Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Eucalyptus camaldulensis Dehnh., or River Red Gum, is a commercially valuable yet recognised invasive alien plant (IAP) of riparian zones throughout South Africa. The invasive potential of E. camaldulensis is widely recognised, with specific regulations aimed at the management of E. camaldulensis. E. camaldulensis is known to use large amounts of water, reduce biodiversity, change river morphology and impact hydrological regimes of rivers. In the native range throughout Australia, E. camaldulensis displays a distinct relationship between rainfall, and flood events, for seed dispersal, germination and establishment, and consequently spatial extent, yet little is known about the relationships in the South African context. The aim of this project was to assess the impact of high rainfall and flood events on the establishment and distribution of E. camaldulensis along the Middle Breede River, between Worcester and Swellendam in the Western Cape, by establishing the current spatial extent of E. camaldulensis along the river, identifying flood events since 1950 and evaluating the impact rainfall and flood events had on the spatial extent thereof. Aerial imagery, rainfall, discharge and river level data was obtained dating back to 1980, as well as field data comprising of GPS-bounding of E. camaldulensis stands. Additionally, density measurements were obtained and interviews conducted with land users. Spatial analysis of aerial imagery, coupled with perimeter (GPS) data and density data were used to conduct spatio-temporal analysis, employing GIS and conventional statistical approaches to address the various objectives. Results indicated E. camaldulensis stands had a small overall increase in spatial extent since 1980. Flooding and rainfall events coincided with an increase in occurrence of E. camaldulensis with elevated river levels and frequent flooding, while spatial variation of this relationship was observed. The hydrological regime of the Breede River coincides with a slow increase in spatial extent of E. camaldulensis stands, but no affirmation of a positive real-world relationship was possible using the available data. Results further suggested, based on the current age class composition, that existing stands originated roughly during 1980, possibly due to commercial forestry related seeding into the river. Reduced fragmentation between stakeholders, educational programmes and improved reporting systems were recommended for improved IAP management within the area. / AFRIKAANSE OPSOMMING: Eucalyptus camaldulensis, of Rooibloekom (RB), is ‘n waardevolle kommersiële, maar erkende indringer plantspesie (IP) wat veral oewersones in Suid-Afrika indring. Die indringerpotensiaal van E. camaldulensis is welbekend, en spesifieke regulasies, gemik op die bestuur van RB en ander spesies is reeds aangeneem. E. camaldulensis is veral bekend vir sy hoë watergebruik, sy vermindering van biodiversiteit, sy vermoë om riviervorme te verander en sy algehele impak op die hidrologiese patroon van riviere waarmee dit in aanraking kom. In sy oorspronklike verspreidingsgebied in Australië toon E. camaldulensis ‘n bepaalde verhouding tussen reënval en vloedgebeurtenisse vir saadverspreiding, ontkieming en vestiging en derhalwe die ruimtelike verspreiding van die spesie; alhoewel hierdie verhouding in die Suid-Afrikaanse konteks steeds redelik onverduidelik bly. Die doelwit van hierdie studie was dus om die impak van hoë reënval en vloedgebeurtenisse op die ruimtelike verspreiding en vestiging van E. camaldulensis teenaan die Middel Breëde Rivier, spesifiek tussen Worcester en Swellendam, te evalueer. Hierdie doelwit was bereik deur die historiese ruimtelike verspreiding teenaan die rivier te meet, hoë reënval en vloedgebeurtenisse vanaf 1980 te identifiseer, en die huidige verspreiding en omtrek met GPS te meet. Digtheidafmetings, sowel as onderhoude met belanghebbendes teenaan die rivier was ook opgeneem. Visuele interpretatasie van lugfotos, sowel as omtrek (GPS) en digtheid-data was gebruik om ruimtelike analise uit te voer, deur die gebruik van GIS en konvensionele statistiese metodes, ten einde die doelwitte te evalueer. Resultate dui aan dat E. camaldulensis areas ‘n klein algemene groei getoon het sedert 1980. Hoë-reënval en gereëlde vloedgebeurtenisse het ook gepaard gegaan met ‘n groei van E. camaldulensis oppervlak, alhoewel hierdie verhouding ruimtelike variasie getoon het, met ‘n algemene groei patroon gemerk oor die volledige studietydperk. Ook geen stimulerende verhouding kon vanuit die beskikbare data bevestig word nie. Addisionele resultate het aangedui dat die verspreiding van E. camaldulensis ongeveer 1980 onstaan het, moontlik as gevolg van kommersiële bosbou-aanplanting en verwante saadverspreiding in die rivier vanaf daardie tyd. Aanbevelings ten opsigte van verbeterde indringerbestuur sluit in die beperking van huidige fragmentasie tussen belanghebbendes en betrokke verwyderingsorganisasies, addisionele onderrigprogramme sowel as die verbetering van terugvoersisteme.

