Coral reef degradation is happening at an alarming rate all over the world due to multiple stressors with elevated sea surface temperature being the root cause. Using the Regional Ocean Modelling System and an individual-based model for the western Indian Ocean, this thesis explored the general circulation patterns (both large and mesoscale) important to dispersal and connectivity of broadcast corals while identifying regions that act as a source of larvae and those that receive larvae. Because habitat destruction and fragmentation through severe bleaching and mortality threaten coral reef health, projected thermal stress from Global Climate Models was explored to quantify future bleaching scenarios that might impact the reproductive timing and larval dispersal. Evaluation of the ROMS configuration for the western Indian Ocean shows that the basin-scale circulation patterns of the region are appropriately captured with the mean volume transports consistent with those derived from observation. Using the eddy detection algorithm, a description of the Southern Gyre as a key aspect of the Somali Current system was identified. The Southern Gyre is associated with barotropic instabilities associated with the northward flowing Somali Current. Rossby waves arriving at the East African coast and the strength of the monsoon winds are also responsible for the evolution and intensification of the gyre. The aggregated trajectories from the Lagrangian model highlight the dominant dispersal pathways and barriers to dispersal following release. The general circulation plays an important role in the dispersal of reef larvae over the study region. At a short pelagic larval duration, most of the released larvae settle back to or near natal reefs, but as the pelagic duration increases, the number of isolated reefs and islands decreases. Even with increased pelagic duration, some reefs (e.g., Agalega and Tromelin) are completely isolated. The mean dispersal distance from release to settlement varied across the region with larvae released along the East African coast dispersed an average of 405 km before settling while those in the Seychelles archipelago dispersed about 101 km. Different blocks of clusters were observed with 16 clusters observed when the pelagic duration is shorter (5 days), compared to seven clusters when the pelagic duration is longer (60 days). The warming trends and bleaching thermal stress shows that among the 636 reef pixels in the study region, about 56% showed positive sea surface temperature trends during the study period (1985- 2016). The frequency of bleaching level thermal stress has also increased over the same period, a tendency that climate models project to continue. Even under optimistic scenarios (such as the Representative Concentration Pathway RCP 4.5), most coral reefs are projected to experience severe bleaching and possible mortality by the 2050s. Low to moderate thermal stress are projected over reefs along the East African coast and near the northwest tip of Madagascar and thus these regions may act as potential climate refugia while increasing the potential of reefs to cope with climate change.

Includes bibliographical references / Nitrification is the oxidation of ammonium to nitrate through a two step biological process. Nitrification in the euphotic zone has, in the past, been considered negligible even though quantifying this process correctly is important when linking carbon export to nitrate uptake by phytoplankton. However, studies of both nitrogen uptake and nitrification rates in surface waters are rare. This thesis presents such data for the Southern Ocean and St-Helena Bay, located in the Southern Benguela upwelling system. Using 15N tracers, Nitrogen uptake and regeneration rates were measured in the Southern Ocean (during a winter cruise in July 2012 and a summer cruise in February-March 2013) and St-Helena Bay (during three studies in November 2011, March 2012 and March 2013). In St-Helena Bay, the upwelling (bloom) cycle was one of the main drivers of the nitrogen cycle. As the bloom cycle started, nitrate uptake rates (5:47 ± 670:48nmol∙L⁻¹∙h⁻¹) and nitrite regeneration (4:36 - 1:28 ± 22:83 - 1:63nmol∙L⁻¹∙h⁻¹) were high but the contribution of nitrification to the nitrate demand was low. Nitrite regeneration at this time could have been driven by phytoplankton excretion. In contrast, at the end of the bloom cycle, nitrate uptake rates were low and was exceeded by nitrate regeneration rates (25:34 - 6:16 ± 82:74 - 34:41nmol∙L⁻¹∙h⁻¹). Nitrite regeneration decreased and was most likely due to ammonium oxidation at this stage of the upwelling cycle. Nitrification in the Southern Ocean was more variable than in St-Helena Bay. It was only detected at five stations out of fifteen and the accuracy of the high nitrite oxidation rates (37:21 - 9:13 ± 217 - 88nmol∙L⁻¹∙h⁻¹) observed can only be assessed with repeat measurements. Nitrate uptake rates ranged from 0.07 to 57:00nmol∙L⁻¹∙h⁻¹ while ammonium uptake rates ranged from 0.81 - 160:94nmol∙L⁻¹∙h⁻¹. The nitrogen uptake rates were similar for both seasons. Using multivariate statistical approach, it was found that during winter, in the Southern Ocean, light and ammonium availability were the most important factors regulating nitrogen uptake while in the late summer, changes in the mixed layer depth had a larger effect. This study provides new observational data for two undersampled regions and contributes to further the mechanistic understanding of the factors regulating nitrogen uptake and nitrification in the Southern Ocean and St-Helena Bay.

