Colonisation and succession of fishes in Lake Liambezi, a shallow ephemeral floodplain lake in Southern Africa
- Authors: Peel, Richard Anthony
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/65211 , vital:28707
- Description: Expected release date-May 2019
- Full Text:
- Date Issued: 2017
- Authors: Peel, Richard Anthony
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/65211 , vital:28707
- Description: Expected release date-May 2019
- Full Text:
- Date Issued: 2017
Geomorphological connectivity and sensitivity examined in a recently degraded gravel-bed stream: implications for river-floodplain rehabilitation
- Authors: Powell, Rebecca
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/53722 , vital:26313
- Description: The study of river complexity and sensitivity to future human land-use activities and climate change is a fast growing field within the discipline of fluvial geomorphology. Associated with this is a need to improve river rehabilitation and catchment management approach, design and effectiveness. This study aimed to investigate drivers of the recent geomorphological sensitivity of the Baviaanskloof River-floodplain, an upland system in South Africa, by integrating the concepts of geomorphological connectivity and Panarchy. The understanding generated was used to evaluate the approach of the State agency, Working for Wetlands (WfWet), to river-floodplain rehabilitation in the catchment.The concepts of geomorphological connectivity and Panarchy provide useful frameworks for understanding interactions between geomorphological processes and structure across scales of space and time. Geomorphological connectivity explains the degree to which water and sediment is linked in a river landscape, determined by the distribution of erosional and depositional landforms (Brierley et al. 2006; Fryirs et al. 2007a; Fryirs et al. 2007b). Panarchy attempts to explain lagged response to disturbances, non-linear interactions, and sudden shifts in system state, and has been applied largely to ecological systems. Panarchy theory, when combined with the concept of geomorphological connectivity, provides a guiding framework for understanding river complexity in greater depth. The first results chapter of this study investigated river long-term and recent geomorphological history, towards understanding the nature and timing of river geomorphological cycling between erosion and deposition. Optically Stimulated Luminescence dating of alluvial fan and floodplain sedimentary units was conducted, for analysis of river-floodplain long-term history (100s to 1 000s of years). Interviews with 11 local landowners, combined with analysis of historic aerial imagery and river-floodplain topographic surveys, provided a means of describing recent (last few decades) geomorphological dynamics. The results indicated that the Baviaanskloof is naturally a cut- and-fill landscape over scales of several hundred to thousands of years, characterized by the alternation between phases of high fluvial energy and alluvial fan expansion, and low energy conditions associated with floodplain accretion. Recent and widespread river-floodplain degradation was compressed into a short period of approximately 30 years, suggesting that one or more drivers have pushed the system beyond a threshold, resulting in increased water and sediment connectivity. The second results chapter investigated the role of human land-use activities and flooding frequency and magnitude, as drivers of recent river-floodplain degradation. Human impacts were investigated by describing land-use activities for the preceding 80 years, and relating these activities to changes in river-floodplain form and behavior. Temporal trends in flood events of different frequency and magnitude were investigated by analyzing rainfall data, integrated with landowner reports of flood-inducing rainfall magnitudes. The findings indicated that human land-use activities have been an important driver of recent river- floodplain degradation, through the enhancement of water and sediment connectivity across spatial scales of the catchment. Episodic and high magnitude floods synergized with human driven increased connectivity, precipitating stream power and geomorphological threshold breaches, resulting in a shift in river behaviour. The third results chapter investigated the influence of tributary-junction streams and fans on the geomorphological form, behavior and sensitivity of the Baviaanskloof River. Local- scale topographic impacts of tributary fans and streams were described using topographic surveys and geomorphological mapping techniques. Tributary streams form a major control on the behaviour of the river, by influencing the degree of coarse sediment connectivity with the main channel. Although tributary fans buffer the river from disturbances occurring in the wider catchment, they initiate topographic variations along the floodplain, influencing local-scale patterns of deposition and erosion along the river. The main river responds to water and sediment inputs from tributary junction streams by locally adjusting longitudinal slope, maintaining an overall constant slope of 0.0066 m/m. The response of the Baviaanskloof River to tributary junction fans and streams is however variable, and is fashioned by complex interactions between geomorphological and anthropogenic factors. The final two chapters of the thesis evaluate the findings of the study within the context of river-floodplain rehabilitation approaches in South Africa, and within the theoretical, philosophical and methodological context of the research. The first of these two chapters evaluates the approach of the WfWet programme to river-floodplain rehabilitation in the Baviaanskloof. The chapter indicates that the present practice of WfWet is to reinstate a pre-degradation state, which is not suited to the Baviaanskloof River-floodplain, since the river-floodplain has passed a geomorphological threshold, resulting in a new set of interacting processes and landforms. The author presents a conceptual model illustrating the existence of geomorphological adaptive cycles interacting across spatial and temporal scales, thereby attempting to explain a river Panarchy specific to the Baviaanskloof. From this conceptual model, a hierarchical rehabilitation framework, targeting geomorphological processes and structure situated at different spatial and temporal scales of the landscape is suggested. The final chapter discusses the implications of integrating the concepts of geomorphological connectivity and river Panarchy theory in studies of river complexity and sensitivity to geomorphological change. The author suggests that there is scope for further investigation of the application of the two concepts within the discipline of fluvial geomorphology, particularly with regard to developing quantitative approaches to measuring and describing connectivity and Panarchy.
- Full Text:
- Date Issued: 2017
- Authors: Powell, Rebecca
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/53722 , vital:26313
- Description: The study of river complexity and sensitivity to future human land-use activities and climate change is a fast growing field within the discipline of fluvial geomorphology. Associated with this is a need to improve river rehabilitation and catchment management approach, design and effectiveness. This study aimed to investigate drivers of the recent geomorphological sensitivity of the Baviaanskloof River-floodplain, an upland system in South Africa, by integrating the concepts of geomorphological connectivity and Panarchy. The understanding generated was used to evaluate the approach of the State agency, Working for Wetlands (WfWet), to river-floodplain rehabilitation in the catchment.The concepts of geomorphological connectivity and Panarchy provide useful frameworks for understanding interactions between geomorphological processes and structure across scales of space and time. Geomorphological connectivity explains the degree to which water and sediment is linked in a river landscape, determined by the distribution of erosional and depositional landforms (Brierley et al. 2006; Fryirs et al. 2007a; Fryirs et al. 2007b). Panarchy attempts to explain lagged response to disturbances, non-linear interactions, and sudden shifts in system state, and has been applied largely to ecological systems. Panarchy theory, when combined with the concept of geomorphological connectivity, provides a guiding framework for understanding river complexity in greater depth. The first results chapter of this study investigated river long-term and recent geomorphological history, towards understanding the nature and timing of river geomorphological cycling between erosion and deposition. Optically Stimulated Luminescence dating of alluvial fan and floodplain sedimentary units was conducted, for analysis of river-floodplain long-term history (100s to 1 000s of years). Interviews with 11 local landowners, combined with analysis of historic aerial imagery and river-floodplain topographic surveys, provided a means of describing recent (last few decades) geomorphological dynamics. The results indicated that the Baviaanskloof is naturally a cut- and-fill landscape over scales of several hundred to thousands of years, characterized by the alternation between phases of high fluvial energy and alluvial fan expansion, and low energy conditions associated with floodplain accretion. Recent and widespread river-floodplain degradation was compressed into a short period of approximately 30 years, suggesting that one or more drivers have pushed the system beyond a threshold, resulting in increased water and sediment connectivity. The second results chapter investigated the role of human land-use activities and flooding frequency and magnitude, as drivers of recent river-floodplain degradation. Human impacts were investigated by describing land-use activities for the preceding 80 years, and relating these activities to changes in river-floodplain form and behavior. Temporal trends in flood events of different frequency and magnitude were investigated by analyzing rainfall data, integrated with landowner reports of flood-inducing rainfall magnitudes. The findings indicated that human land-use activities have been an important driver of recent river- floodplain degradation, through the enhancement of water and sediment connectivity across spatial scales of the catchment. Episodic and high magnitude floods synergized with human driven increased connectivity, precipitating stream power and geomorphological threshold breaches, resulting in a shift in river behaviour. The third results chapter investigated the influence of tributary-junction streams and fans on the geomorphological form, behavior and sensitivity of the Baviaanskloof River. Local- scale topographic impacts of tributary fans and streams were described using topographic surveys and geomorphological mapping techniques. Tributary streams form a major control on the behaviour of the river, by influencing the degree of coarse sediment connectivity with the main channel. Although tributary fans buffer the river from disturbances occurring in the wider catchment, they initiate topographic variations along the floodplain, influencing local-scale patterns of deposition and erosion along the river. The main river responds to water and sediment inputs from tributary junction streams by locally adjusting longitudinal slope, maintaining an overall constant slope of 0.0066 m/m. The response of the Baviaanskloof River to tributary junction fans and streams is however variable, and is fashioned by complex interactions between geomorphological and anthropogenic factors. The final two chapters of the thesis evaluate the findings of the study within the context of river-floodplain rehabilitation approaches in South Africa, and within the theoretical, philosophical and methodological context of the research. The first of these two chapters evaluates the approach of the WfWet programme to river-floodplain rehabilitation in the Baviaanskloof. The chapter indicates that the present practice of WfWet is to reinstate a pre-degradation state, which is not suited to the Baviaanskloof River-floodplain, since the river-floodplain has passed a geomorphological threshold, resulting in a new set of interacting processes and landforms. The author presents a conceptual model illustrating the existence of geomorphological adaptive cycles interacting across spatial and temporal scales, thereby attempting to explain a river Panarchy specific to the Baviaanskloof. From this conceptual model, a hierarchical rehabilitation framework, targeting geomorphological processes and structure situated at different spatial and temporal scales of the landscape is suggested. The final chapter discusses the implications of integrating the concepts of geomorphological connectivity and river Panarchy theory in studies of river complexity and sensitivity to geomorphological change. The author suggests that there is scope for further investigation of the application of the two concepts within the discipline of fluvial geomorphology, particularly with regard to developing quantitative approaches to measuring and describing connectivity and Panarchy.