Biological invasions are reportedly one of the major contributory factors to biodiversity loss worldwide. The impacts of invasive alien plant (IAP) species on native communities are widely documented in the scientific literature, however, there is still a lack of detailed information on their impacts within the most vulnerable habitats. Riparian habitats are highly dynamic systems and naturally disturbed, making them particularly vulnerable to invasion. Climate change, directly or indirectly, is also predicted to adversely impact river systems, which may subsequently alter invasion rates and the impacts of IAPs. However, the interactions between climate and IAPs and their combined effects on vegetation have rarely been examined. To address these knowledge gaps, this thesis investigates: (1) the role of environmental variables, such as sediment loading or climate-related changes to river flow regime, on the abundance of IAPs within riparian zones; (2) how variation in IAP abundance impacts native vegetation, relative to the effects of native dominant plant species and (3) some of the mechanisms underlying the effects of IAPs in riparian habitats. Historic and recent field survey data were used to investigate changes in riparian vegetation on British rivers during the last 20 years. Analyses indicate that IAPs had a negative but small effect on native plant diversity. Overall, changes in land use and differences in flow regime between recording periods were the most important predictors of plant community change. Specifically, IAPs had a greater probability of being present along lowland rivers that experienced increased frequency of high flow events. On a local scale across rivers in Scotland, the abundance of IAPs was constrained by greater soil moisture in summer, whilst greater abundance was associated with tree-lined banks. Both native dominant species and IAPs negatively affected subordinate species abundance to a greater extent than species richness, although this effect varied spatially with bank elevation. Artificial turf mats were used to quantify viable propagules within riverine sediment deposited over-winter along invaded riverbanks. The data indicate that there is a legacy effect of IAP abundance, with the most invaded sites being associated with higher sediment loading the following year, though, contrary to the general pattern, 12 sediment associated propagules were scarcer at invaded sites. Moreover, lower above-ground native diversity was associated with sites which had been previously invaded. Plant species composition in the propagule bank and above-ground vegetation were highly dissimilar, particularly closest to the water’s edge at highly invaded sites. This suggests that mono-specific stands of IAPs proliferate best under less disturbed environmental conditions, although fluvial disturbance events may be required to create opportunities for initial establishment. The propagule bank contributed very little to the above-ground vegetation, nor did it limit invasion, suggesting that above-ground plant composition is largely dictated by competitive interactions. The findings presented in this thesis suggest that invasion by IAPs is an additional stressor for native vegetation within riparian habitats, modifying above-ground plant communities via competition and suppressing recruitment from the propagule bank. However, native dominant species common in riparian habitats also negatively impact, subordinate species via competition, in some cases equalling the effect of IAPs. Native dominant and IAP species are differently affected by environmental factors operating in the riparian zone, which may provide future opportunities for reducing and managing invasions.

