Estuaries worldwide are being subjected to various degrees of catchment degradation, which is having severe consequences on the integrity of these aquatic ecosystems and their ability to function properly. This thesis investigated the relationship between catchment land-cover and estuarine health in four temporarily open/closed estuarine systems (TOCEs) in South Africa, namely the Groot Brak, East Kleinemonde, Mdloti and Tongati. GIS techniques were employed to delineate catchments, lower sections of catchments, 1 km and 100 m buffer zones, and to quantify the extent of land-cover classes present within these delineations. Anthropogenic activities outlined by the Department of Water Affairs and Forestry (DWAF) Resource Directed Measures (RDM) studies and their associated land-cover classes were described. The possible links between catchment and buffer zone land-cover class composition and health of the estuaries were explored. Results indicated that there was a relationship between catchment and estuarine health within the Coastal Protection Zone (CPZ) (1 km and 100 m) buffers, but not at a broader catchment level. Out of natural, urban built-up and cultivation land-cover classes, natural land was determined to be the best predictor of estuarine health within the CPZs. A method of rapidly assessing South African TOCE condition was applied and could be used to prioritise these estuaries for rehabilitation and/or conservation.

The ecologist Garrett Hardin (1968) introduced a useful concept called the tragedy of the commons, which describes how ecological resources become threatened or lost. The term “commons” is based on the commons of old English villages and is symbolic of a resource that is shared by a group of people. If every person were to use each resource in a sustainable fashion it would be available in perpetuity. However, if people use more than their share they would only increase their personal wealth to the detriment of others. In addition, an increase in the population would mean that the size of each share would have to decrease to accommodate the larger number of people. As a result, resources are threatened by personal greed and uncontrolled population growth. Freshwater is an example of a common resource that is under threat in South Africa where the average annual rainfall is less than 60 percent of the global average (Mukheibir & Sparks 2006). The increasing demands for freshwater as well as its eutrophication are major concerns with regards to estuarine health, environmental resource management and human health. The correct management of water is necessary to ensure that it is utilised in a sustainable manner. The National Water Act (No. 36 of 1998) has provided the rights to water for basic human needs and for sustainable ecological function; the Basic Human Needs Reserve and Ecological Reserve are both provided as a right in law. The amount of water necessary for an estuary to retain an acceptable ecological status, known as the Estuarine Ecological Reserve, is determined through the implementation of procedures (rapid, intermediate or comprehensive) compiled by the Department of Water Affairs and Forestry (1999) in its Resource Directed Measures (RDM) for the Protection of Water Resources. The impact of restricted flow on estuaries can be reduced by manipulating the water released from impoundments, the regulation of water abstractions within the river catchment or both (Hirji et al. 2002). The reserve assessment method is designed to evaluate ecosystem requirements by employing groups of specialists from different disciplines. In South Africa, this includes hydrologists, sedimentologists, water chemists and biologists (including microalgae specialists). The use of microalgae in ecological assessments has largely been based on research that was initiated at the Nelson Mandela Metropolitan University (formerly University of Port Elizabeth) and subsequently at Rhodes University (Grahamstown) and the University of KwaZulu Natal (Durban). The microalgal research can be divided into two main focus areas; phytoplankton and benthic microalgae

From Introduction: Energy passes through an ecosystem via a multiplicity of interconnected routes, which can be broadly categorised into trophic and detrital pathways. The "metabolic activity" of most lakes will be governed predcminantly at the base of these two routes; namely, the primary producer and decanposer levels, respectively (Wetzel and Allen, 1972). The importance of the littoral primary producers (especially the aquatic macrophytes) in the functioning of the Swartvlei ecosystem has been emphasised in a comprehensive report by Howard-Williams and Allanson (1978) dealing with the lake system fran 1975 to 1978. They noted that although the littoral shelf (<2m below low water level) occupies only 43% of the lake's surface area it contributed 64% of the total annual primary production during the period investigated. This was largely due to the dense Potamogeton pectinatus stands which alone accounted for 52% of the total carbon input into the lake by plants. The fact that the production/biomass ratio for P. pectinatus was only 1,2:1 suggested that its importance as a primary producer in Swartvlei was largely due to its high bianass. (Biomass, or standing stock, is used in this report as defined by Waters (1977); namely, "the amount present at a point in time, expressed best as quantity per spatial unit".)

