Chlorophyll-a concentration is a measure of phytoplankton biomass and is therefore used as a proxy for primary production. The chlorophyll bloom occurring in the South western Indian Ocean is one of the major blooms in the open ocean and is subject to controversies about its formation, propagation and termination mechanisms. In this study, the region was divided into two sub-regions, the South East region (48°E-66°E, 24°S-30°S) and the East region (70°E-88°E, 24°S-30°S) and satellite datasets of chlorophyll-a, sea surface temperature, wind speed and direction and sea surface height were analysed. A bloom was characterized by twice the mean level of the sub-region (~0.08mg/m3) and three bloom years were identified: 2004, 2006 and 2008. The timing, propagation and termination of the bloom showed spatial and temporal variability. The wavelet analysis revealed a semi-annual signal for 2006 and 2008 and an annual one in 2004 due to the gradual decline in the concentration of chlorophyll-a. The transport of the bloom is affected by the passage of eddies where the concentration of chlorophyll-a is higher in the core and around the edges in cyclonic and anticyclonic eddies respectively. The bloom could be present at the sub-surface level throughout the years but is only apparent at the surface during specific years.

The spiny lobster Jasus tristani inhabits the Tristan da Cunha Island archipelago in the South Atlantic Ocean 2,400km from the West coast of South Africa. It is commercially exploited across the archipelago and is the main economic source of income for the local government as it accounts for nearly 80% of the local gross domestic product. The commercial rock lobster industry was established in 1949, and the fishery is currently recognised as sustainable, and as a result was awarded a Marine Stewardship Council Certification in 2011. That same year however, the sinking of the OLIVA at Nightingale Island spilt 60,000 tonnes of soya beans (Glycine max), greatly affecting the local benthic environment, and with probable consequences for the local food web, including the diet of J. tristani. It is still unclear whether the soya beans are still on the seafloor at Nightingale Island as there have been no scientific surveys conducted since the spill. Using samples from 2015, I assessed whether the diet of the lobsters from Nightingale Island differs from that of lobsters from the unaffected Tristan and Inaccessible Islands, and whether there is any evidence of soya in the diet of the lobsters from Nightingale Island. In addition, I examined whether diet differed between lobsters of small or large size, and between shallow and deep depths. In total, 540 lobsters were sampled across the three islands, and a combination of gut content and stable isotope (SI) analysis was conducted to assess the dietary components of the lobsters. Gut fullness was significantly less at Nightingale Island suggesting there may be less food available on the reef. Statistical analyses showed that diet differed between all islands, depths and sizes, although this was difficult to ascertain from visual multidimensional scaling plots as diet showed considerable overlap and variability both within and between islands, depths and sizes. The stable isotope analysis showed significant differences in nitrogen levels among the three

Includes bibliographical references (leaves 83-88). / Small pelagic fish populations in productive upwelling systems are characterised by long-term patterns of alternating dominance. Sardine and anchovy are the most important small pelagic species in the southern Benguela ecosystem, which has been shown to have undergone regime shifts during the past 50 years. Modelling regime shifts at an ecosystem scale can be of great importance in fisheries management, to aid in long-term planning and fishing strategy evaluation. Frame-based modelling has been successfully applied to regime shift dynamics in terrestrial ecosystems. The pattern of abrupt shifts between quasi-stable regimes suggests the usefulness of a frame-based approach in the southern Benguela ecosystem, with separate frames describing each small pelagic fish dominance pattern. Frame-based modelling is applied to sardine/anchovy dynamics under the influence of climate variability involving interaction with the small pelagic fishery. Four frames are used in the model: Both Species High; Sardine High / Anchovy Low; Anchovy High / Sardine Low; and Both Species Low. Switching rules for transition between the frames are described. Rapid prototyping is used to construct and test first- and second-generation prototypes of a frame-based model. A sensitivity analysis of the model is performed, and the model is found to be sensitive to the frame switching rules. The model is also reasonably sensitive to the sardine population model parameters, and the influence of juvenile sardine bycatch is noticeable in the "Sardine Low" frames. The model behaviour is relatively insensitive to climate variability, but the inherent degree of stochasticity in the sardine recruitment calls for continuous population monitoring and adjustment of fishing levels to avoid crashing the modelled sardine stock. Frame behaviour in the model is sensitive to sardine fishing activity. The model is exercised in a variety of scenario analyses, and confidence in the model is strengthened by the observed parallels to the real world. The use of the model as a "test platform" is explored to improve understanding of fishing impact on the dynamics of small pelagic populations. Previously identified advantages of the frame-based modelling technique include their particular usefulness in inter-disciplinary teams and the ease with which a frame-based model can be expanded and modified, and the experiences of this project support these findings. The use of frames as indicators adds information about the condition of the modelled stock at a given point beyond what can be inferred by population levels alone. Frame-based modelling is also found to be an approach well-suited to the development and maintenance of the computer software which encapsulates the model, and as a common interface between biologists, programmers and non-specialist model users. Suggested applications of the model include deriving "probabilities of change" for use in an expert system to predict long-term ecosystem changes. Applications of the model in understanding the impact of survey data error and compliance issues are discussed.