The most recent surveys in South Africa estimate that invasions are still increasing, despite substantial clearing efforts. Riparian systems in South Africa are particularly vulnerable to invasion by woody IAPs. This thesis addresses the restoration of alien‐invaded riparian systems, by investigating the factors that facilitate or constrain spontaneous recovery and influence the trajectories of succession. These factors include invasion history and management history, especially the use of fire. A seedling emergence approach was used to test the presence of a viable pre‐fire seedbank, and the effect of fire on the seed bank. The efficacy of some active restoration interventions was also tested, with the aim to return invasion‐resistant, indigenous vegetation with a structure and function representative of uninvaded sites. The findings of this study indicated the presence of a viable and persistent riparian soil seed bank, even after 30 years of intermtittent invasion as well as two fire cycles under invasion. It shows that the management practice of fell‐and‐burn resulted in high soil temperatures, and that this reduced the indigenous soil seed bank density, especially in the upper soil layer. Clear germination sequences and patterns of emergence over time for different species were observed during this study, with many species exhibiting delayed emergence relative to the timing of the fire event. It is proposed that manipulation of the season of fire could be used to selectively optimise the order of arrival and therefore superior recruitment of some species over others in the Eastern Cape fynbos, and thus alter the trajectories of recovery of vegetation towards a more desired state. Active restoration in the form of indigenous seed and plant additions resulted in a significantly higher indigenous cover after seven months, compared to a control (passive restoration) or restoring with grass. Indigenous cover and composition was also strongly influenced by lateral zonation, and some key guilds and species were missing or present in much lower densities compared to reference sites. Grass restoration significantly suppressed the regeneration of A. longifolia, as well as the regeneration of indigenous species. Biotic resistance can thus be achieved through restoration, and it could be a powerful tool in the management of IAPs, although the deliberate introduction of grass after clearing in fynbos also reduces biodiversity and could have unforeseen consequences to riparian function.

MENVM / Department of Ecology and Resource Management

PhD (Microbiology) / Department of Microbiology / See the attached abstract below

Thesis (MScConsEcol (Conservation Ecology and Entomology))--Stellenbosch University, 2008. / In the Mediterranean climate regions of the world, agricultural practices have caused considerable landscape transformation and lead to introduction of alien species that now dominate secondary succession on abandoned agricultural fields. Various restoration attempts have been made to reduce alien plant species cover, and to enhance the re-establishment and cover of native plant species. However, results and successes were mostly short-term due to re-growth and persistence of the weedy alien species, which has been suggested to be caused by land use history, especially the nutrient enrichment of soil, and particularly phosphorus and nitrogen. This study investigated different soil properties (pH, electrical conductivity (EC), soil moisture, as well as available phosphorus (P) and total nitrogen (N)) on 10 and 20 year old abandoned fields, as a function of depth in three habitats (ridge (old cultivated area), ditch (old drainage line) and slope (intermediate zone between ridge and ditch)) on the old fields. The relationship between these soil properties and the vegetation occurring on the two old fields was established. At the same time, restoration treatments (autumn burn, combination of autumn burn and herbicide, herbicide application alone, as well as spring burn) were conducted to reduce the cover and abundance of non-native plant species and Cynodon dactylon, and to enhance cover of native species. Results from the study show that levels of all investigated soil properties were higher on the younger field. The highest difference was observed in EC and pH. Seasonal differences in both soil properties could also be observed. A principal component analysis indicated that the dynamic of all soil properties shaped the vegetation type on old fields, with the main soil properties being dependent on land-use history and time since abandonment. This study suggests that EC and pH could be part of parameters that drive the persistence of undesirable species persistence on old fields and inhibit native plant species instead.