- Full Text:
- Date Issued: 2017
Investigating herbivory and plant origin on tall-statured grasses in South Africa
- Authors: Canavan, Kim
- Date: 2017
- Subjects: Insects as biological pest control agents -- South Africa , Arundo donax , Giant reed -- South Africa , Giant reed -- Biological control -- South Africa , Phragmites australis , Phragmites mauritianus , Phragmites , Tetramesa romana , Biological invasions -- South Africa , Wasps -- Host plants , Wasps -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/6147 , vital:21051
- Description: South African riparian zones have been heavily degraded through anthropogenic activities such as dam construction and extraction of water for irrigation, which has resulted in a loss of ecosystem services and functioning. A consequence of such disturbances to riparian areas is in their susceptibility to invasive alien species (IAS). One such IAS is the giant reed, Arundo donax L. (Poaceae), introduced to South Africa in the 1700s largely for erosion control. Arundo donax has since greatly expanded in the country and is now one of the most abundant IAS. Arundo donax has been found to displace native vegetation and in South Africa this will most likely lead to the displacement of the native tall-statured grasses, Phragmites australis (Cav.) Trin. ex Steud. and Phragmites mauritianus Kunth. This study aimed to enhance our understanding of the tall-statured grasses A. donax, P. australis and P. mauritianus to better manage them in riparian areas. For A. donax, biological control is seen as the most viable option to control stands in the long-term. However, before such a programme is put in place, it is important to first collect baseline data that can be used to guide the direction of the biological control project in South Africa. For the Phragmites spp., despite being a dominant vegetative type in riparian areas, very little is known about their status in South Africa. Furthermore, there have been increasing reports of both Phragmites species having an expansion of their range and abundance. In North America, there has been a similar trend of reed expansion and through molecular work it was determined that a cryptic invasion has occurred with the introduction of an invasive non-native haplotype from Europe. It is therefore unknown if Phragmites spp. populations are expanding due to anthropogenic activities or due to a cryptic invasion. To address these shortfalls in knowledge the study investigated the tall-statured grasses in two parts; firstly, molecular techniques are used to explore the plant origin and genetic diversity of A. donax, P. australis and P. mauritianus and secondly using the Enemy Release Hypothesis as a framework, herbivore assemblages for each reed was determined across their distribution in South Africa. Molecular-techniques determined that both P. australis and P. mauritianus had only one haplotype - known as haplotype K and haplotype V respectively, across their distribution. For P. australis, haplotype K shares a close connection with populations from a Mediterranean lineage and this was further confirmed with a shared grass-waxy band. The direction and timing of genetic exchange between the two regions could not be ascertained and thus still remains unknown. Microsatellite analysis determined that both Phragmites spp. had a high genetic diversity compared to worldwide lineages. With no evidence of any cryptic invasions of haplotypes from other regions, both Phragmites spp. populations are likely to be native to South Africa. For A. donax all populations across South Africa were determined to be haplotype M1; a cosmopolitan haplotype that has an ancient native range in Afghanistan and Pakistan (Indus Valley). Populations were found to have no genetic diversity and thus can be considered one clone. A pre-introductory survey determined a list of herbivores associated with each tall- statured grass. For A. donax, a total of seven herbivores were found. Of these, one herbivore, a galling wasp, Tetramesa romana Walker (Hymenoptera: Eurytomidae) was found to be highly abundant and widely distributed in South Africa. Tetramesa romana is already a biological control agent in North America and thus is likely exerting some pressure on A. donax populations in South Africa. For both Phragmites spp. a total of ten herbivores were found, although having higher species richness compared to A. donax, when compared to other regions, these native species have a relatively low species richness. Providing baseline data on plant origin, genetic diversity and herbivory on A. donax, P. australis and P. mauritianus has provided important information on managing these species in riparian ecosystems in South Africa. For the Phragmites spp. with no evidence of any cryptic invasions, it is recommended that reed stands continue to be managed as native species. Phragmites spp. are important dominant vegetative species and thus should be protected; however, if reed stands become expansive, control methods can be put in place to focus on managing spread and abundance. For A. donax, this study was able to provide pivotal information in guiding the biological control programme. By determining the ancient lineage of South African populations, research can be focused in this area to find potential biological control agents. Lastly, the pre-introductory survey determined that a biological control agent, T. romana was already established with an unknown introduction and also highlighted potential plant parts that should be targeted. In particular, no rhizome feeding herbivores were found in South Africa and therefore this highlights an important niche that should be explored in biological control agents.
- Full Text:
- Date Issued: 2017
- Authors: Canavan, Kim
- Date: 2017
- Subjects: Insects as biological pest control agents -- South Africa , Arundo donax , Giant reed -- South Africa , Giant reed -- Biological control -- South Africa , Phragmites australis , Phragmites mauritianus , Phragmites , Tetramesa romana , Biological invasions -- South Africa , Wasps -- Host plants , Wasps -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/6147 , vital:21051
- Description: South African riparian zones have been heavily degraded through anthropogenic activities such as dam construction and extraction of water for irrigation, which has resulted in a loss of ecosystem services and functioning. A consequence of such disturbances to riparian areas is in their susceptibility to invasive alien species (IAS). One such IAS is the giant reed, Arundo donax L. (Poaceae), introduced to South Africa in the 1700s largely for erosion control. Arundo donax has since greatly expanded in the country and is now one of the most abundant IAS. Arundo donax has been found to displace native vegetation and in South Africa this will most likely lead to the displacement of the native tall-statured grasses, Phragmites australis (Cav.) Trin. ex Steud. and Phragmites mauritianus Kunth. This study aimed to enhance our understanding of the tall-statured grasses A. donax, P. australis and P. mauritianus to better manage them in riparian areas. For A. donax, biological control is seen as the most viable option to control stands in the long-term. However, before such a programme is put in place, it is important to first collect baseline data that can be used to guide the direction of the biological control project in South Africa. For the Phragmites spp., despite being a dominant vegetative type in riparian areas, very little is known about their status in South Africa. Furthermore, there have been increasing reports of both Phragmites species having an expansion of their range and abundance. In North America, there has been a similar trend of reed expansion and through molecular work it was determined that a cryptic invasion has occurred with the introduction of an invasive non-native haplotype from Europe. It is therefore unknown if Phragmites spp. populations are expanding due to anthropogenic activities or due to a cryptic invasion. To address these shortfalls in knowledge the study investigated the tall-statured grasses in two parts; firstly, molecular techniques are used to explore the plant origin and genetic diversity of A. donax, P. australis and P. mauritianus and secondly using the Enemy Release Hypothesis as a framework, herbivore assemblages for each reed was determined across their distribution in South Africa. Molecular-techniques determined that both P. australis and P. mauritianus had only one haplotype - known as haplotype K and haplotype V respectively, across their distribution. For P. australis, haplotype K shares a close connection with populations from a Mediterranean lineage and this was further confirmed with a shared grass-waxy band. The direction and timing of genetic exchange between the two regions could not be ascertained and thus still remains unknown. Microsatellite analysis determined that both Phragmites spp. had a high genetic diversity compared to worldwide lineages. With no evidence of any cryptic invasions of haplotypes from other regions, both Phragmites spp. populations are likely to be native to South Africa. For A. donax all populations across South Africa were determined to be haplotype M1; a cosmopolitan haplotype that has an ancient native range in Afghanistan and Pakistan (Indus Valley). Populations were found to have no genetic diversity and thus can be considered one clone. A pre-introductory survey determined a list of herbivores associated with each tall- statured grass. For A. donax, a total of seven herbivores were found. Of these, one herbivore, a galling wasp, Tetramesa romana Walker (Hymenoptera: Eurytomidae) was found to be highly abundant and widely distributed in South Africa. Tetramesa romana is already a biological control agent in North America and thus is likely exerting some pressure on A. donax populations in South Africa. For both Phragmites spp. a total of ten herbivores were found, although having higher species richness compared to A. donax, when compared to other regions, these native species have a relatively low species richness. Providing baseline data on plant origin, genetic diversity and herbivory on A. donax, P. australis and P. mauritianus has provided important information on managing these species in riparian ecosystems in South Africa. For the Phragmites spp. with no evidence of any cryptic invasions, it is recommended that reed stands continue to be managed as native species. Phragmites spp. are important dominant vegetative species and thus should be protected; however, if reed stands become expansive, control methods can be put in place to focus on managing spread and abundance. For A. donax, this study was able to provide pivotal information in guiding the biological control programme. By determining the ancient lineage of South African populations, research can be focused in this area to find potential biological control agents. Lastly, the pre-introductory survey determined that a biological control agent, T. romana was already established with an unknown introduction and also highlighted potential plant parts that should be targeted. In particular, no rhizome feeding herbivores were found in South Africa and therefore this highlights an important niche that should be explored in biological control agents.
- Full Text:
- Date Issued: 2017
Ngomso 'special school': contestations of morality and education in the Eastern Cape
- Authors: Pattenden, Oliver
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/65200 , vital:28704
- Description: Expected release date-May 2019
- Full Text:
- Date Issued: 2017
- Authors: Pattenden, Oliver
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/65200 , vital:28704
- Description: Expected release date-May 2019
- Full Text:
- Date Issued: 2017
Synthesis and biological evaluation of anti-HIV-I integrase agents
- Jesumoroti, Omobolanle Janet
- Authors: Jesumoroti, Omobolanle Janet
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/59215 , vital:27479
- Description: Expected release date-April 2019
- Full Text:
- Date Issued: 2017
- Authors: Jesumoroti, Omobolanle Janet
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/59215 , vital:27479
- Description: Expected release date-April 2019
- Full Text:
- Date Issued: 2017
Systematics and biogeography of forest snails, chondrocyclus (mollusca: gastropoda: caenogastropoda: cyclophoridae) in Southern Africa
- Authors: Cole, Mary Louise
- Date: 2017
- Subjects: Chondrocyclus , Mollusks -- South Africa , Cyclophoridae -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/4356 , vital:20651
- Description: This study presents a molecular phylogeny and systematic revision of Chondrocyclus, the major South African group of the large family of operculate terrestrial molluscs, the Cyclophoridae. Chondrocyclus snails are small gastropods found in forest and moist thicket throughout South Africa. This is the first detailed systematic treatment of a group of Cyclophoridae in mainland Africa and the first to provide molecular data. This study complements regional studies on the systematics of the family in Asia and provides comparative data for studies of higher level relationships within the Cyclophoridae. Phylogenetic reconstruction by BI and ML methods of combined and single gene datasets of 16S and CO 1 all showed Chondrocyclus to be monophyletic and recovered five well-supported clades that corresponded to groups of populations identifiable on the basis of combinations of morphological characters. Species were diagnosed morphologically and were shown to be genetically distinct lineages. Informative morphological features include shell dimensions, protoconch, periostracum, operculum, radula and penis. Two species in Afromontane regions of Zimbabwe and Malawi respectively are excluded from Chondrocyclus based on morphology and tentatively placed in Cyathopoma. Diversity recognised within the genus more than doubled, from a previous seven South African species to seventeen. Re-descriptions of established species and descriptions of new species are provided, together with photographs of morphological characteristics. New taxon names and nomenclatural acts within it are disclaimed and are therefore not available in the sense of the International Code of Zoological Nomenclature until validly published elsewhere. Several cryptic species within previously widespread “species” and unrecorded narrowly endemic species were documented. The clade consisting of populations of “Chondrocyclus isipingoensis”, now considered to be a species complex, was sister to a group containing the other four clades. The “Isipingoensis” clade occurs widely in Afromontane regions, along the Great Escarpment, and on the south-east coast. The other four clades occur from Zululand to the Cape Peninsula with a pattern of east-west lineage turnover. The biogeography of Chondrocyclus is interpreted by comparison with concordant patterns in other terrestrial molluscs and unrelated taxa with poor dispersal ability. This study complements other research on composition, spatial distribution and phylogenetic diversity of low-vagility invertebrates and expands the data available for biodiversity conservation in South Africa.
- Full Text:
- Date Issued: 2017
- Authors: Cole, Mary Louise
- Date: 2017
- Subjects: Chondrocyclus , Mollusks -- South Africa , Cyclophoridae -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/4356 , vital:20651
- Description: This study presents a molecular phylogeny and systematic revision of Chondrocyclus, the major South African group of the large family of operculate terrestrial molluscs, the Cyclophoridae. Chondrocyclus snails are small gastropods found in forest and moist thicket throughout South Africa. This is the first detailed systematic treatment of a group of Cyclophoridae in mainland Africa and the first to provide molecular data. This study complements regional studies on the systematics of the family in Asia and provides comparative data for studies of higher level relationships within the Cyclophoridae. Phylogenetic reconstruction by BI and ML methods of combined and single gene datasets of 16S and CO 1 all showed Chondrocyclus to be monophyletic and recovered five well-supported clades that corresponded to groups of populations identifiable on the basis of combinations of morphological characters. Species were diagnosed morphologically and were shown to be genetically distinct lineages. Informative morphological features include shell dimensions, protoconch, periostracum, operculum, radula and penis. Two species in Afromontane regions of Zimbabwe and Malawi respectively are excluded from Chondrocyclus based on morphology and tentatively placed in Cyathopoma. Diversity recognised within the genus more than doubled, from a previous seven South African species to seventeen. Re-descriptions of established species and descriptions of new species are provided, together with photographs of morphological characteristics. New taxon names and nomenclatural acts within it are disclaimed and are therefore not available in the sense of the International Code of Zoological Nomenclature until validly published elsewhere. Several cryptic species within previously widespread “species” and unrecorded narrowly endemic species were documented. The clade consisting of populations of “Chondrocyclus isipingoensis”, now considered to be a species complex, was sister to a group containing the other four clades. The “Isipingoensis” clade occurs widely in Afromontane regions, along the Great Escarpment, and on the south-east coast. The other four clades occur from Zululand to the Cape Peninsula with a pattern of east-west lineage turnover. The biogeography of Chondrocyclus is interpreted by comparison with concordant patterns in other terrestrial molluscs and unrelated taxa with poor dispersal ability. This study complements other research on composition, spatial distribution and phylogenetic diversity of low-vagility invertebrates and expands the data available for biodiversity conservation in South Africa.
