Doctoral Degrees (Botany and Zoology)

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    Linking physiological, genomic, and ecological functioning in the seagrass, Zostera capensis
    (Stellenbosch : Stellenbosch University, 2024-03) Mokumo, Mosihla Frederick; Von der Heyden, Sophie ; Midgley, Guy F. ; Adams, Janine Barbara; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
    ENGLISH ABSTRACT: In South Africa, the most abundant seagrass, Zostera capensis, occurs in predominantly open and sheltered estuaries and carpets intertidal and subtidal zones. Zostera capensis exhibit a wide yet discontinuous distributional range, limited to estuaries in the cool-temperate biogeographic region along the west coast as well as estuaries in the warm-temperate south coast and the sub-tropical east coast of South Africa. Due to its continued population decline, small area of occupancy and its extirpation status in Durban Bay and St Lucia, Z. capensis is now categorised as Endangered. In South Africa, Z. capensis serves as nursery and foraging grounds for organisms of high conservation importance such as the seahorse Hippocampus capensis, pipefish Syngnathus watermeyeri and klipfish Clinus spatulatus, among others. With over 90 years of research, however, Z. capensis remains poorly protected and severely fragmented, with continued exposure to anthropogenically induced pressures, where eutrophication (leading to agal bloom) and effects of heavy exploitation for bait considered the main pressures in systems such as the Knysna Estuarine Bay. Currently, less is known regarding intertidal and subtidal differences and their responses to global climate change. South Africa is also trailing behind in terms of restoration and rehabilitation trials. Considering these scientific gaps and the continued decline in Z. capensis, this PhD took a broad experimental approach to investigate aspects around morpho-physiological variations between intertidal and subtidal plants, their photophysiological and genotypic responses to thermal stress, as well as investigating transplantation as a mechanism for seagrass conservation. To understand the morpho-physiological responses of plants to their local environmental conditions, an in situ study was conducted in a permanently open estuary (Knysna Estuarine Bay) and a temporarily closed estuary (TCE), Klein Brak Estuary. Generally, seagrasses with ecotypes spanning across bathymetric cline exhibit intertidal ecotypes (exposed twice daily), which are exposed to fluctuating irradiance and temperature regime, and subtidal ecotypes (always submerged) which experience relatively narrower temperature changes but affected by light attenuation, especially in eutrophic systems. Therefore, both ecotypes or plants show morphological and photophysiological differences, with intertidal ecotypes expected to show narrower and shorter leaf width and length (to decrease leaf surface area for light absorption), decreased photophysiological responses (Fv/Fm) but increased shoot and leaf density and the subsequent seagrass %cover (to induce self-shading). These response mechanisms are important for seagrass meadows exposed to high temperatures and light irradiance. For subtidal ecotypes in light attenuated areas, meadows usually show increased leaf length and width as a mechanism to capture light needed for photochemistry. In addition, ecotypes show decreased leaf and shoot density to reduce competition for light, this also affect their %cover which is then decreased in these ecotypes. Seagrass responses occur at leaf-scale (Fv/Fm, and all photosynthesis-related changes), shoot-scale (leaf length and width) and meadow-scale (shoot and leaf density and %cover). To investigate these differences in Knysna, leaf-, shoot-, and meadow-scale responses were determined in each tidal zone at the upper, middle, and lower reaches. Results showed that seagrass responses are localised due to topographical attributes of the estuary and that leaf-scale responses, which are modulated in seconds, were not significantly different at upper estuary, with Fv/Fm values in intertidal ecotypes decreased due to higher light intensities measured at the time of sampling. Results also showed that both intertidal and subtidal plants at the middle estuary suffered mechanical damage, with intertidal plants at the lower estuary showing significantly lower %cover due to anthropogenic effects and sandy and mobile sediment. In Klein Brak Estuary, the same methods were used, however, the estuary was experiencing a drought event and closed estuary moth, therefore, there was no tidal influences. However, exposed plants showed higher Fv/Fm than submerged plants. Nonetheless, shoot- and meadow-scale responses were consistent with other studies. However, the seagrass in this estuary is highly variable due to drought and flooding events associated with South African estuaries, especially TCEs. Collectively, these results formed the basis and highlighted the need for spatiotemporal and seasonal monitoring of Z. capensis to identify meadows that are more permanent and can be used as donor sites for restoration trials. This PhD also investigated the use of different planting patterns (straight-line, compact, and star) and core sizes (11, 18, and 25 cm Ø) in transplanting intertidal and subtidal plants in the Knysna and Klein Brak estuaries in South