School of Animal, Plant and Environmental Sciences (ETDs)

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Assessment of the Environmental Authorisation Processes and Mining Right Applications for Improved Environmental Outcomes
(University of the Witwatersrand, Johannesburg, 2023) Antoniades, Maria; Watson, Ingrid
This study investigates alignment of South African mining right and environmental authorisation application processes to determine their adequacy in catering for optimised early mine planning seeking to achieve enhanced environmental outcomes. First the legislative requirements for mining right and environmental authorisation applications are evaluated. Results are critically analysed, including an assessment of process alignments and disjunctions. Secondly, integration of the application study processes in practice are investigated. The practical implications of the application requirements are qualitatively examined through key informant and case study analysis. It is shown that integrated planning is not a legislated requirement nor readily adopted by proponents. Environmental planning conforms to technical outputs as tick-box exercises rather than being iterative and co-operative. Workstreams misalignments result in poor planning to the detriment of environmental outcomes. Finally, a practical guidance is presented for early integrated study processes aimed at meaningful project design through parallel planning to optimise environmental results.
Effects and consequences of natural and artificial light at night on small mammals in peri-urban Johannesburg, South Africa
(University of the Witwatersrand, Johannesburg, 2024) Oosthuizen, Tasha; Pillay, Neville; Oosthuizen, Marietjie
Studies investigating artificial light at night (ALAN) have increased over recent years. However, research examining the influence of ALAN on southern African small mammal species are lacking and even information on their basic biology is scarce. To close this knowledge gap, I investigated the effect of ALAN on different facets of animal behaviour in African small mammals. Firstly, I evaluated the impact of the natural (lunar cycle) and ALAN on the community composition and species abundance in two populations of small mammals. I chose two field sites: one facing Johannesburg (exposed to ALAN) and one facing away. I conducted mark-recapture trapping to ascertain the occurrence and abundance of small mammals. The Light site had both a higher species composition and a higher animal abundance when compared to the composition and abundance of the Dark site. The lunar cycle had an effect; on nights with a full moon, the species composition and animal abundance of both study sites declined, while on new moon nights, the opposite occurred, with an increase in both the species composition and abundance on the Light and Dark sites. The absence of a negative ALAN effect on the Light site can potentially be ascribed to the availability of microhabitats for small mammals to escape illumination, leaving them seemingly unaffected. Next, I assessed the locomotor activity of three species of commonly occurring rodents on the study area, one crepuscular (19 single-striped grass mice, Lemniscomys rosalia), one species with reportedly variable activity (19 angoni vlei rats, Otomys angoniensis) and one nocturnal (19 southern multimammate mice, Mastomys coucha). They were captured at a different location than the mark-recapture study sites and tested in captivity under natural (exposed to natural light and temperature changes), laboratory (standard laboratory conditions; 12h light:12h dark and constant temperature) and ALAN treatments. Lemniscomys rosalia exhibited crepuscular activity under all three experimental treatments, Otomys angoniensis was mostly nocturnal with some diurnal activity. The temporal activity profiles of the two species that showed some activity during the light hours were unaffected by ALAN. Mastomys coucha displayed strictly nocturnal activity during the natural and laboratory treatments, but during ALAN treatments the temporal activity profiles of some animals shifted so that they were active during the start of the day. Lemniscomys rosalia and O. angoniensis were more active under the natural treatment, whilst M. coucha was more active in the laboratory treatment. When exposed to 2 Lux ALAN presented remotely, there was no effect on the level of activity in O. angoniensis, L. rosalia showed a reduction of about 20% in its activity, whereas M. coucha reduced its activity by more than 50%. Finally, I studied how ALAN impacted the foraging behaviour of the three species under four treatments (during the day, at night, 2 Lux ALAN and 10 Lux ALAN). Foraging behaviour differed in the three species under different light conditions. Lemniscomys rosalia was risk-averse when feeding during the diurnal and nocturnal (no light at night) treatments. Otomys angoniensis showed irregular responses in their foraging behaviour under all foraging treatments. Mastomys coucha showed no differences when feeding under any of the nocturnal treatments, but it was inactive under the diurnal treatment. Overall, my study revealed that the effect of ALAN is not similar for all small mammalian species and appear to depend on both the spatial and temporal niches that the different species occupy. Strictly nocturnal animals seem to be affected the most, whereas animals that are active during the day showed lesser responses. Given the rapid increase in urbanisation and anthropogenic disturbances, more and more species are exposed to ALAN. Species that prefer darker, more secluded habitats appear to be more vulnerable and at higher risk of local extinctions as a result of disturbances, such as ALAN and habitat transformation. My study highlights that ALAN affects both nocturnal and diurnal rodents to the extent that it can have fitness consequences, including changed active times, foraging efficiency, movement patterns and susceptibility to predation. Finally, the disruption of rodent behaviour can have cascading effects for ecosystems and my study also emphasises the importance of safeguarding our night skies to protect biodiversity.