- Full Text:
- Date Issued: 2017
The epidemiology of African horse sickness in the Eastern Cape, South Africa
- Authors: Riddin, Megan Amy
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64460 , vital:28546
- Description: Expected release date-May 2019
- Full Text:
- Date Issued: 2017
- Authors: Riddin, Megan Amy
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64460 , vital:28546
- Description: Expected release date-May 2019
- Full Text:
- Date Issued: 2017
The isolation and genetic characterisation of a novel alphabaculovirus for the microbial control of Cryptophlebia peltastica and closely related tortricid pests
- Authors: Marsberg, Tamryn
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/59292 , vital:27543
- Description: Cryptophlebia peltastica (Meyrick) (Lepidoptera: Tortricidae) is an economically damaging pest of litchis and macadamias in South Africa. Cryptophlebia peltastica causes both pre- and post-harvest damage to litchis, reducing overall yields and thus classifying the pest as a phytosanitary risk. Various control methods have been implemented against C. peltastica in an integrated pest management programme. These control methods include chemical control, cultural control and biological control. However, these methods have not yet provided satisfactory control as of yet. As a result, an alternative control option needs to be identified and implemented into the IPM programme. An alternative method of control that has proved successful in other agricultural sectors and not yet implemented in the control of C. peltastica is that of microbial control, specifically the use of baculovirus biopesticides. This study aimed to isolate and characterise a novel baculovirus from a laboratory culture of C. peltastica that could be used as a commercially available baculovirus biopesticide. In order to isolate a baculovirus a laboratory culture of C. peltastica was successfully established at Rhodes University, Grahamstown, South Africa. This is the first time a laboratory culture of C. peltastica has been established. This allowed for various biological aspects of the pest to be determined, which included: length of the life cycle, fecundity and time to oviposition, egg and larval development and percentage hatch. The results obtained from these studies found that the biology of C. peltastica was similar to that of Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae). Once the laboratory culture had reached high densities, larvae showing symptoms of baculovirus infection were observed. Symptomatic larvae were collected and examined for the presence of a baculovirus. An alphabaculovirus (NPV) was successfully isolated and morphologically identified using purified OBs that were sectioned and observed by transmission electron microscopy. This was then confirmed by amplifying the polyhedrin gene region using degenerate primers. A BLAST analysis found a 93% similarity to a partial polyhedrin gene sequence to be that of Epinotia granitalis (Butler) (Lepidoptera: Tortricidae). The alphabaculovirus was then genetically characterised by generating restriction profiles and sequencing the whole genome. Due to the novelty of the virus, no comparison could be made. The biological activity of the alphabaculovirus was then tested against C. peltastica and two closely related Tortricidae pests: T. leucotreta and Cydiapomonella (Linnaeous) (Lepidoptera: Tortricidae). The alphabaculovirus was highly virulent against all three species. The lethal concentrations (LC50 and LC90) for the virus against C. peltastica was 8.19 x 103 and 3.33 x 105 OBs/ml. The LC50 and LC90 for T. leucotreta was 2.29 x 103 and 9.97 x 104 OBs/ml, respectively and C. pomonella had a LC50 of 1.43 x 103 OBs/ml and LC90 1.26 x 104 OBs/ml. The virus was particularly virulent against T. leucotreta and C. pomonella as compared to C. peltastica. The biological activity of the alphabaculovirus was also tested against CpGV resistant European C. pomonella. From the results it was observed that the virus had the ability to overcome the resistance in C. pomonella and could potentially be used in the resistance management of C. pomonella. With the successful biological activity results obtained from this study, preliminary investigation were made into the mass production of the alphabaculovirus using both the in vivo and in vitro production methods. For in vivo production both the homologous host (C. peltastica) and a heterologous host (T leucotreta) were investigated. Preliminary studies focused on determining the biological activity in fifth instars of both hosts. Fifth instar LC50 and LC90 values for C. peltastica were 3.43 x 103 and 1.11 x 107 OBs/ml and for T. leucotreta the LC50 and LC90 values were 2.53 x 103 and 8.82 x 106 OBs/ml, respectively. The average yield of virus produced in each species was also determined. Cryptophlebia peltastica had the highest viral yield of 5.37 x 1010 OBs/larva and 2.93 x 1010 OBs/larva for T. leucotreta. The results obtained, from the preliminary investigation concluded that the virus could be produced in vivo in both C. peltastica and T. leucotreta, however further research is required into the mass production in both hosts. The in vitro production of the virus was also considered and the susceptibility of the virus was tested against the C. pomonella cell line, Cp14R. After infection of the Cp14R cells with budded virus collected from fifth instar C. peltastica larvae, OBs could be observed after three days. Thus, the alphabaculovirus is susceptible to the Cp14R cell line, thus has the potential to be produced in vitro and further characterised. This study is the first to report of the identification and characterisation of a novel alphabaculovirus isolated from a laboratory reared culture of C. peltastica and the potential for it to be commercially developed into a bipoesticide and used against Tortricidae pests.
- Full Text:
- Date Issued: 2017
- Authors: Marsberg, Tamryn
- Date: 2017
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/59292 , vital:27543
- Description: Cryptophlebia peltastica (Meyrick) (Lepidoptera: Tortricidae) is an economically damaging pest of litchis and macadamias in South Africa. Cryptophlebia peltastica causes both pre- and post-harvest damage to litchis, reducing overall yields and thus classifying the pest as a phytosanitary risk. Various control methods have been implemented against C. peltastica in an integrated pest management programme. These control methods include chemical control, cultural control and biological control. However, these methods have not yet provided satisfactory control as of yet. As a result, an alternative control option needs to be identified and implemented into the IPM programme. An alternative method of control that has proved successful in other agricultural sectors and not yet implemented in the control of C. peltastica is that of microbial control, specifically the use of baculovirus biopesticides. This study aimed to isolate and characterise a novel baculovirus from a laboratory culture of C. peltastica that could be used as a commercially available baculovirus biopesticide. In order to isolate a baculovirus a laboratory culture of C. peltastica was successfully established at Rhodes University, Grahamstown, South Africa. This is the first time a laboratory culture of C. peltastica has been established. This allowed for various biological aspects of the pest to be determined, which included: length of the life cycle, fecundity and time to oviposition, egg and larval development and percentage hatch. The results obtained from these studies found that the biology of C. peltastica was similar to that of Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae). Once the laboratory culture had reached high densities, larvae showing symptoms of baculovirus infection were observed. Symptomatic larvae were collected and examined for the presence of a baculovirus. An alphabaculovirus (NPV) was successfully isolated and morphologically identified using purified OBs that were sectioned and observed by transmission electron microscopy. This was then confirmed by amplifying the polyhedrin gene region using degenerate primers. A BLAST analysis found a 93% similarity to a partial polyhedrin gene sequence to be that of Epinotia granitalis (Butler) (Lepidoptera: Tortricidae). The alphabaculovirus was then genetically characterised by generating restriction profiles and sequencing the whole genome. Due to the novelty of the virus, no comparison could be made. The biological activity of the alphabaculovirus was then tested against C. peltastica and two closely related Tortricidae pests: T. leucotreta and Cydiapomonella (Linnaeous) (Lepidoptera: Tortricidae). The alphabaculovirus was highly virulent against all three species. The lethal concentrations (LC50 and LC90) for the virus against C. peltastica was 8.19 x 103 and 3.33 x 105 OBs/ml. The LC50 and LC90 for T. leucotreta was 2.29 x 103 and 9.97 x 104 OBs/ml, respectively and C. pomonella had a LC50 of 1.43 x 103 OBs/ml and LC90 1.26 x 104 OBs/ml. The virus was particularly virulent against T. leucotreta and C. pomonella as compared to C. peltastica. The biological activity of the alphabaculovirus was also tested against CpGV resistant European C. pomonella. From the results it was observed that the virus had the ability to overcome the resistance in C. pomonella and could potentially be used in the resistance management of C. pomonella. With the successful biological activity results obtained from this study, preliminary investigation were made into the mass production of the alphabaculovirus using both the in vivo and in vitro production methods. For in vivo production both the homologous host (C. peltastica) and a heterologous host (T leucotreta) were investigated. Preliminary studies focused on determining the biological activity in fifth instars of both hosts. Fifth instar LC50 and LC90 values for C. peltastica were 3.43 x 103 and 1.11 x 107 OBs/ml and for T. leucotreta the LC50 and LC90 values were 2.53 x 103 and 8.82 x 106 OBs/ml, respectively. The average yield of virus produced in each species was also determined. Cryptophlebia peltastica had the highest viral yield of 5.37 x 1010 OBs/larva and 2.93 x 1010 OBs/larva for T. leucotreta. The results obtained, from the preliminary investigation concluded that the virus could be produced in vivo in both C. peltastica and T. leucotreta, however further research is required into the mass production in both hosts. The in vitro production of the virus was also considered and the susceptibility of the virus was tested against the C. pomonella cell line, Cp14R. After infection of the Cp14R cells with budded virus collected from fifth instar C. peltastica larvae, OBs could be observed after three days. Thus, the alphabaculovirus is susceptible to the Cp14R cell line, thus has the potential to be produced in vitro and further characterised. This study is the first to report of the identification and characterisation of a novel alphabaculovirus isolated from a laboratory reared culture of C. peltastica and the potential for it to be commercially developed into a bipoesticide and used against Tortricidae pests.
