Doctoral Degrees (Conservation Ecology and Entomology)
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- ItemSimulating natural processes to scale-up ecological restoration in lowland sand fynbos(Stellenbosch : Stellenbosch University, 2023-03) Ngwenya, Duduzile K; Esler, Karen J.; Holmes, Patricia M.; Geerts, Sjirk; Stellenbosch University. Faculty of Agrisciences. Dept. of Conservation Ecology and Entomology.ENGLISH ABSTRACT: The restoration of degraded ecosystems is set to gain momentum given that natural resources are dwindling and there is a need to mitigate the impacts of climate change. There is some reliance on ecological restoration to reverse environmental degradation and to facilitate sustainable economic development. Global initiatives such as the United Nation’s Decade on Ecosystem Restoration and the Global Biodiversity Framework have placed ecological restoration at the forefront of reversing environmental degradation while the Sustainable Development Goals embed biodiversity at the core of sustainability. Ecological restoration is set to direct degraded ecosystems on a restoration trajectory and recover the ecosystem’s composition, structure, and function. However, there is a mismatch between the extent of environmental degradation and that of restoration efforts. Consequently, the net contribution of current restoration efforts towards reversing environmental degradation is limited. What is lacking is an approach which converges the contributions made from different extents of restoration efforts into a global contribution. This is caused by the lack of a framing tool to guide the design and implementation of restoration interventions towards closing the gap between the extents of environmental degradation and restoration efforts. Environmental degradation is widespread and caused by various factors including biological invasions. Plant invasions are problematic in South Africa, particularly in the Greater Cape Floristic Region (GCFR), where they cause biodiversity loss. These invasions are usually dominated by the alien trees and shrubs native to the Mediterranean climate regions of the globe. Restoration efforts may be undermined because the invading species originate from similar, fire-prone environments with similar drivers of regeneration. This way, the invading species can easily adapt in fynbos environments and respond positively to restoration treatments meant to regenerate native vegetation. Therefore, the use of fire treatments to regenerate these fynbos types when they are heavily invaded by fire-adapted species is challenged by the invader’s equal responsiveness to fire treatments. A prime example is using fire treatments to regenerate Lowland Sand Fynbos found within the GCFR when it is heavily invaded by Australian Acacia saligna. In this case, fire treatments stimulate high- density, post-fire acacia recruitment instead of native species. This high-density acacia recruitment outcompetes the sparsely recruited native species which fail to establish thereafter. By coupling alien clearing interventions with restoration of native vegetation, the research sought ways to improve and scale-up ecological restoration efforts currently underway in Lowland Sand Fynbos. Alternative ways were sought to encourage native species regeneration while discouraging the invading species from resurging. Therefore, this dissertation investigated the efficacy of simulating and side-stepping the effects of fire to avoid high-density post-fire acacia recruitment. Guided by the findings from the reviewed literature, two restoration treatments were designed and trialled in Lowland Sand Fynbos ecosystems long invaded by A. saligna. These treatments were designed to improve the regeneration of native species by reducing the density of acacia emergence after clearing acacia stands. Regeneration of natives was encouraged by simulating the effects of fire required to stimulate the germination of native species and by sowing pre-treated native species to boost the depleted native seed bank. The recruitment of acacia was discouraged by avoiding and delaying the use of fire treatments when the acacia seed bank was relatively large and through follow-up clearing of recruited acacia. That is, the cleared areas were either sown without burning the acacia slash (“Fell, Stack & No Burn” treatment) or they were fallowed before burning the slash and sowing pre-treated seeds (“Fell, Fallow & Burn” treatment). By avoiding fire treatments, the recruitment of acacia was discouraged by depriving acacia of its fire-related heat pulse germination cue. This resulted in sparse recruitment of acacia which allowed the native species to germinate from pre-treated seeds and to establish. However, the recovered vegetation did not yet approach a structure comparable