Includes abstract. / Includes bibliographical references (leaves 137-145). / Southern Hemisphere atmospheric circulation and sea surface temperatures in the South Indian Ocean, associated with the South Indian Convergence Zone (SICZ), the main rain producing system over southern Africa, and links with rainfall over Mozambique, are analysed. Cluster analysis applied to gridded outgoing long-wave radiation data, were used to identify convective activity related to the tropical temperate troughs that collectively form the SICZ. Intraseasonal and inter-annual variability of these systems and their contribution to the anomalies of rainfall over Mozambique were explored using composite, correlation and regression analyses for both the early (October to December) and the late (January to March) summer.

Bibliography: leaves 98-103. / The shaping of SOFAR signals by topographic interference and the depth of the source relative to the axis of the sound channel is investigated. Eight shot signals from five different sites near Cape Town were received at three widely spaced hydrophones at Ascension over a number of 4.4 Megametre lines. These signals show the effects of (1) sources at different depths relative to the axis of the sound channel, (2) blocking and partial blocking of direct rays by seamounts and narrow undersea ridges and (3) a sound speed profile displaced downwards by a filament of warm surface water. Comparisons with ray trace and normal mode models show that some of the received signals consist of a combination of slower, refracted rays and faster rays reflected off Walvis ridge. The reflected energy starts earlier and has a greater amplitude than would be expected from ray trace modelling. This energy will act as noise and make ATOC (Acoustic Thermometry of Ocean Climate) determinations more difficult.

Includes bibliography. / A first picture of the Agulhas current is obtained from data of the Quasi synoptic Agulhas current cruise of March 1969. Reinterpretation of other hydrographic data was possible in the light of the 1969 cruise and the information obtained from satellite tracked buoys. For the 1969 cruise acceleration potential diagrams on various sigma-t levels are discussed and indicate that certain features in the current are of such a scale (length and time) that only closely spaced synoptic stations will show them. Of special interest are the following features: two main supplies to the current; a region of dynamical upwelling between East London and Port Elizabeth; the region where the eastward (retroflection); the interaction with the South East Atlantic ocean; the planetary waves in the Agulhas return current over and east of the Agulhas plateau. Volume flux calculations (reference 1100m.) show that the two supplies to the Agulhas current could be estimated at 15 sverdrups each. The main part of the current turns back into the South West Indian ocean. An amount of roughly 5 sverdrups was lost East Atlantic. Property distributions although difficult to interpret, were used to construct the acceleration potential diagrams as the contouring of these diagrams was not always obvious. For a more detailed discussion of the combined data the current system was divided into areas. These areas are: Source area (including the inflow south of Durban and the countercurrent at Durban; Dynamical upwelling region; Mixing and retroflection area; Planetary wave region.

Two coupled physical-biogeochemical models namely, (Regional Ocean Modelling System and Biogeochemical of Eastern Boundary Upwelling Systems) ROMS-BioEBUS (3D) and (Nucleus for European Modelling of the Ocean and Biogeochemical Flux Model) NEMO-BFM (1D) are applied in the Benguela upwelling system to understand biogeochemical interactions and their related feedback processes. The models are formulated differently but achieve similar objectives with respect to the physics and biogeochemistry. The BioEBUS model is used to simulate nitrogen processes under oxic and suboxic conditions in upwelling systems with no option for other cycles. Intermediary nitrogen processes, nitrous oxide production and nitrogen loss mechanisms are studied using this model. Physical and advection processes that drive the oceanic nitrogen cycle in the region are also studied with BioEBUS. The BFM is used to understand the implications of the nitrogen loss and suboxic-anoxic conditions on related biogeochemical cycles. The 1D model was selected for its low computational costs and flexibility for addition of new code. BFM includes the carbon, nitrogen, phosphorus, silicate, iron cycles and hydrogen sulphide production, which is a known occurrence in the Namibian shelf waters. New variables, nitrite and nitrous oxide production, are added in BFM to complete the nitrogen cycle. The nitrification process in BFM is also formulated in two stages as in BioEBUS to obtain comparative results in both models. Both models are compared and validated with data from the Maria S. Merian (MSM) 19/1b cruise and available products respectively. Simulated results from BioEBUS show primary and secondary nitrite maxima in the Benguela shelf waters. The primary nitrite maxima are attributed to nitrification and nitrate assimilation. Secondary nitrite maxima accumulate in the Angola-Benguela Front (ABF) oxygen minimum zone (OMZ) and are attributed to denitrification. Off Walvis Bay, these secondary nitrite maxima and ammonium are thought to be consumed by high rates of anaerobic ammonium oxidation (anammox). The nitrite maxima are restricted to the shelf off Walvis Bay and advected offshore in the ABF region. Interchanges between the poleward South Atlantic Central Water (SACW) and the equatorward, well-oxygenated Eastern South Atlantic Central Water (ESACW) drive the seasonality of nitrogen processes in the Benguela. Nitrous oxide concentrations are high in the ABF as a result of nitrification and accelerated production under suboxic conditions. Off Walvis Bay, nitrous oxide production is low when compared to the ABF. Nitrous oxide production in the ABF occurs in thermocline, intermediate and deeper water masses. Off Walvis Bay, nitrous oxide production in deeper water masses is missing because of the shallow coast. High fixed nitrogen fluxes in the Benguela are attributed to nitrification rather than anammox and denitrification. Simulated results show denitrification to be the dominant nitrogen loss mechanism in the Benguela shelf waters. Simulated results from BFM show higher nitrogen uptake rates than phosphate in shelf and offshore stations. The uptake rates are high on the shallow shelf due to luxury nutrient uptake. High N:P ratios occur at the stations at 21ᵒS than off Walvis Bay and are attributed to the presence of nutrient-rich, oxygen depleted SACW and denitrification respectively. Increased fixed nitrogen deficits (N*) occur in surface and subsurface waters at shallow stations as opposed to offshore. The positive N* anomalies off Walvis Bay are attributed to organic matter remineralization in deep, offshore stations. In contrast, increased phosphate (P*) concentrations occur in surface and subsurface waters. Phosphate is regenerated in subsurface waters and released under suboxic-anoxic conditions increasing P* concentrations. Nitrogen loss coupled with hydrogen sulphide production accelerate phosphate release in suboxic-anoxic bottom waters. The N:P stoichiometry, uptake rates, N* and P* concentrations appear to have considerable implications on potential estimated nitrogen fixation in the Benguela. BFM results suggest that the Benguela is a system characterized by excess nitrate in relation to silicate. This has been drawn from the low Si:N ratios observed at the simulated stations. A secondary Si:N peak is shown on the shallow coast due to high denitrification rates in suboxic waters. Note that high silicate concentrations occur in suboxic conditions and can be attributed to organic matter remineralization. The high silicate concentrations in the well-oxygenated offshore station are linked to sinking particles in deep waters. Increased silicate dissolution occurs in warm, surface waters and the particles that pass through the water column undissolved settle at the bottom where dissolution continues. From these results, it can be assumed that increased warming in the Benguela coastal waters should result in silicate being a limiting nutrient. This could affect carbon export as it has been shown that increased POC export is high in coastal waters due to ballasting of diatom biomass. The models used in this study simulated biogeochemical interactions in the Benguela fairly-well and can be applied in other regions.