Evaluation of the JSE’s environmental reporting requirements of South African listed companies
(University of the Witwatersrand, Johannesburg, 2024) Hariram, Viratha; Schwaibold, Ute
Through its mandatory environmental reporting requirements, the Johannesburg Stock Exchange (JSE) plays a pivotal role in the private sector to align to Environmental, Social and Governance frameworks and disclose information of a company’s environmental priorities and performance in addressing areas of concern. While there are attempts to safeguard the environment from damage and degradation, it is unclear if this framework is suitable at appropriately addressing the environmental areas of concern facing South Africa. In order to evaluate the JSE’s environmental requirements on listed companies, this study aimed to identify the local and global environmental priorities via the South African State of Environment Outlook Report (local view), National Development Plan (local view) and Sustainable Development Goals (global view) and thereafter determine if the Global Reporting Initiative, the only set of mandatory environmental requirements of the JSE, was adequately addressing the indicators they outlined. Furthermore, using a scoring system from zero to four, the study evaluated the alignment of ten randomly selected JSE listed companies against the requirements of the Global Reporting Initiative to note their level of adherence and alignment to the South African State of Environment Outlook Report, National Development Plan and Sustainable Development Goals. The results indicate that the Global Reporting Initiative (GRI) covers 73% of environmental priorities discussed in the South African State of Environment Outlook Report, National Development Plan and Sustainable Development Goals. Of the total 74 indicators of environmental concern identified from the three reports, the GRI did not require disclosure for 20 indicators. Only three indicators that were required to be disclosed by the GRI had scored a four on the rating scale due to it being an integrated disclosure that takes into account one or more other related environmental categories. The evaluation of the sampled listed company’s adherence to the GRI via their sustainability reports and integrated annual reports indicated that none of the companies had provided sufficient disclosures to meet the requirements of the GRI. 80% of the sampled listed companies made a strong alignment to the Sustainable Development Goals in their sustainability reports and / or integrated annual reports. A shortcoming of the JSE that was stated by all four sustainability experts interviewed was the lack of enforcement for listed companies to make quality and comprehensive disclosures or accountability expected from listed companies. There is no formal process of review or consequences for listed companies who do not comply.
Farming systems in South Africa beyond 2020: a scenario-based study, using systems analysis, of the connectivity between farming systems in the Vhembe district, Limpopo, South Africa
(University of the Witwatersrand, Johannesburg, 2024) Materechera-Mitochi, Fenji; Scholes, Mary
Agriculture is a significant contributor to the South African economy and overall development as it contributes to poverty reduction and food security. It is against this backdrop that agricultural development becomes a focus area for decision making amongst stakeholders, as it is directly linked to food systems. The traditional approach to agricultural production in the country has been one that views farming as mainly based on land ownership and yield in isolation from the broader context of the four drivers of production namely land, labour, capital and enterprise. The concept of farming systems provides a broader perspective on farming and encompasses the entire value chain for a commodity which includes production, management practices, marketing, value addition, financial resources, and policies. The South African agrarian structure is characterised by a dualism in which large-scale commercial farmers co-exist alongside small-scale farmers. This is a legacy of the apartheid system of governance. Large-scale commercial farmers, who are mostly capital intensive, have historically been regarded as the main drivers of national food security while small-scale farmers on the other hand are viewed as significant contributors to food security at a household level. Both farmers are therefore important contributors to the national agricultural economy. Research on the two types of farmers in the South African context is usually focused on the respective farmers’ approaches to production individually and does not consider them as joint ventures. This study was aimed at providing an alternative approach to viewing South Africa’s farming systems by evaluating current farming systems in the Vhembe district of Limpopo, South Africa, using systems analysis as a tool to highlight the connectivity of the interactions within and between them. The study also aimed to conceptualize scenarios for sustainable future farming systems in South Africa. The Vhembe district in the Limpopo province was chosen for the study because both largescale commercial and small-scale farmers occur and due to the favourable sub-tropical climate, the area has become a hub for the farming of numerous high value crops that contribute positively to the country’s agricultural economy. The study made use of a mixed methods approach that combined the analysis of primary data obtained from in-depth interviews and secondary data obtained from an agricultural database to identify and characterize large-scale commercial and small-scale farming systems in the Vhembe district. The study examined the drivers of production for three different commodities, macadamia nuts, mangos and avocado iii pears, the two types of farming systems and their connectivity. The study was grounded on the conceptual framework of systems thinking and used a systems analysis tool i.e., causal loop diagrams to analyse the connectivity between the two farming systems. Lastly, the study developed conceptual scenarios using a deductive scenario method to conceptualise scenarios for the future of the two farming systems and the different commodities. Key findings of the study showed that farming systems need to be understood through the lens of the four drivers of production. Land as a driver of production interacts with multiple other factors in shaping the management of a sustainable farming system. Examples of these factors include the link between land availability, ownership and farm size, decision-making and resource allocation tied to land management practices, and socio-economic considerations including the diversification of livelihoods by incorporating non-farm income and the farmers’ adaptability to uncertainties such as climate change. The findings also revealed that there are interconnections between the two types of farming systems presenting potential for enhanced production and commercial opportunities. The conceptual scenarios developed in the study and the systems thinking tool of causal loop diagrams proved to be valuable tools to inform decision making and policy development. The study’s main conclusion points to the potential of large-scale commercial and small-scale farming systems in South Africa operating as joint ventures in the future and enhancing the sustainability of agricultural production and livelihoods. It also recommends the use of systems thinking that includes social, financial and environmental values and impacts in decision making for agricultural development.
