Phosphorus is an essential element since it controls primary productivity in aquatic ecosystems and its excess can lead to eutrophication in receiving systems. The aim of this project was to determine phosphorus distribution in biotic and abiotic nutrient pools of two KwaZulu-Natal estuaries. Samples of dissolved inorganic phosphorus (DIP), particulate phosphorus (PP), phytoplankton, microphytobenthos, zooplankton, macrozoobenthos and sediment were collected in the temporarily open/closed Mpenjati (MP) and permanently open Mlalazi Estuary (ML) during May (ML), September (MP) and November (ML+MP) using standard methods. Chlorophyll a concentrations as well as species richness, abundance and biomass of zooplankton and macrozoobenthos were analysed. Living and non living nutrient pools were analysed for phosphorus and were compared between stations, sampling sessions, estuaries and taxa. Zooplankton abundance and biomass in the Mlalazi Estuary was higher during May than November. In the Mpenjati Estuary highest zooplankton abundance and biomass was recorded during September than November. No significant differences were apparent in abundance (p = 0.217) and biomass (p = 0.974) of zooplankton between the two estuaries. Macrozoobenthos abundance and biomass in the Mlalazi Estuary was higher during May than November. In the Mpenjati Estuary macrozoobenthos abundance and biomass was higher during November than September. Significant differences in abundance (p = 0.003) and biomass (p = 0.020) were apparent between the estuaries. Sediment to a depth of 10 cm comprised the highest phosphorus biomass than any other nutrient pool in both Mlalazi (4871.1 mgP·m⁻² ± 5888.9 SD) and Mpenjati (2578.6 mgP·m⁻² ± 1828.0 SD) estuaries followed by DIP (120.5 mgP·m⁻² ± 177.7 SD and 5.9 mgP·m⁻² ± 6.1 SD respectively). In both estuaries, the lowest phosphorus biomass was contained in zooplankton with both estuaries containing zooplankton P biomass of 0.001 mgP·m⁻² ± 0.002 SD. Particulate phosphorus and DIP concentrations were higher in the upper reaches in both estuaries indicating that rivers were the main sources of this nutrient in these systems. The Mlalazi Estuary had higher nutrient levels than the Mpenjati Estuary. Such elevated nutrients can be enhanced by the continuous river flow into the permanently open estuary. In both estuaries, no significant differences were apparent in zooplankton and macrozoobenthos P content between different taxa. / M.Sc. University of KwaZulu-Natal, Durban 2013.

Marine protected areas (MPAs) have been established along the East African coast to protect coral communities from human and natural disturbance. Their success is dependent on the degree to which resource populations are self-seeding or otherwise connected. Estimates of contemporary gene flow on or between south-east African reefs are thus required to reveal the interdependence of the South African coral communities and those to the north. Accordingly, the ecologically relevant (1 or 2 generations) connectivity of two broadcast-spawning corals, Acropora austera and Platygyra daedalea, was assessed on reefs in the region, from the Chagos Archipelago to Bazaruto Island in Mozambique and Sodwana Bay in South Africa, using hyper-variable genetic markers. Analysis of genetic diversity and differentiation provided evidence for the existence of four discrete genetic populations of A. austera and five of P. daedalea in the sampled area. Higher genetic diversity was found on northern South African reefs (Nine-mile Reef and Rabbit Rock) and migration patterns inferred from assignment tests suggested that, at ecological time scales, South African reefs are disconnected from those in Mozambique and might originate from a source of gene flow that was not sampled. The analysis of fine-scale genetic connectivity conducted on Two-mile Reef (TMR) demonstrated the existence of significant spatial genetic structure at the reefal scale that might be related to the non-random dispersal of coral larvae, putatively explaining the genetic discontinuity observed in the region. Altogether, the results are consistent with the isolation observed in other studies using less variable markers, and support the hypothesis that there is demographic discontinuity between the coral populations along the south-east African coast. More importantly, Acropora austera and P. daedalea represent different life strategies in the South African reef communities yet manifested similar genetic patterns, suggesting that these corals are responding similarly to forces that are driving genetic connectivity in the region. For management purposes, the genetically distinct populations identified at each of the spatial scales analysed in this study may correspond to management units, or evolutionarily significant units. Furthermore, since some reefs appear to act as “landing-sites” for migrants (Nine-mile Reef) and there is evidence of significant within-reef genetic structure (TMR), an adaptive management framework would be the best option for the MPA in the region. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2014.