Includes bibliographical references. / The purpose of this research is to quantify where, how much and by what mechanisms water leaves or comes on to the Namibian shelf and secondly to gain a better understanding into the circulation associated with upwelling filaments in the northern Benguela region and quantify their contribution to the exchange across the shelf edge. For the analyses results from a MOM-4 regional ecosystem model are combined with remote sensing and cruise data.

Includes bibliographical references. / The Knysna Estuary is the largest estuarine ecosystem in the warm temperate coastal region of South Africa. The estuary remains oligotrophic (chlorophyll-a < 5 mg l-1) despite increases in anthropogenic input of nitrogen and phosphate associated with the rapidly increasing urbanization of its littoral and catchment. This dissertation relies on original data, which includes the measuring of concentrations of ammonium, nitrates (nitrate and nitrite), dissolved inorganic phosphate and urea in the water column quarterly for one year at 21 stations. It estimates the contribution to these nutrients from rivers, storm drains and rainfall entering the estuary during this year by monitoring concentration and flow in these source waters. Seasonal, tidal and post-flood patterns of nutrient concentration in the water column are assessed with respect to nutrient loading to determine if variations in concentration are the result of loading or processes in the estuary.

The estimation of annual potential new production at a regional scale for the decade of the 1980s provides the main focus of this thesis. New production is the proportion of total primary production which relies on the uptake of NO₃-N by the phytoplankton while potential new production assumes that all the NO₃-N available to primary producers is assimilated. The Redfield ratio between carbon and nitrogen in the marine environment was used to express rates of potential new production in terms of carbon. In order to arrive at annual estimates of potential new production it was necessary to progress from the event-scale to the annual scale. This was achieved by the adoption of two novel methods of approach. Event-scale estimates of potential new production were made by assessing the amount of NO₃-N present in the nominal euphotic zone as a result of upwelling. Remotely-sensed images of sea surface temperature (SST) coincident with or shortly after upwelling events were used in combination with a derived relationship between SST and NO₃-N concentrations integrated over the depth range of the productive surface layer in the southern Benguela region. In this way it was possible to overcome the main shortcoming of passive satellite imagery by quantifying a sub-surface variable. The event-scale estimates of potential new production were extrapolated to the annual-scale by taking into account the dynamics of the system. Sea level fluctuation at the coast preceding upwelling events was found to be related to the event-scale estimates of introduced NO₃-N and hence used as a proxy for upwelling. Using a ten year record of sea level, estimates of annual potential new production, spanning the period June to May inclusive, were made for the period 1980/81 to 1989/90. Bibliography: pages 92-108.

This study aims to evaluate various existing models for the estimation of PP in the southern Benguela ecosystem, and to investigate the photophysiological responses of phytoplankton to changes in environmental conditions.