Seasonal abundance and diversity of mites in Coffea arabica L. at Beaver Creek Coffee Estate, South Africa
(University of the Witwatersrand, Johannesburg, 2023) Chikomo, Nontobeko Natasha; Situngu, Sivuyisiwe
The presence of multiple species of mites inside the leaf domatia of Coffea arabica is well documented by various studies. This study examined the influence of seasonal changes on the abundance and diversity of mites in the leaf domatia of Coffea arabica. The study furthermore documented the species of predatory mites that were associated with coffee. The results of the study showed that there was a significant variation in the abundance of mites due to changes in season. Mite counts were significantly higher in spring followed by autumn and lowest in summer. There was no correlation between the number of mites and temperature and relative humidity. Therefore, this study could not establish what drives the seasonal changes in the mite populations and we postulate that this was because we did not measure the microclimate of the individual trees we sampled. This would have given us more accurate data on the temperature and relative humidity experienced by these mites. The Shannon-Weiner Diversity Index was found to be highest in summer and lowest in winter. The Phytoseiidae, Tydeidae, Stigmaeidae, and Tenuipalpidae were found to be the predominant families in this study. This study is one of the few studies in South Africa to directly investigate the effects of seasonal changes in mite abundance, and could potentially open avenues for further research, particularly on what seasonal parameters drive the mite population changes. We recommend that future studies use Ibuttons to get a true measure of the climatic variables that are experienced by the mites sampled at a tree level
Tolerance, uptake, and translocation of platinum (Pt), nickel (Ni), and cobalt (Co) by Tamarix usneoides E. Mey. ex Bunge
(University of the Witwatersrand, Johannesburg, 2022) Mader, Anthony E.; Weiersbye, Isabel M.; Mycock David J.
The intensification of platinum (Pt), cobalt (Co) and nickel (Ni) mining and processing results in the release of salts and metals into the environment. This calls for the identification of halophytes with an ability to tolerate and desalinate metal-contaminated sites while simultaneously allocating metals (Pt, Ni, and Co) into harvestable biomass. Tamarix usneoides E. Mey ex Bunge is an indigenous exo-recretohalophyte that has been used for erosion control and for the desalination and allocation of metals from gold and uranium mine tailings and land contaminated by metallurgical effluent. The aim of this study was to investigate the uptake, translocation, and tolerance of Pt, Ni, and Co by T. usneoides from liquid medium (in vitro) and soil contaminated by base metal refinery effluent spillages and previous overspray from the enhanced evaporation spray system (in situ). More specifically, the in situ study investigated the utility of mature T. usneoides trees in the desalination of soil contaminated by previous metallurgical spillages and overspray emissions through the extraction of sulphur and metals Pt, Ni, and Co into harvestable biomass. Four T. usneoides trees were categorised into different size classes based on tree measurements and allometric equations. Seven soil pits (four “planted” and three “unplanted” – control) were excavated and opposite faces of the soil profile were sampled at 20 different intervals (0 – 340 cm). Soil samples were freeze-dried and analysed for total element concentrations. Root systems were harvested by excavating soil pits (maximum depth of 3.5 meters) using a mechanical excavator. Trees were harvested and immediately separated into above (leaves, twigs, wood, and flowers) and belowground (coarse and fine roots) plant organs. Tree biomass was further separated into different above (outer bark, inner bark, and sapwood and heartwood) and belowground (epidermis, cortex, and stele) tissue types. Plant material was rinsed three times in tap water to remove unbound residual metals and residual substrate from root and shoot surfaces. It must be noted that the determined metal concentrations are a combined measure of metals adsorbed on the root surface, assimilated in planta, and excreted on the plant surface from the foliar salt glands. Metals were allocated in trees (across plant organs and tissue types) in the order: Ni (59.46 ± 4.67 mg/kg) > Co (2.65 ± 0.34 mg/kg) > Pt (50 ± 6 µg/kg) whereas sulphur (S) was hyperaccumulated in tree leaves [39 900 ± 861 mg/kg (3.9% ± 0.7 %)]. Platinum was bioaccumulated [bioconcentration factor (BCF) > 