Marine benthic (epilithic) diatom communities along the coast of South Africa: A contribution to their diversity, spatio-temporal variations, and ecology
- Authors: Cotiyane-Pondo, Phumlile
- Date: 2023-12
- Subjects: Marine ecology , Marine biodiversity , Coastal ecology
- Language: English
- Type: Doctorate Dissertation , text
- Identifier: http://hdl.handle.net/10948/62453 , vital:72754
- Description: Diatoms remain one of the most diverse and ecologically important microorganisms within microphytobenthos. The highly variable South African coastline, comprised of heterogeneous rocky intertidal habitats provides the ideal study area to investigate epilithic microphytobenthos and their associated influential drivers. In South Africa, in-depth taxonomic research on marine littoral diatoms exists, however, quantitative research and knowledge on their abundance, diversity, community composition and distribution remain limited. Thus, the main aim of this research was to explore the spatial and temporal variability of marine benthic (epilithic) diatoms, in relation to the variable physico-chemical conditions in the nearshore intertidal environments along the coastline of South Africa. To achieve this, field-based observational (natural substrata) and experimental (artificial substrata) studies were conducted on selected locations around the coastline, with a large focus on south coast localities. For the Spatial studies, large (i.e., encompassing all three biogeographical regions) and small-scale (i.e., coastal island in the warm temperate region) surveys of epilithic diatom assemblages from natural rocky substrata were conducted. Large-scale investigation results revealed highly variable diatom assemblages, diversity and distribution, with compositional differences observed between the coastal sections (around the coastline). A total of 85 diatom taxa from 31 genera were observed at 15 sites, and the number of taxa varied un-systematically along coastline. Genera with noticeable contribution included Nitzschia, Cocconeis and Achnanthes. On the coastal Bird Island (small-scale), similar variability was observed, but with a much higher diatom diversity and number of rarely observed species (e.g. Actinoptychus senarius (Ehrenberg) Ehrenberg, Cocconeis capensis (Cholnoky) Witkowski, Fragilariopsis kerguelensis (O’Meara) Hustedt, Striatella unipunctata (Lyngbye) Agardh. Seventy-two (72) species from 35 genera were recorded with a varied abundance and diversity around the island. The study also revealed a high contribution of typical benthic diatom species to the surf zone environment around the island. To study temporal variations, medium-term compositional differences on natural substrata were assessed monthly over an annual cycle at a single site. A paucity of diatom material was evident during this study and observations indicated a trend of presence and absence of diatom taxa from the study site. Nineteen (19) diatom genera were identified and those observed, albeit as one or two individual valves, included taxa from several genera including Biddulphia, Diploneis, Campyloneis, Trachyneis and Triceratium. Noteworthy was a seasonal increase in the number of diatom valves encountered, with the highest diatom abundance observed during spring (September) and the genera Cocconeis, Grammatophora and Navicula appearing regularly. To complement the sparse data from the long-term temporal study, a short-term experimental study on artificial substrata (Plexiglass) revealed rapid temporal variations of benthic diatom assemblages. The composition differed spatio-temporally during the experimental period, with fluctuating species occurrences and abundances between the two study sites. The experimental study also revealed the highest number of diatom species observed during this research (134 species belonging to 44 genera). While Cocconeis (13 species) and Nitzschia (9 species) were the dominant genera, 48% of the diatomcomposition was composed of rarely observed taxa that included Cocconeis testudo Giffen, Donkinia sp., Paralia sulcata (Ehrenberg) Cleve. Regarding environmental drivers, the findings indicated the importance of temperature and nutrients in driving diatom spatial abundance and composition along the coastline, as well as the island. However, the potential influence of the interplay between measured variables and unexplored coastal oceanographic processes (e.g., wave action) was noted. Temporally, from the annual study, the nature of the rocky substrate (rock type) rather than environmental conditions was postulated to have been the influential factor that resulted in the low diatom abundance data, however this requires further in-depth investigations on the influence of rock microtopography on microphytobenthos in this region. Contrastingly, the experimental study results indicated environmental variables having varying influences on the diatom diversity indices, however, study site and sampling occasion were revealed as the most important predictors of the observed variability. Further, site-specific biofilm processes, including biological interaction (e.g. grazing), were shown to alter biofilm succession, thus influencing the observed diatom assemblages. Overall, this research provided new and relevant knowledge on the variability of benthic (epilithic) diatom composition, biodiversity and distribution along the coastline, further contributing to our understanding of marine benthic diatoms ecology, their ecological role in the context of intertidal food web and their potential as bioindicators of change in the coastal ecosystems in Southern Africa. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2023
- Full Text:
- Date Issued: 2023-12
- Authors: Cotiyane-Pondo, Phumlile
