Biological Sciences

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Identification of Macrourus species (Teleostei: Gadiformes) found near Prince Edward Islands in the Southern Ocean using molecular and morphological analyse.
(2021) Shadamorgan, Vineshree.; Miya, Tshoanelo Portia.
The genus Macrourus belongs to the family Macrouridae that consist mainly of deep-sea fish. Macrourus contains five species that have a polar distribution, with one species, M. berglax, found in the Atlantic Ocean, and the other four species, M. carinatus, M. holotrachys, M. whitsoni and M. caml, found in the Southern Ocean. The species found in the Southern Ocean are morphologically similar to each other and have overlapping distributional patterns, as a result there have been instances of misidentifications within this genus. Based on morphological characteristics, previous studies have grouped the Southern Ocean Macrourus species into two pairs, viz M. carinatus and M. holotrachys, and M. whitsoni and M. caml. Despite overlapping occurrence elsewhere, morphological studies conducted in the Prince Edward Islands (PEIs) located in the Southern Ocean, have identified only one Macrourus species, M. carinatus. Since there are known cases of species misidentification using morphological identification and distribution overlap within this genus, there is a need for a molecular study that will complement the morphological data. There are no published molecular studies that reviewed species identification in these islands. This study aimed to identify Macrourus specimens found near the PEIs using molecular and morphological analyses. This assessment was done by sequencing the cytochrome c oxidase subunit 1 gene, and by measuring and counting morphometric and meristic characters. The BLAST search which had a sequence similarity of 99 – 100%, showed that there are two species represented in this dataset which were identified as M. carinatus and M. holotrachys. This observation was supported by both the phylogenetic and haplotype network trees, which formed two distinct clades. On the other hand, the morphological data did not separate the two species, supporting previous studies that discovered high levels of morphological similarity between M. carinatus and M. holotrachys, which ultimately led to their grouping and/or misidentification. It can therefore be concluded that there are at least two Macrourus species inhabiting waters around PEIs, which are morphologically similar.
Metagenomics assessment of Anthropogenic impact on coral reef-associated microorganisms on the Kenyan Indian Ocean.
(2020) Wambua, Sammy Musee.; Macdonald, Angus Hector Harold.; De Villiers, Santie.
The Western Indian Ocean (WIO) is the world’s second richest marine biodiversity hotspot. It is characterized by a diverse range of ecologically and nutritionally rich marine ecosystems that are increasingly under pressure from the impacts of human population growth and coastal development. A comprehensive understanding of variations of marine microbial community composition with environmental conditions is key to understanding and predicting responses to human and climate pressures because microorganisms are the main drivers of biogeographical processes, and they respond and adapt fast to climatic patterns. Also, because unique environments harbour unique microorganisms with unique properties, genomic exploration of marine microorganisms may lead to discovery of novel metabolic processes, and bioactive products with potential for novel biotechnological applications. This project aimed to assess the effect of local anthropogenic impacts on the community structure and the functional potential of microorganisms inhabiting the WIO coral reefs along the Kenyan coast by metagenomics. Reasons for low application of genomics specifically in marine research in the WIO region were examined through literature review and in-depth interviews with scientists in the region. Coral reef seawater and sediment samples were collected, for microbial assessments, along gradients of human impacts and protection regimes. Environmental variables were estimated, and microbial taxonomic and functional diversity analysed by metagenomic approaches. Comparisons were done between sites with differential human impacts, and with oceanic metagenomes from Tara Oceans expedition. Compartmentalised training of marine scientists and lack of collaboration with molecular scientists are key reasons highlighted for poor uptake of genomics in marine research. Significant differences in taxonomic and functional composition were observed between the coral reef and Tara Oceans datasets. Coral reef metagenomes had more diverse and even microbial taxa and gene groups. Tara Oceans metagenomes were enriched with groups of genes of functions in keeping with oligotrophic conditions, and reefs metagenomes with genes for functions related to adaptations to heterogenous environments. E. coli density decreased with increasing degree of protection, but physicochemical and nutrient variables did not differ across coral reefs in the protected coral reefs. Variations in relative abundances of copiotrophic bacteria and coliphages were observed in coral reefs corresponding to magnitude of the neighbouring human impacts. Malindi and Mombasa marine parks, the coral reef sites experiencing degradative human impacts, were significantly enriched with genes for functions suggestive of mitigation of environment perturbations e.g. capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. This study establishes essential baselines for microbiome studies in the WIO region and provides insights to anthropogenic impact on microbial structure and functions, and potential indicators of health status coral reef ecosystems.
Population connectivity of stylophora pistillata and sinularia brassica between KwaZulu-Natal marine protected areas.
(2021) Gilmore, Jessica Rose.; Pearton, David James.; Macdonald, Angus Hector Harold.
Marine Protected Areas are a valuable tool for ecosystem protection and to enhance resilience in the face of global stressors such as global warming and ocean acidification. There is currently an incomplete understanding regarding the level to which MPAs in KwaZulu-Natal protect existing biodiversity and provide benefits beyond their boundaries. The focus of this study was to determine the extent to which the current MPA network acts to facilitate connectivity of sessile benthic species, the role of oceanographic processes, and whether these processes will persist under global change. The population connectivity of two coral species, a hard coral (Scleractinia), Stylophora pistillata, and a soft coral (Alcyonacea), Sinularia brassica, within and between the MPA network on the east coast of South Africa was studied using both traditional markers and RADSeq, a reduced representation genomic sequencing technique. Sampling locations were selected in three existing MPAs and on a representative reef located in the “gap” in between. These MPAs span the tropical Delagoa and subtropical Natal Bioregions. Stylophora pistillata in South Africa is split into two non-hybridizing clades with clear differences in distribution. Clade 2 was confined to the subtropical Delagoa bioregion whereas clade 3 was found throughout the study region from the tropical Delagoa bioregion down to the southern boundary of the warm temperate Natal bioregion. ITS data indicated that there is a complex population structure of the clade 2 potentially driven by a combination of currents, ecological selection, and distance. A subset of Stylophora clade 2 samples was analysed using a RADSeq approach which clarified the structure suggested by the ITS data and clearly identified three distinct populations across four reefs (Leadsman Shoal, Blood Reef, Aliwal Shoal and Aliwal Deep) spanning the Delagoa/Natal biogeographic break. These populations did not appear to be structured solely by geographic distance, with one population comprising samples from two sites (Blood Reef and Aliwal Deep) that were non-adjacent and at different depths (12-18 m vs >30 m), while a geographically adjacent population (Aliwal Shallow) at 12-18 m constituted a distinct population. This suggests that ecological selection might be involved in structuring the population over short distances for this coral. Sinularia brassica was not found south of the iSimangaliso Wetland Park in this study, despite it being recorded in the southern sites in previous surveys. Analyses of COI and mtMutS sequences revealed that there are potentially multiple clades present in the IWP population and that there is a poleward decrease in genetic diversity. Neither of these clades showed any clear geographical or genetic population structure between the reef complexes but additional studies using RADSeq may help to clarify the situation.

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