Thesis (MSc)--Stellenbosch University, 2008. / ENGLISH ABSTRACT: Alien trees, Pinus spp. and Eucalyptus spp., affect ants negatively in the Cape Floristic Region (CFR), a global biodiversity hotspot in South Africa. They reduce ant abundance and species richness, thus also changing ant assemblage structure. This is alarming, because almost 1300 species of plant species in the CFR are dispersed by certain indigenous ants, and thus there is concern for an indirect effect on indigenous plant assemblages. One of the most impacting ant species on seed dispersal is the invasive Argentine ant (Linepithema humile (Mayr)), which discards seeds outside its nest, where they do not germinate. Ten sites, on Vergelegen Wine Estate, were selected to explore these effects of alien plants. These varied from invaded to non-invaded sites. Each site consisted of six sampling points, which in turn consisted of four pitfall traps left out for seven days, during December 2005, February 2006, May 2006 and September 2006. Forty species of ant were sampled, and various analyses used to illustrate the comparative effects of plant invasion. All analytical methods showed that invasive alien plants had a significant impact on the abundance and richness of the ant species assemblage, by creating a dense canopy cover that changed the abiotic environment of the epigaeic ants’ habitat. Furthermore, increased alien tree invasion correlated significantly with Argentine ant abundances. The Argentine ant displaced Pheidole capensis and Camponotus spp., while it decreased the abundances of commonly-occurring indigenous ants, such as Lepisiota capensis and Plagiolepis spp. Displacement by the Argentine ant may be a result of indirect competition for food resources. The effects of invasive aliens are synergistic in that there is a cascade effects from initial plant invasions to subsequent animal invasion. / AFRIKAANSE OPSOMMING: Indringer bome, Pinus en Eucalyptus, affekteer miere op negatiewe wyse in die Kaap Florsitiese Streek (KFR), ‘n area in Suid Afrika van belang t.o.v. globale biodiversiteit. Hierdie uitheemse indringer bome verminder hulle hoeveelheid en spesies rykheid. Die bogenoemde is kommerwekkend omdat meer as 1300 plant spesies in the KFR versprei word deur miere. Die verandering in hoeveelheid en versameling van inheemse miere kan dus ernstige implikasies hê op die saad verspreiding van inheemse plant spesies. Een van die mees verwoestende effekte op saad verspreiding is veroorsaak deur die indringer Argentynse mier (Linepithema humile (Mayr)), wat sade neer werp buite hulle neste, waar hulle nie suksesvol kan ontkiem nie. Tien monsterings-tereine was geselekteer om die bogenoemde effekte te ondersoek op Vergelegen Landgoed. Hierdie het afgewissel van indringer tot skoon tereine. Elke terrein is op ses versamelings-plekke gemonster, met vier pitvalle, wat oopgelê het vir sewe dae gedurende Desember 2005, Februarie 2006, Mei 2006 en September 2006. 40 spesies van miere was gemonster. Indringer plante het ‚n betekenisvolle impak gehad het op die hoeveelheid en rykheid van die mier gemeenskappe, deur die skepping van ‚n dig baldakyn wat die abiotiese omgewing van die miere se habitat verander het. Die vermeerdering van indringer plante veroorsaak die vermeerdering van Argentyne miere. Kanonieke Mede-Respons Analise illustreer dat die Argentynse mier Pheidole capensis en Camponotus spp. verplaas het, terwyl dit ander inheemse mier getalle verminder het, soos Lepisiota capensis en Plagiolepis spp. Die verplasing deur die Argentynse mier mag die resultaat wees van indirekte wedywering vir hulpbronne. Die effekte van indringer species is dus sinergisties deur dat ‚n kaskade effek ontstaan vanaf plant tot dier indringer spesies.

Thesis (MSc)--University of Stellenbosch, 2005. / ENGLISH ABSTRACT: Invasive alien trees, especially Acacia species, are a great threat to biodiversity in South African rivers. The national Working for Water Programme is addressing the alien problem by removing alien trees from river margins. The concern is that this may be creating even further disturbance by affecting water quality and habitats. In particular, how is this affecting rare and endemic species? Benthic macro invertebrates and aerial odonates were assessed along five Western Cape rivers in alien-invaded, cleared and natural sites between December and March. The aim was to assess the effect of both alien invasion and alien clearing on aquatic invertebrates. Odonata, being easily sampled, were also assessed as they are severely affected by the lack of understorey plants in shaded, alien-invaded sites. Odonata and benthic macroinvertebrates were treated as two separate studies and no attempt was made to correlate the results obtained from both studies. SASS5, a qualitative, rapid bioassessment technique, based on the sensitivity of the families