College of Agriculture, Engineering and Science

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Decadal changes in land-use, water quality and fish assemblages in a KwaZulu-Natal urban and non-urban estuary.
(2021) Van Schoor, Nikita.; Weerts, Steven.; Mackay, Christine Fiona.
Globally, estuaries are recognised as highly dynamic environments which support diverse and productive flora and fauna, and provide numerous goods and services for human wellbeing. These systems are under threat from growing coastal populations that demand the transformation of natural land to accommodate urbanisation, agriculture, harbour, and infrastructure developments. Direct and indirect land-use/land-cover (LULC) changes adversely affect estuarine water quality, directly impacting estuarine biota such as fishes. While the short links between these components are known, few studies have attempted to integrate these links, particularly within the South African context. Therefore, this study aimed to integrate different levels of assessment (LULC and estuarine water quality) to describe changes in estuarine fish ecology over space and time. The study compared two permanently open estuaries in KwaZulu-Natal with distinct land-cover types, namely the uMgeni and uMlalazi estuaries. The uMgeni Estuary is surrounded by urban features and is situated in a highly developed catchment, whereas the uMlalazi is near-natural, with some surrounding agricultural areas. Historical land-cover imagery from the estuary to the 20 m topographical contour (inclusive of the Estuary Functional Zone), the estuary catchment land-cover, water quality and ichthyofauna data were collected. Land-cover types were grouped into eight categories and 42 feature classes based on modifications to the South African National Land Cover system, the United States Geological Survey and the Coastal Change Analysis Program. Multivariate statistical analysis identified two distinct groupings of land-cover types, Period 1 (before 1989) and Period 2 (during and after 1989). This period factor was then further used throughout the study to determine associated (temporal) responses in water quality and fish assemblages. Strong negative correlations were observed between dissolved oxygen and artificial land-cover types in the uMgeni Estuary. The results suggested that the uMgeni Estuary receives nutrient inputs from various urban activities, which reduce oxygen levels within the water column. Alterations to the hierarchical ichthyofauna structure in the uMgeni occurred on a year to year basis, relative to these anthropogenic impacts. In contrast, good water quality likely associated with fewer developments within the Estuarine Functional Zone has allowed the hierarchical fish structure in the uMlalazi Estuary to remain the same over time, although minor species level differences have occurred. The current state of each estuary was then investigated by measuring water quality parameters and sampling fish communities along the respective estuary gradients as determined by salinity penetration. Ichthyofauna and water quality data (salinity, turbidity, pH, dissolved oxygen) were collected within the lower, middle, upper and riverine reaches of each estuary. Each fish species sampled was assigned a functional guild depending on their use of the estuary and their feeding methods. The highly urbanised uMgeni Estuary was found to have an exceptionally degraded water quality in the upper reaches (average dissolved oxygen 3.78 mg l⁻¹). It supported a relatively low number of fish species (30) at a total catch per unit effort of 1488.7. In comparison, the less urbanised uMlalazi Estuary displayed much healthier water quality (average dissolved oxygen 6.94 mg l⁻¹), double the number of fish species (60) and higher total fish abundance (catch per unit effort of 2283.67). Salinity was primarily responsible for the longitudinal gradients in fish assemblage, reflecting the role of tidal influence in permanently open estuaries. Differences in fish communities between estuaries, however, were strongly influenced by oxygen levels within the water column. The uMgeni was primarily a detritus-based system that mostly supports small estuarine species (Ambassidae), detritivores (Mugilidae), and freshwater opportunists (Cichlidae). The uMlalazi Estuary is also a detritus based system, however, the diversity and fish assemblage suggests a more complex food web system across various feeding guilds, including piscivores, and is utilised extensively by marine and estuarine species. The results of this study highlighted the usefulness of incorporating guild and taxonomic distinctness tests in ecological studies. Additionally, they suggest that for the systems studied here, impacts of urban and land-use adjacent to estuaries are more detrimental to estuarine function than forestry or sugarcane cultivation. The results lend support to estuarine management and coastal development goals that aim to limit development in and around estuaries.
