This study represents an integrated and holistic assessment of the eziMbokodweni Estuary’s water and sediment quality. The estuary was once relatively un-impacted but now flows through a highly anthropogenically-modified catchment, comprising industrial and residential developments (formal and informal), and the eziMbokodweni Wastewater Treatment Works, furthermore the floodplain has been completely transformed to accommodate the Amanzimtoti golf course. Flow from the highly degraded Isipingo River and Estuary is occasionally diverted into the eziMbokodweni and the Southern Sewage Works Outfall, one of the largest deep sea sewage outfalls in the eThekwini Municipality, is located at sea, approximately 1.5 km south of the estuary mouth. Estuarine health can be studied on various fronts, in this study, the following variables were monitored in the water and sediment columns, seasonally for spring and neap tides: heavy metals, nutrients, bacteria and selected physico-chemical parameters. The results demonstrated that the eziMbokodweni catchment was a major contributor of heavy metals and nutrients to the estuarine system. The quantity of the majority of heavy metals and nutrients transported by the river at the upper estuary exceeded the amount exported to sea at the estuary mouth-nearshore interface, resulting in the estuary accruing large quantities of material seasonality. It was noted that the nearshore waters are enriched, as a variety of heavy metals and nutrients entered the estuary mouth during flood tide episodes. A range of heavy metals were detected within the sediment profiles obtained from the estuary, with fine to medium grained sediment exhibiting greater heavy metal content, in some cases, multi-fold higher than that detected in medium to coarse grained sediment. Geochemical indices were employed to ascertain the extent to which these metals constituted a pollution threat to the environment. The contamination factor calculated for all sediment layers and sampling sites implied low contamination. The enrichment factor calculated for the majority of heavy metals alluded to natural causes while some heavy metals exhibited significant to extremely high levels of enrichment thus implicating anthropogenic causes as likely sources of these heavy metals. The degree of contamination of the estuary was classified as low. Overall, the heavy metal and nutrient content detected in the sediments were low as compared to the large quantities detected from the budget. This indicates that natural mechanisms exist which facilitate the utilization or removal of these heavy metals and nutrients from the estuary. It is proposed that the most significant manner by which these heavy metals and nutrients are eliminated from the estuary is through episodic flood events that scour and strip fine grained sediment from the estuary bed. The pH assessment of the estuary revealed that this environment was slightly basic through most of the year with mildly acidic conditions noted during winter. The average Dissolved Oxygen levels were within acceptable levels, with the exception of winter when levels were very close to hypoxic conditions. The average Total Dissolved Solid content indicated that the estuary was compliant with the target water quality range for domestic use on selected seasonal-tidal cycles, and the average Electrical Conductivity levels were compliant with the ideal target water quality range for aquatic ecosystems and domestic use as per the South African water quality guidelines (DWAF, 1996a-e). A salinity gradient was evident in the estuary, as salinity levels decreased with distance from the estuary mouth. The saline nature of the lower estuary provided for the flocculation of material, which was alarming as large quantities of heavy metals and nutrients were detected in the estuary. The lower estuary is therefore susceptible to contamination due to the salinity regime and the dominance of fine grained sediment. The demand for oxygen in the estuary was high during summer, autumn and spring, and within acceptable levels for natural waters during winter. Extremely high levels of Chemical Oxygen Demand were recorded in the estuary which provides prime growth and survival opportunities for bacteria. This correlated with the results from microbiological investigations as high levels of bacteria were noted within the estuary, in both the sediment and water columns. The detected quantities of Total Coliforms, Faecal Coliforms and Escherichia Coliforms exceeded the target water quality thresholds for domestic and full contact recreational use. While at selected sites, the recorded Faecal Coliforms and Escherichia Coliforms levels were deemed compliant for intermediate contact recreational use. However, these sites were not compliant throughout the sampling period. Overall, the upper and mid-estuary exhibited greater counts of bacteria, in both the sediment and water column, than the estuary mouth and was attributed to factors such as flushing, sediment particle size, salinity and the ‘dilution effect’. Furthermore, the sediment of the eziMbokodweni Estuary is serving as a reservoir for bacteria. A number of options have been proposed to improve the degraded state of the eziMbokodweni Estuary and are ultimately aimed at curbing the anthropogenic input of these contaminants. The insight gained from this study provides the database from which more integrated and holistic estuarine management strategies can stem, that are applicable not just to the eziMbokodweni Estuary but estuaries in general. / M.Sc. University of KwaZulu-Natal, Durban 2013.