present, was used as a measure of river health and, indirectly, of water quality. SASS indicated a decline in water quality conditions after alien clearing, a likely response to the greater insolation as well as erosion of cleared banks, resulting in elevated temperatures and suspended solids and lowered oxygen levels. Community responses to alien disturbance and other environmental factors were analysed using PRIMER and CANOCO software. Assemblages of Odonata were found to provide a rapid, cost-effective means of assessment and monitoring. Potential indicator and detector species were also identified using the lndicator Value method. Assemblage patterns of aquatic invertebrates, however, were dominated by between-river and seasonal effects. Therefore, while SASS detected overall changes in river health, without identifying the cause, potential aquatic detector taxa were identified that may be useful for linking general disturbance to alien invasion or clearing. All indicator and detector taxa identified in both studies can be used for long-term monitoring and for identifying biodiverse areas for clearing or protection. In both studies, sensitive, endemic taxa were lost after clearing, being replaced by more tolerant, widespread taxa. Recovery of the biota appears to follow the recovery succession of the vegetation, with most sensitive or endemic taxa only appearing after the recovery of indigenous plants. A number of recommendations are made regarding the restoration of both water quality (particularly with respect to shade and soil erosion) and biotope availability (particularly in terms of the recultivation of indigenous plants) in order to achieve biodiversity objectives. The role of catchment management, prioritisation procedures and long-term monitoring are also discussed. / AFRIKAANSE OPSOMMING: Uitheemse, indringerbome, veral Acacia spesies, is 'n groot bedreiging vir biodiversiteit in Suid- Afrikaanse riviere. Die nasionale Werk vir Water-projek spreek hierdie probleem aan deur uitheemse bome van rivieroewers te verwyder. Die kommer is dat water kwaliteit en habitatte sodoende verder versteur kan word. Byvoorbeeld, hoe word endemiese en bedreigde spesies geraak? Akwatiese makroinvertebrate en volwasse Odonata in vyf Wes-Kaapse riviere is tussen Desember en Maart bestudeer en gemonster in natuurlike gebiede, in gebiede waar indringerbome teenwoordig is, en in gebiede waar hulle verwyder is. Die doel was om die effek van indringerverwante impakte op akwatiese invertebrate vas te stel. Odonata is ook bestudeer omdat hulle maklik gemonster kan word en omdat hulle ernstig geraak word deur indringers. Die uitheemse plantegroei oorskadu die oewers en verhoed die groei van inheemse oewerplante. Die bentiese makro-invertebrate en Odonata is as twee aparte studies behandel en geen poging is gemaak om die resultate van die twee te vergelyk nie. SASSS, 'n kwalitatiewe, bioasseseringsmetode wat op die sensitiwiteit van die aanwesige families baseer word, is gebruik om waterkwaliteit op 'n indirekte manier te bepaal. SASS het aangedui dat daar 'n afname in waterkwaliteit is nadat indringerplante verwyder is. Dit is moontlik as 'n gevolg van groter blootstelling aan sonskyn en erosie van rivieroewers wat veroorsaak dat temperature en die hoeveelheid gesuspendeerde materiaal verhoog word, en dat suurstof konsentrasies verminder word. Die gevolge van indringerplante en ander omgewingsfaktore op akwatiese gemeenskappe is met PRlMER en CANOCO sagteware ontleed. Groepering van Odonata kan gebruik word om op 'n maklike en koste-effektiewe manier om die impak van indringerplante en hul verwydering te bepaal en te monitor. Aanwyserspesies is ook deur middel van die 'Indicator Value' metode geïdentifiseer. Die verspreidingspatrone van invertebraatspesies word deur geografiese en seisoenale effekte oorheers. Dus, terwyl SASS veranderinge in waterkwaliteit kan aantoon, sonder om die oorsaak daarvan te identifiseer, kan aanwyserspesies gebruik word om meer spesifieke impakte deur indringerplantegroei, of indringerverwydering, te bepaal en te monitor. Hulle kan ook gebruik word om gebiede met hoë biodiversiteit vir bewaring of indringerverwydering te identifiseer. Beide studies dui aan dat sensitiewe en endemiese taksa na indringerverwydering verlore gaan, en vervang word met meer geharde, wydverspreide taksa. Herstel van die biota volg op die herstel van die plant gemeenskappe, en die mees sensitiewe of endemiese taksa herstel eers nadat die inheemse plantegroei herstel het. 'n Aantal aanbevelings in verband met die restorasie van waterkwaliteit (veral in terme van die hoeveelheid skaduwee en erosie) en die beskikbaarheid van biotope (veral in terme van inheemse plante) om biodiversiteitsdoelwitte te bereik word gemaak. Die rol van opvanggebied bestuur, voorrang prosedures en lang termyn monitering word ook bespreek.

