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:
- Date Issued: 2023-03-29
- 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:
- Date Issued: 2023-03-29
The biology of Oreochromis mossambicus and vulnerability to the invasion of Oreochromis niloticus
- Authors: Mpanza, Nobuhle Phumzile
- Date: 2022-10-14
- Subjects: Ecomorphology , Mozambique tilapia , Nile tilapia , Introduced fishes , Predatory aquatic animals , Predation (Biology) , Otoliths , Von Bertalanffy function
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362983 , vital:65380
- Description: Mozambique tilapia, Oreochromis mossambicus, a native southern African species now co-occurs with invasive Nile tilapia, Oreochromis niloticus throughout much of the distribution of the former. The spread of O. niloticus in South Africa has been attributed to escapees from aquaculture facilities, placing O. mossambicus at risk through competition for habitat and food resources, as well as through hybridisation. To better manage invasions, a comprehensive understanding of the biology, ecology and behaviour of both native and invasive species is required. The aim of this research was to comparatively assess the biology of O. mossambicus and O. niloticus, their food resource use characteristics and potential competitive interactions to infer impact risks associated with O. niloticus invasion dynamics. In addition to lack of sufficient autecological knowledge on O. niloticus in general, the challenge in the Eastern Cape is that relatively little regional knowledge is available on the biology and ecology of the native O. mossambicus. To address this, a total of 101 O. mossambicus individuals (32 - 297 mm LT) were sampled from the Sunday River catchment and their age and growth determined using sectioned sagittal otoliths. The largest female was 288.8 mm with a parameter estimate of LT (mm) = 272 (1-e-0.331(t=0.772)) and the largest male was 297 mm described as LT (mm) = 331.9 (1-e-0.167(t=1.192)). The growth parameter estimate age for combined sexes was best described as LT (mm) = 322.5 (1-e-0.201(t=1.027)). The growth rate was initially rapid for O. mossambicus and the asymptotic length reached after four years. The length-at-50% maturity was reached at 106.45 mm LT (R2 = 0.57) for the entire population. There was a significant difference (ᵡ2 = 8,047, df = 1, p-value = 0.0045) in the sex ratio between males and females which was skewed towards males 1:1.89 (F:M). Comparisons with O. niloticus were based on literature and these showed that O. niloticus had faster growth rates than O. mossambicus. These results serve as a baseline study in predicting the potential impacts of O. niloticus if it was to be introduced in the Eastern Cape region. Furthermore, although these two species are known to share habitat and food resources, feeding dynamics within the context of relative impact on prey resources, and competition potential between the species, are largely lacking. I used experimental functional response procedures to contrast the food consumption dynamics of each species and to assess for any multiple predator effects (MPEs) between these two closely related fishes. This was done by contrasting functional responses between individual species under single predator scenarios, predicted multiple predator functional response dynamics based on the individual species outputs, and actually observed functional responses under multiple predator conditions. Results showed that both Nile tilapia and Mozambique tilapia depicted a destabilizing Type II functional response. In both single and conspecific pairing Nile tilapia had significantly greater functional responses than Mozambique tilapia, hence greater overall predatory potential than its native congeneric Mozambique tilapia. Attack rates were also greater for Nile tilapia than Mozambique tilapia with both species showing similar handling times in single trials. However, no evidence for MPEs were detected, given lack of differences between predicted and observed functional responses under heterospecific conditions. These results suggest that Nile tilapia do not adjust their food intake in the presence of heterospecific competitors, but do consume more than Mozambique tilapia and are better at finding food when it is present at low densities. Feeding-related morphological characteristics may influence predatory performance of a species and can further provide information on the species’ capacity to locate, attack and consume different prey items. The feeding capacities between O. mossambicus and O. niloticus were compared based on morphological traits in order to determine whether differences existed, and if these differences place the invasive O. niloticus at an advantageous position in terms of resource acquisition and consumption over its native congener. Principal component analysis for functional morphology traits showed overlap between O. niloticus and O. mossambicus. Oreochromis niloticus had distinctively larger lower jaw closing force, gill resistance and gill raker length which facilitated greater feeding capacities for the invasive species over the native O. mossambicus. Trophic profiles depicted high dietary overlap between the two species. Although O. niloticus had a greater feeding capacity towards phytoplankton, plants, fish (ambush), fish (pursuit) and larvae, while O. mossambicus only showed greater feeding capacity towards zooplankton. While dietary overlap and similarities in morphological traits between native and invasive species may result in exploitative competition between the species, O. niloticus seems to be more versatile in its feeding and capable of consuming food web components that O. mossambicus may not be able to handle. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Mpanza, Nobuhle Phumzile
- Date: 2022-10-14
- Subjects: Ecomorphology , Mozambique tilapia , Nile tilapia , Introduced fishes , Predatory aquatic animals , Predation (Biology) , Otoliths , Von Bertalanffy function
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362983 , vital:65380