Worldwide, numerous shark populations are in rapid decline due to chronic overfishing. Their slow reproductive capacity make them susceptible to extinction. To monitor the status of chondrichthyan species, the method or combination of methods used should be non-selective, applicable in a variety of habitats and under most environmental conditions. Baited Remote Underwater Video (BRUV) surveys have shown major benefits over traditional capture-based survey methods in multiple areas. They have been shown to be non-extractive, causing no major disturbance to the substrata and its epibenthos. Large, mobile animals that avoid divers and active fishing surveys are detected. The recorded video removes the need for specialist observers to conduct all the fieldwork. The video allows impartial and repeatable measurements and standardizes data collection and training in association with remote taxonomists. The method is also cheaper than alternatives. Ninety-five sites were sampled with 60 minute video recordings across the whole of False Bay during the period of June-July 2012. Fifteen species of chondrichthyans were recorded, of which Haploblepharus edwardsii was the most abundant, being observed at 83 of 95 sites. One hour was sufficient to capture all the chondrichthyans within the observed area as the average time of arrival was about half an hour into the recording. The distribution of the chondrichthyan population was remarkably uniform across the bay. Depth, habitat and substrate type were significant predictors of species composition (P = 0.004, 0.025 and 0.001 respectively). Opportunistic encounters (one individual observed) included Carcharodon carcharias, Squalus megalops, Rhinobatos annulatus and Myliobatis aquila.

Previous studies, using a variety of methods such as photographic identification, fisheries observer programs, or genetic testing, on Indo-Pacific bottlenose dolphins (Tursiops aduncus) around Zanzibar Island, Tanzania, suggest separate populations around the north and south coasts. However, most research around the island has focused on the south coast, and movement of dolphins around the coastline is poorly understood. Photographic identification data, consisting of dorsal fin images, and acoustic data from dolphin whistles, both collected in 2008, were analysed to examine linkages between north and south Zanzibar. Photographic identification data was applied in a Mark-Recapture framework, using open population models, to generate abundance estimates of 149 (95% CI 128-173) and 120 (95% CI 97-149) individuals for the north and south coasts of Zanzibar respectively. As 16 individuals had moved from the south to the north coast of Zanzibar during the two month study, a combined population estimate of 353 (95% CI 290-430) individuals for Zanzibar Island was also generated. Acoustic analysis of standard whistle parameters was used to investigate whether these learned signals shared features between the putative populations, using whistle data collected in Plettenberg Bay, South Africa as an out-group. Discriminant function analysis of whistle parameters indicated high classification success of whistles recorded from animals in the north location (86.2%), moderate classification success for the outgroup (61.8%), and zero classification success for Zanzibar's south coast population. High misclassification rates for south Zanzibar suggest that these whistles cannot be readily discriminated from those of north Zanzibar. Shared whistle features suggest that learning may take place between individuals moving between localities. Coupled with previous genetic studies, this study suggests female philopatry and male mediated gene flow between the two areas; however, more genetic markers are necessary to test this interpretation. Further work is also necessary to quantify the degree of movement of dolphins around Zanzibar Island, and potential migration into the area, which will assist in developing management plans.