to the reference site because it lacked representation of a few plant guilds, e.g., proteoids and geophytes, and the species richness within individual plant guilds was poor. Delaying using fire treatments allowed the acacia seed bank to reduce in size, translating to reduced acacia seedling densities that allowed the recruited native seedlings to establish rapidly. However, this reduced post-fire acacia recruitment still yielded a dense acacia stand in competition with the recruited native species. But the cover from recruited annual species helped to suppress the establishment of dense acacia cover. When the annuals died back, follow-up clearing of acacia seedlings was necessary to facilitate the establishment of perennial species thereafter. Improving the management of alien plant invasions can be better executed by combining insights, efforts, and experiences from the fields of invasion and restoration ecology to inform restoration practice and the selection of suitable restoration treatments. Therefore, this research examined the effectiveness of treatments that side- stepped or simulated natural processes to scale-up native species recovery in a highly threatened Cape Floristic Region habitat. The technical and financial effectiveness of various treatments were compared and indicated context-specific outcomes. There was no ideal treatment which incurred the lowest cost but yielded the best outcomes in all categories of restoration outcomes. Instead, there were trade-offs between costs and outcomes in each treatment. For example, despite being able to recover good native cover and minimising acacia recruitment at lowest costs, the “Fell, Stack & No Burn” treatment retained the highest acacia seed bank after two years. The “Fell, Fallow & Burn” treatment resulted in the highest native cover after two years but it did not improve the species richness of the recruited native species and it was more expensive than the “Fell, Stack & No Burn” treatment. However, the resultant effects of fallowing and high-density post-fire acacia emergence yielded the lowest residual acacia seed bank compared to other treatments. Within the monitored period, none of the treatments allowed the restoration sites to approach an ecosystem structure that was comparable to reference conditions. The restored areas lacked the representation of a few plant guilds, e.g., the overstorey proteoid guild, geophytes and some ericoid resprouter shrubs. Furthermore, species richness within each recovered plant guild was low. The greatest barrier to stimulating the regeneration of a species-diverse Lowland Sand Fynbos ecosystem is likely to be the depleted native seed bank more than the effects of fire or the high-density post-fire acacia resurgence. A depleted native seed bank restoration intervention requires the addition of species-diverse seed mixes irrespective of the treatment, but seed supplies remain limited. The high-density acacia resurgence can be managed by manual removal of acacia saplings within the first year of sowing, though it is expensive and laborious to implement over large areas. An avenue for future research is to explore seed enhancement technologies such as polymer coating, since the combination of restoration treatments with follow-up clearing treatments can improve the establishment of native species in the field. Therefore, practitioners can use seed pre-treatments to enhance the germination of species that are easy to collect and re-establish in the field and plant nodes of rootstock for species and plant guilds that fail to establish from seeds. The choice of management approach depends on the budget constraints, priorities, context, and scope of the intervention. Despite the lack of an ideal treatment and an inconclusive evaluation, the synthesis of research findings indicated some best-practise management options that practitioners can adopt in future restoration efforts. Firstly, it was recommended that when restoring fynbos vegetation types that are heavily invaded with acacia, fires should be delayed until the risk of high-density post-fire acacia recruitment posed by the acacia seed bank is low. Secondly, the persistent portion of the acacia seed bank poses an ongoing risk of reinvasion and therefore requires long-term management planning and budget for follow-up clearing. Thirdly, given the dearth of available native seeds for active restoration in Cape Flats Sand Fynbos, scaling-up ecological restoration may require seed enhancement technologies to boost the depleted native seed bank and help to restore ecosystems that are species diverse, resilient, and resemble reference conditions. Lastly, restoration of functioning ecosystems takes time, over several fire cycles, and requires continuous improvement from the initial interventions.