Estuarine ecosystems are among the most biologically productive areas and they provide important ecosystem services such as erosion control, habitat and refugia for several species. These environments are characterized by the presence of a variety of organic matter sources due to their transitional position between rivers and the sea. The biotic compositions can undergo spatial and seasonal changes along the estuary due to the spatial and temporal fluctuations of environmental factors such as salinity, temperature and seston loads. Therefore, the different combinations of biotic and abiotic factors make each estuary a unique ecosystem. Because of this spatial and temporal complexity, the understanding of estuarine food web structure and which factors affect the trophic relationships within the ecosystem through space and time represent challenging tasks. Furthermore, estuaries are under an increasing number of anthropogenic perturbations because of the growing concentration of human populations in coastal areas. Knowledge of ecosystem structure and functioning is essential for effective conservation and management planning of coastal areas.In this dissertation, I combine the utilization of biological tracers to examine spatial and temporal variability in the food web structure within a small temperate and microtidal estuary located in South Africa. To this end, fatty acid profiles and stable isotope signatures were measured in several primary organic matter sources and consumers (including zooplankton, fishes and benthic invertebrates) during four consecutive seasons and in three different estuarine regions: upper, middle, and lower reaches. The three reaches had distinct habitat features of vegetation type and morphology, and in particular the lower reaches were colonized by the marsh grass Spartina maritima. Isotopic mixing models were used to estimate the relative contribution of each food source to the diets of invertebrates and fishes within the estuarine food web. The isotopic and fatty acid data showed similar results. In general, the lower reaches of the estuary were characterized by a higher deposition and assimilation by brachyuran crabs of carbon derived from marsh grass detritus, whiletowards the upper reaches a mixture of microphytobenthos and particulate organic matter (phytoplankton and detritus) was deposited and sustained the pelagic and benthic fauna. The highest deposition and assimilation of marsh grass detritus in the lower reaches of the estuary occurred during periods of low freshwater discharge (autumn and winter). In the upper reaches, microphytobenthos and suspended particulate organic matter were dominant basal food resources for the food web during all seasons. These results indicated that benthic consumers incorporated mainly local carbon sources from their local habitat.To clarify isotopic and fatty acid patterns I examined the trophic behaviour of the sesarmid crab Sesarma catenata through laboratory feeding experiments. Results from these experiments validated that decomposed leaves of riparian trees and the salt marsh plant S. maritima were the preferred food of the sesarmid crabs, potentially due to high bacterial loads. The remaining leaf material not assimilated by crabs, together with faecal material, are likely important subsidies for adjacent environments, hence representing an important energy pathway involving the microbial food chain. Furthermore, this dissertation showed the importance of mobile top predators as vectors energetically connecting distinct food chains within the estuary (i.e. littoral, benthic and pelagic). I concluded that a combination of physical (i.e. patterns of freshwater discharge and estuary morphology) and biological factors (i.e. organism feeding behaviour, mobility, primary productivity, the local vegetation type) influence the pattern of dominant primary organic matter sources, and therefore the food web structure along the estuarine environment. In particular, marsh grass detritus contributed substantially to the diets of estuarine fauna during periods of low freshwater discharge. Given the importance of the salt marsh habitat in providing trophic resources, it is important to preserve this environment to sustain the natural biota and ecosystem functioning.

This study investigated the response of macrophytes to physico-chemical factors in seven South African estuaries and showed that dominant salt marsh species that occur in different estuaries respond to the same environmental factors. The most important variables influencing distribution were elevation, water level, sediment- and groundwater electrical conductivity and depth to the water table. In permanently open estuaries (Kromme and Olifants) transect surveys identified three distinct vegetation zones i.e. submerged macrophytes, intertidal salt marsh and supratidal salt marsh. In the Kromme Estuary intertidal salt marsh (81.2 ha) covered extensive areas, whereas supratidal (143 ha) and floodplain (797.1 ha) salt marsh were dominant in the Olifants Estuary. Transect surveys identified four distinct vegetation zones (submerged macrophytes, intertidal salt marsh, supratidal salt marsh and reeds and sedges) in the temporarily open/closed estuaries (Mngazi, Great Brak, East Kleinemonde and Seekoei estuaries), although all zones did not occur in all of the estuaries sampled. In the Mngazi Estuary reeds and sedges (1.09 ha) covered extensive areas (no submerged or salt marsh vegetation was present), whereas salt marsh (Great Brak 24.45 ha, East Kleinemonde 17.44 ha and Seekoei 12.9 ha) vegetation was dominant in the other estuaries. Despite the geographic differences, environmental factors influencing macrophyte distribution were similar in all estuaries. Canonical Correspondence Analysis showed that vegetation distribution was significantly affected by elevation, groundwater and sediment electrical conductivity and depth to groundwater. Supratidal species were associated with a greater depth to groundwater (1.2 ± 0.04 m; n = 153) compared to intertidal species (0.5 ± 0.01 m; n = 361). Correlation analysis showed that water level and rainfall were correlated with groundwater electrical conductivity in the lower and upper intertidal zones for all the estuaries sampled. These data indicate the influence of the estuary channel on the physico-chemical conditions of the salt marsh. Low rainfall (16 ± 3.3 mm per annum) in the Olifants Estuary (30-100 mS cm-1) and lack of freshwater flooding in the Kromme Estuary (42-115 mS cm-1) have resulted in high sediment electrical conductivity by comparison with the other estuaries sampled. In the Orange River Estuary approximately 70 ha of salt marsh have been lost through the building of a causeway and flood control levees. Even though salt marsh vegetation can tolerate hypersaline sediments by using the less saline water table, the groundwater at the Orange River Estuary was too saline (avg. of 90.3 ± 6.55 mS cm-1, n = 38) to be of use to the dominant floodplain species, Sarcocornia pillansii. Freshwater inflow to estuaries is important in maintaining longitudinal salinity gradients and reducing hypersaline conditions. In the Olifants Estuary and the Orange River Estuary where supratidal salt marsh is dominant, freshwater inflow is important in raising the water level and maintaining the depth to groundwater and salinity. Lack of freshwater inflow to the Kromme Estuary has highlighted the importance of rainfall in maintaining sediment salinity within acceptable ranges for the salt marsh. Macrophytes are relatively good indicators of physico-chemical factors in estuaries. From an understanding of the response of specific species to environmental variables, ecological water requirements can be set and sensitive areas can be rehabilitated.