Africa. Planting patterns, ecotypes and size did not influence persistence; however, smaller cores should be used as these have less impact on donor meadows. Although transplants did not persist for more than three months in both estuaries, our study demonstrated that seagrass restoration in South Africa is challenging due to limited suitable habitats (in Knysna) and strong environmental variability (in Klein Brak) in estuarine ecosystems. Results also showed that restoration trials be prioritised in predominantly open estuaries and that monitoring of donor sites is an important aspect to consider in restoration studies. This PhD also investigated the transcriptomic and photophysiological (Fv/Fm) responses of intertidal and subtidal plants to a simulated acute MHW (36 °C), with results showing that plants respond in a similar manner as no differentially expressed genes (DEGs) were detected, though Fv/Fm showed significant differences between plants during the MHW. However, DEGs were observed during the MHW and after the seven-days long recovery phase. Generally, Z. capensis show a downregulation of DEGs than upregulation following a heat stress. During the recovery phase, Fv/Fm was significantly decreased in both plants compared to control condition. This was complemented by the DEGs which showed downregulation of genes associated with Photosystem I and II, the most sensitive yet important machinery in photochemistry. These results showed that an acute 36 °C is above the tolerant threshold for Z. capensis, and that the species will disappear under these conditions.
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    Exchange of carbon dioxide, water and energy in South African semi-arid ecosystems
    (Stellenbosch : Stellenbosch University, 2024-03) Maluleke, Amukelani; Midgley, Guy F. ; Feig, Timothy Gregor; Brummer, Christian; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
    ENGLISH ABSTRACT: Recent research indicates that semi-arid regions contribute more than previously understood to global atmospheric carbon dioxide growth rates. Human activities and rising atmospheric carbon dioxide can alter ecosystem and biogeochemical processes in African drylands, potentially affecting land-atmosphere feedbacks. In terms of primary productivity and water-use efficiency, semi-arid ecosystems are expected to respond to these drivers more strongly. A paired-site eddy covariance (EC) based technique was used in the study to assess the fluxes of carbon, water, and energy across two semi-arid vegetation types that represent different semi-arid biomes in southern Africa: the Nama-Karoo and the Savanna. The Nama Karoo Site recorded -160 g C m⁻² over 33 months, while the Savanna Site recorded -567 g C m⁻². The mean net ecosystem exchange (NEE) was -189 g C m⁻² y⁻¹ for the Savanna site and -53 g C m⁻² y⁻¹ for the Nama Karoo Site. NEE was driven by incoming radiation, vapour pressure deficit (VPD), and air temperature, with soil moisture being a critical explanatory variable for productivity. The Nama-Karoo site had better ecosystem water-use efficiency (WUE) than the Savanna site while a greater closure rate of 96% was observed at the Savanna site compared to the Nama-Karoo site's 80%, with Energy Balance Ratios of 0.93 and 0.88 for each site, respectively. The responses of NEE, gross primary productivity (GPP), ecosystem respiration (ER) and evapotranspiration (ET) to wetting events showed that NEE generally peaked after five days, corresponding with GPP and ER peaks during the wet season while no significant peaks were observed during the dry season with both ecosystems remaining neutral. After wetting, ET rates peaks immediately and decreases to pre-wetting levels after around eight days during the wet season. At the Savanna site, rainfall thresholds that initiated sustained photosynthesis (point at which GPP surpasses ER and NEE denotes net uptake for a duration longer than 15 days) varied from 131 mm to 172 mm, whereas at the Nama-Karoo site, they varied from 98 mm to 165 mm. The second period had higher rainfall thresholds, possibly due to fire delaying the growing season. Although rainfall is a significant productivity driver, semi-arid ecosystems are likely to translate wetting events into productivity due to a combination of factors including temperature, vegetation status, soil properties, and preceding soil wetness conditions. Lastly, the study assessed the use of Sentinel-2 vegetation indices to estimate GPP from three semi-arid sites. The indices (the normalized difference vegetation index (NDVI), enhanced vegetation index (EVI), and land surface water index (LSWI)) were evaluated independently and in conjunction with meteorological factors. Results showed that adding meteorological factors to single vegetation index estimations could improve GPP estimation accuracy. The phase of productivity in semi-arid ecosystems is better represented by standard MODIS products than its amplitude, accounting for 68-83% of GPP variability. The study contributes to the understanding of the role of semi-arid ecosystems in climate change and in the global carbon cycle. It addresses uncertainties in these ecosystems, which make up half of Africa. This expertise is crucial for informed resource allocation and policy formulation for ecosystem restoration, mitigation, and resilience, essential for the continent's growing population.