- ItemCharacterisation of soil macro- and mesofauna diversity and their contribution to soil health in grain agroecosystems(Stellenbosch : Stellenbosch University, 2023-03) Mamabolo, Emogine; Pryke, James S. ; Gaigher, Rene; Stellenbosch University. Faculty of Agrisciences. Dept. of Conservation Ecology and Entomology.ENGLISH ABSTRACT: Agriculture is the most important source of food and critical to the South African economy, yet it is detrimental to the environment, including the soil. We need to find innovative ways to achieve agricultural sustainability. Sustainable models are increasingly being adopted, but the major challenge remains measuring their effectiveness. Soils are inextricably linked to sustainable agriculture, as good soils promote crop growth and yields, while sensitive to chemical inputs that farmers place on the croplands. Due to the importance and sensitivity of soil, the assessment of soil health and soil fauna biodiversity has been proposed as an indicator of sustainability yet rarely considered when making recommendation for sustainable agricultural intensification. This dissertation explores the differences in diversity of soil macro-and mesofauna (from here on called soil fauna) under different agricultural land uses, namely conventional, conservation, integrated and natural grasslands, and how this affects the soil physicochemical environment and decomposition processes. The status of macrofauna as bioindicators of soil health was explored to provide a more direct tool in measuring soil function and sustainability. Biodiversity metrics revealed that cultivation under minimum soil disturbance coupled with complex vegetation and soil cover benefited soil fauna and allowed the establishment of most functional groups, which are crucial for pest control, nutrient cycling, and decomposition. Therefore, reduced tillage and increased structural complexity are recommended for preserving soil arthropod diversity and associated ecosystem services. Litter decomposition was positively linked to soil fauna species richness and not abundance or diversity. Results also showed that, soil fauna significantly contributed to decomposition, but contributions are highly depended on temperature, soil moisture and land use intensity. These findings highlight the importance in understanding management effects on soil fauna functional roles in maintaining nutrient cycling and soil health. Soil characterisation showed that conventional land uses favoured some important soil properties, however the overall effects of the soil physicochemical environment on fauna were complex, implying that sustainable intensification will not only be beneficial for productivity but also for the promotion of soil fauna and ecosystem services. Multivariate analyses of soil health characterisation allowed for the development of a simple but robust soil health assessment tool using soil macrofauna as indicators. The tool is important for assessing land use management and associated effects on soil health and ecosystem function. Overall, this dissertation shows that sustainable management, increased biodiversity, and increased soil health complement each other. Compared to their conventional counterparts, the conservation and livestock integrated land uses optimised favourable and stable conditions for various soil fauna groups and were more like that of the natural grasslands. As some of the important soil variables are favoured by more intensive land uses, designing sustainable and functional schemes is a lengthy process which requires patience, as soil itself is an ever-evolving entity which needs time to generate and/or restore. Here it is shown that low intensity agriculture promotes health soil fauna, thus sustainable management of soils in agriculture has the potential to increase the overall soil health, biodiversity, and function, meaning they (ecosystem engineers) can restore degraded soils and ecosystem services.
- Item“A social-ecological systems approach to sustainable production of endemic rooibos (Aspalathus linearis) and honeybush (Cyclopia spp.) species amongst agrarian communities in the Cape Floristic Region (CFR)”(Stellenbosch : Stellenbosch University, 2022-12) Malgas, Rhoda Ronette; Esler, Karen J.; Jacobs, Shayne Martin; Schaminee, Joop Hendrik Jacque; Stellenbosch University. Faculty of AgriSciences. Dept. of Conservation Ecology and Entomology.ENGLISH ABSTRACT: How do we ensure sustainable biomass production of Fynbos endemic plant species to support the livelihoods of small-scale producers in geographically delimited production areas of the Cape Floristic Region (CFR)? This research aims to address that question for the South African small-scale rooibos (Aspalathus linearis) and honeybush (Cyclopia spp.) sectors by applying a systems approach. Social-ecological (SE) variables and their interactions were described and mapped using Ostrom’s Social Ecological Systems Framework (SESF), a novel undertaking for Fynbos-based sectors. The SESF is a conceptual tool designed to describe, characterize, and analyse social-ecological systems (SES). It is used to diagnose problems and to elicit principles for improved SES outcomes, such as sustainable harvesting, agroecological production, sustainable livelihoods and maintaining the ecological integrity of wild rooibos and honeybush populations in natural Cape Fynbos plant communities. Pitfalls and pathways to sustainability were identified by analysing SE variables and their interactions. Variable identification was achieved through three inter-related studies. First, to anchor the conceptual work in a real-life focal action situation, the historical practice of wild-harvesting and contemporary production of honeybush at Genadendal (The Overberg, Western Cape) was used as a case. Interviews with 32 local ecological knowledge (LEK) holders formed the basis for a) collation of LEK to understand the mental models¹ or local perceptions resource-users have of local honeybush species and b) characterisation of LEK in the context of the SESF and potential sustainability outcomes in contemporary harvest systems of honeybush, and sister species, rooibos. Correlations between knowledge-bearer biographies and LEK, and details of knowledge transfer and LEK valuation were amongst the emerging themes. Findings from LEK also included details of species habitats, harvest sites, morphological features, and the status of local wild honeybush. Secondly, barriers that local land-users at Genadendal face in adopting honeybush production as a viable livelihood option were explored