River inflow is one of the most important factors influencing the density and biomass of estuarine biotic communities. The aim of this study was to obtain an understanding of the ecosystem functioning of selected estuaries on the east coast of South Africa and to represent their dynamics through ecosystem models. The responses of water column nutrients, plankton density and biomass to inlet phase changes for 16 temporarily open/closed estuaries (TOCEs) in South Africa were first determined. This analysis demonstrated that inlet phase and the duration of mouth closure were the most important factors determining plankton density and biomass of the analysed TOCEs. Estimates of planktonic standing stocks for four of these estuaries revealed that stocks can be from 26 to 10 000 times higher during the closed compared to the open phase. Also, slightly higher variability of planktonic density and biomass was recorded during the closed phase of TOCEs. The second major thrust of this study was to analyse the variability and temporal stability of planktonic and macrobenthic invertebrate density and biomass in two KwaZulu-Natal estuaries over a dry/wet cycle. The results suggest that “stable” variability and species synchronization could be the mechanisms whereby the estuarine biota of these systems compensate for environmental changes and attain a degree of environmental homeostasis. The third major thrust involved an assessment of the spatio-temporal variations in the elemental composition and stoichiometry of suspended and sediment detritus, zooplankton and macrobenthic taxa from two estuaries over a dry/wet cycle. Significant seasonal variations in the elemental composition of detritus, zooplankton and macrobenthic species were found, with the variations in the elemental content of sediment and suspended detritus being related to the seasonal changes in river inflow, while the among-taxa variability was mainly explained by feeding mode. Finally, static seasonal carbon and nitrogen ecosystem network models were developed for the East Kleinemonde, Mlalazi and Mpenjati estuaries to investigate their nutrient dynamics and ecosystem functioning. The results indicated that the East Kleinemonde and Mpenjati estuaries were mainly dependent on primary producers during the dry season, especially the high standing stocks of phytoplankton and microphytobenthos. Similarly, the dependency on detritus was higher during the wet season due to the high riverine imports during this season. Consequently, higher detritivory was recorded in all three study systems during the wet season. Cycling of nitrogen was higher than of carbon on a seasonal basis, with higher recycling of nitrogen during the dry season implying a lower availability of this element due to reduced freshwater inflow and nutrient input during the low rainfall period. System indices indicated that the organization of these systems was higher during the dry season, while the overheads on imports and exports peaked during the wet season. The ecosystem models analysed here provide an initial insight into the overall carbon and nitrogen dynamics of estuaries on the east coast of South Africa. / M.Sc. University of KwaZulu-Natal, Durban 2013.