- Full Text:
- Date Issued: 2017
Aquatic–terrestrial trophic linkages via riverine invertebrates in a South African catchment
- Authors: Moyo, Sydney
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54427 , vital:26564
- Description: Rivers play a vital role in human livelihoods and are likely to undergo substantial alteration due to climate and land use changes from an increasing human population. Mitigating the pressures facing rivers in the world requires scientists and environmental managers to understand the ecological mechanisms, and ultimately the strength, of connections between ecosystems. This understanding of connections between adjacent habitats will enable environmental managers to predict the consequences of perturbing these linkages in the future. In this thesis, aquatic-terrestrial linkages in rivers were investigated using ecologically meaningful variables including abundances, biomasses, stable isotopes and fatty acids. This study is part of a larger project entitled “Connectivity through allochthony: reciprocal links between adjacent aquatic and terrestrial ecosystems in South Africa”, in which a team of researchers assessed a variety of pathways connecting riverine and estuarine systems to land within a catchment in the Eastern Cape, South Africa. I conceptualised the flow of energy within a temperate southern hemisphere river (the Kowie River) within theoretical models of energy flow such as the River Continuum Concept (RCC; presents lotic systems as being longitudinally linked with food webs in shaded headwaters being principally driven by allochthonous energy, with the addition of autochthonous food as a minor carbon source in the lower reaches) and the Riverine Productivity Model (RPM; proposes consumers derive most of their energy from local production of phytoplankton, benthic algae and aquatic plants, as well as directly from riparian zones via terrestrial leaf litter). Using the RCC as a starting point, I collected macroinvertebrates (September 2012 to May 2013) along a longitudinal gradient and grouped them into functional feeding groups (FFGs). The results revealed that gatherers and filterers dominated in the Kowie River, and together represented 50 – 83% of the invertebrate assemblages. There was a general paucity of shredders (relative abundance was ≤ 10% across all sites and seasons). The changes in relative abundances of different FFGs did not follow predictions of the RCC along the longitudinal gradient, as there were no correlations of community structure with some physical attributes (stream width, canopy cover, distance of river) that changed along the river continuum. However, FFG abundances were related to water velocity, total dissolved solids and canopy cover. Broadly, the Kowie River data showed that changes in relative abundances of FFGs along the river continuum could not be explained by changes in physical attributes alone, and may be highly influenced by the availability of food and the chemistry of the stream. Analysis of stable carbon (δ13C) and nitrogen (δ15N) isotopes was used to estimate the contributions of algal and land-based production to consumers over space (six sites) and time (November 2012 to September 2013). Carbon contributions determined by the use of mixing models (Stable Isotope Analysis in R) revealed that consumers in the headwater assimilated mainly terrestrially-derived organic matter, with consumers in the middle and lower reaches assimilating autochthonous basal resources (macrophytes and algae). The findings from this river supported aspects of the RCC (at the headwaters; terrestrial organic matter made up 41% of consumer diets), but overall the data supported the predictions of the RPM (local production made the highest contributions of 50 – 86% to all FFGs across all seasons). The carbon isotopes of consumers and their food sources changed substantially every season, indicating that samples of food sources and consumers should be analysed many times throughout the year to capture that variability and to ensure that ephemeral components of the food web are not missed. To validate the findings from the isotope data, fatty acids were used as complementary tracers to determine the contributions of algal versus terrestrial organic matter to the consumers. Fatty acid tracers for terrestrial (Ʃω3/Ʃω6; 18:2ω6; 18:3ω3) vs aquatic (Ʃω3/Ʃω6; 20:5ω3) sources corroborated the findings from the isotope data set, as the mean ratio of Ʃω3/Ʃω6 in consumers was less than one at the headwaters (indicating allochthony), while middle and lower reaches were associated with Ʃω3/Ʃω6 > 1 (indicating autochthony). In addition to the tracer and FFG analyses for examining trophic connections between land and river, the bidirectional exchange of organisms between the riparian zone and the river was assessed using floating pyramidal traps (to measure emergence) and pan traps (for infalling invertebrates) placed at different sites in the river and the biomass in each trap was determined. The exchanges were variable over space and time, with emergence peaking in summer (169 to 1402 mg m-2 day-1) and declining in winter (3 to 28 mg m-2 day-1). Similarly, infalling invertebrates increased in summer (413 to 679 mg m-2 day-1) and declined in winter (11 to 220 mg m-2 day-1). Biomass measurements are indications of quantity that ignore nutritional quality, so I determined the bidirectional flow of invertebrates using absolute concentrations of physiologically important biochemical compounds (essential and polyunsaturated fatty acids). The fluxes of emergent and infalling arthropods peaked in summer (emergence = 0.3 to 18 mg m-2 day-1 and terrestrial infall = 0.3 to 3 mg m-2 day-1) and declined in winter (emergence = 0.01 to 0.51 mg m-2 day-1 and terrestrial infall = 0.01 to 0.03 mg m-2 day-1). However, during some seasons, no significant differences in polyunsaturated fatty acid flux in either direction were observed; this finding indicated the balance of reciprocal subsidisation via reciprocal flows of animals. Factors such as air temperature and algal productivity affected the reciprocal flows between adjacent habitats, with algal productivity being positively related to emergence while air temperature was positively correlated to infalling terrestrial invertebrates. This research enhances the growing body of literature on the function of riverine systems and offers some invaluable information on the flow of energy and the role played by invertebrates in translocating nutrients from terrestrial systems to aquatic systems and vice versa. This study unifies the concepts of the RCC and RPM and shows that these concepts are not limited only to large rivers, but are applicable to small southern temperate rivers too. However, some tenets of the theoretical models were challenged. For example, it challenges the proposition by the RCC that the fine particulate organic matter leaked from upstream breakdown of coarse particulate organic matter is predominantly allochthonous. Additionally, this study showed that in the headwaters, the RPM underestimated the role of autochthony. Overall, the results showed that the Kowie River and its riparian area are intrinsically connected. Once we understand the mechanisms controlling connections and subsidies across ecotones, we can then start to predict the consequences of disruptions to these connections by climate change and/or land use changes. To make predictions about future perturbations to rivers and riparian zones, studies like this, which considers the form and magnitude of subsidies, are needed to provide baseline information. Algal resources (e.g. epiphyton), macrophytes, riparian plants, terrestrial organisms and aquatic organisms all contributed to aquatic and terrestrial linkages in the Kowie River; therefore, it is important to conserve the different components of these ecosystems.
- Full Text:
- Date Issued: 2016
- Authors: Moyo, Sydney
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54427 , vital:26564
- Description: Rivers play a vital role in human livelihoods and are likely to undergo substantial alteration due to climate and land use changes from an increasing human population. Mitigating the pressures facing rivers in the world requires scientists and environmental managers to understand the ecological mechanisms, and ultimately the strength, of connections between ecosystems. This understanding of connections between adjacent habitats will enable environmental managers to predict the consequences of perturbing these linkages in the future. In this thesis, aquatic-terrestrial linkages in rivers were investigated using ecologically meaningful variables including abundances, biomasses, stable isotopes and fatty acids. This study is part of a larger project entitled “Connectivity through allochthony: reciprocal links between adjacent aquatic and terrestrial ecosystems in South Africa”, in which a team of researchers assessed a variety of pathways connecting riverine and estuarine systems to land within a catchment in the Eastern Cape, South Africa. I conceptualised the flow of energy within a temperate southern hemisphere river (the Kowie River) within theoretical models of energy flow such as the River Continuum Concept (RCC; presents lotic systems as being longitudinally linked with food webs in shaded headwaters being principally driven by allochthonous energy, with the addition of autochthonous food as a minor carbon source in the lower reaches) and the Riverine Productivity Model (RPM; proposes consumers derive most of their energy from local production of phytoplankton, benthic algae and aquatic plants, as well as directly from riparian zones via terrestrial leaf litter). Using the RCC as a starting point, I collected macroinvertebrates (September 2012 to May 2013) along a longitudinal gradient and grouped them into functional feeding groups (FFGs). The results revealed that gatherers and filterers dominated in the Kowie River, and together represented 50 – 83% of the invertebrate assemblages. There was a general paucity of shredders (relative abundance was ≤ 10% across all sites and seasons). The changes in relative abundances of different FFGs did not follow predictions of the RCC along the longitudinal gradient, as there were no correlations of community structure with some physical attributes (stream width, canopy cover, distance of river) that changed along the river continuum. However, FFG abundances were related to water velocity, total dissolved solids and canopy cover. Broadly, the Kowie River data showed that changes in relative abundances of FFGs along the river continuum could not be explained by changes in physical attributes alone, and may be highly influenced by the availability of food and the chemistry of the stream. Analysis of stable carbon (δ13C) and nitrogen (δ15N) isotopes was used to estimate the contributions of algal and land-based production to consumers over space (six sites) and time (November 2012 to September 2013). Carbon contributions determined by the use of mixing models (Stable Isotope Analysis in R) revealed that consumers in the headwater assimilated mainly terrestrially-derived organic matter, with consumers in the middle and lower reaches assimilating autochthonous basal resources (macrophytes and algae). The findings from this river supported aspects of the RCC (at the headwaters; terrestrial organic matter made up 41% of consumer diets), but overall the data supported the predictions of the RPM (local production made the highest contributions of 50 – 86% to all FFGs across all seasons). The carbon isotopes of consumers and their food sources changed substantially every season, indicating that samples of food sources and consumers should be analysed many times throughout the year to capture that variability and to ensure that ephemeral components of the food web are not missed. To validate the findings from the isotope data, fatty acids were used as complementary tracers to determine the contributions of algal versus terrestrial organic matter to the consumers. Fatty acid tracers for terrestrial (Ʃω3/Ʃω6; 18:2ω6; 18:3ω3) vs aquatic (Ʃω3/Ʃω6; 20:5ω3) sources corroborated the findings from the isotope data set, as the mean ratio of Ʃω3/Ʃω6 in consumers was less than one at the headwaters (indicating allochthony), while middle and lower reaches were associated with Ʃω3/Ʃω6 > 1 (indicating autochthony). In addition to the tracer and FFG analyses for examining trophic connections between land and river, the bidirectional exchange of organisms between the riparian zone and the river was assessed using floating pyramidal traps (to measure emergence) and pan traps (for infalling invertebrates) placed at different sites in the river and the biomass in each trap was determined. The exchanges were variable over space and time, with emergence peaking in summer (169 to 1402 mg m-2 day-1) and declining in winter (3 to 28 mg m-2 day-1). Similarly, infalling invertebrates increased in summer (413 to 679 mg m-2 day-1) and declined in winter (11 to 220 mg m-2 day-1). Biomass measurements are indications of quantity that ignore nutritional quality, so I determined the bidirectional flow of invertebrates using absolute concentrations of physiologically important biochemical compounds (essential and polyunsaturated fatty acids). The fluxes of emergent and infalling arthropods peaked in summer (emergence = 0.3 to 18 mg m-2 day-1 and terrestrial infall = 0.3 to 3 mg m-2 day-1) and declined in winter (emergence = 0.01 to 0.51 mg m-2 day-1 and terrestrial infall = 0.01 to 0.03 mg m-2 day-1). However, during some seasons, no significant differences in polyunsaturated fatty acid flux in either direction were observed; this finding indicated the balance of reciprocal subsidisation via reciprocal flows of animals. Factors such as air temperature and algal productivity affected the reciprocal flows between adjacent habitats, with algal productivity being positively related to emergence while air temperature was positively correlated to infalling terrestrial invertebrates. This research enhances the growing body of literature on the function of riverine systems and offers some invaluable information on the flow of energy and the role played by invertebrates in translocating nutrients from terrestrial systems to aquatic systems and vice versa. This study unifies the concepts of the RCC and RPM and shows that these concepts are not limited only to large rivers, but are applicable to small southern temperate rivers too. However, some tenets of the theoretical models were challenged. For example, it challenges the proposition by the RCC that the fine particulate organic matter leaked from upstream breakdown of coarse particulate organic matter is predominantly allochthonous. Additionally, this study showed that in the headwaters, the RPM underestimated the role of autochthony. Overall, the results showed that the Kowie River and its riparian area are intrinsically connected. Once we understand the mechanisms controlling connections and subsidies across ecotones, we can then start to predict the consequences of disruptions to these connections by climate change and/or land use changes. To make predictions about future perturbations to rivers and riparian zones, studies like this, which considers the form and magnitude of subsidies, are needed to provide baseline information. Algal resources (e.g. epiphyton), macrophytes, riparian plants, terrestrial organisms and aquatic organisms all contributed to aquatic and terrestrial linkages in the Kowie River; therefore, it is important to conserve the different components of these ecosystems.
