D.Sc. (Freshwater Biology) / Please refer to full text to view abstract

M.Sc. (Aquatic Health) / Aquatic ecosystems in rural South Africa have been impacted over many years by commercial and subsistence anthropogenic activities (DWAF, 2001). These impacts include commercial and subsistence farming, domestic use (e.g. washing of clothes, cars and bathing) and recreational use (e.g. fishing). In the northern parts of the Limpopo Province of South Africa (Vhembe District) the land use is primarily dominated by various agricultural activities and human settlements. Rivers in this region flow through mixed agricultural use, including commercial agriculture (tea and timber plantations) as well as subsistence farming and housing. Perennial rivers in this region include the Mutale, Mutshindudi and Tshinane rivers. These rivers are located in the Water Management Area 2 (WMA 2 Luvuvhu-Letaba) (Kleynhans, et al., 2007a). They are highland river systems, originating in the nearby Soutpansberg Mountain, and these rivers all form part of the larger drainage system of the Luvuvhu River, a tributary of the Limpopo River. The wetlands in the catchment of these rivers are also heavily utilised by the local communities (Working on Wetlands, 2013) used for grazing, sand mining and subsistence cultivation, thus providing a livelihood for the surrounding communities (SANBI, 2012). The aim of the study was to assess aspects of the biological integrity of the Mutale, Mutshindudi and Tshinane rivers. This study formed part of a larger study that included assessments of both abiotic and biotic aspects of these river systems. For this study, the focus was on assessing the fish community structure through the application of Fish Response Assessment Index (FRAI), riparian vegetation through the application of Vegetation Response Assessment Index (VEGRAI) and fish health aspects with special reference to liver and gonadal histopathology. Water quality parameters were found to be within the target water quality range for aquatic ecosystems. The results did however vary between upstream and downstream sampling sites. Similarly, compared to upstream sites, the FRAI showed the Mutale River to improve in fish community structure whereas the Tshinane and Mutshindudi rivers showed a decrease in the FRAI score. The VEGRAI results showed a decrease in EcoCondition in the Mutale and Mutshindudi rivers whereas the Tshinane indicated an increase. This can be attributed to land use change up to the edge of the river systems. Visual observation at the various study sites showed a definite localised impact of human activities on the beds and banks of many parts of the rivers. No histological alterations were identified in any of the gonadal or liver tissue of the Chiloglanis pretoriae (Shortspine suckermouth) (Van der Horst, 1931) and the fish were found to be in a healthy condition according to the selected parameters (gonads and livers) assessed. The fish community structure of the three rivers were found to be in a moderately to largely modified condition according to the ecological state categories calculated. However, the fish health assessment showed no histological alterations in the sampled fish. It is proposed that future studies investigate the influence of the domestic use of the rivers as well as attempt to quantify the impact of agriculture on the system.