- Date: 2023-12
- Subjects: Marine ecology , Marine biodiversity , Coastal ecology
- Language: English
- Type: Doctorate Dissertation , text
- Identifier: http://hdl.handle.net/10948/62453 , vital:72754
- Description: Diatoms remain one of the most diverse and ecologically important microorganisms within microphytobenthos. The highly variable South African coastline, comprised of heterogeneous rocky intertidal habitats provides the ideal study area to investigate epilithic microphytobenthos and their associated influential drivers. In South Africa, in-depth taxonomic research on marine littoral diatoms exists, however, quantitative research and knowledge on their abundance, diversity, community composition and distribution remain limited. Thus, the main aim of this research was to explore the spatial and temporal variability of marine benthic (epilithic) diatoms, in relation to the variable physico-chemical conditions in the nearshore intertidal environments along the coastline of South Africa. To achieve this, field-based observational (natural substrata) and experimental (artificial substrata) studies were conducted on selected locations around the coastline, with a large focus on south coast localities. For the Spatial studies, large (i.e., encompassing all three biogeographical regions) and small-scale (i.e., coastal island in the warm temperate region) surveys of epilithic diatom assemblages from natural rocky substrata were conducted. Large-scale investigation results revealed highly variable diatom assemblages, diversity and distribution, with compositional differences observed between the coastal sections (around the coastline). A total of 85 diatom taxa from 31 genera were observed at 15 sites, and the number of taxa varied un-systematically along coastline. Genera with noticeable contribution included Nitzschia, Cocconeis and Achnanthes. On the coastal Bird Island (small-scale), similar variability was observed, but with a much higher diatom diversity and number of rarely observed species (e.g. Actinoptychus senarius (Ehrenberg) Ehrenberg, Cocconeis capensis (Cholnoky) Witkowski, Fragilariopsis kerguelensis (O’Meara) Hustedt, Striatella unipunctata (Lyngbye) Agardh. Seventy-two (72) species from 35 genera were recorded with a varied abundance and diversity around the island. The study also revealed a high contribution of typical benthic diatom species to the surf zone environment around the island. To study temporal variations, medium-term compositional differences on natural substrata were assessed monthly over an annual cycle at a single site. A paucity of diatom material was evident during this study and observations indicated a trend of presence and absence of diatom taxa from the study site. Nineteen (19) diatom genera were identified and those observed, albeit as one or two individual valves, included taxa from several genera including Biddulphia, Diploneis, Campyloneis, Trachyneis and Triceratium. Noteworthy was a seasonal increase in the number of diatom valves encountered, with the highest diatom abundance observed during spring (September) and the genera Cocconeis, Grammatophora and Navicula appearing regularly. To complement the sparse data from the long-term temporal study, a short-term experimental study on artificial substrata (Plexiglass) revealed rapid temporal variations of benthic diatom assemblages. The composition differed spatio-temporally during the experimental period, with fluctuating species occurrences and abundances between the two study sites. The experimental study also revealed the highest number of diatom species observed during this research (134 species belonging to 44 genera). While Cocconeis (13 species) and Nitzschia (9 species) were the dominant genera, 48% of the diatomcomposition was composed of rarely observed taxa that included Cocconeis testudo Giffen, Donkinia sp., Paralia sulcata (Ehrenberg) Cleve. Regarding environmental drivers, the findings indicated the importance of temperature and nutrients in driving diatom spatial abundance and composition along the coastline, as well as the island. However, the potential influence of the interplay between measured variables and unexplored coastal oceanographic processes (e.g., wave action) was noted. Temporally, from the annual study, the nature of the rocky substrate (rock type) rather than environmental conditions was postulated to have been the influential factor that resulted in the low diatom abundance data, however this requires further in-depth investigations on the influence of rock microtopography on microphytobenthos in this region. Contrastingly, the experimental study results indicated environmental variables having varying influences on the diatom diversity indices, however, study site and sampling occasion were revealed as the most important predictors of the observed variability. Further, site-specific biofilm processes, including biological interaction (e.g. grazing), were shown to alter biofilm succession, thus influencing the observed diatom assemblages. Overall, this research provided new and relevant knowledge on the variability of benthic (epilithic) diatom composition, biodiversity and distribution along the coastline, further contributing to our understanding of marine benthic diatoms ecology, their ecological role in the context of intertidal food web and their potential as bioindicators of change in the coastal ecosystems in Southern Africa. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2023
- Full Text:
- Date Issued: 2023-12
The effect of the anaesthetics 1 Clove oil and MS-222 on the sedation, recovery, survival, population growth and fecundity of the calanoid copepod, Pseudodiaptomus hessei Copepoda Calanoida under culture conditions.