The invasion of Acacia mearnsii in the Kouga catchment, Eastern Cape, South Africa, has various negative impacts on the ecosystem. These impacts include: reduced species richness, increased water use, increased nutrients and increased N cycling rates. The native shrubby fynbos vegetation has adapted to the acidic nutrient poor soils and Mediterranean climate of the Kouga Mountains. Fynbos, however, is currently being out competed by the much taller Acacia mearnsii trees, due to their competitive nature and ability to fix nitrogen, thereby enriching the soil. The invaded sections of the valley bottoms and lower hill slopes are characterised by an almost complete monoculture of Acacia mearnsii, with very few fynbos species still present. The Department of Water and Environmental Affairs sponsored Working for Water programme started clearing Acacia mearnsii in 1996 in the Kouga Mountains. Cleared sites have remained bare for long periods, indicating that soil properties are not favourable for indigenous propagule re-establishment. The aim of this research was to assess how A. mearnsii invasion and clearing affect fynbos recovery through its impact on soils. This was done by characterising vegetation and soil properties on fynbos, infested and cleared slopes. Vegetation cover for various growth forms was determined and a species list was compiled for each plot. The slope angle, surface hardness, litter cover, bare ground cover and soil depth were measured in the field, whereas water repellency, particle size and the chemical composition were measured in the laboratory. Furthermore, the plant establishment capacity of soils from fynbos, infested and cleared slopes was calculated. This was done by germinating fynbos seeds and growing fynbos plants in soils from the various slopes. The effect that invasion and clearing has on soil erosion was quantified using erosion plots on fynbos, infested and cleared slopes. The invasion and clearing of Acacia mearnsii led to an increase in soil nutrients, especially nitrogen, phosphorus, potassium, carbon and manganese. Furthermore, soils became more acidic, with increased water repellency and reduced surface hardness. The vegetation changed to a tree-dominated structure, replacing the native species. Native plant germination was relatively unaffected by invasion and clearing, with an increase in germination just after clearing. Plant growth of a native grass, Themeda triandra, and herb, Helichrysum umbraculigerum, has increased on soils from cleared slopes. This study showed that soil movement increased on slopes which are invaded and cleared of Acacia mearnsii, with erosion rates doubling on invaded slopes

Invasive alien plants have widespread ecological and socioeconomic impacts throughout many parts of the world, including Swaziland where the government declared them a national disaster. Control of these species requires knowledge on the invasion ecology of each species including how they interact with the invaded environment. Species distribution models are vital for providing solutions to such problems including the prediction of their niche and distribution. Various modelling approaches are used for species distribution modelling albeit with limitations resulting from statistical assumptions, implementation and interpretation of outputs. This study explores the usefulness of Bayesian networks (BNs) due their ability to model stochastic, nonlinear inter-causal relationships and uncertainty. Data-driven BNs were used to explore patterns and processes influencing the spatial distribution of 16 priority invasive alien plants in Swaziland. Various BN structure learning algorithms were applied within the Weka software to build models from a set of 170 variables incorporating climatic, anthropogenic, topo-edaphic and landscape factors. While all the BN models produced accurate predictions of alien plant invasion, the globally scored networks, particularly the hill climbing algorithms, performed relatively well. However, when considering the probabilistic outputs, the constraint-based Inferred Causation algorithm which attempts to generate a causal BN structure, performed relatively better. The learned BNs reveal that the main pathways of alien plants into new areas are ruderal areas such as road verges and riverbanks whilst humans and human activity are key driving factors and the main dispersal mechanism. However, the distribution of most of the species is constrained by climate particularly tolerance to very low temperatures and precipitation seasonality. Biotic interactions and/or associations among the species are also prevalent. The findings suggest that most of the species will proliferate by extending their range resulting in the whole country being at risk of further invasion. The ability of BNs to express uncertain, rather complex conditional and probabilistic dependencies and to combine multisource data makes them an attractive technique for species distribution modeling, especially as joint invasive species distribution models (JiSDM). Suggestions for further research are provided including the need for rigorous invasive species monitoring, data stewardship and testing more BN learning algorithms. / Environmental Sciences / D. Phil. (Environmental Science)