Studies on morphological variation are important as it can depict the relationship with environmental factors clearly and convey an understanding of the manner, mechanism and factors influencing plant adaptation and evolution. Although many studies have been conducted on South African salt marsh plant physiology and phytosociology there are at present very few morphological studies on estuarine plants. The aim of this study was to compare the morphological variation of estuarine macrophytes in three different estuary types in the warm temperate biogeographic zone of South Africa and to compare characters used in the taxonomic descriptions of species with those measured in the field. Permanently open estuaries investigated were Ngqusi (WC), Kowie (KW) and Swartkops (SW) estuaries. The Knysna Estuary (KN) was the estuarine bay investigated and the temporarily open/ closed estuaries (TOCEs) were the East Kleinemonde (EK) and Great Brak (GB) estuaries. Macrophytes were morphologically different across different estuary types. This suggests that there were different factors operating between these estuary types that would directly influence the morphology of species. The variation of plant height with different estuary types can be attributed to the fact that smaller salt marshes also have smaller habitat ranges compared to larger ones. The variation in morphological characteristics such as plant height can also be attributed to biogeographical range. Most morphological characteristics measured in the field fall within previously published ranges, and so these characters are useful in delimiting species. There were significant relationships between phenotypic variables and multivariate environmental variables. The most important of these variables were soil electrical conductivity, soil organic content and soil water content. Specifically, plant height increased with water content and decreased with salinity, flower stalk length had strong significant positive correlations with moisture content, organic content and pH while there were strong significant correlations with redox potential and electrical conductivity. Salt marshes are considered ideal for studying variation of species due to the explicit environmental gradients and plants occurring in salt marshes are halophytes that exhibit a range of morphological traits that allows for growth and reproduction under the stressful and extreme conditions. Considering recent climate change predictions and the consequent effects on South African estuaries this study provides significant information with regard to the response of species to a changing environment. The study was also aimed at updating the existing botanical database for South African estuaries in terms of species occurrence in South African estuaries, taxonomic name changes of existing species, new species, common names and habitats. Species diversity indices were also calculated for different estuaries, estuary types and biogeographic zones and diagnostic descriptions of the dominant salt marsh species were developed. The objective of this was that these data should provide baseline information for determining habitat richness and plant species diversity of South African estuaries which in turn should be used in determining priority estuaries for conservation and management. The identification key, developed using the DELTA software, would also aid researchers, managers and laymen in identifying salt marsh species. Results showed that the total number of macrophyte species, including intraspecific taxa and macroalgae, was 242 in 53 estuaries that were updated . There was an increase in the number of taxa recorded in the database primarily due to 1) research focus and full taxonomic surveys on larger estuaries and the big research projects has led to the identification of more species, 2) the addition of species that are not characteristically known as estuarine species, 3) the addition of 50 macroalgal taxa and 4) minor changes due to taxonomic revisions of species and the addition of newly described species. The Shannon diversity index showed that greater species diversity was found in the Berg (Groot) Estuary (4.220) and the Uilkraals Estuary (4.025). The cool temperate bioregion was the most diverse in the number of taxa (58) with the highest Shannon index (4.736). Permanently open estuaries were the most diverse in the number of unique taxa (56) with the highest Shannon index (4.867). Estuarine managers need to be aware of the species diversity in different estuarine types as well as the associated impacts on them. Conservation planning must therefore include species. Diagnostic features of INTKEY indicated that all 57 taxa were distinguishable from each other. Contrary to expectations plant height and not floral morphology was the best diagnostic characteristic. Ecological information such as the estuarine habitat, where different life forms occur, was important in delimiting species.

