Microbial and extracellular polymeric substance dynamics in arid–zone temporary pan ecosystems
- Authors: Bute, Tafara Frank
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422258 , vital:71925
- Description: Microbial communities of bacteria, viruses, algae, protozoans and fungi participate profoundly in aquatic systems, particularly in mediating processes such as primary production, decomposition, and biogeochemical cycles. In addition, microbiomes produce extracellular polymeric substances (EPS) which encompass a hydrated exopolymer mainly constituted of carbohydrates and proteins. The exopolymer aid proliferation and persistence of biofilms on their resident surfaces. There is however paucity of data on functional diversity of microbiomes in arid zone temporary wetlands with previous research having mainly focused on permanent systems in the northern hemisphere. In the face of ongoing climatic changes and anthropogenic threats to wetlands, it is imperative to assess the health status of aquatic systems in relation to microbial productivity dynamics. In this thesis, colorimetric methods and sequence–based metagenomics were conducted to quantify microbial EPS production and bacterial metagenome functions, respectively. This study was conducted in Khakhea–Bray region (North–West, South Africa) in June 2021 and January 2022 with a focus on evaluating microbial patterns of distribution between seasons (i.e., Dry and Wet) and varying depth i.e., deepest zones (Deep), intermediate depth (Mid) and shallowest regions (Edge). Additionally, potential relationships between EPS and either water content or organic matter content (OM content) were evaluated. In this study it was hypothesized that wet phases and deeper zones will have high EPS production and support more functions in comparison to shallowest regions and dry phases. Carbohydrates and proteins were quantified using the Dubois method and modified Lowry procedure, respectively. Carbohydrates generally occurred in higher proportions than proteins, suggesting that EPS found in these systems was largely diatom produced. The wet phases (wet season and inundation periods) supported more EPS production compared to the dry phases. The results of principal components analysis (PCA) and Spearman’s correlations suggested that EPS was highly correlated with sediment water content among other assessed variables. No significant associations were established between EPS and organic matter content. Spatial distribution of EPS demonstrated similar patterns between the deepest (Deep) and the intermediate depth zones (Mid) however the shallow regions (Edge) had significantly lower concentrations. Bacterial characterization was established by amplification of the 16S rRNA gene using illumina–sequencing protocol. Enzyme functions associated with biogeochemical pathways were predicted in PICRUSt2 bioinformatics pipeline. A total of 15 042 Unique Amplicon Sequence Variants (ASVs) were observed to be affiliated to 51 bacterial phyla and 1 127 genera. All top genera had commonality in heat tolerance. Firmicutes, dominated at phyla level with 59 % (mean ± sd, 19 ± 13 %) relative abundance followed by Actinobacteria and Proteobacteria both at 34 % (18 ± 7 %) and (18 ± 6 %), respectively. Microbial diversity matrices highlighted significant differences in beta diversity more than alpha diversity. Bacterial microbiomes were more distinct between seasons compared to within season, suggesting that functions were seasonally driven. These findings were supported by highest rates of denitrification, carbohydrate degradation and EPS production by core microbiomes in the wet season as compared to low rates of nitrogen mineralisation, carbon fixation and nitrification in the dry season. The present findings represent a first attempt in evaluating sequence–based metagenomics in semi–arid southern African temporary pan ecosystem. Both microbial EPS and bacterial functional potential were highly driven by water availability, with highest rates mainly associated with maximum inundation compared to dry states of pans. It can therefore be suggested that extended dry periods are threatening to microbially mediated processes in temporary wetlands, with implications to loss of biodiversity due to desiccation resulting in poor nutrient cycling. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Date Issued: 2023-03-29
- Authors: Bute, Tafara Frank
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422258 , vital:71925
- Description: Microbial communities of bacteria, viruses, algae, protozoans and fungi participate profoundly in aquatic systems, particularly in mediating processes such as primary production, decomposition, and biogeochemical cycles. In addition, microbiomes produce extracellular polymeric substances (EPS) which encompass a hydrated exopolymer mainly constituted of carbohydrates and proteins. The exopolymer aid proliferation and persistence of biofilms on their resident surfaces. There is however paucity of data on functional diversity of microbiomes in arid zone temporary wetlands with previous research having mainly focused on permanent systems in the northern hemisphere. In the face of ongoing climatic changes and anthropogenic threats to wetlands, it is imperative to assess the health status of aquatic systems in relation to microbial productivity dynamics. In this thesis, colorimetric methods and sequence–based metagenomics were conducted to quantify microbial EPS production and bacterial metagenome functions, respectively. This study was conducted in Khakhea–Bray region (North–West, South Africa) in June 2021 and January 2022 with a focus on evaluating microbial patterns of distribution between seasons (i.e., Dry and Wet) and varying depth i.e., deepest zones (Deep), intermediate depth (Mid) and shallowest regions (Edge). Additionally, potential relationships between EPS and either water content or organic matter content (OM content) were evaluated. In this study it was hypothesized that wet phases and deeper zones will have high EPS production and support more functions in comparison to shallowest regions and dry phases. Carbohydrates and proteins were quantified using the Dubois method and modified Lowry procedure, respectively. Carbohydrates generally occurred in higher proportions than proteins, suggesting that EPS found in these systems was largely diatom produced. The wet phases (wet season and inundation periods) supported more EPS production compared to the dry phases. The results of principal components analysis (PCA) and Spearman’s correlations suggested that EPS was highly correlated with sediment water content among other assessed variables. No significant associations were established between EPS and organic matter content. Spatial distribution of EPS demonstrated similar patterns between the deepest (Deep) and the intermediate depth zones (Mid) however the shallow regions (Edge) had significantly lower concentrations. Bacterial characterization was established by amplification of the 16S rRNA gene using illumina–sequencing protocol. Enzyme functions associated with biogeochemical pathways were predicted in PICRUSt2 bioinformatics pipeline. A total of 15 042 Unique Amplicon Sequence Variants (ASVs) were observed to be affiliated to 51 bacterial phyla and 1 127 genera. All top genera had commonality in heat tolerance. Firmicutes, dominated at phyla level with 59 % (mean ± sd, 19 ± 13 %) relative abundance followed by Actinobacteria and Proteobacteria both at 34 % (18 ± 7 %) and (18 ± 6 %), respectively. Microbial diversity matrices highlighted significant differences in beta diversity more than alpha diversity. Bacterial microbiomes were more distinct between seasons compared to within season, suggesting that functions were seasonally driven. These findings were supported by highest rates of denitrification, carbohydrate degradation and EPS production by core microbiomes in the wet season as compared to low rates of nitrogen mineralisation, carbon fixation and nitrification in the dry season. The present findings represent a first attempt in evaluating sequence–based metagenomics in semi–arid southern African temporary pan ecosystem. Both microbial EPS and bacterial functional potential were highly driven by water availability, with highest rates mainly associated with maximum inundation compared to dry states of pans. It can therefore be suggested that extended dry periods are threatening to microbially mediated processes in temporary wetlands, with implications to loss of biodiversity due to desiccation resulting in poor nutrient cycling. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Date Issued: 2023-03-29
The influence of immuno-contraception on the ecology of African savanna elephants (Loxodonta africana) in a small game reserve in the Eastern Cape, South Africa
- Authors: Fowler, Natalie
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422269 , vital:71926
- Description: African savanna elephants (Loxodonta africana) can alter the vegetation structure on a landscape which has both positive and negative consequences for biodiversity. This ecological role can be dependent on the density of elephants in a given area and how the area is transformed. Elephants are currently listed as an endangered species on the International Union for Conservation of Nature (IUCN) global red list. Despite this endangered status, strong conservation efforts in southern Africa have increased elephant numbers in protected areas. In South Africa, many of these protected areas are small (<1000 km2) and fenced. Thus, without the freedom to roam over large areas, elephant impacts on vegetation and other ecosystem processes may be exacerbated. Increased growth rates and higher population densities, have prompted wildlife managers to explore several population-level management techniques to slow elephant growth rates in small, protected areas. One such technique is the use of immuno-contraception. My study focused on three datasets (Pre, During and Post porcine zona pellucida (PZP) treatments) of one elephant population over an 18-year period in a small game reserve in the Eastern Cape, South Africa. The first aim of my study was to compare the female demography and reproductive parameters of treated (with PZP) and non-treated females (no PZP). I predicted that the population growth would decrease as more elephant cows were contracepted as well as them having longer inter-calving intervals than non-treated cows. Further, I predicted that there would be a skewed sex ratio of male calves born to treated cows. Lastly, I predicted that fertility rates would be lower in treated cows than in non-treated cows. I calculated the annual population growth rates, inter-calving intervals, sex ratios, age at first calving, fecundity rates and fertility rates of all breeding cows. Population growth rates were similar to other managed populations although, compared to a relatively untouched elephant population, annual growth rates in my study site were high. The inter-calving intervals and age at first birth were low compared to other African protected areas which were most likely influenced by the use of PZP, rainfall and a lack of density dependence. Treated cows did not have longer inter-calving intervals compared to non-treated cows nor was there a male biased sex ratio of the offspring of treated cows. The second aim was to assess the spatial ecology of this elephant population and how it may be influenced by immuno-contraception. I predicted that the use of PZP would increase