Microbial and extracellular polymeric substance dynamics in arid–zone temporary pan ecosystems
- Authors: Bute, Tafara Frank
- Date: 2023-03-29
- Subjects: Extracellular polymeric substances , Biofilms , Vernal pools , Microbiomes , Sediment–water interface
- 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:
- Authors: Bute, Tafara Frank
- Date: 2023-03-29
- Subjects: Extracellular polymeric substances , Biofilms , Vernal pools , Microbiomes , Sediment–water interface
- 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
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Perceptions of the role of Lantana camara on human well-being and rural livelihoods in Vhembe Biosphere Reserve, South Africa
- Authors: Mhlongo, Edward Swazi
- Date: 2021-04
- Subjects: Lantana camara -- South Africa -- Vhembe District Municipality , Introduced organisms -- South Africa -- Vhembe District Municipality , Biological invasions -- South Africa -- Vhembe District Municipality , Plant invasions -- South Africa -- Vhembe District Municipality , Lantana camara -- Control -- South Africa -- Vhembe District Municipality , South Africa -- Rural conditions , Ethnoscience -- South Africa -- Vhembe District Municipality
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177952 , vital:42893
- Description: In the past, social aspects on biological invasions were less documented, this hindered the development of sound and effective management of Invasive Alien Species (IAS). However, there has been a shift in trends with more studies on biological invasions integrating local knowledge together with ecological studies to develop effective management interventions. Invasive Alien Species are widespread throughout Southern Africa and are usually prevalent in the rural areas. Limpopo province consists of large rural areas where people depend on natural resources, wild and exotic species for their livelihoods. Lantana camara is one of the major invaders that is problematic worldwide having detrimental impacts on biodiversity, ecosystem functions, and economies. This study assessed the perceptions of the role of L. camara on the well-being and rural livelihoods of local communities in the Vhembe Biosphere Reserve using household surveys. A total of 300 surveys were administered in six villages. The study further used a two-pronged approach to examine invasion extent and management options. The two-pronged approach included (i) detailed vegetation surveys in 50 household yards within each village, and (ii) focus group to solicit local knowledge of invasion extent and managing L. camara by the rural communities. The results of the study showed that almost all the respondents knew L. camara and could describe it. Most of the respondents were of the view that L. camara had no negative impacts on their livelihoods. Other respondents stated costs associated with L. camara were more than benefits and wanted a reduction in L. camara densities in the area. Most respondents wanted more government intervention to help in managing L. camara, this is because of the perceived future impacts of L. camara. Vegetation survey results showed no significant difference in L. camara abundances and plant heights among the six study villages. The average number of L. camara counted per household yard in all villages was (2.41 ± 0.20) plants, with average plant basal diameter of (0.94 ± 0.02 cm). There were significant differences in canopy width of L. camara among the six study villages. Plant basal diameter was high in Tshakhuma (1.05 ± 0.04 m) and Duthuni (1.00 ± 0.04 m) villages, and low in Ha Mutsha village (0.82 ± 0.03 m). Lantana camara canopy width at household level across all villages averaged 1.34 ± 0.03 m. Canopy cover was high in Tshakhuma village (1.70 ± 0.09 m) and low at Ha Mutsha village (1.03 ± 0.03 m). In all six village focus group discussions, it was noted that mechanical clearing of L. camara was the most used method, but they reported minimum help from the government particularly Working for Water (WfW). The study concludes that L. camara has no substantial adverse impacts to most of the respondents. The study further noted that L. camara is dominant in most household yards ii and that management is taking place however current control options are not enough on their own. Suggestions for further research are to explore more alternative indigenous species present or easily accessible to the community members which may offer the same benefits as IAS. Furthermore, additional research at local level is required for implementing management techniques best suited for the area. , Thesis (MSc) -- Faculty of Science, Environmental Science, 2021
- Full Text:
- Authors: Mhlongo, Edward Swazi
- Date: 2021-04
- Subjects: Lantana camara -- South Africa -- Vhembe District Municipality , Introduced organisms -- South Africa -- Vhembe District Municipality , Biological invasions -- South Africa -- Vhembe District Municipality , Plant invasions -- South Africa -- Vhembe District Municipality , Lantana camara -- Control -- South Africa -- Vhembe District Municipality , South Africa -- Rural conditions , Ethnoscience -- South Africa -- Vhembe District Municipality
- Language: English
- Type: thesis , text , Masters , MSc
- Identifier: http://hdl.handle.net/10962/177952 , vital:42893