Global warming from anthropogenic greenhouse gas emissions causes temperature increases in aquatic ecosystems. The rise in environmental temperatures places sensitive organisms under thermal stress. Reef-building corals are a critically important group of animals that provide many ecosystem services for coral reef ecology and the economy and are at a high risk of loss from thermal stress. Thermal stress causes corals to lose their colour, i.e. become bleached, resulting from the loss of symbiont zooxanthellae. This diminishes the energetic benefits that zooxanthellae provide to corals leading to a decline in coral health and high mortality rates. However, corals are also predators and can thus draw nutrients from zooplankton prey to supplement their nutritional requirements. This study investigated whether heterotrophic feeding can ameliorate the effects of thermal stress on coral physiology by providing an alternative energy source to zooxanthellar photosynthesis. Fragmented Pocillopora damicornis coral colonies were exposed to daily maximum temperatures of up to 31°C while being either starved or fed. During the experimental period coral nubbins were monitored for changes in polyp extension, oxygen consumption rate, feeding rate, colour, chlorophyll a content, zooxanthellae density, antioxidant potentials and DNA integrity during stress and after a short recovery period. It was found that, as expected, coral polyp extension, oxygen consumption rate, colour health, chlorophyll a content, zooxanthellae density and DNA integrity were all adversely affected by thermal stress. This indicted that all these measurements were viable biomarkers for assessing the negative effects of thermal stress on coral health. Coral colour, oxygen consumption rate, chlorophyll a content, lipid content, antioxidant potential and DNA integrity were all significantly improved by feeding. These results indicate that feeding does play a role in improving overall coral health and supports the physiological processes in coral tissue during and after thermal stress. The conclusions from this study also have great significance for coral reef ecology and management as predictions of reef resilience can be made from zooplankton ecology and boosting zooplankton availability to corals may be considered to mitigate the harmful effects of thermal stress and bleaching. / M.Sc. University of KwaZulu-Natal, Durban 2013.

The Natal Bight off the east coast of South Africa is a unique shelf habitat, exhibiting high secondary productivity and supporting high diversity. Ecosystem attributes are influenced by local oceanographic features and outwelling via one of the largest rivers in the country. This study forms part of a larger, multi-institutional, multi-disciplinary study under the second phase of the African Coelacanth Ecosystem Programme (ACEP II) Natal Bight Project, investigating how material sources, posited to be derived from these features, shape the ecological structure and functioning of the region. Macrobenthic samples were collected along cross shelf transects off Richard’s Bay, Durban and the Thukela River mouth during two cruises, corresponding with periods of variable rainfall. Macrobenthic communities were classified taxonomically, to the lowest level possible, and functionally. Community patterns were investigated within and between feature areas and related to measurable environmental factors in order to determine environmental drivers and assess the importance of identified oceanographic features. Environmental parameters measured included sedimentary characteristics as well as physico-chemical conditions in the surrounding pelagic milieu. A total of 38 215 individuals belonging to 826 taxa were recorded from the three feature areas, of which the majority were Polychaeta and Crustacea. An in-depth investigation of the polychaete component has shown that this group can be used as a proxy for the whole macrobenthic community which has important implications for future studies. Facultative feeding modes dominated the trophic functioning macrobenthic communities sampled on the Natal Bight. Primary community metrics of abundance and numbers of macrobenthic taxa were reduced from the high to low rainfall period but differences were not significant, probably due to the lack of temporal repetition. The Thukela feature area was found to support the most abundant and taxon rich macrobenthic community. Mid-shelf stations sampled along the Thukela and Durban transects were in close proximity to the coarse paleo-dune cordon, running along the 60 m isobath and supported a diverse assemblage. Despite the lack of temporal repetition in the present study, there were significant short-term changes in the structure and functioning of macrobenthic communities on the Thukela shelf. This suggests that Thukela River outflow has a significant effect on the functioning of the Natal Bight ecosystem. This was surprising given the importance which has previously been placed on the Cape St. Lucia upwelling cell in terms of contributing nutrients and sustaining biological productivity and diversity on the Natal Bight. / Thesis (M.Sc.)-University of KwaZulu-Natal, Durban, 2013.