Understanding the mechanisms and adaptations that allow only certain species to thrive in the potentially stressful foredune environment requires a knowledge of the basic ecophysiology of foredune species. Ecophysiological measurements were conducted on the foredune pioneer species Arctotheca populifolia (Berg.) Norl., Ipomoea pes-caprae(L.) R. Br. and Scaevola plumieri (L.) Vahl. and showed significant differences among species with respect to the physiology associated with biomass production, water and nutrient relations. Differences related to CO₂ assimilation included differences in photosynthetic and respiratory rates, susceptibility to light stress and leaf and stem non-structural carbohydrate concentrations. These resulted in differences in primary production rates of shoots. Mechanisms leading to the differences in CO₂ assimilation among species included differences in stomatal behaviour, carboxylation efficiencies, efficiencies of utilisation of incident photosynthetic photon flux density (PPFD) and rates of ribulose-1,6-bisphosphate (RuBP) regeneration. Correlated with differences in photosynthetic capacity were differences in chlorophyll contents but not differences in leaf nitrogen content. Differences in interspecific stomatal behaviour resulted in significantly different transpiration rates which in combination with differences in assimilation rates resulted in differences in water-use efficiency. The absolute amounts of water transpired, although significantly different among species, were moderate to high in comparison with species from other ecosystems and were typical of mesophytes. Transpiration rates in combination with plant hydraulic conductances and soil water availability resulted in leaf water potentials that were not very negative and none of the investigated species showed evidence of osmotic adjustment. The volume of water transpired by each of the species per unit land surface area was estimated from the relationship between abiotic factors and plant water loss. These relationships varied among species and had varying degrees of predictability as a result of differences in stomatal behaviour between the three species. The water requirements of A. populifolia and S. plumieri were adequately met by the water supplied by rainfall and the water stored in the dune sands. It was therefore not necessary to invoke the utilisation of ground water or the process of internal dew formation to supply sufficient water to meet the requirements. However, I. pes-caprae despite its lower transpiration rates and due to its higher biomass, lost greater volumes of water per unit dune surface area than either A. populifolia or S. plumieri. This resulted in periods of potential water limitation for I. pes-caprae. Incident light was the most important determinant of leaf photosynthetic CO₂ assimilation and transpiration, particularly as a linear relationship between incident PPFD and atmospheric vapour pressure deficit (VPD) could be demonstrated. Whole plant photosynthetic production by S. plumieri was shown to be light limited as a result of mutual shading despite high incident and reflected PPFD occurring in the foredune environment. The leaf hair-layer of A. populifolia was shown to be important in reducing transmitted UV and hence reducing photoinhibition but it also caused reduced transpiration rates because of the thicker boundary layer and thus increased leaf temperatures. The nutrient content of above-ground plant parts of the investigated species were typical of higher plants despite the low nutrient content measured for the dune soils. With the possible exception of nitrogen the nutrient demand created by above-ground production was adequately met by the supply of nutrients either from sand-water or from aquifer-water transpired by the plants. Differences in the volumes of water transpired, and hence the quantity of nutrients potentially taken up via the transpiration stream, resulted in interspecific differences in above-ground plant macronutrient content. The reallocation patterns of nutrients differed both between the various nutrients measured and interspecifically. Standing biomass and the density of plants per unit land area was low in comparison to that of other ecosystems and was different among investigated species. This may be important in maintaining the adequate supply of resources (water, nutrients and light). As a result of the interspecific differences in biomass when production was expressed per unit land surface area the resultant productivity was not dissimilar among species. Productivity was high when comparisons were made with species from other ecosystems. No single resource (water, nutrients or light) could be identified as the controlling factor in the foredune environment and a combination of both resource stress and environmental disturbance are likely to be involved. Physiology, production, growth and growth characteristics conveyed certain adaptive advantages to these species in respect to both resource stress and environmental disturbance. Interspecific differences in these adaptations can be used to offer explanations for the observed microhabitat preferences of the three investigated species. Furthermore features common to all three species offer some explanations as to why these species and not others are able to inhabit the foredunes.