- Full Text:
- Date Issued: 2016
Community structure and trophic ecology of shallow and deep rocky reefs in a well-established marine protected area
- Authors: Heyns, Elodie R
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54438 , vital:26565
- Description: The now formally adopted ecosystem approach to fisheries (EAF) considers not only commercially important species, but the entire ecosystem and the processes that support these species. A key component of EAF management is the implementation of no-take Marine Protected Areas (MPAs). Shallow water fish stocks are depleted and fishing effort is moving deeper and further offshore to keep up with demands. This situation calls for a detailed investigation of deep nearshore reefs to provide critical information relevant to policy uptake and management decisions regarding existing and new MPAs in terms of zonation and use. To address this need, the aim of this thesis was to investigate reefs that lie between 45 and 75 m and compare them in terms of community structure and function to the relatively well-studied shallow reefs that lie within SCUBA diving depth (<25 m). Ecological collections were made in the centre of a large and well-established MPA, Tsitsikamma National Park, to ensure that data represented non-anthropogenically impacted communities. Data were collected from two study sites; Rheeders Reef, (shallow reef) and Middlebank, a deep reef complex situated near the Storms River Mouth. The first step to address the aim of this study was to obtain baseline data on the distribution patterns of both the macrobenthic invertebrates and fish assemblages. Baseline data were obtained by underwater video methods and included the use of a remotely operated vehicle, baited remote underwater stereo-video systems (stereo-BRUVs) and traditional underwater camera equipment operated by SCUBA divers. To establish functional differences between the two study sites, fatty acid (FA) and stable isotope (SI) analyses were employed. These biomarker techniques provided insight into the importance of different sources of primary production, nutritional condition and species packing. From 360 photoquadrats examined for macrobenthic invertebrate distribution patterns, 161 invertebrates were identified that demonstrated a clear changeover of species along the depth gradient. Species richness was highest on the shallow reef and decreased with an increase in depth. To understand how the measured environmental variables impacted the macrobenthic assemblage data a LINKTREE analysis was performed. LINKTREEs produce hierarchical cluster analysis based on the macrobenthic assemblage data and provide a threshold of environmental variables that correspond to each cluster. The outcome of the LINKTREE analysis indicated that the changeover of species resulted in four distinct clusters, each cluster associated with a particular set of environmental variables that fell within a depth range. On the shallowest sites, the high energy environment resulting from wave action and surge prevented the settlement of suspended particles. The high energy environment of the shallow reef selected for low-growing encrusting species. High light intensities supported great abundances of benthic algae, and as light was lost with increasing depth, algal cover gradually diminished until it was completely absent on the deep reef. The reduced impact of surface wave action on the deep reef caused increased levels of settled suspended particles. The high levels of settled particles likely caused clogging of feeding parts of the encrusting species. Consequently, upright growth forms were more common in the lower energy environment of the deep reef. A total of 48 fish species were identified from 51 stereo-BRUVs samples. Fish assemblages differed significantly between the shallow and deep reefs. The shallowest sites were characterised by many small and juvenile fish species that fed at lower trophic levels. The deep reef supported the majority of the large predatory fish that fed at higher trophic levels. Many species demonstrated depth-related ontogenetic shifts in habitat use, and as such the deep reef hosted the majority of the sexually mature individuals. The fish assemblages also demonstrated a strong association with the macrobenthic clusters identified as habitat types by the LINKTREE analysis. The results from 201 FA and 191 SI samples provided information on specific feeding interactions, but more importantly shed some light on different processes that supported the shallow and deep reef communities. The shallow reef community was characterised by greater diversity of food sources, a pattern that could be explained by the presence of benthic algae and terrestrial inputs. Greater diversity of carbon sources at the bottom of the food web meant that a larger variety of species could be supported. Higher species richness increased the number of distinct taxa that performed similar functions, rendering the shallow reef more redundant and consequently more resilient to disturbance. In contrast, the deep reef demonstrated a food web supported mainly by pelagic production, which was more variable both over space and time. The deep reef was less redundant when compared to the shallow reef, as fewer species demonstrated similar trophic niches. These factors, in addition to the increased presence of sensitive calcareous macrobenthic species on the deep study site, rendered the deep reef more vulnerable to disturbance when compared to the shallow reef. Although the data presented here were from a single study area, the limitations typically associated with these inaccessible and challenging sampling environments made the dataset a significant contribution to the knowledge of reef ecosystems. The study addressed priority research questions for South Africa as identified during the National Biodiversity Assessment. The observable differences in structure, function and vulnerability point to the need for continued protection of our shallow reefs and offshore expansion of our MPA networks. Future research should determine if the patterns identified here are common throughout the Agulhas Ecoregion to provide managers with robust evidence for the extension our MPAs offshore.
- Full Text:
- Date Issued: 2016
- Authors: Heyns, Elodie R
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54438 , vital:26565
- Description: The now formally adopted ecosystem approach to fisheries (EAF) considers not only commercially important species, but the entire ecosystem and the processes that support these species. A key component of EAF management is the implementation of no-take Marine Protected Areas (MPAs). Shallow water fish stocks are depleted and fishing effort is moving deeper and further offshore to keep up with demands. This situation calls for a detailed investigation of deep nearshore reefs to provide critical information relevant to policy uptake and management decisions regarding existing and new MPAs in terms of zonation and use. To address this need, the aim of this thesis was to investigate reefs that lie between 45 and 75 m and compare them in terms of community structure and function to the relatively well-studied shallow reefs that lie within SCUBA diving depth (<25 m). Ecological collections were made in the centre of a large and well-established MPA, Tsitsikamma National Park, to ensure that data represented non-anthropogenically impacted communities. Data were collected from two study sites; Rheeders Reef, (shallow reef) and Middlebank, a deep reef complex situated near the Storms River Mouth. The first step to address the aim of this study was to obtain baseline data on the distribution patterns of both the macrobenthic invertebrates and fish assemblages. Baseline data were obtained by underwater video methods and included the use of a remotely operated vehicle, baited remote underwater stereo-video systems (stereo-BRUVs) and traditional underwater camera equipment operated by SCUBA divers. To establish functional differences between the two study sites, fatty acid (FA) and stable isotope (SI) analyses were employed. These biomarker techniques provided insight into the importance of different sources of primary production, nutritional condition and species packing. From 360 photoquadrats examined for macrobenthic invertebrate distribution patterns, 161 invertebrates were identified that demonstrated a clear changeover of species along the depth gradient. Species richness was highest on the shallow reef and decreased with an increase in depth. To understand how the measured environmental variables impacted the macrobenthic assemblage data a LINKTREE analysis was performed. LINKTREEs produce hierarchical cluster analysis based on the macrobenthic assemblage data and provide a threshold of environmental variables that correspond to each cluster. The outcome of the LINKTREE analysis indicated that the changeover of species resulted in four distinct clusters, each cluster associated with a particular set of environmental variables that fell within a depth range. On the shallowest sites, the high energy environment resulting from wave action and surge prevented the settlement of suspended particles. The high energy environment of the shallow reef selected for low-growing encrusting species. High light intensities supported great abundances of benthic algae, and as light was lost with increasing depth, algal cover gradually diminished until it was completely absent on the deep reef. The reduced impact of surface wave action on the deep reef caused increased levels of settled suspended particles. The high levels of settled particles likely caused clogging of feeding parts of the encrusting species. Consequently, upright growth forms were more common in the lower energy environment of the deep reef. A total of 48 fish species were identified from 51 stereo-BRUVs samples. Fish assemblages differed significantly between the shallow and deep reefs. The shallowest sites were characterised by many small and juvenile fish species that fed at lower trophic levels. The deep reef supported the majority of the large predatory fish that fed at higher trophic levels. Many species demonstrated depth-related ontogenetic shifts in habitat use, and as such the deep reef hosted the majority of the sexually mature individuals. The fish assemblages also demonstrated a strong association with the macrobenthic clusters identified as habitat types by the LINKTREE analysis. The results from 201 FA and 191 SI samples provided information on specific feeding interactions, but more importantly shed some light on different processes that supported the shallow and deep reef communities. The shallow reef community was characterised by greater diversity of food sources, a pattern that could be explained by the presence of benthic algae and terrestrial inputs. Greater diversity of carbon sources at the bottom of the food web meant that a larger variety of species could be supported. Higher species richness increased the number of distinct taxa that performed similar functions, rendering the shallow reef more redundant and consequently more resilient to disturbance. In contrast, the deep reef demonstrated a food web supported mainly by pelagic production, which was more variable both over space and time. The deep reef was less redundant when compared to the shallow reef, as fewer species demonstrated similar trophic niches. These factors, in addition to the increased presence of sensitive calcareous macrobenthic species on the deep study site, rendered the deep reef more vulnerable to disturbance when compared to the shallow reef. Although the data presented here were from a single study area, the limitations typically associated with these inaccessible and challenging sampling environments made the dataset a significant contribution to the knowledge of reef ecosystems. The study addressed priority research questions for South Africa as identified during the National Biodiversity Assessment. The observable differences in structure, function and vulnerability point to the need for continued protection of our shallow reefs and offshore expansion of our MPA networks. Future research should determine if the patterns identified here are common throughout the Agulhas Ecoregion to provide managers with robust evidence for the extension our MPAs offshore.
- Full Text:
- Date Issued: 2016
Phylogenetics and historical biogeography of the Teloganodidae (Ephemeroptera)
- Pereira da Conceicoa, Lyndall Louise
- Authors: Pereira da Conceicoa, Lyndall Louise
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64900 , vital:28629
- Description: The Teloganodidae are a mayfly family endemic to the southwestern Cape (South Africa), with relatives in Madagascar and Asia. Like many other aquatic invertebrates in Africa, they have been considerably understudied. Research into biodiversity and biogeography allows an understanding of the earth’s biota, producing knowledge which can be used to develop strategies to preserve and monitor this biota. Mismanagement of water systems places biodiversity of river fauna under an ever-increasing extinction threat. This investigation explores rivers in under-collected areas to determine how well teloganodids have been represented in the literature, with four genera and five species described at the onset of this study. A lectotype for Lestagella penicillata Barnard (1940) has been elected and described in detail, setting “benchmark” characters for future descriptions. Standard DNA sequencing methods provide portions of three mitochondrial genes; cytochrome oxidase subunit I (COI), small subunit ribosomal 16S RNA (16S), 12S ribosomal DNA (12S) and two nuclear genes, Histone 3 (H3) and 28S ribosomal DNA (28S) for up to 255 specimens. Fore and hind wings of 79 teloganodid adults were used to examine phylogenetic signal and evolutionary divergence using geometric morphometrics. A multi-faceted approach is used to investigate relationships between clades and the effects of deep-time climatic and landform changes which have influenced the diversity and distribution seen today. Tree (Bayesian Inference and Maximum Likelihood) and network (parsimony) phylogenies, ancestral reconstruction, historical biogeography and wingevolution of the Teloganodidae are investigated. Species tree analyses discovered 27 species and six genera. Distinct lineages are restricted to catchments, and strong phylogeographic structure was found within most genera. Southern African Teloganodidae are shown to have originated in the Cretaceous, with divergence and dispersal of lineages depended on their established locality at the time of tectonic events (uplift) and climatic changes (sea level regressions and transgressions). Geographic clines in wing-shape of Lestagella across its range imply evolutionary adaptations to specific catchment landscape and environment. A detailed analysis of biodiversity has many valuable contributions, from directing future research, understanding adaptive processes, fine-tuning phylogeographical and evolutionary hypotheses, to improving management and conservation decisions in order to preserve endemic biodiversity hotspots.
