The epidemiology of African horse sickness in the Eastern Cape, South Africa

Expected release date-May 201

Investigating the enzymatic mechanism of platinum nanoparticle synthesis in sulfate-reducing bacteria

Efforts to discover an efficient yet environmentally friendly mode of metal nanoparticle (NP) synthesis are increasing rapidly. A ‘green’ route that avoids the high costs, toxic wastes and complicated protocols associated with chemical synthesis methods is therefore highly sought after. A biologically based protocol will provide the possibility of gaining control over the mechanism merely by manipulating the experimental conditions of the system. Given that the properties of nanoparticles are highly dependant on the morphology of the particles themselves, this mechanistic control will provide significant industrial advantages with regards to tailoring specific properties of the nanoparticles produced. The key objectives of this study were to: a) determine whether a consortium of sulfate-reducing bacteria was capable of platinum nanoparticle synthesis, b) elucidate the bioreductive, enzymatic mechanism responsible, and c) attempt to control the morphologies of the particles produced. A consortium of sulfate-reducing bacteria (SRB), isolated from sewage sludge, was used in these investigations due to the advantages a consortium provides in comparison to pure cultures. The syntrophic relationships established within the constituent species not only prevent the growth of contaminant microbes, but increases the oxygen-tolerance of the system as a whole. The sulfate-reducing consortium was shown to possess an aerobic mechanism for Pt(IV) reduction which, though different from the anaerobic bioreductive mechanism previously identified in literature, did not require an exogenous electron donor. It was demonstrated that the Pt(IV) ion becomes reduced to Pt(0) via a two-cycle mechanism involving Pt(II) as the intermediate. Further investigation elucidated the reduction of Pt(IV) to Pt(II) to be dependant on a novel Pt(IV) reductase which becomes upregulated in the presence of Cu(II), while the reduction of Pt(II) to Pt(0) occurred by means of a periplasmic hydrogenase. To our knowledge, this is the first time a coupled mechanism for Pt(IV) reduction by micro-organisms has been proposed. A cell-free, crude protein solution from the consortium produced both geometric and irregular platinum nanoparticles. The wavelength of 334 nm was chosen as a nonquantitative indicator of Pt(0) nanoparticle formation over time. The optimum conditions for nanoparticle synthesis were pH 9.0, 65 ˚C and 0.75 mM Pt(IV) as H2PtCl6 salt. In the absence of a buffer a Pt(IV) concentration > 1 mM resulted in the precipitation of protein-nanoparticle bioconjugates, due to unfavourable acidic conditions. This demonstrated that the nanoparticles were binding to and becoming stabilised by general protein in the cell-free solution. Upon addition of a sodium-bicarbonate buffer, a general increase in Pt(IV) reduction to Pt(II) was observed. The addition of the buffer also resulted in an unexplained change in particle morphology and for this reason was not used in subsequent investigations. Polyvinylpyrrolidone (PVP) was shown to compromise the reduction rate of the Pt(IV) ion by SRB cells. The presence of extracellular NP’s was suggested by the colour of the supernatant turning brown and the A334 increasing over time. Attempts to visualise the particles by transmission electron microscopy (TEM) resulted in an unexpected phenomenon where nanoparticles could be observed to form dynamically upon irradiation by the electron beam. Extended irradiation by the electron beam also resulted in structural changes of the particles occurring during observation. An increase in temperature was shown to increase the reduction rate which in turn resulted in particles decreasing in size. The starting pH was shown to have a significant effect on the reduction rate and particle morphology although specific trends could not be identified. In conclusion, the cell-soluble extract from the sulfate-reducing consortium investigated, is capable of Pt(0) nanoparticle synthesis. Precise control over the particle morphology was not attained although the mechanism was further clarified and optimal conditions for nanoparticle synthesis were determined

Dynamics of macrophytes in the East Kleinemonde, a small temporarily open/closed South Afrcan Estuary