Climate change is a reality. One of the main ecological concerns regarding climate change is the predicted increase in atmospheric and sea temperatures. The latter is expected to rise by roughly 2.5°C by the end of 2050 with dramatic impacts on marine ecosystems predicted around the world. Seagrass ecosystems are a good example of vital ecosystems that are threatened by climate change and other anthropogenic factors. A decline in global seagrass cover of 29% has been estimated over the last century, and at a local level, cover of the seagrass Zostera capensis has declined by 38% over the last 50 years in Langebaan Lagoon, with associated losses of invertebrate abundance by 70% in certain areas. Two limpets, Siphonaria compressa and Fissurella mutabilis depend on Zostera capensis for their survival in Langebaan Lagoon, feeding on epiphytic diatoms, filamentous algae and bacteria growing on blades on seagrass. Siphonaria compressa occurs exclusively in beds of Zostera capensis and is currently listed as critically endangered. Increasing sea temperatures have been found to directly and indirectly affect seagrass growth and survival. Temperature changes influence epiphytic microalgal growth on seagrass blades, thereby limiting light and nutrient availability to seagrasses. Key grazers, however, can potentially limit microalgal growth on seagrasses, but this function is dependant on how they respond to temperature change. Therefore, understanding the effects of temperature on seagrasses and their grazing limpets is vital to seagrass health and ultimately their persistence in marine ecosystems. To quantify the latter, a mesocosm experiment was conducted to assess the interactive effect of temperature changes and grazing by the limpets S. compressa and F. mutabilis on the seagrass Z. capensis. One of the main outcomes of the experiment was that Increasing temperatures significantly enhanced algae biomass fouling seagrass leaves. At the same time, limpet feeding significantly decreases algal fouling, especially at higher temperatures. S. compressa was significantly more effective at removing algae from the blades of Z. capensis than F. mutabilis, particularly at higher temperatures. Increasing temperatures and the feedback from grazer presence had no substantial impact on the growth of Z. capensis but vi significantly influenced the survival of the seagrass blades. Another important result for predicting future effects of temperature rise on seagrass ecosystems was that mortality of F. mutabilis was significantly greater than S. compressa at higher temperatures. Overall, the study demonstrates that increasing temperatures clearly impacts the dynamics of seagrass ecosystems, either directly by impacting seagrasses or indirectly, by increasing algal fouling. The presence of limpets is also vital in controlling the levels of algae, with S. compressa performing more of a beneficial role in keeping blades of seagrass free of fouling. These findings are relevant for the conservation of seagrasses in Langebaan Lagoon, as they indicate the importance of preserving populations of the endangered limpet S. compressa in order to maintain healthy functioning seagrass ecosystems under future warming scenarios.

A variety of cetacean species make use of the bays along the South African coast for different purposes, including feeding, mating and calving. Sightings of five species of cetaceans were recorded from shore based locations between February 2010 and August 2014 in Mossel Bay, Western Cape. In this study, we aimed to examine the underlying environmental variables: sea surface temperature (°C), chlorophyll a concentration (mg.m-3) and moon brightness (as % of full) that potentially affect presence patterns within the bay, and several temporal scales (diurnal, monthly, seasonal, annual). The study focused on three whale species: the southern right whale (Eubalaena australis), humpback whale (Megaptera novaeangliae) and Bryde's whale (Balaenoptera brydei); and two dolphin species: the Indo- Pacific bottlenose dolphin (Tursiops aduncus), and the Indian Ocean humpback dolphin (Sousa plumbea). Generalized additive models (GAM) were used to model the sighting rate of the common cetacean species in the area, by relating sighting rate to the environmental variables. Cow-calf groups and adults-only groups were modelled separately for humpback and southern right whales. Chlorophyll a concentration is commonly indicative of high trophic productivity, and sea surface temperature is indicative of biophysical processes that influence cetacean distribution, as well as cetacean migration preferences. Change in sea surface temperature (over the study period) was a significant contributing factor to the sighting rate of cow-calf paired groups and adults-only groups of both right whales and humpback whales, underlying their greater sighting rate during the winter and spring months annually; thus, conforming to the seasonal migration from Antarctica for breeding and calving. Chlorophyll a concentration was a significant factor contributing to Bryde's whale, bottlenose and humpback dolphin distribution. These species reside along the South African coast all year round, but are more frequently seen when trophic productivity is high. During 2011, sea surface temperature values were lower and chlorophyll a concentrations greater than average in Mossel Bay, due to the La Niña effect. This was found to positively correlate with the use of Mossel Bay by the cetacean species in the area. This paper highlights the importance of biophysical processes on cetacean distribution at various temporal scales (diurnal, monthly, seasonal and annual), and the information it provides may be used for conservation planning management.