in comparison with accounts from rooibos and honeybush small-scale farmers elsewhere in the CFR to formulate a composite framework. Research outcomes highlight biophysical, institutional, and interpersonal barriers that these actors face in deciding whether to adopt indigenous rooibos or honeybush crops into their livelihood strategies. Thirdly, sets of ecological variables were identified from literature on Fynbos ecological research. Phytosocialogical data were used to highlight how conserving wild rooibos and honeybush habitats inadvertently conserve the habitats of co-occurring Fynbos species and concomitant ecological processes across a range of Fynbos vegetation types. A review of published research pointed to guides and recommendations for sustainable ¹ In the language of Ostrom’s Social Ecological Systems Framework, mental models refer to the conceptual ideas people commonly hold of the natural resource and how they interact with it. For instance, Sarah Ives (2014) describes this extensively for rooibos tea amongst different farmer groups. In her paper, she reflects on how the plants are associated with land and patriotism, whereas coloured producers consider the tea part of their heritage as First Nations descendants. biomass production, helping to identify plant functional traits and ecological parameters explicit in biomass production. Abstraction of ecological drivers in rooibos and honeybush sectors highlighted the “ecological rules” implicit in Fynbos-based production systems, but that are often neglected in previous iterations of the SESF. The study thus also addresses the theoretical gap of the “missing E” in SES previously reported in SES research by emphasising how foundational ecological factors are in endemic Fynbos production systems. Pathways to sustainability outcomes were devised by reviewing findings from the studies with conceptual constructs and principles theoretically associated with sustainability outcomes. Ostrom’s SESF has been widely applied to diverse SES across the world, but has rarely been used in South Africa, and to date, has not been operationalised for any of the Fynbos-based sectors, despite their apparent eligibility for its application. This research adds to SESF theory with a unique contribution from the Cape Fynbos and its unique ecology. A grounded approach to SES variable identification focused attention on two entities often neglected in mainstream research: Fynbos genetic crop wild relatives and the small- scale producers who rely on them for their livelihoods. The dissertation concludes with a sector-specific SESF refined for application in the rooibos and honeybush sectors. Ultimately, the result is a revised SESF that may find application in other Fynbos-based SES where sustainable wild-harvesting and sustainable agricultural production are desired outcomes.
- ItemFungal endophyte assemblages associated with twigs of olives in the Core Cape Subregion, South Africa(Stellenbosch : Stellenbosch University, 2022-04) Ngubane, Nombuso Portia; Roets, Francois; Dreyer, L. L.; Slippers, Bernard; Kemler, Martin; Stellenbosch University. Faculty of AgriSciences. Dept. of Conservation Ecology and Entomology.ENGLISH ABSTRACT: Fungal endophytes are increasingly gaining recognition for their role in plant health. In the face of global change and unprecedented biodiversity loss, it has become an urgent concern to understand these valuable microbes. The main objectives of the work presented here were two-fold, 1) to gain better understanding of the fungal endophytes in a threatened biodiversity hotspot and 2) to improve our understanding of fungal endophyte assemblages associated with ecologically and agriculturally important Olea species. The Core Cape Subregion provides a rare and important study area since it is one of the few areas of olive cultivation with close native relatives, including O. europaea subsp. cuspidata. Many olive (O. europaea subsp. europaea) orchards in the Core Cape Subregion are near natural O. europaea subsp. cuspidata populations. In Chapter 2, I investigated the role of host identity and geographic distance on fungal endophyte assemblages associated with the two Olea europaea subspecies in South Africa. Although many taxa were shared between these hosts, the native host harboured significantly higher alpha diversity. The beta diversity of fungal endophytes also differed significantly between hosts. Geographic distances played a significant role in shaping fungal endophyte assemblages of both hosts, more so in the native host. The native O. europaea subsp. cuspidata is a widely distributed plant growing across a variety of habitats that is also a favoured shade plant, planted in gardens, parks and roadsides. In Chapter 3, the response of fungal endophytes to different levels of disturbance (habitat context) and to differences in surrounding vegetation types (vegetation contrast) were assessed. Endophyte species richness was influenced by habitat context and vegetation contrast. However, fungal endophyte assemblage composition was only affected by habitat context. This suggests that although the host can tolerate different habitat context levels, its fungal endophytes are particularly sensitive to even the mildest of disturbances found in the semi-natural habitat context. In the Core Cape Subregion, two additional Olea species (O. capensis and O. exasperata) are native to South Africa. This made it possible to assess the impact of host identity and relatedness on fungal endophyte assemblages of native hosts (Chapter 4). Fungal endophytes were documented in five native hosts (three Olea and two non-Olea hosts) in the Kogelberg Biosphere. Although fungal endophyte assemblages were significantly different between hosts, this was not correlated to host relatedness (phylogeny). Other factors, other than host phylogeny, were more important to fungal endophytes in this area. The lack of a phylogenetic signal reflected in fungal endophyte assemblages of native Oleaceae hosts suggests that the differences in fungal endophyte assemblages between O. europaea susp. europaea and O. europaea susp. cuspidata are likely due to differences in their histories. The differences in planted African olive trees versus those in the natural context, and the differences between the cultivated and the native olives demonstrate the importance of habitat context. The dynamic nature and diversity of fungal endophytes within the investigated hosts highlights the need to improve our understanding of fungal endophytes in South Africa, especially in native hosts.