The East Kleinemonde Estuary is one of 175 temporarily open/closed estuaries (TOCEs) that represent 70 percent of estuaries in South Africa. TOCEs are small (mostly less than 100 ha), shallow estuaries (average depth 30 ppt) and high water level (> 1.6 m amsl) in the estuary. Water level increased by up to 0.33 m due to large volumetric changes and salinity was significantly higher in the 16 month closed euhaline phase after the breach (31 ± 0.9 ppt) compared to 21.9 ± 0.9 ppt in the closed polyhaline phase before the September 2008 breach. This increase in salinity significantly reduced the cover of the submerged macrophytes Ruppia cirrhosa and Chara vulgaris. They were replaced by macroalgae during this high salinity phase. The cover of supratidal salt marsh and reed habitats was also significantly reduced during the high water level phase, which in turn would lead to the potential for bank destabilisation and erosion. Based on the average elevation above sea level position of the macrophytes in the East Kleinemonde iv Estuary, a threshold water level was identified as 1.55 amsl. This was taken to be the height above sea level at which there was a maximum cover change for each macrophyte habitat. Above this water level emergent macrophyte habitat would mainly be inundated. This, together with 30 ppt salinity, was identified as the two thresholds for macrophyte change in the East Kleinemonde Estuary. From these thresholds and the 5 year dataset four biotic states were identified as State A: open and tidal, State B: closed with a water level below 1.55 m amsl and salinity between 18 to 30 ppt, State C: closed and water level above 1.55 m amsl and salinity between 18 to 30 ppt and State D: closed and water level above 1.55 m amsl and salinity above 30 ppt. Intertidal salt marsh, reeds and sedges were dominant during the open phase. Submerged macrophytes were dominant during the closed polyhaline state and macroalgae during the closed euhaline state. The high variability of abiotic factors common in TOCEs and the response of macrophyte habitat indicated that macrophytes were resilient to changing states provided they were of relatively short (< 3 months) duration. Macrophytes in the East Kleinemonde Estuary were found to have fast growth rates and large seed reserves in the sediment. The seed banks in the East Kleinemonde, as well as the adjacent temporarily open/closed West Kleinemonde Estuary were quantified for the first time in a South African estuary. The averaged data from both estuaries showed that Charophyte öospores represented almost 72 percent of the sexual propagules in the sediment with a mean öospore density of 31 306 ± 2 293 m-2. This was despite the Charophytes being sparsely located and only representing a maximum of 32.5 percent cover in the above ground vegetation. Historically there must have been stands of Charophytes in the East Kleinemonde Estuary, such that öospores could accumulate to such high density found in this study. The second highest seed density was for the intertidal salt marsh plant Sarcocornia tegetaria (18 percent) (7 929 ± 688 seed m-2), followed by the submerged angiosperm Ruppia cirrhosa (7 percent) (2 852 ± 327 seeds m-2). Although seed density did not differ significantly with sediment depth, seeds still occurred at 20 cm below the surface of the sediment providing a regeneration source in the event of sediment scouring during a flood event. Germination studies in the greenhouse showed that most seeds were viable and Sarcocornia tegetaria began to germinate after 3 days to a maximum of 82 percent after 91 days. Submerged species only germinated after 18 days with a low maximum germination of between 11 and 15 percent. This study has made an original contribution to the field of knowledge on macrophyte responses in a small TOCE as it showed that macrophyte habitats in the East Kleinemonde Estuary have a high natural variability in cover over time, they respond quickly after a disturbance event such as a mouth breach and there are large sediment seed reserves that remain viable