- Description: In the past, social aspects on biological invasions were less documented, this hindered the development of sound and effective management of Invasive Alien Species (IAS). However, there has been a shift in trends with more studies on biological invasions integrating local knowledge together with ecological studies to develop effective management interventions. Invasive Alien Species are widespread throughout Southern Africa and are usually prevalent in the rural areas. Limpopo province consists of large rural areas where people depend on natural resources, wild and exotic species for their livelihoods. Lantana camara is one of the major invaders that is problematic worldwide having detrimental impacts on biodiversity, ecosystem functions, and economies. This study assessed the perceptions of the role of L. camara on the well-being and rural livelihoods of local communities in the Vhembe Biosphere Reserve using household surveys. A total of 300 surveys were administered in six villages. The study further used a two-pronged approach to examine invasion extent and management options. The two-pronged approach included (i) detailed vegetation surveys in 50 household yards within each village, and (ii) focus group to solicit local knowledge of invasion extent and managing L. camara by the rural communities. The results of the study showed that almost all the respondents knew L. camara and could describe it. Most of the respondents were of the view that L. camara had no negative impacts on their livelihoods. Other respondents stated costs associated with L. camara were more than benefits and wanted a reduction in L. camara densities in the area. Most respondents wanted more government intervention to help in managing L. camara, this is because of the perceived future impacts of L. camara. Vegetation survey results showed no significant difference in L. camara abundances and plant heights among the six study villages. The average number of L. camara counted per household yard in all villages was (2.41 ± 0.20) plants, with average plant basal diameter of (0.94 ± 0.02 cm). There were significant differences in canopy width of L. camara among the six study villages. Plant basal diameter was high in Tshakhuma (1.05 ± 0.04 m) and Duthuni (1.00 ± 0.04 m) villages, and low in Ha Mutsha village (0.82 ± 0.03 m). Lantana camara canopy width at household level across all villages averaged 1.34 ± 0.03 m. Canopy cover was high in Tshakhuma village (1.70 ± 0.09 m) and low at Ha Mutsha village (1.03 ± 0.03 m). In all six village focus group discussions, it was noted that mechanical clearing of L. camara was the most used method, but they reported minimum help from the government particularly Working for Water (WfW). The study concludes that L. camara has no substantial adverse impacts to most of the respondents. The study further noted that L. camara is dominant in most household yards ii and that management is taking place however current control options are not enough on their own. Suggestions for further research are to explore more alternative indigenous species present or easily accessible to the community members which may offer the same benefits as IAS. Furthermore, additional research at local level is required for implementing management techniques best suited for the area. , Thesis (MSc) -- Faculty of Science, Environmental Science, 2021
- Full Text:
A community–wide trophic structure analysis in intertidal ecosystems on the south coast of South Africa
- Authors: Gusha, Molline Natanah C
- Date: 2018
- Subjects: Food chains (Ecology) , Coastal ecology -- South Africa , Intertidal ecology -- South Africa , Marine animals -- Climatic factors -- South Africa , Marine animals -- Food -- South Africa , Marine animals -- Habitat -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63312 , vital:28392
- Description: Coastal ecosystems are more than microhabitats for marine species. Acting as atmospheric carbon filters, species in coastal environments are directly and/or indirectly associated with transferring organic carbon to species at higher trophic levels. However, the progressing change in global climatic conditions has created the need to assess the consequences of the shifting conditions on both direct and indirect interactions of physical and biological parameters at species and/or community levels. From these perturbations, the effects of biotic homogenization on ecosystem functioning and resilience can also be realised. Herein, I discuss the effects of temperature, nutrients, biotic interactions and habitat characteristics on community dynamics within intertidal rock pool systems on the south coast of South Africa using complementary qualitative and quantitative analytical methods. Seasonality had a significant impact on rock pool species with changes in composition and higher richness in winter than summer. The first two axes of the Canonical Correspondence Analysis (CCA) of the plant and animal communities each explained ~20% of the relationship between physico-chemical parameters and biological variables. The CCA highlighted that seasonal shifts in chlorophyll-a, conductivity, salinity, water depth, surface area and substratum type indirectly influenced species composition. For example, pools with heterogenous substratum comprising a mixture of sand and rock exhibited higher species diversity than homogenously bedded pools. Furthermore, a Bayesian analysis of community structure based on stable isotope ratios was used to assess how trophic pathways of carbon and nitrogen elements reflected community composition and richness. Isotopic biplots showed an increase in food web size, food chain length and the trophic positions of fish and some gastropods in winter compared to summer. There was greater dietary overlap among species in larger pools. In addition, while isotopic nearest neighbour