1.5] and translocated [translocation factor (TF) > 1] in the leafy shoots of one individual tree, Ni in one (BCF = 1.03), and Co in another replicate (BCF = 1.02). Soil chemical properties (pH, electrical conductivity, and redox potential) differed between planted and unplanted pits whereby pH and EC were lower in planted pits [pH 6.0; EC = 3 499 µS/cm (34.99 mM NaCl)] compared with unplanted [pH 7.6; EC = 9 644 µS/cm (96.44 mM NaCl)] (ANOVA, p < 0.01). The lower EC, along with S hyperaccumulation (BCF > 20; TF > 1), supports the potential use of T. usneoides for phytoextraction of S and Ni in shoot tissues and Co and Pt in roots. At a spacing of 1333 trees / ha, T. usneoides trees could remove an estimated 2.23 ± 0.30 mg Pt/ha, 3.02 ± 0.83 kg Ni/ha, 1.28 ± 0.90 kg Co/ha, and 1.28 ± 0.09 tons S/ha, excluding excreted salts. Excreted salts were visible but could not be quantified without confounding surface dust contamination. The first in vitro study determined factors influencing the rhizogenesis of T. usneoides in order to develop a mass propagation protocol. Explant establishment in vitro was influenced by various donor plant factors, viz. growing conditions (contaminated < non-contaminated; Kruskal-Wallis (KW), p < 0.05), physiological age (younger > older donor plants; ANOVA, p < 0.05), genotype (KW, p < 0.001), season of culturing (higher establishment in winter; KW, p < 0.05), length of explant (40 mm > 25 mm; KW, p < 0.05), and volume of growth vial (50 mL > 15 mL; KW, p < 0.05) but not pH, chronological age, strength of plant growth medium, or auxin pulse treatments. This study indicates that propagation protocols can be developed by controlling factors influencing explant establishment. A standardised and rapid in vitro protocol was developed for the mass propagation of T. usneoides explants. This in vitro protocol was used for the metal uptake studies whereby established explants were exposed to 25 % Murashige and Skoog standard plant growth medium supplemented with Pt, Co, or Ni (as sulphate complexes) at 0, 25, 50, or 100 mg/L at pH 5.5 or 7.5 over a 14-day exposure period. On completion of the metal exposure period, plantlets were harvested, separated into roots and shoots, freeze-dried, and analysed for metal concentrations. Higher metal concentrations (Ni > Co >> Pt) were accumulated in roots (combined measure of metals adsorbed on the root surface and assimilated in planta) compared with shoots whereby BCF > 1 (excluding Pt) and TF < 1. Metal BCF (Ni > Co >> Pt; KW, p < 0.05) and TF (Co > Ni >> Pt; KW, p < 0.05) increased in a dose-dependent fashion and were not influenced by pH level. Cobalt and Ni (≤ 50 mg/L) uptake dynamics did not v differ suggesting similar uptake dynamics, when treated separately. Platinum (defined in this study as Pt > 1 – 4 mg/kg), Ni (> 1 000 mg/kg), and Co (> 300 mg/kg) were hyperaccumulated in roots (“rhizo-hyperaccumulation”) across treatments with possible Co-hyperaccumulation in shoots by two genotypes. Genotype influenced Co allocation in shoots but not Ni or Pt. Tolerance indices did not differ [Co (97 %) > Pt (82 %) > Ni (77 %)] between pH, metal, treatment concentration, or the interplay between these factors. Metal treatments did not impact measured morphological parameters (excluding Ni treatments which promoted shoot length increment) (KW, p < 0.05). Plantlet survival differed between pH and metals [Pt (90 %) > Ni (81 %) > Co (62 %)] (KW, p < 0.05). Variability in Co accumulation capacity between genotypes indicated that selective breeding, using the developed in vitro mass propagation protocol, for improved rhizofiltration and phytoextraction traits is feasible. Results demonstrate that T. usneoides has the potential for recovery of Ni and Co (and Pt to a lesser degree) from effluents, exhibiting a tolerance to Ni, Co, and Pt at 1, 10, and 10,000 times the average soil crustal abundance, respectively, under moderately acidic (pH 5.5) and alkaline (pH 7.5) conditions and across a wide metal concentration range. Results from the in situ study indicate that 9- year-old T. usneoides trees can be used for the decontamination of sulphate-contaminated soils under study site conditions which are more conducive to the survival of glycophytes. Tamarix usneoides is thus able to assimilate, translocate, and tolerate Ni, Co, and Pt (to a lesser degree) when exposed to metals across a wide pH and metal concentration range, under different (in situ and in vitro) experimental conditions. This opens the possibility for the species to be used in a range of phytotechnologies.

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