from 2 to more than 5 years. This ensures habitat persistence even under unfavourable conditions, such as prolonged periods of mouth closure with high water level and flooding which causes loss of salt marsh species. Given this natural variability it is necessary to predict responses both spatially and temporally in order to manage and maintain ecological functioning in TOCEs. This study identified dominant macrophyte habitat for different abiotic states through the use of water level and salinity thresholds. In the determination of the freshwater requirements of any South African estuary freshwater inflow rates are provided for each estuary's past, present and possible future freshwater inflow scenarios. These flow data are generated by hydrological models and simulated monthly inflow volumes for a period of about 72 years are provided. For the East Kleinemonde freshwater requirement study for any year in that 70-odd year period, the number of high flow and low flow mouth breaches were predicted, as well as the closed state periods. The threshold water level of 1.55 m amsl was also used to filter past, present and future inflow monthly volumes to determine the frequency of the four abiotic states identified in this study. It was based on a water level/water volume equation calculation from a digital elevation model. Results showed that the total closed period in the present state was 83 percent, made up of 48 percent of the time in a polyhaline state (State C) and 35 percent in a euahaline state (State D). A second method was used to quantify available spatial habitat under different water level scenarios. A spatial model was written in Model Builder, an application in ArcGIS that allowed a series of processes to be built. A habitat map was overlaid with a bathymetric map and by selecting water level, available habitat areas were determined and empirical equations of water level versus available habitat were produced. These equations were then used to calculate the available habitat areas for monthly water level conditions from the freshwater requirement study for the past, present and two future inflow scenarios. Using both the threshold water level method and the spatial availability model method it was possible to assess the effect of the two future inflow scenarios on macrophyte habitat vi response. Scenario 1 had a 16 percent reduction in mean annual runoff (MAR) generating low flows for 88.6 percent of the time and a 3.5 percent reduction in flood events. In Scenario 2 there would be a 12 percent reduction in MAR with low flows occurring for 87.5 percent of the year, a 5.3 percent reduction in floods and an 11.5 percent reduction in the open mouth state. The model showed that Scenario 1 would have the highest submerged macrophyte area (12.56 ha versus 12.48 ha in Scenario 2), whereas Scenario 2 produced the largest mudflat and intertidal salt marsh area (7.11 ha versus 7.34 ha) due to lower water level in conjunction with the bathymetry of the estuary. A reduction in freshwater inflow to TOCEs either due to anthropogenic influences or natural precipitation cycles is one of the main threats to the optimum functioning of these estuaries. The results from this study and the two methods of assessing the effect of freshwater inflow scenarios on macrophytes in TOCEs can be integrated into the current freshwater inflow assessment methodology in South Africa, as well as adding to our understanding of the ecological functioning of these small, highly variable estuaries. The methods provide a quick assessment of macrophyte habitat associated with abiotic states under past, present and future inflow scenarios. All that is required to predict macrophyte habitat for different freshwater inflow scenarios (present, past and future) is a habitat map, a bathymetric map and the elevation range of macrophytes in the TOCE being assessed. This, together with the knowledge of response rates, provides invaluable information for the management of TOCEs to maintain their ecological functioning under altered freshwater inflow regimes