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    Shared marking site use in African wild dogs (Lycaon pictus)
    (Stellenbosch : Stellenbosch University, 2024-03) Claase, Megan Jane; Cherry, Michael ; Jordan, Neil R.; McNutt, John W.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
    ENGLISH ABSTRACT: African wild dogs (Lycaon pictus) have recently been shown to use latrines, or shared marking sites (SMSs), which are long lasting communal areas where multiple packs visit to deposit scent marks. The aim of this study is to understand how wild dogs use these locations, and what this behaviour means for communication and territoriality in this species. Chapter one explores seasonal variation in visitation rates across the study period, and aims to determine habitat selection of SMS locations in the landscape. Results indicate a seasonal difference in how often wild dogs visit SMS, with visits significantly decreasing during the annual denning season. Despite this dip in visitation during denning when their ranges are substantially contracted, wild dogs visit SMSs year-round. This supports the theory that SMSs play a key role in territorial advertisement and inter-pack communication in this species. SMSs are more likely to be found closer to roads, while grassland and permanent water areas are not selected for, patterns consistent with our existing knowledge of wild dog movement ecology. The second chapter aims to identify and explore the intrinsic and extrinsic characteristics driving individual scent marking patterns in both the inter- and intra-pack contexts. Dominant wild dogs scent mark more than subdominants, while patterns observed between the sexes appear to be context dependant. Dominant females overmark more than dominant males in the inter-pack context, while the opposite is seen in the intra-pack context. These results are consistent with a resource defence function of wild dog latrines, but suggest that the resource defended may differ between the sexes. Females may be more invested in the physical territory, while males may be more invested in advertising a bonded pair, likely a critical component of communicating with neighbouring packs. The final chapter explores how resident packs may tailor their territorial behaviour in response to rival identity, specifically determining if they exhibit a “dear enemy” or “nasty neighbour” response. Using behavioural data captured from camera traps as a natural experiment, results show that wild dogs generally exhibit a dear enemy response at the group level, but that this response is moderated by pack size, with larger packs exhibiting a nasty neighbour response. Data show individual, wild dogs from larger packs overmark larger groups more than they overmark small groups, while individuals from small packs avoid overmarking large groups. These patterns may be driven by variation in the size of intruding groups representing different threat, and serve to highlight key variables which may be overlooked in scent presentation experiments. Overall, this study provides detailed insights into SMSs use in wild dogs which offer insights into territoriality and communication in this endangered species. This information may be used to assist in their conservation such efforts to manipulate their ranging behaviour artificially using scent.