Deep-water trawling (>200 m deep) for crustaceans in the South West Indian Ocean (SWIO) yields catches of several species, including prawns (Haliporoides triarthrus, Aristaeomorpha foliacea, Aristeus antennatus and Aristeus virilis), langoustine (Metanephrops mozambicus), spiny lobster (Palinurus delagoae) and geryonid crab (Chaceon macphersoni). Infrequent deep-water trawling takes place off Tanzania, Kenya and Madagascar; however, well-established fisheries operate off Mozambique and South Africa. Regular trawling off South Africa started in the 1970’s, mainly targeting M .mozambicus and H. triarthrus. Catch and effort data for the South African fishery were regularly recorded in skipper logbooks over a 23 year period (1988 – 2010); this database was obtained from the Department of Agriculture, Forestry and Fisheries (DAFF) in order to assess abundance trends of M. mozambicus and H. triarthrus. Generalized linear models (GLM) were used to quantify the effects of year, month, depth and vessel on catch per unit effort (CPUE). By year, the standardized CPUE of M. mozambicus increased, and three factors (or a combination of them) could explain the trend: reduced effort saturation, improved gear and technology, or an increase in abundance. By month, CPUE peaked in July and was highest between depths of 300 and 399 m. The standardized CPUE of H. triarthrus fluctuated more by year than for M. mozambicus, possibly because it is a shorter-lived and faster growing species. The monthly CPUE peaked in March, and was highest between depths of 400 and 499 m. Totals of 2 033 M. mozambicus (1 041 males and 992 females) and 5 927 H. triarthrus (2 938 males and 2 989 females) were sampled at sea between December 2010 and March 2012, during quarterly trips on-board a fishing trawler. A GLM framework was used to explore their size composition, sex ratio variability, size at maturity and reproductive cycles. Male and female M. mozambicus size distributions were similar, but varied by month and decreased as depth increased. Female H. triarthrus were significant larger than males; size structure varied by month, but showed no change over depth. The sex ratio of M. mozambicus favoured males (1 : 0.89), but was close to parity in all months, except November when males predominated. H. triarthrus exhibited parity (1 : 1.002) with no significant variations in sex ratios by month. The proportion of egg-bearing M. mozambicus in the population declined between March and August (hatching period) and then increased until December (spawning period). The L₅₀ (length at 50% maturity) of M. mozambicus was estimated to be 49.4 mm carapace length (CL), and the smallest and largest observed egg-bearing females were 33.5 and 68.6 mm, respectively. No reproductively active female H. triarthrus were recorded during the sampling period. Growth parameter estimates for M. mozambicus (male and female combined) using Fabens method were K = 0.48 yearˉ¹ and L∞ = 76.4 mm CL. Estimates for the von Bertalanffy growth formula (VBGF) were: K = 0.45 yearˉ¹ and L∞ = 76.4 mm CL. H. triarthrus male and female growth parameter were estimated separately. For males they were K = 0.5 yearˉ¹ and L∞ = 46.6 mm CL using Fabens method, and K = 0.76 yearˉ¹ and L∞ = 46.6 mm CL using the VBGF. For females they were K = 0.3 yearˉ¹ and L∞ = 62.9 mm CL using Fabens method, and K = 0.47 yearˉ¹ and L∞ = 62.9 mm CL using the VBGF. CL to total weight regressions were calculated for both species; no significant differences were found between male and female M. mozambicus, although H. triarthrus females became larger and heavier than males. Comparisons with three earlier studies (Berry, 1969; Berry et al., 1975; Tomalin et al., 1997) revealed no major changes in the biology of either species off eastern South Africa. Stocks appear to be stable at current levels of fishing pressure, although some factors are not yet fully understood. Disturbance caused by continual trawling over a spatially limited fishing ground may affect distribution and abundance patterns, especially in M. mozambicus, which was less abundant in the depth range trawled most frequently. The absence of reproductive H. triarthrus in samples suggests that they occur elsewhere, and there is some evidence of a possible spawning migration northwards to Mozambique; this suggests that H. triarthrus is a shared stock between South Africa and Mozambique. The results from this thesis will add to the knowledge of M. mozambicus and H. triarthrus in the SWIO, and provide a basis for developing sustainable management strategies for the deep-water crustacean trawl fishery off eastern South Africa. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.

