Browsing by Author "Pfaff, Maya"

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    Marine algal virus communities along Southern African coasts
    (2015) Morrissey, Kathryn Lee; Rybicki, Edward P; Pfaff, Maya; Schroeder, Declan
    Southern Africa is home to highly diverse marine environments along its coasts. The main reason for the contrasting environments is the two major boundary currents, the Benguela and Agulhas currents, and their interaction around the tip of South Africa. Algal blooms are known to proliferate predominantly off the nutrient - rich west coast, however, sporadic inshore upwelling on the east coast can also illicit these events. In addition, solar salt - pans located on the coast that draw their water from the bay area are affected by bloom events. Algal viruses play a key role in regulating phytoplankton communities and modulate the dynamics of these bloom events. Identifying the viruses associated with algal blooms is the first step in determining the role they play in the bloom dynamics. Here I chose to focus on phycodnaviruses, known agents of bloom termination. Samples were taken from two specific algal blooms that occurred in 2013 in different bioregions namely Elands Bay (west coast) and Algoa Bay (east coast). Additionally the Cerebos solar salt pans located along the west coast were selected as sample sites to investigate viral composition. DNA polymerase (pol) gene fragments were amplified from environmental samples using algal - virus specific PCR primers AVS1 and POL. Amplified fragments were then sequenced. Viral sequences were identified and mapped to existing virus families. Amplicon specific primers were designed for select dominant virus group identified for both bloom events. These were used to screen across all samples to determine viral prevalence. Phylogenetic analysis of viral sequences revealed new clades of Phycodnaviridae in the Elands Bay and Algoa Bay regions. A bloom terminating virus, EB1, is proposed for the Elands Bay bloom event. The Cerebos salt pans showed the greatest diversity of all samples analysed and novel halophilic algal viruses were identified in regions with the highest salinity.
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    Short-term dynamics of nano- and picoplankton in the southern Benguela upwelling system
    (2022) Dames, Nicole Rebecca; Moloney, Coleen L; Rocke, Emma; Rybicki, Edward; Pfaff, Maya
    Wind driven coastal upwelling influences the overall physical and chemical properties of coastal regions, as well as the small phytoplankton and microbial communities responsible for the productivity and biogeochemistry governing many of these properties. These environmental changes can influence picoplankton (0.3–3 µm) and nano-picoplankton (0.3–10 µm) at different time scales; in this thesis daily changes were of interest because of the cyclic (3–7 days) nature of wind-driven upwelling. Daily variability of picoplankton was studied during an upwelling cycle at a single station in Elands Bay. Using amplicon sequencing of the 16S and 18S rRNA gene region, as well as additional supplementary environmental data, it was found that picoplankton diversity, community structure and primary metabolism varied between the active and relaxation periods of an upwelling cycle. The results highlighted the complexity of picoplankton dynamics in variable environmental settings. However, the question then became whether nano-picoplankton dynamics were as complex in a post-upwelling setting. This was assessed in autumn (post-upwelling period) in St. Helena Bay by measuring primary productivity and nitrogen cycling over five days from three depths at a single station. Using stable isotope tracer and flow cytometry analyses it was determined that primary productivity was supported by regenerated production and that nano-picoplankton were responsible for up to 90% of the net primary production, with nanoeukaryotes and heterotrophic bacteria dominating at the surface and at depth. Increased resolution of nano-picoplankton community composition, structure and potential metabolism was obtained using metagenomic analyses of samples taken at the same depths and days as the productivity study. A strong depth-differentiation in community structure and potential metabolism was found over the five-day period, with little variability observed from day to day. Metagenome abundances of transporter genes for processes like ammonium uptake and nitrite oxidation were found to be good indicators of measured process rates using isotope tracers. This research has highlighted the complex structure of picoplankton and nano-picoplankton communities in a coastal setting, and has shown how diversity, function and biotic interactions are strongly influenced by the properties of the surrounding water column.
