Browsing by Author "Rocke, Emma"

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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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    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