distance and species evenness also showed a positive increase with pool size in summer, the same metrics were almost constant across all pool sizes in winter. These changes in food web packing and species evenness suggest seasonal preferences or migration of species in summer from small pools to larger pools with stable physico-chemical parameters. Furthermore, the presence of fish was seen to promote trophic diversity within some pools. The results from laboratory microcosm grazing experiments demonstrated significant direct and indirect effects of temperature and nutrients within plankton communities. Copepod grazing had an indirect positive influence on phytoplankton biomass and size structure while the interactive effects of temperature and nutrients had contrasting effects on both phytoplankton communities and copepod biomass. Shifts in water chemistry and nutrient treatments were also observed in the presence of copepods. Phosphate addition had a recognisable impact on plankton communities. The presented synthesis of the literature mainly highlighted that positive effects at one trophic level do not always positively cascade into the next trophic level which is evidence of complex interactive biotic, habitat and water chemistry effects within these intertidal ecosystems. Thus, to further understand cascading effects or community structure functioning in general, there may be a need to incorporate and understand species functional traits and how they contribute to trophic diversity, community restructuring and functioning in coastal habitats.
- Full Text:
- Authors: Gusha, Molline Natanah C
- Date: 2018
- Subjects: Food chains (Ecology) , Coastal ecology -- South Africa , Intertidal ecology -- South Africa , Marine animals -- Climatic factors -- South Africa , Marine animals -- Food -- South Africa , Marine animals -- Habitat -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63312 , vital:28392
- Description: Coastal ecosystems are more than microhabitats for marine species. Acting as atmospheric carbon filters, species in coastal environments are directly and/or indirectly associated with transferring organic carbon to species at higher trophic levels. However, the progressing change in global climatic conditions has created the need to assess the consequences of the shifting conditions on both direct and indirect interactions of physical and biological parameters at species and/or community levels. From these perturbations, the effects of biotic homogenization on ecosystem functioning and resilience can also be realised. Herein, I discuss the effects of temperature, nutrients, biotic interactions and habitat characteristics on community dynamics within intertidal rock pool systems on the south coast of South Africa using complementary qualitative and quantitative analytical methods. Seasonality had a significant impact on rock pool species with changes in composition and higher richness in winter than summer. The first two axes of the Canonical Correspondence Analysis (CCA) of the plant and animal communities each explained ~20% of the relationship between physico-chemical parameters and biological variables. The CCA highlighted that seasonal shifts in chlorophyll-a, conductivity, salinity, water depth, surface area and substratum type indirectly influenced species composition. For example, pools with heterogenous substratum comprising a mixture of sand and rock exhibited higher species diversity than homogenously bedded pools. Furthermore, a Bayesian analysis of community structure based on stable isotope ratios was used to assess how trophic pathways of carbon and nitrogen elements reflected community composition and richness. Isotopic biplots showed an increase in food web size, food chain length and the trophic positions of fish and some gastropods in winter compared to summer. There was greater dietary overlap among species in larger pools. In addition, while isotopic nearest neighbour distance and species evenness also showed a positive increase with pool size in summer, the same metrics were almost constant across all pool sizes in winter. These changes in food web packing and species evenness suggest seasonal preferences or migration of species in summer from small pools to larger pools with stable physico-chemical parameters. Furthermore, the presence of fish was seen to promote trophic diversity within some pools. The results from laboratory microcosm grazing experiments demonstrated significant direct and indirect effects of temperature and nutrients within plankton communities. Copepod grazing had an indirect positive influence on phytoplankton biomass and size structure while the interactive effects of temperature and nutrients had contrasting effects on both phytoplankton communities and copepod biomass. Shifts in water chemistry and nutrient treatments were also observed in the presence of copepods. Phosphate addition had a recognisable impact on plankton communities. The presented synthesis of the literature mainly highlighted that positive effects at one trophic level do not always positively cascade into the next trophic level which is evidence of complex interactive biotic, habitat and water chemistry effects within these intertidal ecosystems. Thus, to further understand cascading effects or community structure functioning in general, there may be a need to incorporate and understand species functional traits and how they contribute to trophic diversity, community restructuring and functioning in coastal habitats.
- Full Text:
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