Oceanic pelagic shark species are under threat worldwide as fishing effort increases and they are taken as both targeted and bycatch. It is widely recognized that the life history characteristics of sharks make them inherently susceptible to overexploitation and as a result many shark-directed fisheries have collapsed. It is therefore essential that good-quality data are collected and analyzed in order to provide fisheries managers with the right information to manage these species sustainably. South Africa has a pelagic longline fishery which includes tuna-, swordfish-, and shark-directed vessels. This study analyzed logbook (1998 – 2010) and observer data (2002 – 2010) provided by the Department of Agriculture, Forestry and Fisheries in order to assess the catch composition and standardized catch-per-unit-effort (CPUE) of sharks captured as both targeted catch and bycatch. The study area consisted of four zones moving east of the 20°E meridian: the Agulhas Bank (20°E – 24°E), South Coast (25°E – 29°E), East Coast 1 (30°E – 32.8°E), and East Coast 2 (32.9°E – 36.5°E). The majority of fishing effort targeted at tuna was focused on the Agulhas Bank and consisted of foreign vessels which operated over the winter months, whereas local vessels targeted swordfish with consistent year-round effort along the upper east coast. Sharks made up 13% of total catches according to logbook data and catch composition was dominated by blue shark (Prionace glauca) and shortfin mako shark (Isurus oxyrinchus). Observer data identified a larger number of shark species than shown by logbooks, and notably, the crocodile shark (Pseudocarcharias kamoharai) made up 22.5% of shark bycatch on swordfish-directed vessels operating along the upper east coast. In addition, the observer data showed that although blue and mako shark dominated catches in the Agulhas Bank and South coast zones, carcharhinid sharks were more prevalent further east. Generalized linear models explained 54% of the variation in CPUE of shark bycatch, with year and target species being the two most important explanatory variables. The standardized CPUE index based on logbook data suggested a slightly increasing shark abundance trend between 1998 and 2010, but conversely, the index based on observer data suggested a decline between 2002 and 2010. Assuming that the observer data best reflected the actual CPUE trend (i.e. a declining trend), the increasing trend shown by logbooks over the same period most likely stems from initial under-reporting of shark capture events by skippers, followed by improved reporting in later years, thus masking the declining trend. Catch by target species revealed that swordfish vessels caught significantly more sharks per 1000 hooks than tuna vessels. The shortfin mako shark was one of the most common bycatch species, and also the primary target species of the shark-directed fishery. Generalized linear models of shortfin mako shark CPUE using the delta method produced similar trends than models of total shark bycatch; i.e. trends based on logbook data appeared stable but observer data showed a declining trend over time. Shortfin mako sharks were more abundant in the Agulhas Bank and South coast zones than along the East coast. A total of 817 shortfin mako shark samples were collected onboard a South African shark-directed pelagic longline vessel operating out of Cape Town and by the KwaZulu-Natal Sharks Board bather protection nets, set close inshore. Sharks collected inshore (from nets) were significantly larger than those collected offshore. More males than females were collected from the nets (2.3 males : 1 female), whereas the ratio for offshore samples was 1.1 : 1. Age and growth parameters were estimated from 89 sectioned vertebral samples consisting of 43 females and 46 males ranging in size from 90 cm to 299.4 cm fork length (FL). Annual band-pair deposition was assumed and growth was analyzed by fitting 3-parameter von Bertalanffy and Gompertz growth models. Parameter estimates for the Gompertz model were: K = 0.152 year¯¹ for males and 0.127 yearˉ¹ for females; L0 = 85 cm; L∞ = 295 cm for males and 315 cm for females; and longevity was 17 and 21 years for males and females respectively. Estimates for the von Bertalanffy model were: K = 0.08 yearˉ¹ for both sexes; L0 = 85 cm; L∞ = 354 cm for males and 321 cm for females; and longevity was 34 and 31 years for males and females respectively. Using these data, age and length at 50% maturity were calculated at 7 years and 199.1 cm FL for males, and 14 years and 252.8 cm for females. Litter size was in agreement with previous studies (9 to 14 pups). The gestation period was not estimated but parturition may be in late winter to spring. The stomach contents of 817 sharks showed that shortfin mako sharks are opportunistic feeders; elasmobranchs dominated in stomachs collected from sharks caught in nets near the shore (%F = 63.54%) whereas shark stomachs collected from the offshore contained mainly teleosts (70%). Length-frequency analyses revealed that large and reproductively active shortfin mako sharks were more common along the upper east coast and in the inshore environment, whereas juveniles and subadults preferred the oceanic environment, particularly over the Agulhas Bank and South Coast zones. The findings from the present study are a significant step forward towards developing a management strategy for protecting shortfin mako sharks in the South West Indian Ocean region. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.