- Full Text:
- Date Issued: 2016
- Authors: Pereira da Conceicoa, Lyndall Louise
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64900 , vital:28629
- Description: The Teloganodidae are a mayfly family endemic to the southwestern Cape (South Africa), with relatives in Madagascar and Asia. Like many other aquatic invertebrates in Africa, they have been considerably understudied. Research into biodiversity and biogeography allows an understanding of the earth’s biota, producing knowledge which can be used to develop strategies to preserve and monitor this biota. Mismanagement of water systems places biodiversity of river fauna under an ever-increasing extinction threat. This investigation explores rivers in under-collected areas to determine how well teloganodids have been represented in the literature, with four genera and five species described at the onset of this study. A lectotype for Lestagella penicillata Barnard (1940) has been elected and described in detail, setting “benchmark” characters for future descriptions. Standard DNA sequencing methods provide portions of three mitochondrial genes; cytochrome oxidase subunit I (COI), small subunit ribosomal 16S RNA (16S), 12S ribosomal DNA (12S) and two nuclear genes, Histone 3 (H3) and 28S ribosomal DNA (28S) for up to 255 specimens. Fore and hind wings of 79 teloganodid adults were used to examine phylogenetic signal and evolutionary divergence using geometric morphometrics. A multi-faceted approach is used to investigate relationships between clades and the effects of deep-time climatic and landform changes which have influenced the diversity and distribution seen today. Tree (Bayesian Inference and Maximum Likelihood) and network (parsimony) phylogenies, ancestral reconstruction, historical biogeography and wingevolution of the Teloganodidae are investigated. Species tree analyses discovered 27 species and six genera. Distinct lineages are restricted to catchments, and strong phylogeographic structure was found within most genera. Southern African Teloganodidae are shown to have originated in the Cretaceous, with divergence and dispersal of lineages depended on their established locality at the time of tectonic events (uplift) and climatic changes (sea level regressions and transgressions). Geographic clines in wing-shape of Lestagella across its range imply evolutionary adaptations to specific catchment landscape and environment. A detailed analysis of biodiversity has many valuable contributions, from directing future research, understanding adaptive processes, fine-tuning phylogeographical and evolutionary hypotheses, to improving management and conservation decisions in order to preserve endemic biodiversity hotspots.
- Full Text:
- Date Issued: 2016
Predators of aerial insects and riparian cross-boundary trophic dynamics: web-building spiders, dragonflies and damselflies
- Authors: Chari, Lenin Dzibakwe
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/55791 , vital:26734
- Description: This thesis characterises the cross-boundary trophic interactions of a relatively small model ecosystem, the Kowie River (Eastern Cape of South Africa), to explore their epistemic implications for systems ecology. Using web-building spiders and odonates (dragonflies and damselflies) as model organisms, I sought to investigate whether the diets of predators of aerial insects could be used to assess the strength of the trophic connectivity between freshwater and terrestrial systems in relation to variables such as stream width, distance from the river and aquatic insect emergence rates and abundances. Predator diet composition was determined by using a combination of diet analysis tools: direct observations of cross-subsidies, naturally-abundant stable (carbon and nitrogen) isotope analysis and fatty acid analysis. I also sought to reveal feeding niches and guilds among riparian aerial predators and investigate how the environment influenced predators’ access to aquatic prey subsidies. As emergent aquatic insect abundances decreased with an increase in distance from the river, and increased with stream width and seasonal changes from winter to summer, stable isotope and fatty acid analyses revealed distinct changes in web-building spider diet composition. Examination of the fatty acid eicosapentaenoic acid, a component commonly used as an indicator of consumer reliance on aquatic nutritional subsidies, showed that aquatic subsidies extended further inland at the wider sections of the river. Spiders and odonates at the wider sections of the Kowie River generally received more subsidies (56 – 70%) than those at the narrower sections (25 – 60%). When terrestrial insect biomass was distinctly low in winter, the benefit of aquatic subsidisation to spiders was relatively lower at the narrower sections of the Kowie River relative to the wide sections. As such, riparian areas adjacent to wide parts of the river were more likely to support larger populations of aerial predators than those at the narrow sections. Apart from the diet changes across time and space, there was evidence of inter-specific niche partitioning in both spiders and odonates, but no differences were observed between males and females of the same species. Results showed odonates of different sizes and hunting strategies had separate dietary niches, hence varied access to aquatic nutritional subsidies. The larger odonate taxa that frequently foraged mid-air had more varied diets and relied less on aquatic emergent insects than the smaller odonates that foraged from perches near the river. There was also evidence of niche partitioning amongst the spiders, as those that built horizontal webs captured more aquatic insects (40 – 78%) than the vertical orb-web builders (20 – 66%). This study showed that the nature and extent of trophic cross-boundary linkages in riparian areas largely depended on the availability of subsidies that varied seasonally and spatially. The width of the stream and seasonal variability emerged as important predictors of emergent insect abundances/biomasses that influenced predator feeding niches. The high mobility of odonates made their reliance on aquatic nutritional subsidies different from the less mobile spiders. The link between the width of the river and the extent of trophic connectivity has implications for riparian area management and definition of riparian buffer zones. However, the variation in diet niches amongst terrestrial consumers makes the results area-specific, and more studies are required that incorporate additional terrestrial predators in other fluvial systems so that we can make some generalizations on the dynamics of riparian trophic cross-boundary links.
- Full Text:
- Date Issued: 2016
- Authors: Chari, Lenin Dzibakwe
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/55791 , vital:26734
- Description: This thesis characterises the cross-boundary trophic interactions of a relatively small model ecosystem, the Kowie River (Eastern Cape of South Africa), to explore their epistemic implications for systems ecology. Using web-building spiders and odonates (dragonflies and damselflies) as model organisms, I sought to investigate whether the diets of predators of aerial insects could be used to assess the strength of the trophic connectivity between freshwater and terrestrial systems in relation to variables such as stream width, distance from the river and aquatic insect emergence rates and abundances. Predator diet composition was determined by using a combination of diet analysis tools: direct observations of cross-subsidies, naturally-abundant stable (carbon and nitrogen) isotope analysis and fatty acid analysis. I also sought to reveal feeding niches and guilds among riparian aerial predators and investigate how the environment influenced predators’ access to aquatic prey subsidies. As emergent aquatic insect abundances decreased with an increase in distance from the river, and increased with stream width and seasonal changes from winter to summer, stable isotope and fatty acid analyses revealed distinct changes in web-building spider diet composition. Examination of the fatty acid eicosapentaenoic acid, a component commonly used as an indicator of consumer reliance on aquatic nutritional subsidies, showed that aquatic subsidies extended further inland at the wider sections of the river. Spiders and odonates at the wider sections of the Kowie River generally received more subsidies (56 – 70%) than those at the narrower sections (25 – 60%). When terrestrial insect biomass was distinctly low in winter, the benefit of aquatic subsidisation to spiders was relatively lower at the narrower sections of the Kowie River relative to the wide sections. As such, riparian areas adjacent to wide parts of the river were more likely to support larger populations of aerial predators than those at the narrow sections. Apart from the diet changes across time and space, there was evidence of inter-specific niche partitioning in both spiders and odonates, but no differences were observed between males and females of the same species. Results showed odonates of different sizes and hunting strategies had separate dietary niches, hence varied access to aquatic nutritional subsidies. The larger odonate taxa that frequently foraged mid-air had more varied diets and relied less on aquatic emergent insects than the smaller odonates that foraged from perches near the river. There was also evidence of niche partitioning amongst the spiders, as those that built horizontal webs captured more aquatic insects (40 – 78%) than the vertical orb-web builders (20 – 66%). This study showed that the nature and extent of trophic cross-boundary linkages in riparian areas largely depended on the availability of subsidies that varied seasonally and spatially. The width of the stream and seasonal variability emerged as important predictors of emergent insect abundances/biomasses that influenced predator feeding niches. The high mobility of odonates made their reliance on aquatic nutritional subsidies different from the less mobile spiders. The link between the width of the river and the extent of trophic connectivity has implications for riparian area management and definition of riparian buffer zones. However, the variation in diet niches amongst terrestrial consumers makes the results area-specific, and more studies are required that incorporate additional terrestrial predators in other fluvial systems so that we can make some generalizations on the dynamics of riparian trophic cross-boundary links.
- Full Text:
- Date Issued: 2016
Synthesis and biological evaluation of novel thiazole-based compounds
- Authors: Olawode, Emmanual Oladayo
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62955 , vital:28325
- Description: Thesis embargoed for one-year period. Expected date of release: April 2019
- Full Text:
- Date Issued: 2016
- Authors: Olawode, Emmanual Oladayo
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62955 , vital:28325
- Description: Thesis embargoed for one-year period. Expected date of release: April 2019
- Full Text:
- Date Issued: 2016
The trophic ecology of waterbirds in a small temperate estuary: a stable isotope and lipid tracer approach
- Authors: Hean, Jeffrey William
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54356 , vital:26557
- Description: Waterbirds are often overlooked as predators in aquatic ecosystems, despite the fact that waterbirds congregate in great numbers in and around waterways, notably estuaries. To fully appreciate the effect that aquatic feeding waterbird species may have on aquatic prey communities and the role that they play in estuarine food webs, stable isotopes and fatty acid profiles were employed to examine the seasonal diet of selected waterbirds in the Kowie Estuary, Eastern Cape Province, South Africa. Population counts were conducted every month for four seasons to examine the demography of waterbirds in the lower reaches of the estuary. The mean monthly energy consumption, along with dry matter intake of all waterbird species observed, were calculated and compared to similar estuaries in South Africa and elsewhere. Three duck species, one migrant sandpiper and one piscivore were selected for more detailed investigation at several temporal scales. This thesis has revealed that stable isotope analysis of waterbird tissues provides more informative data than fatty acid analysis for investigating waterbird diet and basal resource-tertiary consumer nutrient coupling. Stable δ15N and δ13C isotopes from several body tissues, in conjunction with SIAR models, were used to determine the seasonal diet of each waterbird species, while fatty acid profiles were investigated to examine the trophic transfer of fatty acids from basal resources to waterbird predators via the benthic fauna. Stable isotopes revealed that Cape Shoveller, Cape Teal and Yellow-Billed Duck shifted their diet over both long and short temporal scales, while the migratory Ruff and piscivorous Little Egret maintained a relatively consistent diet over time. Isopods, amphipods, copepods and Mysidacea were the main foods of all three duck species and the Ruff (>30%). Little Egret fed mainly on flathead mullet throughout the year. Fatty acid analysis revealed evidence for trophic transfer of specific fatty acids from basal resources to waterbirds in the Kowie Estuary but provided little information on seasonal diet of waterbirds. Waterbirds foraging in the Kowie Estuary appeared to shift their diet to coincide with resource abundance pulses, but also displayed seasonal dietary overlap. This study highlights the role that waterbirds play in aquatic food webs. The subject requires more attention so that we can better understand all the predatory drivers on aquatic communities.
- Full Text:
- Date Issued: 2016
- Authors: Hean, Jeffrey William
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54356 , vital:26557
- Description: Waterbirds are often overlooked as predators in aquatic ecosystems, despite the fact that waterbirds congregate in great numbers in and around waterways, notably estuaries. To fully appreciate the effect that aquatic feeding waterbird species may have on aquatic prey communities and the role that they play in estuarine food webs, stable isotopes and fatty acid profiles were employed to examine the seasonal diet of selected waterbirds in the Kowie Estuary, Eastern Cape Province, South Africa. Population counts were conducted every month for four seasons to examine the demography of waterbirds in the lower reaches of the estuary. The mean monthly energy consumption, along with dry matter intake of all waterbird species observed, were calculated and compared to similar estuaries in South Africa and elsewhere. Three duck species, one migrant sandpiper and one piscivore were selected for more detailed investigation at several temporal scales. This thesis has revealed that stable isotope analysis of waterbird tissues provides more informative data than fatty acid analysis for investigating waterbird diet and basal resource-tertiary consumer nutrient coupling. Stable δ15N and δ13C isotopes from several body tissues, in conjunction with SIAR models, were used to determine the seasonal diet of each waterbird species, while fatty acid profiles were investigated to examine the trophic transfer of fatty acids from basal resources to waterbird predators via the benthic fauna. Stable isotopes revealed that Cape Shoveller, Cape Teal and Yellow-Billed Duck shifted their diet over both long and short temporal scales, while the migratory Ruff and piscivorous Little Egret maintained a relatively consistent diet over time. Isopods, amphipods, copepods and Mysidacea were the main foods of all three duck species and the Ruff (>30%). Little Egret fed mainly on flathead mullet throughout the year. Fatty acid analysis revealed evidence for trophic transfer of specific fatty acids from basal resources to waterbirds in the Kowie Estuary but provided little information on seasonal diet of waterbirds. Waterbirds foraging in the Kowie Estuary appeared to shift their diet to coincide with resource abundance pulses, but also displayed seasonal dietary overlap. This study highlights the role that waterbirds play in aquatic food webs. The subject requires more attention so that we can better understand all the predatory drivers on aquatic communities.