the elephant herd’s core range as there were fewer reproducing cows. I also predicted that PZP would alter the elephant’s habitat use making them less selective in terms of the vegetation types they selected. I compared the home ranges of the elephant population among the three treatments (Pre PZP, During PZP and Post PZP treatment). Home ranges were larger when elephants were treated with PZP compared to the Pre and Post treatments. The herd utilized most of the reserve during the use of PZP whereas prior to contraception, their space use was mostly concentrated on the eastern side of the reserve. Additionally, the vegetation utilization was inconsistent across the differing timeframes, specifically between pre PZP and during PZP. Prior to the use of PZP, the elephant herd utilized the old lands and riverine thicket the most whereas during the use of PZP, the grasslands and karroid habitats were used the most. The most likely influence of the changes in home ranges and vegetation utilization were rainfall, the use of PZP and resource availability. My results suggest that the use of PZP is essential for controlling elephant population numbers. However, there may be some long-term effects (e.g., behavioural changes) of the use of PZP in elephant populations in small game reserves. Thus, I recommend continued monitoring of all aspects of elephant ecology on reserves where PZP is used as a contraceptive technique. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Date Issued: 2023-03-29
- Authors: Fowler, Natalie
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422269 , vital:71926
- Description: African savanna elephants (Loxodonta africana) can alter the vegetation structure on a landscape which has both positive and negative consequences for biodiversity. This ecological role can be dependent on the density of elephants in a given area and how the area is transformed. Elephants are currently listed as an endangered species on the International Union for Conservation of Nature (IUCN) global red list. Despite this endangered status, strong conservation efforts in southern Africa have increased elephant numbers in protected areas. In South Africa, many of these protected areas are small (<1000 km2) and fenced. Thus, without the freedom to roam over large areas, elephant impacts on vegetation and other ecosystem processes may be exacerbated. Increased growth rates and higher population densities, have prompted wildlife managers to explore several population-level management techniques to slow elephant growth rates in small, protected areas. One such technique is the use of immuno-contraception. My study focused on three datasets (Pre, During and Post porcine zona pellucida (PZP) treatments) of one elephant population over an 18-year period in a small game reserve in the Eastern Cape, South Africa. The first aim of my study was to compare the female demography and reproductive parameters of treated (with PZP) and non-treated females (no PZP). I predicted that the population growth would decrease as more elephant cows were contracepted as well as them having longer inter-calving intervals than non-treated cows. Further, I predicted that there would be a skewed sex ratio of male calves born to treated cows. Lastly, I predicted that fertility rates would be lower in treated cows than in non-treated cows. I calculated the annual population growth rates, inter-calving intervals, sex ratios, age at first calving, fecundity rates and fertility rates of all breeding cows. Population growth rates were similar to other managed populations although, compared to a relatively untouched elephant population, annual growth rates in my study site were high. The inter-calving intervals and age at first birth were low compared to other African protected areas which were most likely influenced by the use of PZP, rainfall and a lack of density dependence. Treated cows did not have longer inter-calving intervals compared to non-treated cows nor was there a male biased sex ratio of the offspring of treated cows. The second aim was to assess the spatial ecology of this elephant population and how it may be influenced by immuno-contraception. I predicted that the use of PZP would increase the elephant herd’s core range as there were fewer reproducing cows. I also predicted that PZP would alter the elephant’s habitat use making them less selective in terms of the vegetation types they selected. I compared the home ranges of the elephant population among the three treatments (Pre PZP, During PZP and Post PZP treatment). Home ranges were larger when elephants were treated with PZP compared to the Pre and Post treatments. The herd utilized most of the reserve during the use of PZP whereas prior to contraception, their space use was mostly concentrated on the eastern side of the reserve. Additionally, the vegetation utilization was inconsistent across the differing timeframes, specifically between pre PZP and during PZP. Prior to the use of PZP, the elephant herd utilized the old lands and riverine thicket the most whereas during the use of PZP, the grasslands and karroid habitats were used the most. The most likely influence of the changes in home ranges and vegetation utilization were rainfall, the use of PZP and resource availability. My results suggest that the use of PZP is essential for controlling elephant population numbers. However, there may be some long-term effects (e.g., behavioural changes) of the use of PZP in elephant populations in small game reserves. Thus, I recommend continued monitoring of all aspects of elephant ecology on reserves where PZP is used as a contraceptive technique. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Date Issued: 2023-03-29
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