- Description: Mozambique tilapia, Oreochromis mossambicus, a native southern African species now co-occurs with invasive Nile tilapia, Oreochromis niloticus throughout much of the distribution of the former. The spread of O. niloticus in South Africa has been attributed to escapees from aquaculture facilities, placing O. mossambicus at risk through competition for habitat and food resources, as well as through hybridisation. To better manage invasions, a comprehensive understanding of the biology, ecology and behaviour of both native and invasive species is required. The aim of this research was to comparatively assess the biology of O. mossambicus and O. niloticus, their food resource use characteristics and potential competitive interactions to infer impact risks associated with O. niloticus invasion dynamics. In addition to lack of sufficient autecological knowledge on O. niloticus in general, the challenge in the Eastern Cape is that relatively little regional knowledge is available on the biology and ecology of the native O. mossambicus. To address this, a total of 101 O. mossambicus individuals (32 - 297 mm LT) were sampled from the Sunday River catchment and their age and growth determined using sectioned sagittal otoliths. The largest female was 288.8 mm with a parameter estimate of LT (mm) = 272 (1-e-0.331(t=0.772)) and the largest male was 297 mm described as LT (mm) = 331.9 (1-e-0.167(t=1.192)). The growth parameter estimate age for combined sexes was best described as LT (mm) = 322.5 (1-e-0.201(t=1.027)). The growth rate was initially rapid for O. mossambicus and the asymptotic length reached after four years. The length-at-50% maturity was reached at 106.45 mm LT (R2 = 0.57) for the entire population. There was a significant difference (ᵡ2 = 8,047, df = 1, p-value = 0.0045) in the sex ratio between males and females which was skewed towards males 1:1.89 (F:M). Comparisons with O. niloticus were based on literature and these showed that O. niloticus had faster growth rates than O. mossambicus. These results serve as a baseline study in predicting the potential impacts of O. niloticus if it was to be introduced in the Eastern Cape region. Furthermore, although these two species are known to share habitat and food resources, feeding dynamics within the context of relative impact on prey resources, and competition potential between the species, are largely lacking. I used experimental functional response procedures to contrast the food consumption dynamics of each species and to assess for any multiple predator effects (MPEs) between these two closely related fishes. This was done by contrasting functional responses between individual species under single predator scenarios, predicted multiple predator functional response dynamics based on the individual species outputs, and actually observed functional responses under multiple predator conditions. Results showed that both Nile tilapia and Mozambique tilapia depicted a destabilizing Type II functional response. In both single and conspecific pairing Nile tilapia had significantly greater functional responses than Mozambique tilapia, hence greater overall predatory potential than its native congeneric Mozambique tilapia. Attack rates were also greater for Nile tilapia than Mozambique tilapia with both species showing similar handling times in single trials. However, no evidence for MPEs were detected, given lack of differences between predicted and observed functional responses under heterospecific conditions. These results suggest that Nile tilapia do not adjust their food intake in the presence of heterospecific competitors, but do consume more than Mozambique tilapia and are better at finding food when it is present at low densities. Feeding-related morphological characteristics may influence predatory performance of a species and can further provide information on the species’ capacity to locate, attack and consume different prey items. The feeding capacities between O. mossambicus and O. niloticus were compared based on morphological traits in order to determine whether differences existed, and if these differences place the invasive O. niloticus at an advantageous position in terms of resource acquisition and consumption over its native congener. Principal component analysis for functional morphology traits showed overlap between O. niloticus and O. mossambicus. Oreochromis niloticus had distinctively larger lower jaw closing force, gill resistance and gill raker length which facilitated greater feeding capacities for the invasive species over the native O. mossambicus. Trophic profiles depicted high dietary overlap between the two species. Although O. niloticus had a greater feeding capacity towards phytoplankton, plants, fish (ambush), fish (pursuit) and larvae, while O. mossambicus only showed greater feeding capacity towards zooplankton. While dietary overlap and similarities in morphological traits between native and invasive species may result in exploitative competition between the species, O. niloticus seems to be more versatile in its feeding and capable of consuming food web components that O. mossambicus may not be able to handle. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
- Date Issued: 2022-10-14
Understanding biotic interactions in invaded pond communities in the Sundays River irrigation network, South Africa
- Authors: Mofu, Lubabalo
- Date: 2020
- Subjects: Mozambique tilapia -- South Africa -- Sundays River (Eastern Cape) , Western mosquitofish -- South Africa -- Sundays River (Eastern Cape) , Gobiidae -- South Africa -- Sundays River (Eastern Cape) , Clupeidae -- South Africa -- Sundays River (Eastern Cape) , Reservoirs -- South Africa -- Sundays River (Eastern Cape) , Zooplankton -- South Africa -- Sundays River (Eastern Cape) , Freshwater ecology -- South Africa -- Sundays River (Eastern Cape) , Biotic communities -- South Africa -- Sundays River (Eastern Cape) , Fishes -- Effect of temperature on -- South Africa -- Sundays River (Eastern Cape) , Stable isotopes , Relative Impact Potential