Growth and gonad size in cultured South African abalone, Haliotis midae

According to farm records, cultured Haliotis midae (50-70 g.abalone⁻¹) were growing 10% slower in winter when compared to summer. This reduction in growth rate also coincided with enlarged gonads. Initial trials showed that there were differences in mean monthly growth rates ranging from 1.97 – 5.14 g abalone⁻¹ month⁻¹, and gonad bulk index (GBI) also varied between months (GBI range: 26.88 ± 12.87 to 51.03 ± 34.47). The investment of energy into gonad tissue growth did not compromise whole body growth as the abalone continued to gain weight throughout the reproductive periods, probably due to gonadal growth. Growth of this size class of abalone was not influenced by water temperature or day length, suggesting favourable on-farm culture conditions (regression analyses, p > 0.05). There is no need to implement a seasonal dietary regime. Cultured H. midae were fed artificial diets with different protein sources, including only soya, only fishmeal, a combination of soya and fishmeal, and these were compared to kelp-fed abalone. Kelp-fed abalone grew slower than those fed artificial feeds (p>0.05). Gonad growth was the greatest when soya meal was included in the diet (average GBI: 74.91 ± 23.31), while the average gonad size of abalone fed the fishmealbased diet had gonads which were 38% smaller, and kelp-fed abalone had gonads which were 75% smaller than those of the abalone fed on diets containing soya meal. The increased gonad mass in abalone fed on diets including soya meal could be attributed to phytoestrogenic activity, as a result of the presence of isoflavones found in the soya plant; this remains to be tested. The use of soya in brood stock diet development is advised. The influence of dietary protein to energy ratio (1.41 – 2.46 g MJ⁻¹) on growth and gonad size was tested. Protein and energy levels within the ranges tested (22 and 33% protein; 13.5 and 15.6 MJ kg⁻¹) did not interact to influence growth rates of cultured H. midae. GBI increased from 50.67 ± 4.16 to 83.93 ± 9.35 units as a function of dietary protein to energy ratio (y = 42.02 x⁰·⁸¹; r² = 0.19; regression analysis: F₁¸₃₈ = 8.9; p = 0.005). In addition, protein level influenced gonad size, with gonad growth being greater in abalone fed the high protein diet (factorial ANOVA: F₁¸₃₂ = 7.1, p = 0.012). Canning yields were reduced by 7% when the protein content was increased, while increasing the quantity of dietary energy improved canning yields by ~ 6% (one-way ANOVA: F₁¸₂₈ = 14.4, p= 0.001). The present study provided evidence that although growth rates are varying seasonally, reproductive investment is not hindering weight gain. Gonad growth can be influenced if desired by farms, depending on the level of soya inclusion, as well as the protein to energy ratio in the diet. Monthly variation in growth and gonad size, as well as the influence of diet on gonad growth were highlighted, and the implications for farm application and further research were discussed

Systematics and biogeography of Mesobola brevianalis (Boulenger, 1908) (Teleostei: Cyprinidae)

The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for long-term survival and sustainability. Mesobola brevianalis Boulenger, 1908, commonly known as the river sardine, is found in many river systems in southern Africa. Because it exhibits widely separated populations showing subtle differences, particularly in colour, it is thought that there may be cryptic species involved. Standard phylogenetic techniques using three genetic markers (mitochondrial COI, nuclear protein RAG1 and nuclear ribosomal 28S rRNA), enabled the building of phylogenetic networks for M. brevianalis and some outgroup species. Consistent patterns of relationship were seen with 28S supporting monophyly. COI and RAG1 suggested that populations that are currently identified as M. brevianalis in fact represent several species. There was sufficiently strong support for the evolutionary independence of the M. brevianalis populations from the Rovuma, Kunene and Orange River Systems to consider them as independent species. The independence of the genus Mesobola was brought into question because Engraulicypris sardella and Rastrineobola argentea were placed within it phylogenetically.Morphometric methods in the form of multivariate truss network analyses, were performed to locate morphological markers for populations. There was little to no variation among most of the populations synonymized under M. brevianalis. Furthermore, neither latitude nor longitude had an effect on the morphological characters that might be linked to functional evolution. A molecular clock analysis of COI data was used to calibrate a paleobiogeographical model which entailed a divergence of lineages starting from an easterly reigning Paleo-Congo Basin, via a hypothetical Paleo-Kalahari Lake that was fragmented by a series of uplifts and drying events beginning ~65 million years ago. Complete evidence supported the synonymisation of the genera Engraulicypris and Mesobola, the resurrection of the species name gariepinus for the Orange River Systempopulation, and the description of two new species: E. ngalala from the Rovuma River System and E. howesi from the Kunene River System