Coral recruitment is a key process that contributes to the community structure and resilience of coral reefs. As such, quantification of this process is important to assist with the management of these threatened ecosystems. While coral recruitment has been the focus of numerous studies over the past 30 years, an understanding of this process on the high-latitude reefs of South Africa is limited. In addition, variations in methods used in recruitment studies make the results difficult to compare. A rapid in-situ method for universal application in the detection of early post-settled recruits would thus be useful. In this study, scleractinian coral recruitment was investigated at three study sites on Two-mile Reef, over two six-month sampling periods, covering summer and winter. Two components were investigated by attaching settlement tiles consisting of ceramic and marble tiles, and ceramic tiles conditioned with crustose coralline algae (CCA) onto the reef in a spatially structured experimental design. Firstly, coral recruitment was compared on the three different tile surfaces and fluorescence photography was investigated as a rapid in situ technique to detect early post-settled recruits. Fluorescence photography was then used to compare recruitment on tiles with the surrounding natural substrata. Secondly, the spatial and temporal variation in the abundance, composition and size of recruits was investigated. Additionally, the percentage cover of biota surrounding each recruit within three millimeters of its corallum was visually estimated to quantify the microhabitat surroundings of coral recruits. Overall recruitment on the three tile types differed, yet spatial variation in coral recruitment, regardless of tile surface, accounted for most of the variance in recruitment. While the highest recruitment occurred on CCA tiles, this was not significantly greater than ceramic tiles, indicating that the conditioning of ceramic tiles with Mesophyllum funafutiense CCA did not enhance coral settlement in this study. Although many recruits were not detected with fluorescent photography (73%), it proved useful to reveal recruits as small as 0.75 mm in corallum diameter, and indicated that recruitment on the tiles and natural substratum differ significantly. Spatially, the abundance and composition of coral recruits differed between study sites, within sites, and predominantly occurred on tile edges. Coral recruitment was lowest at shallower sites, and was dominated by pocilloporids regardless of study site. Additionally, the abundance and composition of recruits differed between the two sampling periods, with a 6.6-fold decrease in the mean abundance of recruits from summer to winter, with only pocilloporid settlement occurring in the latter season. The majority of recruits were <3 mm, and their microhabitat was dominated by bare substrata and crustose coralline algae. The results suggest that, while the choice of artificial settlement surface used in such studies can have a profound influence on the results, spatial variation in recruitment can be greater. The recovery of scleractinian coral taxa on Two-mile Reef in the event of a severe disturbance is expected to differ, with greatest recovery in areas of high levels of recruitment. The microhabitat surrounding recruits is described here for the first time, suggesting that further research into coral-crustose coralline algae interactions is warranted. Finally, while fluorescence photography has its limitations, it shows promise as a useful tool for rapid qualitative, but not quantitative, assessment of recruitment. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2011.

The development of coral reefs is largely restricted to areas within the tropics where favourable conditions for both coral and reef growth prevail. There is, however, a continuum from these typical, accretive reefs in the tropics to marginal, non-accretive, coral-dominated reef communities which occur at higher latitudes. High-latitude reefs function similarly in many regards to their tropical counterparts and are regulated by similar processes to a varying degree. In this study, the major biological and physico-chemical processes were assessed which directly or indirectly prevent the continued persistence of reefal frameworks and thus hinder reef accretion on high-latitude reefs in the iSimangaliso Wetland Park. These reefs have a high diversity of hard and soft corals with significant reef coverage, yet little evidence of any biogenic accretion has been observed. The scleractinian coral, Acropora austera, is one of the few corals which may be responsible for reef framework production. It exhibits a gregarious growth pattern, forming large, monospecific stands with an interlocking framework characteristic of the early stages of reef accretion. The framebuilding potential of A. austera and the continued persistence of such frameworks were thus determined by in situ monitoring of coral growth, mortality, bioerosion and several physico-chemical parameters. Growth rate and mortality of A. austera branches were measured at three sites of differing stand size and apparent age. This was achieved by repeated image analysis and by staining branches with the vital stain, Alizarin Red S. Both measures of growth yielded a similar linear extension rate of 24.5 mm/yr (n = 467), comparable to related species at similar latitudes. Mean branch mortality was as high as 50%, with clear differences manifested between each A. austera stand. Branch extension rates and branch mortality were inversely related between sites. Small, young stands exhibited significantly faster coral growth rates, lower mortality and a net increase in overall branch length over the study period, whilst the opposite was true of larger, more developed stands. In addition, bioerosion was determined at each site to assess its potential for carbonate removal and its destabilizing effect on reef frameworks. Bioerosion intensity was recorded as “percentage area damage” within cross-sections and “frequency of occurrence” of bioeroding organisms in coral rubble fragments (n = 120). The level of bioerosion was found to be substantial (up to 11.5% loss in weight of coral fragments over the 12-month study period) and was found to decrease significantly with a reduction in size of each A. austera stand. Aragonite saturation state is considered a major factor that limits the geographical range of coral reefs globally. Although previously thought to be limiting in Maputaland, mean ΩArag values of 4.40±0.29 were measured on the reefs in summer and 4.33±0.21 in winter and thus would not have limited reef development. Past studies have noted the turbulence on South African east coast reefs and its adverse effect on reef development. This was corroborated in this study with the measurement of considerable sediment re-suspension (0.17 g cm⁻² day⁻¹) and regular damage to both living coral and the reef framework caused by large swells. These results lead to the theory that Acropora austera stands senesce with increasing size and age. Although large coral frameworks are found on the Maputaland reefs, they do not persist in the long term. High rates of sediment re-suspension prevent infilling of the interstitial spaces and eventual cementation, while high levels of bioerosion lead to framework instability over time. Rough seas further hamper accretion by physical removal of both living coral and the coral-derived framework, thus removing recent growth. This process is suspected to cause an imbalance in the carbonate budget of these marginal reefs, ultimately favoring carbonate removal over carbonate deposition. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2011.