The Bushmans Estuary is one of the few permanently open estuaries in the Eastern Cape that is characterized by large intertidal salt marshes. Freshwater inflow to the estuary has decreased as a result of abstraction by more than 30 weirs and farm dams in the catchment. The mean annual run-off is naturally low (38 x 106 m3 y-1) and thus abstraction and reduction of freshwater inflow to the estuary is expected to cause a number of changes. The aims of this study were to determine the current health/status of the estuary based on the macrophytes and microalgae and identify monitoring indicators for the East London Department of Water Affairs, River Health Programme. Changes in the estuary over time were determined from available historical data which were compared with present data. This analysis showed that under normal average conditions freshwater inflow to the estuary is very low, less that 0.02 m3 s-1 most of the time. Under these conditions the estuary is in a homogenous marine state. Vertical and horizontal salinity gradients only form when high rainfall and run-off occurs (> 5 m3.s-1). Salinity gradients from 30.1 PSU at the mouth to 2.2 PSU in the upper reaches were measured in 2006 after a high flow event. However the estuary quickly reverted back to its homogenous condition within weeks after this flood. This study showed that freshwater inflow increased nutrient input to the estuary. Total oxidised nitrogen (TOxN) and soluble reactive phosphorus (SRP) concentrations were higher in August 2006, after the flood, than during the other low flow sampling sessions. TOxN decreased from a mean concentration of 21.6 μM in 2006 to 1.93 μM in February 2009. SRP decreased from 55.3 μM to 0.2 μM respectively. With the increased nutrient availability, the response in the estuary was an increase in phytoplankton biomass. After the 2006 floods the average water column chlorophyll-a was 9.0 μg l-1, while in the low freshwater inflow years it ranged from 2.1 to 4.8 μg l-1. The composition of the phytoplankton community was always dominated by flagellates and then diatoms, with higher cell numbers in the nutrient-enriched 2006 period. Although the water column nutrient data indicated that the estuary was oligotrophic, benthic microalgal biomass (11.9-16.1 μg.g-1) in the intertidal zone was comparable with nutrient rich estuaries. Benthic species indicative of polluted conditions were found (Nitzschia frustulum, Navicula gregaria, Navicula cryptotenelloides). These benthic species were found at the sites where wastewater / sewage seepage had occurred. Benthic diatom species also indicated freshwater inflow. During the high flow period in 2006 the dominant diatoms were fresh to brackish species that were strongly associated with the high concentrations of TOxN and SRP (Tryblionella constricta, Diploneis smithii, Hippodonta cf. gremainii, and Navicula species). During the freshwater limited period of 2008 and 2009 the benthic diatom species shifted to a group responding to the high salinity, ammonium and silicate concentrations. The species in this group were Nitzschia flexa, Navicula tenneloides, Diploneis elliptica, Amphora subacutiuscula and Nitzschia coarctata. Ordination results showed that the epiphytic diatom species responded to different environmental variables in the different years. Most of the species in 2008/2009 were associated with high salinity, temperature, dissolved oxygen, ammonium and silicate concentrations while the response was towards TOxN and SRP in 2006. The dominant species were Cocconeis placentula v euglyphyta in 2006; Nitzschia frustulum in 2008; and Synedra spp in 2009. The average biomass of the epiphytes was significantly lower in May 2008 than in both August 2006 and February 2009; 88.0 + 17.7 mg.m-2, 1.7 + 0.8 mg.m-2, and 61.8 + 14.4 mg.m-2 respectively. GIS mapping of past and present aerial photographs showed that submerged macrophyte (Zostera capensis) cover in 1966 and 1973 was less than that mapped for 2004. Salt marsh also increased its cover over time, from 86.9 ha in 1966 to 126 ha in 2004, colonizing what were bare sandy areas. Long-term monitoring of the health of the Bushmans Estuary should focus on salinity (as an indicator of inflow or deprivation of freshwater), benthic diatom identification and macrophyte distribution and composition (for the detection of pollution input), and bathymetric surveys (for shallowing of the estuary due to sedimentation).