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    Exploring the restoration of Zostera capensis in Langebaan Lagoon: ecological, molecular and physiological perspectives
    (Stellenbosch : Stellenbosch University, 2024-03) Watson, Katie Margaret; Pillay, Deena; Von der Heyden, Sophie; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
    ENGLISH ABSTRACT: Despite being one of the most valuable natural systems globally, seagrass meadows are also among the most threatened due to global climate change and localised threats. There is growing concern that the ecosystem functions seagrasses perform will be reduced or lost altogether without intervention, as is the case for the endangered Cape dwarf-eelgrass (Zostera capensis) in South Africa, including its declines in Langebaan Lagoon, the focus of this study. Although fast-growing, Z. capensis does not colonise new areas quickly and is highly threatened due to anthropogenic impacts, resulting in population declines and local extinctions. As such, management interventions through integrating seagrass restoration as part of a resilience-based management strategy are urgently needed. However, seagrass restoration has previously been viewed as an unpredictable management strategy, with a mixed history of success. The principal aim of this PhD was to explore the restoration potential of Z. capensis, employing ecological, molecular, and physiological methods. The first chapter aimed to address issues associated with transplantation by investigating Z. capensis restoration using different donor materials (cores and anchored shoots) planted in different spatial arrangements across several sub-sites within Oestewal, Langebaan Lagoon. After 18 months of monitoring, ~58 % plots survived across all treatments, but temporal persistence and area cover increased in transplant plots using cores in a dense pattern towards the upper shoreline, expanding by >400 % in some instances. To identify areas to prioritise for future restoration efforts, Chapter 2 employed habitat suitability modelling (HSM) to explore how environmental data and Z. capensis distribution over time shape habitat suitability at local scales. Remote sensing using supervised semi-automated classification to predict past and current Z. capensis distribution, was used in combination with the preliminary transplant suitability index (PTSI), identifying several priority areas for restoration. The HSM model was validated through post hoc data from the restoration trial in Chapter 1. In Chapter 3, a controlled mesocosm experiment was conducted using two genomically divergent Z. capensis populations, found naturally occurring in Langebaan Lagoon, exposed to a simulated marine heatwave (MHW) event. The experimental procedure allowed the identification of photophysiological responses as well as transcriptomic mechanisms involved in the thermal tolerance of Z. capensis, with the successful activation and regulation of heat-responsive genes involved in plant defence and histone methylation in heated plants potentially supporting processes involved in short-term heat acclimation. Under global-change scenarios, gaining insights into the transcriptional and photophysiological responses of increasing thermal extremes worldwide, such as MHWs, is crucial to understanding the responses of foundational species, with important implications for restoration and conservation management. Chapter 4 presents a review of gene expression studies in seagrasses globally, providing insights into how these studies have the potential to revolutionise seagrass restoration through project co-creation. In conclusion, this thesis explored ecological, molecular, and physiological approaches to enable practitioners to incorporate targeted seagrass conservation and restoration measures as an integral part of Z. capensis management across southern Africa.
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    Patterns and mechanisms of woody plant encroachment and impacts on ecosystem processes and services
    (Stellenbosch : Stellenbosch University, 2023-12) Skhosana, Felix Vusumuzi; Midgley, Guy F. ; Stevens, Nicola; Mateyisi, Mohau Jacob; Von Maltitz, Graham; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
    ENGLISH ABSTRACT: Amid global climate change and heightened population growth especially in Africa, proper management of the grassy ecosystems that offer various services that are crucial to human well-being is paramount. Due to various land-use changes, these systems are transforming from a grassy to a woody- dominated system – a phenomenon termed woody plant encroachment (WPE). Driven by a combination of drivers such as fire suppression overgrazing and rising atmospheric CO2 fertilisation, WPE is affecting ecosystem functioning and services in these grassy ecosystems in Africa and worldwide. Despite this, the diverse impacts of WPE have not yet been comprehensively synthesized and the mechanisms behind WPE impacts and explanations of the associated patterns of change remain contested. The broad-scale impacts of encroachment are also likely to vary depending on the socio-economic status of the region and the dependence of the communities on natural resources. For instance, people in the Global South such as in Africa are likely to have a high reliance on ecosystem services when compared to people in the developed Global North such as in North America. This perspective has not yet been explored directly, though some global scale assessments show that WPE is widespread in grassy and savanna ecosystems globally. At the mechanistic level, the main impact of invading woody plants in grassy systems is assumed to relate to light capture by taller woody plants, determined by plant traits relating to the efficiency of light capture and canopy shading. In water-limited savannas, characterized by limited and stochastic