- Full Text:
- Date Issued: 2016
A constructivist deconstruction of post-apartheid South Africa’s trade negotiation strategies: the politics of development and global value chains
- Authors: Pillay, Morgenie
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64731 , vital:28596
- Description: Expected release date-May 2020
- Full Text:
- Date Issued: 2015
- Authors: Pillay, Morgenie
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64731 , vital:28596
- Description: Expected release date-May 2020
- Full Text:
- Date Issued: 2015
Bacterial degradation of fossil fuel waste in aqueous and solid media
- Authors: Edeki, Oghenekume Gerald
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54565 , vital:26588
- Description: The generation of environmental pollutants worldwide is mainly due to over reliance on fossil fuels as a source of energy. As a result of the negative impacts of these pollutants on the health of humans, animals, plants and microorganisms, global attention has been directed towards ways of containing this problem. Biodegradation of fossil fuel is one of the most effective methods used to remediate contaminated systems. However with regard to coal waste, much of what is known is based on the ability of fungal species to biosolubilize this material under enrichment conditions in a laboratory setting. For effective biodegradation as a remediation technique, there is an immediate need to source, isolate, enrich and incorporate other microorganisms such as bacteria into bioremediation technologies. The goal of this dissertation was to isolate bacteria from fossil fuel contaminated environments and to demonstrate competence for petroleum hydrocarbon degradation which was achieved using a combination of analytical methods such as spectrophotometry, FT-IR, SEM and GC-MS. Screening for biodegradation of coal and petroleum hydrocarbon waste resulted in the isolation of 75 bacterial strains of which 15 showed good potential for use in developing remedial biotechnologies. Spectrophotometric analysis of bacteria both in coal and petroleum hydrocarbons (all in aqueous media) revealed a high proliferation of bacteria in these media suggesting that these microbes can effectively utilize the various substrates as a source of carbon. The isolated bacteria effectively degraded and converted waste coal to humic and fulvic acids; products required to enrich coal mine dumps to support re-vegetation. Scanning electron microscopy showed the attachment of bacteria to waste coal surfaces and the disintegration of coal structures while FT-IR analysis of extracted humic-like substances from biodegraded waste coal revealed these to have the same functional groups as commercial humic acid. Specific consortia which were established using the isolated bacterial strains, showed greater potential to biodegrade coal than did individual isolates. This was evident in experiments carried out on coal and hydrocarbons where the efficient colonization and utilization of these substrates by each bacterial consortium was observed due to the effect of added nutrients such as algae. The biodegradation of liquid petroleum hydrocarbons (diesel and BTEX) was also achieved using the 15 bacterial isolates. GC-MS analysis of extracted residual PHC from aqueous and solid media revealed rapid breakdown of these contaminants by bacteria. Different bacterial consortia established from the individual isolates were shown to be more efficient than single isolates indicating that formulated consortia are the biocatalysts of choice for fossil fuel biodegradation. This study represents one of the most detailed screenings for bacteria from fossil fuel contaminated sites and the isolation of strains with potential to biodegrade coal and petroleum hydrocarbon wastes. Several consortia have been developed and these show potential for further development as biocatalysts for use in bioremediation technology development. An evaluation of efficiency of each established bacterial consortium for biodegradation in a commercial and/or industrial setting at pilot scale is now needed.
- Full Text:
- Date Issued: 2015
- Authors: Edeki, Oghenekume Gerald
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54565 , vital:26588
- Description: The generation of environmental pollutants worldwide is mainly due to over reliance on fossil fuels as a source of energy. As a result of the negative impacts of these pollutants on the health of humans, animals, plants and microorganisms, global attention has been directed towards ways of containing this problem. Biodegradation of fossil fuel is one of the most effective methods used to remediate contaminated systems. However with regard to coal waste, much of what is known is based on the ability of fungal species to biosolubilize this material under enrichment conditions in a laboratory setting. For effective biodegradation as a remediation technique, there is an immediate need to source, isolate, enrich and incorporate other microorganisms such as bacteria into bioremediation technologies. The goal of this dissertation was to isolate bacteria from fossil fuel contaminated environments and to demonstrate competence for petroleum hydrocarbon degradation which was achieved using a combination of analytical methods such as spectrophotometry, FT-IR, SEM and GC-MS. Screening for biodegradation of coal and petroleum hydrocarbon waste resulted in the isolation of 75 bacterial strains of which 15 showed good potential for use in developing remedial biotechnologies. Spectrophotometric analysis of bacteria both in coal and petroleum hydrocarbons (all in aqueous media) revealed a high proliferation of bacteria in these media suggesting that these microbes can effectively utilize the various substrates as a source of carbon. The isolated bacteria effectively degraded and converted waste coal to humic and fulvic acids; products required to enrich coal mine dumps to support re-vegetation. Scanning electron microscopy showed the attachment of bacteria to waste coal surfaces and the disintegration of coal structures while FT-IR analysis of extracted humic-like substances from biodegraded waste coal revealed these to have the same functional groups as commercial humic acid. Specific consortia which were established using the isolated bacterial strains, showed greater potential to biodegrade coal than did individual isolates. This was evident in experiments carried out on coal and hydrocarbons where the efficient colonization and utilization of these substrates by each bacterial consortium was observed due to the effect of added nutrients such as algae. The biodegradation of liquid petroleum hydrocarbons (diesel and BTEX) was also achieved using the 15 bacterial isolates. GC-MS analysis of extracted residual PHC from aqueous and solid media revealed rapid breakdown of these contaminants by bacteria. Different bacterial consortia established from the individual isolates were shown to be more efficient than single isolates indicating that formulated consortia are the biocatalysts of choice for fossil fuel biodegradation. This study represents one of the most detailed screenings for bacteria from fossil fuel contaminated sites and the isolation of strains with potential to biodegrade coal and petroleum hydrocarbon wastes. Several consortia have been developed and these show potential for further development as biocatalysts for use in bioremediation technology development. An evaluation of efficiency of each established bacterial consortium for biodegradation in a commercial and/or industrial setting at pilot scale is now needed.
- Full Text:
- Date Issued: 2015
Characterization of the co-chaperones of Hsp70 and Hsp90 in Trypanosoma brucei and their potential partnerships
- Authors: Mokoena, Fortunate
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54543 , vital:26583
- Description: African Trypanosomiasis, which is caused by Trypanosoma brucei, is one of the crippling agents of social and economic development in Africa. T. brucei cycles between the cold-blooded insect vector, the tsetse fly (Glossina spp), and warm-blooded mammalian hosts. T. brucei, T. cruzi and L. major are mammal infecting kinetoplastid parasites that are collectively referred to as TriTryps. These parasites experience extreme environments as they move between their warm-blooded mammalian hosts and cold-blooded insect vectors which trigger extensive morphological transformations during the life-cycle of the parasite. Molecular chaperones have been implicated in parasite differentiation. TriTryps display significant expansions and diversity in the gene complements encoding molecular chaperones, especially J-proteins. Generally, J-proteins function as co-chaperones of Hsp70s, forming part of vital protein homeostasis processes. Hsp70s show a high degree of conservation, while J-proteins appear to be an extreme case of taxonomic radiation. Although several studies have focused on the molecular and cell biology of Hsp70s in some kinetoplastid parasites, knowledge is still lacking pertaining to J-proteins and their partnerships with Hsp70s. This thesis focused on the classification of kinetoplastid Jproteins into the four types by examining the domain organizations using T. brucei as a guide. The potential partnership of J-proteins and Hsp70s were postulated based on predicted subcellular localization. Kinetoplastid parasites, particularly T. brucei, have evolved an expanded and specialized J-protein machinery, likely to be a consequence of an evolutionary fitness/trait to adapt to diverse environment present in hosts and vectors. These analyses will yield insight into the process of parasite differentiation as well as provide new leads for chemotherapeutic treatments. The presence of the STI1 mediated Hsp90 hetero-complex formation has not been confirmed in T. brucei. To this end, in silico and biochemical techniques were used to characterize the role of TbSTI1, as an adaptor protein of Hsp70 and Hsp90. Through domain architecture analysis, sequence alignments, phylogenetic analysis and three-dimensional structure prediction, TbSTI1 was demonstrated to be the most conserved TPR containing co-chaperone of Hsp70 and Hsp83 in T. brucei and also shown to be highly similar to its eukaryotic homologues. Recombinant TbSTI1 was overproduced and purified in E.coli cells and subsequently shown to associate with TcHsp70 in a concentration dependent manner and associate weakly with TbHsp70.4. TbSTI1 and TbHsp83 were also demonstrated to be expressed and upregulated upon exposure to heat shock at the bloodstream stage of parasite development. In conclusion, this study is the first to report the interaction of TbSTI1 with a chaperone. Interactions between TbSTI1 and Hsp70s were demonstrated and therefore, the formation of the hetero-complex is predicted based the similarity of TbSTI1 to other STI1 proteins.
- Full Text:
- Date Issued: 2015
- Authors: Mokoena, Fortunate
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54543 , vital:26583
- Description: African Trypanosomiasis, which is caused by Trypanosoma brucei, is one of the crippling agents of social and economic development in Africa. T. brucei cycles between the cold-blooded insect vector, the tsetse fly (Glossina spp), and warm-blooded mammalian hosts. T. brucei, T. cruzi and L. major are mammal infecting kinetoplastid parasites that are collectively referred to as TriTryps. These parasites experience extreme environments as they move between their warm-blooded mammalian hosts and cold-blooded insect vectors which trigger extensive morphological transformations during the life-cycle of the parasite. Molecular chaperones have been implicated in parasite differentiation. TriTryps display significant expansions and diversity in the gene complements encoding molecular chaperones, especially J-proteins. Generally, J-proteins function as co-chaperones of Hsp70s, forming part of vital protein homeostasis processes. Hsp70s show a high degree of conservation, while J-proteins appear to be an extreme case of taxonomic radiation. Although several studies have focused on the molecular and cell biology of Hsp70s in some kinetoplastid parasites, knowledge is still lacking pertaining to J-proteins and their partnerships with Hsp70s. This thesis focused on the classification of kinetoplastid Jproteins into the four types by examining the domain organizations using T. brucei as a guide. The potential partnership of J-proteins and Hsp70s were postulated based on predicted subcellular localization. Kinetoplastid parasites, particularly T. brucei, have evolved an expanded and specialized J-protein machinery, likely to be a consequence of an evolutionary fitness/trait to adapt to diverse environment present in hosts and vectors. These analyses will yield insight into the process of parasite differentiation as well as provide new leads for chemotherapeutic treatments. The presence of the STI1 mediated Hsp90 hetero-complex formation has not been confirmed in T. brucei. To this end, in silico and biochemical techniques were used to characterize the role of TbSTI1, as an adaptor protein of Hsp70 and Hsp90. Through domain architecture analysis, sequence alignments, phylogenetic analysis and three-dimensional structure prediction, TbSTI1 was demonstrated to be the most conserved TPR containing co-chaperone of Hsp70 and Hsp83 in T. brucei and also shown to be highly similar to its eukaryotic homologues. Recombinant TbSTI1 was overproduced and purified in E.coli cells and subsequently shown to associate with TcHsp70 in a concentration dependent manner and associate weakly with TbHsp70.4. TbSTI1 and TbHsp83 were also demonstrated to be expressed and upregulated upon exposure to heat shock at the bloodstream stage of parasite development. In conclusion, this study is the first to report the interaction of TbSTI1 with a chaperone. Interactions between TbSTI1 and Hsp70s were demonstrated and therefore, the formation of the hetero-complex is predicted based the similarity of TbSTI1 to other STI1 proteins.