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167089 , vital:41436
- Description: The Sundays River valley irrigation ponds provide a unique opportunity to investigate biotic interactions within a biological invasions context, as they contain both native and non-native fish species. This study focusses on two native species (Glossogobius callidus and Gilchristella aestuaria) and two non-native species (Oreochromis mossambicus and Gambusia affinis). The ecology of the ponds was driven by physico-chemical variables, mainly temperature, but the interactions between fishes were a complex interplay between temperature, pond community ecology and food web structure. Seasonal changes in temperature and subsequent fluctuations in water levels resulted in changes in zooplankton community. Chlorophyll-a, temperature, G. callidus and G. affinis were the drivers of the seasonal changes in macroinvertebrate composition. Stable isotope analysis identified substantial ontogenetic dietary shifts in all species, corresponding to changes in body size. Stable isotope analysis revealed that the niche space occupied by G. affinis was broad and overlapped with that of the other three focal species. Stable isotope metrics showed that G. affinis and O. mossambicus utilised a wide range of resources compared to G. callidus and G. aestuaria. Stomach content analysis showed that G. callidus, O. mossambicus and G. affinis fed predominantly on benthic resources, while G. aestuaria fed mainly plankton resources. Functional response experiments revealed that G. callidus and G. affinis both displayed Type II functional responses. In single fish trials, G. affinis had significantly higher functional responses than G. callidus. In heterospecific G. callidus-G. affinis combinations the functional response of G. callidus was reduced by the presence of G. affinis, whereas, this combination greatly enhanced G. affinis functional response magnitudes. The functional response of G. callidus, O. mossambicus and G. affinis under two temperature treatments along with fish abundance data was used to determine temporal differences in the ecological impacts of each fish species between seasons. The relative impact potential of O. mossambicus was consistently higher than that of G. callidus and G. affinis. This study demonstrates how seasonal temperature fluctuations affect the relative impact capacities of introduced species. Overall, this thesis showed that high temperature along with life-history traits contributes to the biotic interactions between native and non-native species in novel environments.
- Full Text:
- Date Issued: 2020
- Authors: Mofu, Lubabalo
- Date: 2020
- Subjects: Mozambique tilapia -- South Africa -- Sundays River (Eastern Cape) , Western mosquitofish -- South Africa -- Sundays River (Eastern Cape) , Gobiidae -- South Africa -- Sundays River (Eastern Cape) , Clupeidae -- South Africa -- Sundays River (Eastern Cape) , Reservoirs -- South Africa -- Sundays River (Eastern Cape) , Zooplankton -- South Africa -- Sundays River (Eastern Cape) , Freshwater ecology -- South Africa -- Sundays River (Eastern Cape) , Biotic communities -- South Africa -- Sundays River (Eastern Cape) , Fishes -- Effect of temperature on -- South Africa -- Sundays River (Eastern Cape) , Stable isotopes , Relative Impact Potential
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167089 , vital:41436
- Description: The Sundays River valley irrigation ponds provide a unique opportunity to investigate biotic interactions within a biological invasions context, as they contain both native and non-native fish species. This study focusses on two native species (Glossogobius callidus and Gilchristella aestuaria) and two non-native species (Oreochromis mossambicus and Gambusia affinis). The ecology of the ponds was driven by physico-chemical variables, mainly temperature, but the interactions between fishes were a complex interplay between temperature, pond community ecology and food web structure. Seasonal changes in temperature and subsequent fluctuations in water levels resulted in changes in zooplankton community. Chlorophyll-a, temperature, G. callidus and G. affinis were the drivers of the seasonal changes in macroinvertebrate composition. Stable isotope analysis identified substantial ontogenetic dietary shifts in all species, corresponding to changes in body size. Stable isotope analysis revealed that the niche space occupied by G. affinis was broad and overlapped with that of the other three focal species. Stable isotope metrics showed that G. affinis and O. mossambicus utilised a wide range of resources compared to G. callidus and G. aestuaria. Stomach content analysis showed that G. callidus, O. mossambicus and G. affinis fed predominantly on benthic resources, while G. aestuaria fed mainly plankton resources. Functional response experiments revealed that G. callidus and G. affinis both displayed Type II functional responses. In single fish trials, G. affinis had significantly higher functional responses than G. callidus. In heterospecific G. callidus-G. affinis combinations the functional response of G. callidus was reduced by the presence of G. affinis, whereas, this combination greatly enhanced G. affinis functional response magnitudes. The functional response of G. callidus, O. mossambicus and G. affinis under two temperature treatments along with fish abundance data was used to determine temporal differences in the ecological impacts of each fish species between seasons. The relative impact potential of O. mossambicus was consistently higher than that of G. callidus and G. affinis. This study demonstrates how seasonal temperature fluctuations affect the relative impact capacities of introduced species. Overall, this thesis showed that high temperature along with life-history traits contributes to the biotic interactions between native and non-native species in novel environments.
- Full Text:
- Date Issued: 2020
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