Includes bibliographical references (leaves 43-44). / In an attempt to improve the quality of preserving seawater nutrients for delayed analyses, a sample of unfiltered and aged nutrient-depleted seawater was obtained from Marine and Coastal Management (M&CM) and spiked with small different volumes of standard nutrient solutions. These were prepared into 100 mL glass bottles to constitute the lowest, intermediate and highest levels of dissolved inorganic phosphate (0.5, 1.5, 3.0 μM), nitrate (5, 15 and 30 μM) and ammonium (0.5, 1.5, 2.5 μM) that are found in the southern Benguela region. After spiking, the samples were analysed to determine their "true" initial concentrations and immediately quick frozen using liquid nitrogen. A time series analysis (up to seven weeks) was performed by first fast-thawing the samples using a microwave oven and fixing up the nutrients within 20 minutes. Variations in nutrient concentrations did not exceed 7% for phosphate, 4.0% for nitrate at all levels and 8% for ammonium at the intermediate and highest levels, but varied by 19.2% at the lowest level. Statistical tests for significance of the means were made at a = 0.05 level and no difference was found at any level for the nitrate, and the lowest level phosphate. The higher levels of phosphate, and all ammonium were found to be significantly different. Hence, the experimental conditions employed in this paper would not be recommended for the all ammonium and the higher levels of phosphate concentrations. These variations were however not large or regular in pattern but erratic, which suggested that they were not due to microorganisms and optimizing those conditions may well to yield improved results.

Advances in remote sensing and tagging technology have made it possible to investigate the relationship between oceanographic dynamics and the distribution of certain marine species. For this study, surface chlorophyII-a concentration was used as a proxy for underlying related productivity, rather than as a direct indicator of prey density. Post-breeding, adult female southern elephant seals from Marion Island were tagged with conductivity, temperature and depth satellite-relayed data loggers (CTD-SRDL's) and their foraging behaviour was examined in relation to different chlorophyII-a concentrations. Optimal foraging and area restricted search theories predict that travelling speed and turning frequency would be quantifiably affected by prey density, which is in turn affected by the underlying richness of primary producers.

The St Helena Bay Monitoring Line (SHBML) stretches 197 nautical miles off Elands Bay on the west coast of South Africa. It is an extensive long term project on environmental monitoring, running from 2000 till 2012 on an almost monthly basis but currently running on a quarterly basis. It extends through the nursery grounds and part of the transport zone for hydrology and productivity in areas that are significant to early life history of small pelagic fish. Environmental, acoustic and zooplankton data have been collected along the SHBML to obtain information on ocean environment, pelagic fish abundance and also zooplankton abundance. This study used an interdisciplinary approach, analysing historical data collected during biannual surveys of small pelagic fish, to investigate seasonal and spatial variability of pelagic fishes in relation to environmental variability in St Helena Bay. Surface values from 2000 to 2010 of temperature, salinity, oxygen and chlorophyll were analysed in relation to zooplankton and fish densities. The results show partial / weak seasonality of SST in offshore and also in coastal stations. Zooplankton, chlorophyll and oxygen show limited seasonality only in nearshore stations. Strong cross-shelf patterns of SST, chlorophyll, salinity, oxygen, zooplankton biomass and fish abundance were noted. These were expected results from a coastal upwelling system where primary productivity during summer is increased in the nearshore zone. There was a positive relationship between salinity and SST (r = 0.821, p< 0.0001) and a negative relationship between chlorophyll and SST (r = -0.549, p< 0.001), as would be expected in a coastal upwelling environment. When other variables were examined (also in pairs), there were no relationships between SST and oxygen, fish and zooplankton, fish and chlorophyll, fish and SST, fish and oxygen, and chlorophyll and zooplankton. A GLM was fitted to the data to investigate the relationship of pelagic fish density with zooplankton biovolume, chlorophyll, SST and oxygen; the GLM results showed a negative relationship between zooplankton abundance and pelagic fish (t=-1.980, p=0.049). Based on these results, it appears that the SHBML data were not able to pick up seasonal signals but have shown interannual variability and also some inshore-offshore differences.