- Authors: Bulube, Masivuye Nomazizi
- Date: 2023-01
- Subjects: Water quality , Marine biodiversity , Aquatic animals -- Food
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/27524 , vital:67430
- Description: Compared to current live food organisms used in aquaculture, the calanoid copepod, Pseudodiaptomus hessei is smaller and has a superior nutritional value. However, due to their fast and erratic movements, manipulating and counting this species for aquaculture research purposes is difficult. For easier manipulation it is therefore necessary to sedate the copepods. The study aimed to determine the effect of two anaesthetics on sedation, recovery, survival, population growth and fecundity of the calanoid copepod, Pseudodiaptomus hessei, under culture conditions. Male and female P. hessei were exposed to the anaesthetics clove oil and Tricaine Methane sulfonate (MS-222). Twelve replicates of five copepods each were exposedto clove oil at 100, 150 and 200 μL/L, and to MS-222 at 300, 600, 900, 1200 and 1500 mg/Lwith the number of fully sedated copepods being recorded. clove oil sedation only occurredafter 5:23±1:25 minutes in the 100 μL/L treatment while copepods exposed to 150 and200μL/L were anaesthetized within 2:48±0:46 and 0:40±0:07 minutes respectively. Sedation did not occur in MS-222 at concentrations of 300 and 600 mg/L while at 900 mg/L all copepodswere sedated within 4:19±0:41 minutes. Only copepods exposed to 1200 and 1500 mg/L were all fully sedated within 2:26±1:46 and 1:23±0:37 minutes respectively. Clove oil recovery onlyoccurred at 4:40±1:32 minutes in the 100 μL/L treatment while copepods exposed to 150 and200 μL/L recovered at 8:30±1:46 and 12:12±0:59 minutes, respectively. In this study, all MS- 222 treatments showed full recovery at 1:07±0:41 to 1:11±0:41 minutes with 100% survivalrate. The growth development FPN (Final Population Number) for Clove oil, MS-222 and control were not different from the control indicating that exposure to the anaesthetic had no effect on their long-term survival (21 days). The mean clutch size of 34±5 eggs per sac was high compared to other studies on the species. Based on these findings the 150 μL/L Clove oiland 1200 mg/L MS-222 concentrations were the lowest doses of each anaesthetic to induce full sedation within 3 minutes followed by rapid recovery 87 within three minutes without it affecting its short (24 hours) and long-term survival, population growth and fecundity. Basedon sedation and recovery rates, effect on survival, fecundity and growth as well as cost and ease use, the 1200 mg/L MS-222 concentration is the recommended to safely anaesthetize P. hessei. , Thesis (MSci) -- Faculty of Science and Agriculture, 2023
- Full Text:
- Date Issued: 2023-01
- Authors: Bulube, Masivuye Nomazizi
- Date: 2023-01
- Subjects: Water quality , Marine biodiversity , Aquatic animals -- Food
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10353/27524 , vital:67430
- Description: Compared to current live food organisms used in aquaculture, the calanoid copepod, Pseudodiaptomus hessei is smaller and has a superior nutritional value. However, due to their fast and erratic movements, manipulating and counting this species for aquaculture research purposes is difficult. For easier manipulation it is therefore necessary to sedate the copepods. The study aimed to determine the effect of two anaesthetics on sedation, recovery, survival, population growth and fecundity of the calanoid copepod, Pseudodiaptomus hessei, under culture conditions. Male and female P. hessei were exposed to the anaesthetics clove oil and Tricaine Methane sulfonate (MS-222). Twelve replicates of five copepods each were exposedto clove oil at 100, 150 and 200 μL/L, and to MS-222 at 300, 600, 