An estuary, according to the National Water Act of 1998, is a partially or fully enclosed body of water which is open periodically or permanently to the sea within which the sea water can be diluted, to an extent that is measurable with freshwater from inland. Estuaries and the lands surrounding them are places of transition from land to sea, and from freshwater to saltwater. Although influenced by the tides, estuaries are protected from the full force of ocean waves, winds, and storms by the reefs, barrier islands, or fingers of land, mud, or sand that surround them. South Africa’s estuaries are important and irreplaceable habitats, especially for prawns, fish, wading birds and mangroves. They are home to numerous plants and animals that live in water that is partly fresh and partly salty. Estuaries are also homes to growing coastal communities as increasing number of people occupy watersheds. However, estuaries are also threatened. One of the threats is reduced river water inflow. This study applies the contingent valuation method (CVM) to elicit user’s willingness to pay to mitigate the negative impacts of reduced freshwater inflow into selected five Eastern Cape and Kwazulu-Natal estuaries: the Sundays, Gamtoos, Mdloti, Mgeni and Mvoti estuaries. In addition to the contingent valuation method, the travel cost method was used to generate comparative values. The contingent valuation method is a technique to establish the value of a good (or service) that is not bought or sold in an actual market. The CVM establishes the economic value of the good by asking the users of an environmental good to state their willingness to pay (WTP) for a hypothetical project to prevent, or bring about, a change in the current condition of the environmental good. The users’ WTP is aggregated to establish a total willingness to pay (TWTP) for the population of the users of the environmental good.

Phylogeographic patterns of coastal organisms with different life histories and breeding strategies may reveal patterns not consistent with the current delineation of the biogeographic provinces around South Africa. The subdivision of the South African coastline into these three main climatological or biogeographic regions: namely the cool temperate west coast, the warm temperate south coast and the subtropical east coast, is based on average seawater temperatures and hydrological conditions. Genealogies of two estuarine fish species Atherina breviceps, a marine breeder, and Gilchristella aestuaria, an estuarine spawner, were reconstructed using mitochondrial DNA (mtDNA) control region sequences. The study comprised two components, an assessment of a small dataset of both fish species to compare their population structure along the South African coastline and a more comprehensive investigation of the phylogeography of G. aestuaria collected from 21 estuaries around the coast. The comparative study of A. breviceps and G. aestuaria indicate different population distribution patterns along the South African coastline. Results of the A. breviceps analysis demonstrate substantial gene flow due to the random mixing of alleles, while the comparative G. aestuaria dataset indicates a more structured population and considerably less gene flow. The G. aestuaria population demonstrates geographic separation into four groups, namely the west coast (Great Berg), Bot (south coast), Seekoei (south coast) and east coast (Bushmans, Kasouga and Cefane). Results from the larger G. aestuaria dataset indicate that the phylogeographic patterns observed during this study do not conform to existing biogeographic boundaries along the southern African coastline. The delineation identified during this study between the warm temperate and subtropical regions is further south than originally perceived and this southward extension can be ascribed to the prevailing hydrology. The life history patterns and ecology of these two estuarine fish species appears key to understanding their population structure. These factors interact with environmental characteristics such as physical oceanography and the distribution of estuaries (along the coastline) to explain the observed distribution patterns and population structure of A. breviceps and G. aestuaria.

During 1982 benthic and floating filamentous algal mats appeared in the maturation ponds of the Grahamstown Sewage Disposal Works. These mats clogged the ponds and reduced the efficiency by which the effluent was purified. As they continued to be a problem despite numerous efforts to remove them, this study was initiated to investigate the alga, establish why it was successful in the pond environment, and how its growth could be controlled. The physico-chemical environment of a representative maturation pond was characterised while laboratory studies were conducted to investigate the growth, photosynthetic and respiratory characteristics in the alga. The alga was identified as Rhizoclonium riparium (Roth) Harv. although its morphological variability was greater than that reported in the literature. Growth and photosynthetic studies indicated that the alga favoured temperatures between 20 and 30⁰C and relatively high light intensity (700μE.m⁻².s⁻¹) and that it was highly productive. In addition, the alga exhibited photoadaptive ability, although it seemed to be sensitive to photoinhibition. Its success in the maturation pond was attributed to the favourable physico-chemical environment, particularly the high transparency of the effluent which allowed the penetration of PAR to the pond floor and to the alga's ability to adapt to the change in environment when it floated from the pond floor to its surface. Although the algal mats contribute to the oxidation of the effuent within the maturation pond, they are generally detrimental to the system because they shade the water column and inhibit wind-induced mixing. Recommendations on methods of controlling of the mats are presented. / KMBT_363 / Adobe Acrobat 9.53 Paper Capture Plug-in