Browsing by Author "Rocke, Emma"

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    Benthic and pelagic responses to endobenthic bioturbator (Kraussillichirus kraussi) density, temperature and eutrophication in a global change mesocosm experiment
    (2025) Thomas, Cheryl; Pillay, Deena; Marco, Heather; Rocke, Emma
    Coastal ecosystems are increasingly being threatened by global change stressors such as eutrophication and warming, which can impair ecosystem functioning and ultimately affect societal well-being. Addressing this challenge, in part, requires identifying and understanding mechanisms that may enhance ecosystem resilience to global change. The axiid crustacean Kraussillichirus kraussi (sandprawn) plays a critical role as an endobenthic bioturbator in southern African estuaries and coastal ecosystems, with previous research highlighting its role in mediating bentho-pelagic coupling via top-down reductions in phytoplankton biomass, likely through phytoplankton adsorption onto burrow walls during bi-directional water- pumping. This novel finding has the potential to be an important resilience-enhancing mechanism against eutrophication in estuarine and coastal ecosystems locally. However, the robustness of this process, along with other benthic functions provided by sandprawns, is unclear given that they are nested within global change processes such as warming and eutrophication, which have the potential to alter fundamental benthic and pelagic processes mediated by sandprawns. In this context, this thesis addressed critical knowledge gaps in understanding the individual and combined impacts of warming, eutrophication and sandprawn density on ecosystem functions and community dynamics in both pelagic and benthic compartments, using an indoor mesocosm experiment. Results from Chapter 3 of the thesis revealed that sandprawn water filtration (reduction in phytoplankton biomass) remained robust under simulated warming to levels predicted by the year 2100, with elevated temperatures accelerating reductions in phytoplankton biomass. Sandprawn biofiltration also remained robust under eutrophic conditions, reducing phytoplankton biomass by approximately 74%. Importantly, under eutrophic conditions, sandprawn filtration prevented the development of extreme eutrophy, and prevented a switch to nanoplankton dominance, resulting in even contributions of pico- and nanophytoplankton. Findings thus highlight the potential for sandprawn water filtration to be an important natural process that can mitigate eutrophication symptoms under future global change conditions. The observed declines in the abundance of subsurface microphytobenthic algal biomass and abundance generally declined with warming, likely due to physiological intolerance of cool- temperate assemblages to elevated temperatures. Sandprawn induced reductions of cyanobacteria may likely enhance ecosystem resilience to coastal eutrophication by limiting harmful cyanobacterial blooms. However, warming-induced declines in microphytobenthic biomass may have important implications for sediment stability and trophic resource availability for benthic feeders under future global change scenarios. Findings from Chapter 5 highlighted the importance of temperature and sandprawn density rather than eutrophication in determining sandprawn bioturbation rates. Sediment boundary roughness (a proxy for bioturbation) increased by 43% at maximum sandprawn density under high temperatures (29.5℃), suggesting robustness of sandprawn physiology to future warming scenarios, particularly within populations inhabiting cool-temperate distribution ranges. Organic matter degradation rates increased under mesotrophic conditions and warming, particularly at high sandprawn densities, but was suppressed under eutrophic conditions, emphasising the importance of minimising nutrient loading to estuaries to prevent impairment of benthic carbon degradation. Lastly, Chapter 6 explored meiofaunal responses to predictor variables, and highlighted exceptionally complex and varied outcomes and the importance of contextual settings in determining responses to global change. Notably however, findings showed that higher sandprawn densities were associated with increased meiofaunal biomass dominance relative to abundance, even under high temperatures and eutrophic conditions (measured using W-statistics and ABC curves), suggesting that sandprawn bioturbation and associated benthic ecosystem engineering contributes to less perturbed states that facilitate meiobenthic assemblages. Overall, findings of this thesis demonstrate the potential for sandprawns to facilitate the development of less disturbed benthic ecosystems, resulting in meiobenthic attributes indicative of stable communities. Findings also indicate the ability of sandprawns to enhance ecosystem resilience by preventing phytoplankton and cyanobacterial blooms and shifts to nanophytoplankton dominance under eutrophic conditions, including under warming scenarios. These findings highlight the potential of sandprawns to be important nature-based processes that can combat global change challenges, while also emphasising the need to conserve and manage sandprawn populations so that they are included in resilience-based ecosystem management.