Advancing ecosystem accounting in estuaries: Swartkops Estuary case study

Rapid degradation of ecosystems and loss of ecosystem services have sparked interest in developing approaches to report and integrate such change with socio-economic information systems, such as the System of National Accounts. Here we describe an approach and application of ecosystem accounting for individual estuaries, building on approaches previously applied at national and bay levels. Using the Swartkops Estuary as a case study, the focus is on physical accounts for ecosystem extent and condition, as well as accounts for two important ecosystem services (carbon sequestration and recreational use). Pressure accounts are also introduced to demonstrate the value of identifying key areas for management and restoration interventions in response to changes in extent and/or condition accounts. Greater resolution in these account reports, achieved through zoning, provides spatially explicit information on ecosystem assets and their services within an estuary to also inform management decision-making at local level. Further, these accounts can also inform local restoration prioritisation, in support of the UN Decade on Ecosystem Restoration (2021–2030), for example offsetting irreversibly degraded areas in one zone with restoration or maintenance of similar habitats in another. Significance: • This study is the first to apply the ecosystem accounting approach at the individual estuary level. • We provide spatially explicit information on ecosystem assets and their services in support of resource management. • Physical accounts include extent and condition, as well as ecosystem service and pressure accounts. • These accounts inform estuary management and restoration at the local governance level

New possibilities for research on reef fish across the continental shelf of South Africa

[From introduction] Subtidal research presents numerous challenges that restrict the ability to answer fundamental ecological questions related to reef systems. These challenges are closely associated with traditional monitoring methods and include depth restrictions (e.g. safe diving depths for underwater visual census), habitat destruction (e.g. trawling), mortality of target species (e.g. controlled angling and fish traps), and high operating costs (e.g. remotely operated vehicles and large research vessels. Whereas many of these challenges do not apply or are avoidable in the shallow subtidal environment, the difficulties grow as one attempts to sample deeper benthic habitats. This situation has resulted in a paucity of knowledge on the structure and ecology of deep water reef habitats around the coast of South Africa and in most marine areas around the world. Furthermore, the inability to effectively survey deep water benthic environments has limited the capacity of researchers to investigate connectivity between shallow and deep water habitats in a standardised and comparable fashio

Alphaviruses Detected in Mosquitoes in the North-Eastern Regions of South Africa, 2014 to 2018

The prevalence and distribution of African alphaviruses such as chikungunya have increased in recent years. Therefore, a better understanding of the local distribution of alphaviruses in vectors across the African continent is important. Here, entomological surveillance was performed from 2014 to 2018 at selected sites in north-eastern parts of South Africa where alphaviruses have been identified during outbreaks in humans and animals in the past. Mosquitoes were collected using a net, CDC-light, and BG-traps. An alphavirus genus-specific nested RT-PCR was used for screening, and positive pools were confirmed by sequencing and phylogenetic analysis. We collected 64,603 mosquitoes from 11 genera, of which 39,035 females were tested. Overall, 1462 mosquito pools were tested, of which 21 were positive for alphaviruses. Sindbis (61.9%, N = 13) and Middelburg (28.6%, N = 6) viruses were the most prevalent. Ndumu virus was detected in two pools (9.5%, N = 2). No chikungunya positive pools were identified. Arboviral activity was concentrated in peri-urban, rural, and conservation areas. A range of Culicidae species, including Culex univittatus, Cx. pipiens s.l., Aedes durbanensis, and the Ae. dentatus group, were identified as potential vectors. These findings confirm the active circulation and distribution of alphaviruses in regions where human or animal infections were identified in South Africa.publishersversionpublishe

New possibilities for research on reef fish across the continental shelf of South Africa

[From introduction] Subtidal research presents numerous challenges that restrict the ability to answer fundamental ecological questions related to reef systems. These challenges are closely associated with traditional monitoring methods and include depth restrictions (e.g. safe diving depths for underwater visual census), habitat destruction (e.g. trawling), mortality of target species (e.g. controlled angling and fish traps), and high operating costs (e.g. remotely operated vehicles and large research vessels. Whereas many of these challenges do not apply or are avoidable in the shallow subtidal environment, the difficulties grow as one attempts to sample deeper benthic habitats. This situation has resulted in a paucity of knowledge on the structure and ecology of deep water reef habitats around the coast of South Africa and in most marine areas around the world. Furthermore, the inability to effectively survey deep water benthic environments has limited the capacity of researchers to investigate connectivity between shallow and deep water habitats in a standardised and comparable fashion