02 to 0.19 nmol L\(^{-1}\) (at 15 m depth) and 0.02 to 0.11 nmol L\(^{-1}\) (at 150 m) along the north-south transect studied, below the range reported for other open-ocean regions. Measurements with Anodic Stripping Voltammetry (ASV) on four selected profiles from the Tasman Sea established the concentrations of labile Zn (0.6 to 500 pmol L\(^{-1}\)) and Zn-complexing ligands (0.23 to 4.19 nmol L\(^{-1}\)) for the first time in the Tasman Sea. Zn speciation was dominated by complexation to organic ligands (59 to 98%) with the highest percentages in surface. These ligands were closely related to the phytoplankton assemblages found in the studied region (Chlorophytes ~ Haptophytes > Diatoms). The links between chemistry and biology were studied with a simple conceptual ZnPPZZD model. It was parameterised with information gained in the experimental phases of this work, such as the difference of uptake response observed for the two species and range of concentrations measured. The model showed the concentration of ligands and zinc speciation played an important role in the structure of the conceptual phytoplankton assemblages. Further work is required to assess if ligands are produced by the organisms to enhance their uptake or if the chemistry of Zn strongly influences the community for a specific region.

A quasi-two dimensional model for the southern Vancouver Island shelf was developed with the Regional Ocean Modelling System (ROMS) to study coupling of the carbon, oxygen, and nitrogen cycles in a summer wind-driven upwelling region. The physical model is coupled to an ecosystem module that includes a simple representation of a sediment layer and considers non-fixed C:N ratios for detritus and dissolved organic matter (i.e., explicitly modelled pools of carbon and nitrogen for those variables). The model accounts for denitrification within the sediments as well as within the water column when oxygen concentrations are low (below 5 mmol-O2 m-3). The objective is to identify the dominant processes controlling the cycles, their coupling, and their sensitivity to changes in environmental forcing. Results demonstrate how low oxygen and low pH events are tightly coupled in the coastal study region, especially through local ecosystem processes. In particular, exchange with the sediments plays a dominant role in consuming oxygen from and releasing inorganic carbon to the bottom waters on the shelf. Two key features distinguish the southern Vancouver Island shelf from other coastal regions in the California Current System and protect inner shelf waters from severe hypoxia and corrosive (i.e., undersaturated in aragonite) conditions. First, the greater width of the shelf reduces the penetration of subsurface offshore high-carbon and low-oxygen waters into shallower waters; and second, the relatively fresh Vancouver Island Coastal Current (VICC) brings oxygen-rich and carbon-poor waters to the bottom layer over the inner shelf. Sensitivity experiments show that carbon and oxygen cycles on the southern Vancouver Island shelf may be significantly affected by an altered upwelling season, a shallower offshore Oxygen Minimum Zone, a warmer ocean, and a carbon-enriched environment. Combinations of these scenarios suggest a potential increasing risk for the development of coastal hypoxia and corrosive conditions in the future. Further sensitivity simulations indicate that sedimentary denitrification provides an additional coupling between the carbon, oxygen, and nitrogen cycles. Total alkalinity generated by sediment denitrification has the potential to buffer anthropogenic ocean acidification. However, this alkalinity effect over the Vancouver Island shelf in late spring and summer simulations is small compared with studies for other locations at annual scales. Longer time scales need to be examined in this region to confirm whether the role of alkalinity generation in the sediments is significant. In conclusion, this dissertation not only demonstrates the coupled nature of biogeochemical cycles in the coastal ocean, but also the importance of this coupling as we try to estimate how coastal ecosystems will respond to human modifications of shelf waters and the climate.