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    The ecology of picophytoplankton in a coastal upwelling ecosystem
    (2021) Gebe, Zimkhita; Moloney, Coleen; Pfaff, Maya; Rocke, Emma
    The dynamic Benguela Upwelling System is one of four major upwelling regions in the world and is subdivided into two sub-systems, the northern and southern Benguela. This current study was conducted within the southern Benguela, which lies between 27°S and 35°S (Orange River Mouth to East London) and is characterized on the west coast by seasonal, wind-driven, coastal upwelling. The study targeted three picophytoplankton groups, Synechococcus, Prochlorococcus and picoeukaryotes, which are the three most abundant < 2 µm size class phytoplankton. Flow cytometry was employed to enumerate picophytoplankton abundances, using their pigments and cell sizes to identify the different groups. The aim of the study was to investigate the role of picophytoplankton in the southern Benguela coastal upwelling ecosystem. These aims were met by: i) determining the spatiotemporal variability of each of the three picophytoplankton groups over a period of 8 sampling cruises at 44 stations across four latitudinal lines in the study region, ii) determining short-term changes in carbon and nitrogen biomass of picophytoplankton and their growth rates over a 10-day period, using abundance estimates from a station off St. Helena Bay, and iii) estimating mortality of microbial communities in a laboratory study using samples collected from a coastal upwelling environment. Results showed no strong seasonality in picophytoplankton abundances but evidence of latitudinal and zonal effects. Investigations over the short term showed that populations of picophytoplankton in the southern Benguela change on the same timescale of ~3 days as the larger phytoplankton during an upwelling event. Determining mortality rates using a dilution experiment presented some challenges. Instead of increased growth rates, the study showed decreased growth rates as predator numbers decreased. These shortcomings were investigated in a second experiment, which both excluded large predators (<200µm) and also ran a parallel experiment excluding smaller predators (10-200 µm). The last of these experiments resulted in increased growth rates as predator numbers decreased. The complexity of the southern Benguela system, with its pulsed, high productivity and large concentrations of nutrients, traditionally is known to show variability through effects on the biology of large phytoplankton. However, picophytoplankton also were variable in the study area, resulting from bottom up effects of the environment, confounded by biotic factors such as predation, parasitism and competition
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    The effectiveness of Table Mountain National Park Marine Protected Area in the conservation of rocky shore biodiversity
    (2021) Baliwe, Ndiviwe Gabriel; Branch, George M; Pfaff, Maya
    Establishment of marine protected areas (MPAs) has intensified in recent years, and there are now over 6800 MPAs worldwide. However, there is a prominent need to assess their effectiveness in terms of protecting biodiversity. In Chapter 1, I provide the theoretical background to this dissertation and define its central goal, i.e., to assess the effectiveness of no-take (‘restricted') sections of the Table Mountain National Park MPA (TMNP MPA), relative to zones that are designated as ‘controlled', where harvesting can take place under national regulations. Chapter 2 compares the effectiveness of no-take versus harvested areas in the TMNP MPA in protecting the biodiversity of intertidal rocky shores. Surveys were conducted to compare (1) the densities and sizes of exploited species and rarely harvested species, and (2) community composition, between these two levels of protection. Some clear patterns emerged. Firstly, notake areas had significantly greater densities of the commonly harvested limpets Cymbula granatina, C. oculus and Scutellastra argenvillei, most obviously on sandstone ledges where abundances were greatest. In contrast, densities of the rarely harvested limpets, S. cochlear, S. longicosta and S. granularis did not differ in a manner reflecting protection levels. Secondly, C. granatina and S. argenvillei were significantly larger in no-take areas, although C. oculus displayed the opposite pattern. None of the rarely harvested limpets showed differences in sizes between protection levels. Thirdly, community composition differed significantly between protection levels. No-take areas were characterised by a greater abundance of commonly harvested limpets and mussels, while harvested areas were dominated by ephemeral and corticated algae, due to their release from grazing pressure by limpets. Chapter 3 focuses on a subset of the sites, all lying on the west coast and all comprising sandstone rocks. First, in a temporal comparison, I evaluated changes in densities and sizes of limpets and in community composition between historical data from 1970 and my sampling in 2017, at two sites where harvesting has intensified since 1970. This analysis showed three kinds of changes: (1) the appearance of alien species; (2) the effects of increased harvesting; and (3) the direct and indirect effects of these changes on other species. Secondly, to disentangle the effects of harvesting from those of alien invasions, I made spatial comparisons using my 2017 data, between