- ItemA mixed method approach towards the evaluation and assessment of integrative research programme outputs: the case of the invasive alien plant management programme working for water(Stellenbosch : Stellenbosch University, 2022-04) Abrahams, Brent; Esler, Karen J.; Sitas, Nadia; Stellenbosch University. Faculty of AgriSciences. Dept. of Conservation Ecology and Entomology.ENGLISH ABSTRACT: The pervasiveness of threats posed by biological invasions presents significant challenges to human well-being, biodiversity conservation, and natural resource management, which has contributed to the growth of invasion science as a discipline. However, several studies have shown that the social-ecological complexity of invasions, the compartmentalisation of knowledge into disciplines and the lack of integrative research approaches, current invasion research has not informed management decision making effectively. Thus, to maximise the impact of research investments, there is a need to explore and evaluate how research informs management practices and processes linked to biological invasions. Accordingly, this dissertation outlines the state of invasion management-related research in South Africa, using the internationally recognised Working for Water (WfW) programme as a case study. Drawing on insights from science studies and evaluation research, a mixed method approach is used to assess the processes, conditions and outputs associated with research produced under the programme’s auspices. The research comprised two areas of inquiry 1) the exploration of textual information (journal articles, grey literature, and their content), and 2) the social dimensions of research and decision making linked to invasion science and management, with a specific focus on collaborative relationships amongst scientists and decision makers. It sought to determine the extent to which published research aligned with the programme’s needs, research and management strategies. The research also aimed to identify effective ways for organising and producing knowledge relevant to decision making; and to provide insights into how the social dimensions, the people and organisations, their interactions and impact, have shaped research and decision-making processes. Findings suggest that there are significant gaps in the knowledge base particularly in relation to the social dimensions of biological invasions, which were poorly represented and aligned with the mandate and priorities set by the programme. This research showed significant deficiencies in knowledge management and the uptake of research funded by the programme, despite its potential relevance to decision making as evidenced by the recommendations presented in the research. Moreover, research produced under WfW’s auspices was authored by a handful of key researchers who fulfil a significant role in shaping research collaborations both across disciplines and institutions. The loss of these key individuals, including those involved in management-related decision making, would be detrimental to the stability of collaboration networks and research productivity. Finally, findings show that research productivity, collaborative relationships between scientists within and across research organisations, and between research and decision-making processes are positively influenced by collegiality and cooperation between actors, while increased competition and bureaucratisation in the workplace negatively influence research productivity. To address the shortcomings concerning the invasion research and management identified in this dissertation, efforts towards improving the relationship between researchers and decision makers and building more resilient collaboration networks need to be implemented. Firstly, institutions must engage in and fund more targeted, long-term transdisciplinary or integrative research that incorporates appropriate structures that foster collaboration, knowledge coproduction and knowledge sharing. Secondly, systems and strategies for monitoring and evaluating research, including the use of bibliometric indicators, social network analyses and qualitative assessments, should be developed to ensure that research relevant to managing biological invasions is not lost to the decision-making process. Such an undertaking would in turn require the development of an integrated research strategy and action plan that accounts for both the knowledge management and the social processes underpinning research and decision making.