St. Lucia estuarine lake system has a history of episodic droughts and floods leading to a high variability in physico-chemical characteristics which may influence the community structure of nano- and microplankton that are the main primary energy synthesisers in aquatic systems. Originally, the St. Lucia estuary and the Mfolozi River shared the same mouth with the Mfolozi River acting as the main source of fresh water to the system and as stabiliser of the common inlet. Due to prolonged mouth closure from 2001-2012 and high evaporation rates, severe extended droughts and high salinities were experienced in 2001-2012.This project aimed to characterise community composition and biomass of nano-and microplankton (autotrophic and heterotrophic) under the varying and extreme physico-chemical conditions in order to characterize the energy basis of the planktonic food web in St. Lucia. Its main objectives were to compare and add onto Johnson’s (1977) list of phytoplankton taxa in the system, to estimate the biomass (carbon) of nano- and microplankton from cell counts and biovolume measurements, and lastly to understand and establish trends in the change in community structure of these organisms with the varying physico-chemical characteristics. Nano- and microplankton samples were collected monthly from October 2010 to September 2011 at three different sites: Lister’s Point, Charters Creek and the mouth representing the lakes and estuary Channel. Chlorophyll a and physico-chemical parameters were also measured in situ during collection. In the lab, samples were settled using the Utermöhl method and species were identified to at least genus level, counted and cell measurements taken under an inverted microscope for biovolume calculations and biomass thereof. Abundance in cells per liter and biomass (carbon) in pg/L was then analyzed from the counts. The nano-and microplankton groups recorded in the system were cyanobacteria, chlorophytes, cryptophytes, dinoflagellates, ciliates and diatoms. Seventy eight phytoplankton taxa were identified composed of 56 diatoms, eight green algae, one cryptophyte, seven cyanobacteria and six dinoflagellate taxa. Nineteen ciliate taxa were also found. Only 12 of the diatom taxa identified in this study were listed by Johnson (1977), none of the taxa in the other phytoplankton groups was listed by Johnson (1977). The Johnson (1977) study conducted in the system from 1975-1977 listed the phytoplankton taxa occurring at that time. There was no significant difference in the community composition, biovolume and biomass between seasons hence no seasonal trend however, there were significant differences in the nano- and microplankton community composition, biovolume and biomass at the three different sites of the system. Cyanobacteria were the main taxa in the northern embayments dominating in abundance, biovolume and biomass (biological variables), green algae and cryptophytes dominated in abundance, biovolume and biomass in the Channels while in South Lake, green algae dominated in abundance but diatoms dominated in biovolume and biomass. Ciliate biological variables were higher in the northern regions than in the other parts of the estuary. The absence or limited grazing pressure of ciliate predators in the northern region due to their inability to cope with the extreme salinities compared to the other parts of the system explains why the northern embayments had the highest abundance, biovolume and biomass of ciliates. Ciliates and heterotrophic dinoflagellates were the heterotrophs in this study. Autotrophic:heterotrophic biomass ratio was lowest in the northern regions as heterotrophs had a higher biomass there. This ratio was higher in the South Lake and the Channel. The lack of stratification and generally high turbidity in the system made the system unfavourable for dinoflagellate growth. The higher presence of ciliate predators in the South Lake and Channel probably accounts for the low heterotrophic biomass hence high autotrophic:heterotrophic biomass ratio in South Lake and the Channel. Nutrients were not limiting during this study and salinity was the main physico-chemical characteristic accounting for the differences in nano- and microplankton biological variables. The Cyanothece bloom in the northern region was primarily due to high salinities (>150) which also indicated unfavourable conditions for other plankton types. The high diatom biomass in the southern lake was due to low salinities (<28) which favoured their growth, whereas chlorophytes and cryptophytes dominated in the Channel mainly due to low turbidity (median of 11.4NTU) and fresh water input from the Mfolozi lowering salinities (<5). The South Lake and Channel thus had the highest available energy for higher trophic level organism since 1) diatoms and green algae are the most favoured food source for phytoplankton grazers while the cyanobacteria though most abundant are the least favoured food source leaving the northern lake with smaller energy source for higher trophic level organisms and 2) The low autotrophic:heterotrophic biomass ratio in the northern region leaves the region with a lower net carbon biomass than the other parts of the system with a higher autotrophic: heterotrophic biomass. / Thesis (M.Sc.)-University of KwaZulu-Natal, Durban, 2013.