two harvested sites and two sites in a no-take zone. One striking result was transformation of mid-shore zones by the appearance of the invasive Mediterranean mussel Mytilus galloprovincialis, and the indirect effects of this on the demography of the granular limpet Scutellastra granularis. Adults of this limpet have been excluded by the mussel, whereas juveniles find a secondary home on the shells of the mussel. In addition, harvesting has decimated the granite limpet Cymbula granatina and Argenville's limpet Scutellastra argenvillei. This has led to the proliferation of opportunistic seaweeds, such as Ulva spp., or corticated algae, notably Pachymenia orbitosa. The dual effects of alien invasive species and over-harvesting thus have major ecosystem effects. In chapter 4, densities of the limpet Cymbula granatina were manipulated at two sites within a fully-protected no-take area to generate four density levels ranging from zero to maximum natural densities, to evaluate the effects of harvesting this limpet on the community composition. Following removal or substantial thinning of C. granatina, community composition changed, cover of corticated and ephemeral algae increased and recruitment of C. granatina decreased. These outcomes were, however, dependent on the time frame considered, as algae underwent an annual cycle, and the effects of limpet removal were evident only during cooler months when the algae proliferated. All these effects have management implications. Chapter 5 provides an overview of the findings from this dissertation and their management implications. The major limitation of the dissertation is that interpretation of results was clouded by an absence of reliable data on actual harvesting rates as reflected in the numbers and activities of people operating in the restricted and controlled portions of the MPA, and of the efficiency with which law enforcement takes place. Nevertheless, strong evidence emerged that no-take areas within the MPA are effective means of conserving biodiversity, and the effects of harvesting deduced in Chapter 2 and 3 were verified by the experiment undertaken in Chapter 4, in which depletion of a dominant and commonly harvested limpet, Cymbula granatina, did yield algal proliferations like those evident in harvested portions of the park. The fact that this outcome was observed only at certain times of the year points to the need for studies and monitoring to be undertaken over sufficient time scales to produce meaningful results.
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    The effects of microplastic and natural particles on the invasive mussel Mytilus galloprovincialis (Lamarck, 1819) and the native Choromytilus meridionalis
    (2021) Germishuizen, Matthew; Griffiths, Charles; Pfaff, Maya; Lenz, Mark
    Mussels living in coastal environments are often exposed to natural inorganic particles and hence may be well adapted to dealing with high sediment loads. The mechanisms by which they deal with particle loads do, however, cause stress and alter metabolic processes. An increasingly common anthropogenic addition to particle loads in the ocean are microplastic particles. Numerous recent experiments have addressed the impacts of microplastics on metabolic performance, but few of these have used natural reference particles to control for the concurrent effects of particle load itself. This study aims to compare the effects of microplastic and of natural particle exposure on the mussel Mytilus galloprovincialis, an invasive species which has become the dominant mussel in the mid- to low-shore of the south and west coasts of South Africa, but is absent from areas prone to sand inundation. These effects will be compared to those on the native mussel Choromytilus meridionalis, which resides on the low shore, and unlike M. galloprovincialis often occurs in areas prone to sand inundation. Respiration rates, byssus production, clearance rate, body condition (BCI) and survival of mussels exposed to four concentrations of two particle types, polyvinyl chloride (PVC) and red clay were measured. A significant concentration effect was found in the respiration rates of Mytilus galloprovincialis, while C. meridionalis respiration rates were largely unaffected by both particle type and particle concentration. The byssus numbers of M. galloprovincialis were significantly reduced by microplastic exposure, whilst no particle type effects were found in C. meridionalis. Clearance rates of C. meridionalis, on the other hand, were significantly affected by particle concentration, while no effects were found on M. galloprovincialis. The BCI of C. meridionalis was also found to be affected by particle concentrations, while M. galloprovincialis was unaffected. All C. meridionalisindividualssurvived the experiment, while 29 M. galloprovincialis died. Mortality of M. galloprovincialis exposed to the two particle types was not significantly different, although more mortality was suffered in PVC treatments than in red clay treatments. The results reveal that there was indeed a difference in the response of M. galloprovincialis to the different particle types, and that the two species did exhibit different strategies to both particle type, and concentration. Experimental studies of this nature are imperative in order to disentangle microplastic effects from those of particles in general, and to develop a better understanding of potential impacts of plastic debris on marine ecosystems.