Estuaries are dynamic features of a coastline whose sediments are influenced by riverine and marine processes. Periodic events such as floods, as well as variations in mouth status, greatly affect the energy levels within an estuary and subsequently the amount of sediment erosion and deposition that takes place. Concurrently, pollutants are transported and deposited into estuaries and can reside in the sediments for many years. The estuaries of the eThekwini Municipality in KwaZulu-Natal, South Africa, are exposed to a variety of pollutants; however with the expanding industrial sector within this region, metal contamination is of concern. This study investigates the sedimentology and geochemical variations of six estuaries within the municipality namely, the uTongati, uMdloti, uMgeni, Isipingo and uMbokodweni estuaries as well as the Durban Harbour. To determine the spatial variations in estuarine sedimentology, sediment cores were collected longitudinal to the estuary axis. The core samples were analysed for sediment colour, texture and organic matter content. To assess the geochemical variations, core samples were analysed for Zn, Cu, Cr, Ni, Pb, As, Fe, Al, Ca, S, P, Mg, Mn, Cd and V concentrations. Some samples were also carbon dated to provide a temporal aspect to the sediment and geochemical variations. Descriptive and graphic techniques were used to examine the sedimentology within the estuaries; and the geochemical data was analysed with the use of multivariate statistics. Additionally, pollution indices and sediment quality guidelines were utilized to assess the pollution levels within the sediments. The results indicated that lower energy environments caused by protracted mouth closures in the uMdloti and Isipingo estuaries accounted for large amassing of fines. In contrast, the accumulation of mixed coarse and fine sediments in the uTongati and uMgeni estuaries was an indication of high fluvial flows and open mouth conditions. All carbon dated ages for all estuaries were greater than 700 years which may be attributed to a combination of scouring effects from past and recent flood events and also possibly due to the deposition of re-worked older sediments from upstream. Low metal concentrations were found within the sediments of all estuaries, and the presence of fines and organic matter governed their concentration variations with depth. The uMgeni and uMbokodweni estuaries which are located immediately downstream of industrial and urban areas, were found to contain relatively higher concentrations of elements Pb, Cu, As and Ni. These metals showed high enrichment within the sediments; however actual concentrations were below sediment quality guideline levels. General pollution levels within all estuaries were very low, and can be attributed to the climatic influences within this region which has a ‘cleansing’ effect on the estuarine environments in removing contaminants. / Thesis (M.Sc.)-University of KwaZulu-Natal, Durban, 2014.