The ichthyofauna of three small Natal estuaries, the Mhlanga, Damba and Zotsha was sampled over a period of two years. A total of 68 kinds of fishes representing 24 families, 39 genera and 56 species were captured during this study. Forty seven kinds of fishes were recorded in the Mhlanga of which Gilchristella aestuaria,Oreochromis mossambicus, Valamugil cunnesius, Valamugil sp. and juvenile mugilids numerically dominated. In terms of biomass, O. mossambicus, V. cunnesius, Liza alata, Myxus capensis and Mugil cephalus dominated the ichthyofauna of the Mhlanga. In the Damba, 24 kinds of fishes were recorded. The most abundant fishes captured were Glossogobius callidus, M. capensis and O. mossambicus. M. capensis, M. cephalus, O. mossambicus and G. callidus dominated the fish biomass captured in the Damba. A total of 56 kinds of fishes were recorded in the Zotsha during this study. The ichthyofauna of the Zotsha was numerically dominated by juvenile mugilids, G. aestuaria, O. mossambicus, Rhabdosargus holubi, Terapon jarbua, Ambassis productus and G. callidus. The species which dominated the fish biomass in the Zotsha were O. mossambicus, L. alata, Valamugil robustus, Valamugil buchanani, M. capensis, M. cephalus and V. cunnesius. Classifying the species captured according to whether they were resident estuarine species, freshwater species, estuarine-dependent marine species and marine species revealed that the first three groups were all well represented in the systems. The only system in which marine species made any significant contribution to the ichthyofauna was the Zotsha. Oreochromis mossambicus was the dominant freshwater species in all three estuaries during this study. Gilchristella aestuaria and Glossogobius callidus were the principal estuarine species in the Mhlanga and the Damba respectively. Both G. aestuaria and G. callidus were the dominant estuarine species captured in the Zotsha. The principal estuarine-dependent marine fishes captured in the Mhlanga were V. cunnesius, Valamugil sp., juvenile mugilids, M. capensis, M. cephalus and L. alata. In the Damba, M. capensis and M. cephalus were the dominant estuarine-dependent marine species and in the Zotsha juvenile mugilids, R. holubi, T. jarbua, A . productus, M. capensis, V. cunnesius, V. robustus, M. cephalus and L. alata predominated. The results of this study indicate that the estuaries are dominated at different periods by different assemblages of fishes. This is linked to the spawning and migration patterns of the various species as well as the hydrological regime of each estuary. During the winter these systems are normally closed with relatively deep waters and high food resource and habitat availability. Freshwater and estuarine species mainly inhabit the upper reaches of the systems while estuarine-dependent marine species mainly occupy the middle and lower reaches and dominate the fish community. When these systems open with the onset of the spring/summer rains, adult and sub-adult estuarine-dependent marine species emigrate to the marine environment and juveniles begin recruiting into the systems. Spring is also the peak breeding period of resident estuarine and freshwater species, resulting in an increase in the contribution of these fishes to the overall population during this period. When closed estuaries open many of them drain and this results in the fishes concentrating in the lower reaches of the system where moderate water depths are present, thus further contributing to an increase in the proportion of freshwater and estuarine species in this region. The breaching of closed estuaries also results in a slump in food resources and habitat availability. Competition and possible increased vulnerability to avian predation (due to the shallow nature of the systems), may contribute to a decrease in the proportion of estuarine and freshwater species in summer. The prolonged spawning and recruitment of 0+ juveniles of estuarine-dependent marine species results in an increase in the proportion of these fishes present in the estuaries during summer. In autumn, these systems normally close, water levels rise and available food resources and habitat increase. This allows the redistribution of freshwater and estuarine species upstream, leaving estuarine-dependent marine species to dominate the middle and lower reaches. Although temporarily open/closed estuaries along the Natal coast may not be as diverse as permanently open estuaries in terms of their ichthyofauna, their importance must not be underestimated since by providing a continuous sequence of sheltered habitats along the coast they may contribute significantly to the viability of estuarine-dependent marine fish stocks.

Introduction: Phosphorus is an especially scarce element in the aquatic environment, yet it is of vital importance to living organisms: the pyrophosphate bond is the basis of biochemical energy transfer, and phosphate groups make up the backbone of the nucleic acids (Wetzel, 1975). An understanding of phosphorus movements and transformations is thus essential to a study of the biological functioning of a lake. The present report describes a study of phosphorus dynamics inSwartvlei, a lake with an extremely low pelagic primary production rate, in the order of 0,15 gC.m⁻².d⁻¹ (Robarts, 1973; Howard-Williams and Allanson, 1978). The littoral phosphorus dynamics of Swartvlei have been discussed in some detail (Howard-Williams, 1977; Howard-Williams and Allanson, 1978), and what follows is an attempt to quantify the changes in phosphorus concentration occurring in the deeper parts of the lake, which comprise some 57% of the total area.

Temporary rivers in dryland regions are subject to highly variable and unpredictable rainfall and flow, and are considered unstable systems relative to perennial rivers of temperate zones. Little is known of the ecology of South Africa's temporary rivers, despite their abundance. The research presented focusses on the aquatic invertebrates inhabiting intermittently-flowing rivers in the 'arid corridor' of the Eastern Cape, South Africa. The major aims of the work were: to investigate which invertebrates inhabit these rivers, how the fauna is affected by environmental variability at various spatial and temporal scales, whether or not a characteristic fauna can be associated with these rivers or the hydrological phases which characterise them, and to establish to what extent faunal overlap occurs between different temporary rivers and between natural and modified temporary and perennial rivers. Research results indicate that the fauna of the Eastern Cape temporary rivers shows little structure at the scales of investigation, and that communities are generally non-equilibrial in character. The major forces shaping the biota are considered to be physical rather than biological, and the most important of these are: present and antecedent hydrological conditions and their duration; time of year; and biotope character, extent and heterogeneity. Three groups of fauna were identified as inhabitants of the temporary rivers: 'residents', 'facultative taxa' and 'opportunist colonists'. Taxa were tentatively allocated to these groups. Faunal resemblance was fairly high in Eastern Cape temporary rivers at the level of family, but not at more detailed taxonomic levels. A comparison between faunas of temporary and perennial rivers in different regions of South Africa illustrated the influence of geographical location on diversity. Within regions, however, there was no indication that perennial rivers were more diverse than intermittent rivers. The relatively high diversities in temporary rivers in this study are attributed at least in part to the heterogeneity in surface water conditions over time. A conceptual framework envisioning a continuum between perennial and temporary rivers is proposed as a basis for ongoing research into these rivers. A supporting terminology for the range of river flow types in South Africa is presented.