Deep-water prawns Haliporoides triarthrus and langoustines Metanephrops mozambicus are endemic to the South West Indian Ocean (SWIO) region and make up the largest proportion of deep-water crustacean trawl catches in Mozambique and South Africa. Despite their economic importance to these fisheries, little is known about their distribution, biology and genetic population structure. The metapopulation genetic variation of H. triarthrus and M. mozambicus was assessed from 220 specimens per species collected from three sites in Mozambique (Bazaruto A, Boa Paz and Inhaca), two sites in western Madagascar (Morombe and Tulear) and one site in eastern South Africa (Durban). Two fragments of the mitochondrial region were amplified using universal primers ribosomal 16S subunit (16S) and mitochondrial cytochrome oxidase subunit I (COI). From H. triarthrus, fragments of 569 base pair (bp) (16S) and 1300 bp (COI) were amplified. A total of 207 sequences (16S) and 151 sequences (COI) were recovered, and 69 and 78 haplotypes identified, respectively. Metanephrops mozambicus 16S and COI genes produced similar fragment lengths, and 112 (16S) and 127 haplotypes (COI) were recovered. Both species demonstrated high genetic diversity and significant population differentiation in the SWIO region. Two sister-species (or subspecies) of H. triarthrus were identified, one occurring along the African continental shelf and the other off western Madagascar. Furthermore, individual populations making up each lineage were genetically structured, as indicated by the absence of shared haplotypes, and should be recognized as demographically distinct subspecies. Both species have undergone recent population expansions, likely since the late Pleistocene. The large anti-cyclonic and cyclonic eddies prevalent in the Mozambique Channel, and the boundary area between these eddies and upper Agulhas Current are likely factors driving larval retention or return process, thus giving rise to the observed genetically structured populations. The findings from this study are unique for the SWIO region, and may lead to a paradigm shift in the way that deep-water crustacean stocks are perceived by fisheries managers – instead of single shared stocks, they comprise of many isolated ones, in spite of the dispersal potential of larvae in strong ocean current regimes. Thus stocks should be managed as small independent units. / Thesis (M.Sc.)-University of KwaZulu-Natal, Durban, 2013.