A gradient of sea temperatures is created along the South African coastline by the confluence of the cold Benguela Current on the West coast with the warm Agulhas Current on the East coast. This temperature gradient allows for an assortment of species to occupy the variety of microenvironments occurring in this area. Amongst these species is commercially important South African abalone, Haliotis midae, which although being capable of existing across this wide range of temperatures grows larger on the cooler West coast. Abalone reared on the warmer East coast however, experience greater mortalities especially during the more thermally variable summer months. The aim of the study was thus to assess the zone of tolerance for H. midae by exposing abalone to fluctuating temperatures in an attempt to model environmental temperature instability, a scenario which may likely be worsened by global climate change. Animals from the West and East coasts were exposed to two thermal treatments of fluctuating temperatures with the first group being kept at 16°C±2 and the second group kept at 16°C±4. The control group was maintained at a constant 16°C indicating that the mean temperature experienced by all three groups was 16°C. Oxygen consumption, nitrogen excretion and O:N ratio were assessed at the organismal level to give an indication of metabolic rate, amount of protein excreted and type of metabolic substrate utilized respectively. At the biochemical level, D-lactate accumulation was quantified to indicate whether metabolism was proceeding aerobically or anaerobically. Heat shock protein 70 (Hsp70) expression and degree of carbonylation were analyzed at the proteomic level with Hsp70 also being assessed at the transcriptomic level. All biological responses were measured at days 1, 3, 7 and 14 of the two week exposure. Oxygen consumption rates were significantly elevated on day 14 when comparing treatment group animals to control group animals of the same biogeographic region. P < 0.05 for both treatment groups from the West coast, while P < 0.001 for the East coast treatment groups. The ammonia excretion rates of the West coast animals were significantly lower than those of the controls at day 14 with P < 0.001 for both treatment groups, while ammonia excretion rates were elevated in East coast animals at day 14, although not significantly. Trends similar to those seen for ammonia excretion rates were exhibited by O:N ratios. West coast animals showed lower than control O:N ratios at day 14 (P < 0.01 for both treatment groups) while East coast animals displayed higher than control values (P < 0.05 only for the 16°C±2 group) at day 14. D-lactate, having been detected only for the West coast animals, showed no significant differences but large degrees of variation were noted on days 1 and 7. Carbonylation was evident for animals from both biogeographic regions with baseline carbonyl accumulation for East coast animals being greater (non-significantly) than that of the West coast animals. The hsp70 gene expression remained low for both biogeographic groups with West coast animals appearing to show slight elevations in expression at days 1 and 7, days which also displayed high degrees of variability. The West coast animals appeared to be better suited to coping with the thermal fluctuations, as they not only transiently reduced oxygen consumption rate to reduce ROS production, but also utilized the assistance of the D-lactate pathway possibly to maintain metabolism, both of which were not observed in the East coast animals. Although West coast abalone seemed to have slightly elevated hsp70 expression (suggestive of a repair response) when compared to their East counterparts, both groups of abalone were shown to have incurred notable amounts of protein damage (i.e. carbonylation). This suggests impairments in both protective and repair responses for animals from both biogeographic regions. The lack or attenuation of physiological responses noted in East coast abalone may be due to limitations in thermal adaptation but subsequent studies are required to confirm this notion. The information obtained from this study may assist in providing an insight into the mechanisms responsible for thermal limitation in H. midae and how this species is likely to respond to future periods of thermal instability which may be worsened by global climate change. An understanding of the processes leading up to limitations may potentially assist the abalone aquaculture industry in altering culturing practices early on to support optimal performance in abalone. / M.Sc. University of KwaZulu-Natal, Durban 2014.

The St Lucia estuarine system, Africa’s largest estuarine lake, is characterised by cyclic changes from hypersaline to oligo/mesohaline conditions in response to alternations between drought and wetter than average years. In addition, St Lucia also experiences stochastic disturbances, such as flooding events that rapidly decrease salinity levels. Due to their sessile and slow moving nature, bivalves are particularly vulnerable to rapid or prolonged changes in the physico-chemical environment. The recent freshwater deprivation crisis that prevailed for the last decade resulted in a significant loss in bivalve species richness within the system. An annotated and illustrated bivalve census revealed the occurrence of twenty-four species within St Lucia between the years 1925 and 2011. However, only six species were recorded during the most recent survey in March 2011. The infaunal razor clam, Solen cylindraceus, and the epifaunal brackwater mussel, Brachidontes virgiliae, are currently the dominant bivalve species within St Lucia. This study, therefore, aimed to record the species richness of bivalves found in Lake St Lucia and to investigate key biological aspects of the two dominant bivalve taxa within the system, under different salinity regimes. Experiments revealed that S. cylindraceus can tolerate salinities between 15 and 65, while B. virgiliae prefers salinity levels ranging from freshwater to 20. The varying tolerance limits, therefore, dictate the distribution of these species during different climatic conditions within the estuarine lake. During wet periods, S. cylindraceus is restricted to the northern reaches, unable to tolerate the oligohaline conditions present in the rest of the system. Conversely, B. virgiliae, often restricted to the Narrows, becomes ubiquitous throughout the system under such conditions. Solen cylindraceus can reach a maximum length of 95 mm. However, in the St Lucia estuarine system, specimens seldom exceed a length of 55 mm, probably because prevailing/re-occurring harsh conditions prevent them from reaching maximum size. In situ measurements of this species also revealed less growth during the first year of life than for the same species in different systems. While B. virgiliae is substantially smaller than S. cylindraceus, the high densities that this species is able to attain makes it an important grazer with the potential to have significant feeding impacts on the local phytoplankton biomass. Results showed that in localised areas, B. virgiliae populations may consume up to eight times the available phytoplankton biomass. These key bivalve species are strongly influenced by the fluctuation in climatic conditions from wet to dry phases. Thus, understanding the effects that climatic shifts have on key estuarine species is essential, as flood and drought events are predicted to increase in frequency, intensity and duration as a result of global climate change. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2014.