The citrus red mite, Panonychus citri (McGregor), is a relatively new pest to South African citriculture, the first recorded injury to citrus trees was from Rustenberg, Transvaal in 1950 (Smith 1953). In the U.S.A. the biology of this mite has been studied by Quayle (1938), Prendergast (1938), English and Turnipseed (1941), DeBach (1947), DeBach et al. (1950), Ebeling (1959) and Jeppson et al. (1957,1961). However, in South Africa little information is available concerning the ecolopy of the citrus red mite. The majority of the literature pertaining to P. citri in Republic, (Smith (1953), Mentz (1954), Stofberg (1959), Schwartz (1965) and Brodrick (1965) is of a descriptive nature, and mainly concerned with the chemical control of the mite. The only biological investigation on the development of P.citri, and the effect of insecticides and insect predators on its biology, under South African conditions, was made by van Rooyen (1966) at Zebediela, Transvaal. In the control of citrus pests, such as the citrus red mite, that need for a better understanding of their ecology has been well emphasised by DeBach (1951) and Griffiths (1951). DeBach (1951) in particular, stressed the danger of the continued reliance on insecticidal treatment as the only method of nest control, and has pointed out that persistent chemical applications may only serve to intensify the pest problem. He has suggested that a closer study of the environment of the pest species could provide a solution to the problems now encountered as a result of insecticidal control measures. Intro., p. 1-2.

Global trends in teleost fisheries indicate significant population declines. Thus, alternative fisheries are being developed to meet the growing economic and nutritional demands of the expanding human population. Recently, it has been established that elasmobranch fisheries may fulfill these demands. As many elasmobranchs possess life-history characteristics that make them particularly vulnerable to overfishing, it is imperative to develop management strategies prior to the inception of these fisheries to ensure sustainable resource utilisation. In South Africa, elasmobranchs have been commercially exploited since the 1930s. Although generally considered an under-exploited resource, the potential for growth within these fisheries has been recognized. In 2005, the commercial shark fishery will undergo a transition from medium to long-term rights allocations. This represents an ideal opportunity for scientists and managers to develop precautionary species-specific management plans for commercially exploitable elasmobranch species. The soupfin shark (Galeorhinus galeus) is one of the principal target species in South Africa’s shark fisheries. Given its inherent susceptibility to overexploitation, G. galeus was selected as a management priority by South Africa’s regional fisheries organisation. The purpose of this study was to examine and describe the stock status of G. galeus in South Africa, and to develop a precautionary fishery management plan to ensure the sustainability of this resource. Age, growth, and mortality calculations for G. galeus were made from research survey data collected between 1996 and 1999. A small sample size precluded independent analyses of females. The maximum recorded age for G. galeus was 33 years. Estimated von Bertalanffy growth parameters from observed length-at-age for males and combined sexes were: L∞ 1542.8 mm TL, K 0.21 year⁻¹ , t₀ -2.79 year⁻¹ and L∞ 1560.3 mm TL, K 0.19 year¹, t₀ -3.03 year⁻¹, respectively. The age-at-50% maturity was determined to be 6 years, corresponding to 1011 mm TL for males and 1100 mm TL for combined sexes. Natural mortality was calculated as 0.126 yr⁻¹. The rate of instantaneous total mortality was calculated as 0.27 yr⁻¹. Catch trend analysis showed that catches and CPUE of G. galeus are increasing in the demersal longline fishery, and decreasing in the handline fishery. Decreasing catches and CPUE were observed in fishery-independent research survey data. The status of the soupfin shark stock was modelled using per-recruit analysis. The SB/R model indicated the soupfin shark is being optimally exploited and spawner biomass is at 43% of preexploitation levels. Current fishing levels ( F = 0.14 yr⁻¹) approximate the Fsb₄₀ level (F = 0.17 yr¹); thus, an increase in fishing pressure may lead to stock collapse. It was determined that the current age-at-capture (7.9 years) should be increased to 10 years, or 1420 mm TL, to maximize yield and minimize the possibility of recruitment failure. The results of this study indicate a need for immediate scientific and management intervention in South Africa’s soupfin shark fishery. An assessment report and fishery management plan for G. galeus was compiled, and several management options were proposed. These include the implementation of licence and size restrictions, as well as seasonal/area closures. The potential for an experimental gillnet fishery should be investigated.