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    Investigation of the Interactions Between Sea Ice Algae from the Marginal Ice Zone of Antarctica and Artificial Sea Ice
    (2025) Van Niekerk, James; Rampai, Tokoloho; Rocke, Emma
    Sea ice is multi-phase system that plays a major role in the Earth's climate system. Sea ice algae act as primary producers of organic carbon, forming the building blocks
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    Population genetics of the endemic red-chested sea cucumber, Hemiocnus insolens, along the southern coastline of Africa
    (2023) Ho, Yi-Ting; Rocke, Emma; Karenyi Natasha
    Hemiocnus insolens is the endemic red-chested sea cucumber (or holothuroid) of South Africa, found along the coastline spanning from Port Elizabeth, South Africa to Lüderitz, Namibia. They present as three colour variations (red, yellow, and white) prompting the existence of possible cryptic species. The aim of the study is to sequence the genomic markers of each colour variation using Sanger sequencing and metagenomic sequencing to analyse their phylogenetic and associated community structure to delimit whether the colour variations of H. insolens are a single species or a possible species complex. DNA was extracted from tissue of whole preserved (99% ethanol AR) samples and were sequenced for 16S rRNA and COI gene regions (Sanger sequencing) as well as their metagenomes (Oxford Nanopore Technologies). ChromasPro and seaview.exe were used for sequence analysis and tree building, respectively. MGnify and Flye were used for assessing the metagenomics of selected samples. Parsimony-based tree fitting was generated for 16S rRNA and COI which suggested that some differentiation between white samples, and red and yellow samples (BP = 100) (Figure 2.1, Figure 2.2). According to population genetics and phylogeography, these species can be considered as cryptic species due to their phylogeographic breaks bolstering the separation of certain colour variations. Metagenome-assembled genomes (MAGs) were used to further explore the community structure of each sample/colour variation and were holistically compared to the parsimony-based phylogenetic trees to support these differences and provide explanations. Results suggested some differences in gene expression and microbiome diversity between the colour variations; however, these results were preliminary as a result of small sample size and low throughput in sequencing. Metagenome studies provided some insight into creating a conceptual model of how the environment could affect the colour expression of H. insolens.
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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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    Spatial and temporal distribution of a marine microbial parasite, Syndiniales MALV I and II, within St Helena Bay
    (2025) Fourie, Shani; Rocke, Emma
    MALV I and II are globally distributed marine microbial parasites that infect and kill a wide range of phytoplankton hosts. These organisms play an important role in bloom dynamics, are suspected to terminate algal blooms, and contribute significantly to carbon fluxes, an important process required to lock away greenhouse gases. The study aims to investigate the spatial and temporal distribution of MALV I and II and their hosts in the Benguela upwelling system, one of the four major Eastern Boundary Upwelling Systems (EBUS). A Fluorescent In Situ Hybridization (FISH) technique was used to identify and quantify MALV I and II in samples taken at 0m and 10m respectively over the course of 10 consecutive days during an upwelling event in December of 2016, and in samples taken at 1m and 25m respectively over the course of 5 consecutive days during a stratified period in April 2019 within St Helena Bay. Microscopy observations revealed a distinct difference in their infection dynamics between an active upwelling season (austral spring and summer) and a stratified period (austral autumn and winter), with distinctly different phytoplankton communities present in the water column between these two seasons. Whilst temperature and silicate were significant factors correlating with the infection rates at the surface during an upwelling period, biological factors (presence of MALV I and II hosts) appeared to be the most important contributor. Furthermore, 18S rRNA data confirmed that MALV I and II dominated the water column, with group I exhibiting the highest relative abundance, contradicting microscopy observations which showed no significant difference in infection rates between MALV I and II. This shed light on the realities of amplicon data, especially with high gene copy numbers present in MALV rRNA. This study applies a holistic approach to understanding the infection dynamics of MALV I and II and in doing so revealed a transition from diatom hosts during an active upwelling period to dinoflagellate hosts during a stratified period in the same region. Ultimately, the MALV I and II populations are dependent upon available hosts to infect, and the infection rates are driven by multiple environmental and biotic factors.
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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