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.
Macrofauna diversity of unique, fluvially-dependent soft-sediment habitats in the Uthukela Marine Protected Area, South Africa.
(2021) Badenhorst, Stacey.; Mackay, Christine Fiona.
The uThukela shelf is a large section of the KwaZulu-Natal (KZN) Bight, and being situated adjacent to the largest river on South Africa’s east coast and the fluvially-dominated uThukela Estuary, is an excellent example of a fluvially-dependent coastal ecosystem. Previous studies found that this shelf contains structurally and functionally unique macroinvertebrate communities that contributed to the promulgation of the uThukela Marine Protected Area (MPA), as part of the South African MPA network of 20 new or extended systems. This study expands on this evidence using recent samples collected prior to the protection of the uThukela shelf to provide a good baseline database for future monitoring within the MPA. The uThukela macrofauna distributions and the environmental parameters correlated with these patterns were investigated through replicated sediment grabs that were collected with corresponding abiotic parameters, along coast-perpendicular transects. Macrofauna were subsequently classified taxonomically and their functional attributes determined. One replicate collected on the innershelf was particularly noteworthy as the taxa composition was unique and unexpected for a mud depocenter as it was indicative of hard substrata, suggesting a nearby low-lying reef. This habitat anomaly should be further investigated as it may play an important role in biodiversity and ecosystem functioning within the uThukela benthic system that mostly consists of soft sediments. Overall, the uThukela shelf soft-sediment community represented a wide variety of taxa but in low abundance, and was dominated by burrowing polychaetes. These ubiquitous polychaetes exhibited diverse biological traits, and a finding of this study was that this group alone is a potential surrogate for future studies and monitoring of the entire uThukela shelf macroinvertebrate community. This community consisted of mostly facultative deposit feeders that shift to suspension-feeding and rely significantly on terrestrial particulate organic matter (POM) and mud deposited onto the shelf by the fluvially-dominated uThukela Estuary. The adaptive behaviour of these taxa allows intermittent shifts in food acquisition when conditions do not favour this optimal deposition (such as during reduced fluvial outflow), thereby enhancing ecosystem resilience to natural environmental fluxes. Natural fluctuations in the uThukela River flow results in reduced freshwater penetration onto the shelf during the dry (winter) season, and was observed during this study by the higher-than-expected salinity measurements further inshore and the resultant atypical salinity gradient across the uThukela shelf. Salinity, along with dissolved oxygen, were the measured near-bottom water parameters most correlated with macrobenthic distribution. Sediment composition also affected distribution patterns, forming fine-grained and medium-coarse-grained assemblages on the v inner and mid-shelf, and a muddy assemblage on the outer-shelf. The muddy outer-shelf is mostly old deposits that suggests the uThukela has functioned as a fluvially-dominated system for a long time. Overall, sediments contained a large amount of crushed-shell and high Foraminifera abundances, contributing to habitat complexity and increasing diversity. Maintaining macrofauna diversity by preserving benthic habitats is vital in the functional success of marine ecosystems; particularly so in the uThukela system that is classified as strongly benthic-driven. This study provides baseline information contributing to future monitoring of whether the uThukela MPA achieves the aim of protecting rare benthic habitats associated with the connection of the coast to the deep sea and whether macrofauna diversity and associated ecological processes are maintained. In addition, it will support future studies within the MPA that emphasise the importance of the critical role of freshwater to the marine system and that ensure areas important for life-history strategies of vertebrates and invertebrates with high conservation status are conserved.
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.
Molecular phylogenetic structure between geographically distant marine fish Macrourus holotrachys and M. berglax.
(2021) Zuma, Nkululeko.; Miya, Tshoanelo Portia.