- Full Text:
- Date Issued: 2015
Contributions to the study of a class of optimal control problems on the orthogonal groups SO(3) and SO(4)
- Authors: Adams, Ross Montague
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64826 , vital:28608
- Description: In this thesis we investigate a class of invariant optimal control problems, and their associated quadratic Hamilton-Poisson systems, on the orthogonal groups SO(3) and SO(4). Specifically, we are concerned with the class of left-invariant control affine systems. We begin by classifying all cost-extended systems on SO(3) under cost equivalence. (Cost-extended systems are closely related to optimal control problems.) A classification of all quadratic Hamilton-Poisson systems on the (minus) Lie-Poisson space so(3)*, under affine equivalence, is also obtained. For the normal forms obtained in our classification (of Hamilton-Poisson systems) we investigate the (Lyapunov) stability nature of the equilibria using spectral and energy-Casimir methods. For a subclass of these systems, we obtain analytic expressions for the integral curves of the associated Hamiltonian vector fields in terms of (basic) Jacobi elliptic functions. The explicit relationship between the classification of cost-extended systems on SO(3) and the classification of quadratic Hamilton- Poisson systems on so(3)* is provided. On SO(4), a classification of all left-invariant control affine systems under L-equivalence is obtained. We then determine which of these representatives are controllable, thus obtaining a classification under detached feedback equivalence. We also obtain a partial classification of quadratic Hamilton-Poisson systems on the Lie-Poisson space so(4)*. An investigation of the stability nature of the equilibria for a subclass of these systems is also done. Several illustrative examples of optimal control problems on the orthogonal group SO(3) are provided. More specifically, we consider an optimal control problem corresponding to a representative of our classification (of cost-extended system) for each possible number of control inputs. For each of these problems, we obtain explicit expressions for the extremal trajectories on the homogeneous space S2 by projecting the extremal trajectories on the group SO(3). The examples provided show how our classifications of cost-extended systems and Hamilton-Poisson systems can be used to obtain the optimal controls and the extremal trajectories corresponding to a large class of optimal control problems on SO(3). An example of a four-input optimal control problem on SO(4) is also provided. This example is provided to show how the solutions of certain problems on SO(4) can be related to the solutions of certain optimal control problems on SO(3).
- Full Text:
- Date Issued: 2015
- Authors: Adams, Ross Montague
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64826 , vital:28608
- Description: In this thesis we investigate a class of invariant optimal control problems, and their associated quadratic Hamilton-Poisson systems, on the orthogonal groups SO(3) and SO(4). Specifically, we are concerned with the class of left-invariant control affine systems. We begin by classifying all cost-extended systems on SO(3) under cost equivalence. (Cost-extended systems are closely related to optimal control problems.) A classification of all quadratic Hamilton-Poisson systems on the (minus) Lie-Poisson space so(3)*, under affine equivalence, is also obtained. For the normal forms obtained in our classification (of Hamilton-Poisson systems) we investigate the (Lyapunov) stability nature of the equilibria using spectral and energy-Casimir methods. For a subclass of these systems, we obtain analytic expressions for the integral curves of the associated Hamiltonian vector fields in terms of (basic) Jacobi elliptic functions. The explicit relationship between the classification of cost-extended systems on SO(3) and the classification of quadratic Hamilton- Poisson systems on so(3)* is provided. On SO(4), a classification of all left-invariant control affine systems under L-equivalence is obtained. We then determine which of these representatives are controllable, thus obtaining a classification under detached feedback equivalence. We also obtain a partial classification of quadratic Hamilton-Poisson systems on the Lie-Poisson space so(4)*. An investigation of the stability nature of the equilibria for a subclass of these systems is also done. Several illustrative examples of optimal control problems on the orthogonal group SO(3) are provided. More specifically, we consider an optimal control problem corresponding to a representative of our classification (of cost-extended system) for each possible number of control inputs. For each of these problems, we obtain explicit expressions for the extremal trajectories on the homogeneous space S2 by projecting the extremal trajectories on the group SO(3). The examples provided show how our classifications of cost-extended systems and Hamilton-Poisson systems can be used to obtain the optimal controls and the extremal trajectories corresponding to a large class of optimal control problems on SO(3). An example of a four-input optimal control problem on SO(4) is also provided. This example is provided to show how the solutions of certain problems on SO(4) can be related to the solutions of certain optimal control problems on SO(3).
- Full Text:
- Date Issued: 2015
Environmental conflict resolution: a critical analysis of the role of interests and value
- Authors: Mweshi, John
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/55842 , vital:26740
- Description: This thesis intends to contribute to an enhanced understanding of environmental conflicts and their resolution. To accomplish this task the thesis will ascertain the role that value and interests play in environmental conflicts in order to establish an adequate basis upon which they can be resolved. In the process, the thesis will also examine three different approaches, namely, the Standard Approach; the Environmental Impact Assessment (EIA) framework; and the Structured Decision Making (SDM) approach. First, the standard approach is informed by the understanding that focusing on interests instead of human values makes the resolution of conflicts more tractable. In contrast, this thesis argues that an exclusive focus on interests, in the context of environmental conflict resolution, is inadequate in some important respects because there are other factors to be considered such as the environmental impacts at the root of the conflict. Second, the thesis examines the focus on impacts that characterises EIAs. It argues that this approach remedies the limitations of the standard approach insofar as impacts are understood in terms of object value. However, the EIA approach does not provide much guidance on how to deal with conflicting human values. Third, taking into account the fact that the standard approach does not address the question of object value, while the EIA addresses object value but does not deal directly with human values, the thesis examines the SDM approach to environmental risk decisions. The thesis argues that while the SDM approach claims to deal with conflicts involving human values head-on, it does not provide a viable alternative in terms of environmental conflict resolution. This is because it fails to recognise the key distinction between human values and object value despite acknowledging the presence of multiple value dimensions as a major obstacle to value trade-offs and therefore to the resolution of value conflicts. Finally, the thesis recommends an adequate basis upon which environmental conflicts can be resolved.
- Full Text:
- Date Issued: 2015
- Authors: Mweshi, John
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/55842 , vital:26740
- Description: This thesis intends to contribute to an enhanced understanding of environmental conflicts and their resolution. To accomplish this task the thesis will ascertain the role that value and interests play in environmental conflicts in order to establish an adequate basis upon which they can be resolved. In the process, the thesis will also examine three different approaches, namely, the Standard Approach; the Environmental Impact Assessment (EIA) framework; and the Structured Decision Making (SDM) approach. First, the standard approach is informed by the understanding that focusing on interests instead of human values makes the resolution of conflicts more tractable. In contrast, this thesis argues that an exclusive focus on interests, in the context of environmental conflict resolution, is inadequate in some important respects because there are other factors to be considered such as the environmental impacts at the root of the conflict. Second, the thesis examines the focus on impacts that characterises EIAs. It argues that this approach remedies the limitations of the standard approach insofar as impacts are understood in terms of object value. However, the EIA approach does not provide much guidance on how to deal with conflicting human values. Third, taking into account the fact that the standard approach does not address the question of object value, while the EIA addresses object value but does not deal directly with human values, the thesis examines the SDM approach to environmental risk decisions. The thesis argues that while the SDM approach claims to deal with conflicts involving human values head-on, it does not provide a viable alternative in terms of environmental conflict resolution. This is because it fails to recognise the key distinction between human values and object value despite acknowledging the presence of multiple value dimensions as a major obstacle to value trade-offs and therefore to the resolution of value conflicts. Finally, the thesis recommends an adequate basis upon which environmental conflicts can be resolved.
- Full Text:
- Date Issued: 2015
Invariant control systems and sub-Riemannian structures on lie groups: equivalence and isometries
- Authors: Biggs, Rory
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64815 , vital:28607
- Description: In this thesis we consider invariant optimal control problems and invariant sub-Riemannian structures on Lie groups. Primarily, we are concerned with the equivalence and classification of problems (resp. structures). In the first chapter, both the class of invariant optimal control problems and the class of invariant sub-Riemannian structures are organised as categories. The latter category is shown to be functorially equivalent to a subcategory of the former category. Via the Pontryagin Maximum Principle, we associate to each invariant optimal control problem (resp. invariant sub-Riemannian structure) a quadratic Hamilton-Poisson system on the associated Lie-Poisson space. These Hamiltonian systems are also organised as a category and hence the Pontryagin lift is realised as a contravariant functor. Basic properties of these categories are investigated. The rest of this thesis is concerned with the classification (and investigation) of certain subclasses of structures and systems. In the second chapter, the homogeneous positive semidefinite quadratic Hamilton-Poisson systems on three-dimensional Lie-Poisson spaces are classified up to compatibility with a linear isomorphism; a list of 23 normal forms is exhibited. In the third chapter, we classify the invariant sub-Riemannian structures in three dimensions and calculate the isometry group for each normal form. By comparing our results with known results, we show that most isometries (in three dimensions) are in fact the composition of a left translation and a Lie group isomorphism. In the fourth and last chapter of this thesis, we classify the sub-Riemannian and Riemannian structures on the (2n + 1)-dimensional Heisenberg groups. Furthermore, we find the isometry group and geodesics of each normal form.
- Full Text:
- Date Issued: 2015
- Authors: Biggs, Rory
- Date: 2015
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64815 , vital:28607
- Description: In this thesis we consider invariant optimal control problems and invariant sub-Riemannian structures on Lie groups. Primarily, we are concerned with the equivalence and classification of problems (resp. structures). In the first chapter, both the class of invariant optimal control problems and the class of invariant sub-Riemannian structures are organised as categories. The latter category is shown to be functorially equivalent to a subcategory of the former category. Via the Pontryagin Maximum Principle, we associate to each invariant optimal control problem (resp. invariant sub-Riemannian structure) a quadratic Hamilton-Poisson system on the associated Lie-Poisson space. These Hamiltonian systems are also organised as a category and hence the Pontryagin lift is realised as a contravariant functor. Basic properties of these categories are investigated. The rest of this thesis is concerned with the classification (and investigation) of certain subclasses of structures and systems. In the second chapter, the homogeneous positive semidefinite quadratic Hamilton-Poisson systems on three-dimensional Lie-Poisson spaces are classified up to compatibility with a linear isomorphism; a list of 23 normal forms is exhibited. In the third chapter, we classify the invariant sub-Riemannian structures in three dimensions and calculate the isometry group for each normal form. By comparing our results with known results, we show that most isometries (in three dimensions) are in fact the composition of a left translation and a Lie group isomorphism. In the fourth and last chapter of this thesis, we classify the sub-Riemannian and Riemannian structures on the (2n + 1)-dimensional Heisenberg groups. Furthermore, we find the isometry group and geodesics of each normal form.
- Full Text:
- Date Issued: 2015