rainfall, increasing woody cover can reduce plant available water, streamflow, and groundwater by altering evapotranspiration rates and rainfall partitioning in space, but the ecological relevance of this impact has been little studied. The potential inefficiency of water use by woody encroaching species in semi-arid savannas is a cause for concern and warrants the investigation of the influence of woody plant traits that determine rainfall interception via canopy interception in these systems as an alternative mechanism of woody plant impact to that of light capture, and the potential of these mechanisms for patterns and implications of encroachment. To address these issues, I systematically reviewed the literature on the impacts of woody encroachment on ecosystem services within the three broad categories of Nature’s Contributions to People (NCP), namely: material, non-material, and regulating NCP, in North American and African regions with contrasting socio-economic characteristics (Chapter 2), as a broad scale context for further work on the mechanisms involved at local scales in African savannas, I then narrowed focus in two subsequent chapters, exploring the alternative rainfall interception mechanism potentially involved in WPE in Africa as mentioned above. In Chapter 3 I quantified in a field-based study the altered partitioning of rainfall by two dominant woody plant structural types (fine- and broad-leaved trees) across a local gradient of encroachment in a semi-arid savanna in South Africa. I then further determined plant canopy and leaf traits associated with water loss through canopy capture in a series of controlled experiments conducted in the same field environment Chapter 4. From the review work, material NCP benefits were found to be generally more directly relevant to livelihoods in Africa and constituted the provision of wood materials for fuel, building, and browser forage. I found that the material NCP most adversely affected by woody encroachment was the reduction in herbaceous forage availability, leading to reductions in livestock numbers and products on both continents. Negative impacts on Non-Material NCP such as recreation, tourism and social amenities, herding, and pressure to diversify livestock were also reported for Africa. For regulating services, negative effects were reported on both continents in terms of soil health, habitat availability and quality, and on the regulation of hydrological services. Overall African WPE tended to be driven more by fine-leaved N2 fixing species than in North American ecosystems. In Chapter 3, I found that when averaged across both fine- and broad-leaved woody plant functional types, loss of rainfall through canopy interception and subsequent evaporation approximately doubled with a roughly 13-fold increase in woody cover. Changes in water partitioning comprised fourfold increases in stemflow and a decline in throughfall proportion of about two-fifths. Changes in partitioning were dependent on plant functional type. Rainfall interception by the fine-leaved multi-stemmed shrub Dichrostachys cinerea was almost double that of the broad-leaved tree Terminalia sericea at the highest levels of woody encroachment. Partitioning was also dependent on rainfall characteristics, with the proportion of rainfall intercepted inversely related to rainfall event size, and intensity. The observation of higher water loss by fine-leaved over broad-leaved species was consistent with the findings of Chapter 4, where I found that over and above variability among other species, the fine-leaved species recorded a significantly higher storage capacity than the broad-leaved species at both branch complex and leaf levels. Various canopy traits and leaf traits were more influential in contributing to variability among species. At the branch complex level, traits such as the number of leaf clusters and leaves on each branch as well as leaves in totality contributed to most of the variability in species. At the leaf level, leaf type, structure, apex, and laminar shape had the most influence. Canopy storage capacity had a strong positive correlation with the number of leaves, followed by the number of modules and branches, while at the leaf level, storage capacity had a negative correlation with the number of hairs and the number of waves on the leaf. Overall, this study demonstrated that the mechanism of rainfall interception in underpinning patterns of WPE in semi-arid savannas is at least a viable alternative to the ancillary mechanism of light interception. A major novel finding in this study is that increasing tree cover in African grassy ecosystems reduces the amount of canopy throughfall, especially beneath canopies of fine-leaved species in smaller rainfall events. Rainfall interception traits may thus confer a selective advantage, especially for fine-leaved woody plant species in semi-arid savannas. Understanding the relationships between plant traits and canopy water storage capacity can help guide better management of plant communities in these semi-arid regions where water availability is limited. Leaf and canopy traits that determine rainfall interception, stem flow, and canopy throughfall deserve further attention in mechanistic models of this phenomenon, and possibly in assessing the reasons for distinct types of WPE species between African and North America. Finally, while WPE may be seen as having potential benefits of increased above-ground carbon sequestration by woody biomass, the benefits of carbon sequestration through WPE need to be understood in the context of the diverse NCP impacts involved. The need for critical ecosystem services for African livelihoods such as livestock production, tourism revenue, and water provision is thus presented in the context of recommendations to control and reverse WPE in the final summary Chapter 5.