The taxonomic status of Macrourus species has been in disarray due to their morphological similarities and overlapping distribution. Given the number of research that have been conducted in an attempt to resolve the taxonomic confusion in this group, there are still some species with unconfirmed taxonomy. Macrourus holotrachys found in the Southern Ocean and M. berglax from the North Atlantic Ocean, are among the species that need taxonomic review. These species differ morphologically, and the minor differences have been used as a basis to separate them into different species. DNA molecular studies that have reviewed the taxonomy of these species using the cytochrome c oxidase subunit I (COI) gene found low sequence divergence between M. holotrachys and M. berglax. The findings of these studies provide motivation for population genetic studies to compare genetic structure between these distantly distributed species. The present study aimed to close this gap by assessing the genetic structure between M. holotrachys and M. berglax using the COI and displacement loop (D-loop) gene regions. Aligned sequences of these genes were 532 base pairs (bp) and 703 bp long, respectively. The COI gene revealed seven haplotypes from 26 sequences, while D-loop region had eight haplotypes from 55 sequences. The mismatch distribution curves were unimodal and the haplotype network trees had a star shape pattern for both datasets, which is consistent with populations undergoing demographic expansion. Although neutrality test values were not significant, negative values were observed for Tajima’s D, supporting the populations undergoing demographic expansion. The FST pairwise distance method revealed no substantial differentiation between the populations of M. holotrachys and M. berglax. These results suggest that a recent dispersal of populations may have occurred such that there was not enough time for the separated populations to develop different genetic traits. In conclusion, this study demonstrated no significant genetic differentiation between M. holotrachys and M. berglax and confirms that they are one species consisting of North and South Pole populations, respectively. Additionally, this study has added more literature on the population genetic structure of these species.
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.
Population connectivity of Stylophorum pistillata and sinularia brassica between KwaZulu-Natal marine protected areas.
(2021) Gilmore, Jessica Rose.; 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.
Zooplankton dynamics during a regime shift in the St Lucia Estuary, South Africa.
(2021) Govender, Merusha.; Carrasco, Nicola Kim.
The St Lucia Estuary is the largest estuarine lake in Africa and forms part of the iSimangaliso World Heritage Site however historical anthropogenic changes, including the separation of the Mfolozi River from the St Lucia system, have exacerbated periodic drought conditions. A Global Environment Facilitated (GEF) funded project was carried out (June 2016 to July 2017) to relink the Mfolozi River and St Lucia Estuary to allow unimpeded flow of freshwater into the St Lucia Estuary that would alleviate drought conditions and ideally restore natural mouth functioning. This reconnection, combined with increased precipitation from 2017 onwards, initiated a transition to a new wet phase in the estuary. Zooplankton form an essential link between primary producers and higher trophic levels, and they are important indicators of change in aquatic ecosystems. This study aimed to firstly record the changes in the zooplankton community before, during and after the restoration project in the mouth region from February 2015 to November 2018. The zooplankton community structure at the mouth differed significantly before and after the restoration project. Estuarine resident taxa including the mysid Mesopodopsis africana, the copepods Acartiella natalensis and Oithona brevicornis were absent post project completion as mainly freshwater taxa dominated. Both total suspended solids and salinity were identified as major determinants of the zooplankton community structure at the mouth region. Secondly, the study aimed to investigate the system-wide impacts by monitoring the zooplankton community at 5 representative sites within the system as it transitioned from a hypersaline state to a freshwater state from February 2015 to November 2017. Following the reconnection, water levels increased, and salinity levels decreased throughout the lake system, however the reversed salinity gradient persisted with a mean salinity of 23 recorded in the upper reaches of the lake system in 2017. There was a clear shift in the zooplankton community to freshwater taxa such as cyclopoids, rotifers and cladocerans. Resident taxa declined in abundance, as Oithona brevicornis and Acartiella natalensis were virtually absent in 2017, possibly due to low salinity, or increased competition from freshwater taxa. The calanoid copepod Pseudodiaptomus stuhlamnni was still present throughout the lake system (in lower abundance) and the mysid Mesopodopsis africana was restricted to the upper reaches which served as refuge from the low salinity areas. While the increased freshwater input is positive, it has not yet been substantial enough to initiate a mouth breaching event that would flush the system of the excessive silt build-up. Furthermore, continuation of this already extended wet phase could force the exclusion of the estuarine resident zooplankton.

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