Springhare are large, bipedal, nocturnal, herbivorous, burrowing rodents that are found in arid and semi-arid parts of southern and eastern Africa. In this thesis I examine the general ecology, biology and physiology of these animals in the Eastern Cape Province of South Africa. An investigation of their distribution and activity in the study site showed that springhare exhibit a preference for flat, open, recently disturbed habitat that is dominated by the grass Cynodon dactylon and the sedge Cyperus esculentus. These two species constitute a major proportion of their diet. The impact of spring hare on chicory and grazing is also discussed. Nightly activity generally peaks soon after dark and decreases in the 2-4 hour period before sunrise. This pattern is, however, modified by moonlight. Springhare typically respond to moonlight by reducing aboveground activity, shifting their activity to dark moonless periods of the night, and by reducing their use of open space. Contrary to earlier reports, springhare utilise several different burrow systems spread over large areas. They regularly change burrow systems and seldom spend more than a few consecutive days in each. Springhare do not appear to defend territories but recently used burrows appear to be avoided by conspecifics. Males and females on average use a similar number of burrows, scattered over similar sized areas. Burrows are shown to provide a stable microclimate of moderate temperature and high humidity throughout the year. Reproduction is continuous and there is no synchronised breeding season. The ability to reproduce throughout the year is attributed primarily to their ability to utilise subterranean food stores. The overall reproductive strategy of springhare (a single young with long gestation and weaning) is unusual for a mammal of this size but may be linked to low levels of adult and juvenile mortality. Physiologically, springhare are reasonably well adapted to life in hot, arid environments. They produce a concentrated urine, exhibit a high tolerance to dehydration, are good osmoregulators capable of maintaining plasma volume, osmolality and ion balance over long periods of water deprivation, and are able to produce dry faeces. They are also good thermoregulators at low ambient temperatures, which are usually encountered at night, but are poor thermoregulators at high ambient temperatures, which they avoid behaviourally.

The spatial and temporal pattern of ichthyofaunal community composition in relation to selected physico-chemical (temperature and salinity) and biological variables (chlorophyll-a and zooplankton) was investigated at ten stations in the temperate temporarily open/closed Kasouga estuary. In addition, the food web structure in the estuary was investigated using stable carbon isotope analysis. Results of the 5 metre seine net survey indicated that ichthyofaunal composition and biomass in the Kasouga estuary was largely determined by seasonality and mouth condition. Maximum abundance and biomass of ichthyofauna was recorded during summer or during those periods when overtopping occurred. Overtopping coincided with the recruitment of marine estuarine dependant species, which dominated the catches both numerically and in biomass. The recruitment of these species resulted in an increase in diversity of the ichthyofaunal community. There were no significant spatial patterns in the distribution of smaller ichthyofauna (<50mm SL) identified in Bray-Curtis similarity matrices using cluster analysis (Primer 5 v5.2.4). Spearman’s correlation analysis revealed that there were no significant correlations between abundance and biomass of ichthyofauna and selected physico-chemical and biological variables other than salinity (P>0.05 in all other cases). There were two distinct spatial patterns in the distribution of the larger ichthyofauna (>50mm SL). These corresponded to a grouping associated with the mouth region and a grouping associated with the remaining regions of the estuary. Stable isotope analysis indicated that the primary source of carbon utilised by the ichthyofauna of the Kasouga estuary was derived from the channel, most likely microphytobenthic algae. The contributions of the riparian and salt marsh vegetation to the total carbon flow appear to be minimal.