Contaminants introduced in solution to coastal waters eventually accumulate in sediment. Pollution by these contaminants is only evident when biological effects occur. Geochemical procedures lack the ability to identify biological effects of pollution. Biological methods (i.e. community structure analyses and/or bioassays) are currently the best available techniques for pollution assessment. Standardised and locally relevant protocols for pollution assessment are lacking in many developing countries, including South Africa. This study aims to develop a sediment toxicity testing protocol using an amphipod species endemic to South Africa, Grandidierella lignorum. Initial research focussed on establishing ranges of physico-chemical parameters (i.e. salinity, temperature, sediment grain size and organic matter content) within which sediment toxicity tests should be performed. The sensitivity of the amphipod was then determined by exposing the amphipod to cadmium, copper and zinc at various salinities. Lastly, the amphipod was exposed to effluents (to test the amphipod’s sensitivity in water only tests) and whole sediment (to tests the amphipod’s sensitivity to solid phase material). G. lignorum tolerates salinities between 0 and 56, but prefers salinities between 7 and 42. Preferred salinity range is modified by temperature, with salinity of 42 becoming less tolerable. Salinities between 7 and 35 are most preferred at 10-25°C. G. lignorum prefers fine- (27.48±12.13%), medium- (25.11±12.99%) and coarse-grained sand (21.45±8.02%). Sediment with low (≤2%) organic matter content is most preferable, regardless of sediment grain size or type of organic matter (protein-rich vs. carbohydrate-rich). Cadmium toxicity decreased with increasing salinity (LC₅₀: 0.34 ± 0.17 mg l⁻¹ (salinity of 7), 0.73 ± 0.05 mg l⁻¹ (salinity of 21) and 1.08 ± 0.49 mg l⁻¹ (salinity of 35)). Zinc toxicity increased with decreasing salinity (1.56 ± 0.33 mg l⁻¹ at a salinity of 21 to 0.99 ± 0.13 mg l⁻¹ at a salinity of 7) and with increasing salinity (from salinity of 21 to 0.82 ± 0.19 mg l⁻¹ at a salinity of 35). Copper toxicity did not differ significantly with salinity and ranged between 0.72 ± 0.18 mg l⁻¹ (salinity of 35) and 0.89 ± 0.24 mg l⁻¹ (salinity of 21). Toxicity testing using Grandidierella lignorum should be performed in coarse- to fine-grained sediment at salinities of 7 - 35, at 10 – 25°C. Amphipods do not need to be fed during toxicity testing. A control chart using cadmium as a reference toxicant was established to determine the acceptability of toxicity results. Toxicity test results should be accepted when cadmium toxicity falls between 0.49 and 4.02 mg l⁻¹. The amphipod responded consistently to effluents and was able to discriminate polluted and unpolluted sediment in Durban Bay. Recommendations for refining the effluent and sediment toxicity test are suggested. / Ph.D. University of KwaZulu-Natal, Durban 2013.

Among the 155 species of fish recorded so far in the St Lucia estuarine lake, Oreochromis mossambicus and Ambassis ambassis are the two most prominent. Although originally endemic to southern Africa, O. mossambicus is now one of the most widely distributed exotic fish species worldwide. Together with A. ambassis, they have become the dominant fish species in the St Lucia estuarine lake since the closure of the mouth in 2002 and are, therefore, a crucial component of the food webs throughout the system. After a decade dominated by dry and hypersaline conditions, the St Lucia system has changed dramatically in terms of prevailing environmental conditions, as a result of higher than average rainfall at the end of 2011 and the onset of a new wet phase at the start of 2012. In response, A. ambassis, which prefers lower salinity regimes, has expanded its distribution range throughout the estuarine lake. Stable δ¹⁵N and δ¹³C isotope analysis was used in conjunction with gut content analysis to elucidate the diet of these species at sampling localities spanning the geographical range of the system and determine whether these species shift their diet in response to environmental or climatic shifts. From both studies it is evident that from a temporal and spatial scale these two species adopt similar, yet very different, dietary tactics. Oreochromis mossambicus was shown to adopt a generalist feeding strategy, opportunistically feeding on dietary items that are available thus allowing this species to alter its diet according to the environment that it inhabits. Trophic positioning of this species was found to be controlled by salinity in St Lucia as dietary composition differed greatly between sites. In contrast, Ambassis ambassis displayed a more specialist dietary composition, feeding predominantly on zooplankton. However, this species also opportunistically supplements its diet with additional sources when available. Trophic position of A. ambassis was higher in the dry season owing to the increased productivity of the system during the wet season. The success and dominance of both species in the St Lucia system can therefore be attributed to their dietary strategies. Under extreme environmental conditions, O. mossambicus has the added advantage of its wide tolerance of different environmental conditions, particularly salinity, thus allowing it to proliferate. / M.Sc. University of KwaZulu-Natal, Durban 2014.