900, 1200 and 1500 mg/Lwith the number of fully sedated copepods being recorded. clove oil sedation only occurredafter 5:23±1:25 minutes in the 100 μL/L treatment while copepods exposed to 150 and200μL/L were anaesthetized within 2:48±0:46 and 0:40±0:07 minutes respectively. Sedation did not occur in MS-222 at concentrations of 300 and 600 mg/L while at 900 mg/L all copepodswere sedated within 4:19±0:41 minutes. Only copepods exposed to 1200 and 1500 mg/L were all fully sedated within 2:26±1:46 and 1:23±0:37 minutes respectively. Clove oil recovery onlyoccurred at 4:40±1:32 minutes in the 100 μL/L treatment while copepods exposed to 150 and200 μL/L recovered at 8:30±1:46 and 12:12±0:59 minutes, respectively. In this study, all MS- 222 treatments showed full recovery at 1:07±0:41 to 1:11±0:41 minutes with 100% survivalrate. The growth development FPN (Final Population Number) for Clove oil, MS-222 and control were not different from the control indicating that exposure to the anaesthetic had no effect on their long-term survival (21 days). The mean clutch size of 34±5 eggs per sac was high compared to other studies on the species. Based on these findings the 150 μL/L Clove oiland 1200 mg/L MS-222 concentrations were the lowest doses of each anaesthetic to induce full sedation within 3 minutes followed by rapid recovery 87 within three minutes without it affecting its short (24 hours) and long-term survival, population growth and fecundity. Basedon sedation and recovery rates, effect on survival, fecundity and growth as well as cost and ease use, the 1200 mg/L MS-222 concentration is the recommended to safely anaesthetize P. hessei. , Thesis (MSci) -- Faculty of Science and Agriculture, 2023
- Full Text:
- Date Issued: 2023-01
An investigation into the bacterial biosynthetic origins of bioactive natural products isolated from South African latrunculid sponges
- Authors: Waterworth, Samantha Che
- Date: 2018
- Subjects: Marine biodiversity , Metagenomics , Sponges Biotechnology , Spirochetes , Natural products Biotechnology
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61826 , vital:28065
- Description: Several pyrroloiminoquinone alkaloids exhibiting cytotoxic, anti-tumour activity have been isolated from sponges within the Latrunculiidae family that are endemic to the South African coastline. Other, structurally similar pyrroloiminoquinone compounds have been isolated from geographically distant and phylogenetically distinct marine sponges, as well as terrestrial myxomycetes which suggested that sponge-associated bacteria may be the true biosynthetic origin of pyrroloiminoquinone compounds. Previous studies have shown that there is conservation of spirochete and betaproteobacterial species in the bacterial communities associated with South African Latrunculiidae sponges and it was proposed that these conserved bacteria represented candidate pyrroloiminoquinone-producers. This study aimed to confirm the conserved dominance of betaproteobacteria and spirochetes within bacterial communities associated with South African latrunculid sponges and employed a shotgun metagenomic approach to assess the functional and biosynthetic potential of associated microbiota in Tsitsikamma favus sponges. Clustering of assembled contigs revealed twenty-three putative bacterial genomes, of which, two were identified as representatives of the conserved betaproteobacteria and spirochete species previously identified in Tsitsikamma sponges. It was shown that the spirochete was most likely an obligate symbiont that benefitted the host sponge through possible defence against pathogenic bacteria and/or nutrient acquisition. The putative genome representing the conserved betaproteobacteria was found to be heavily contaminated and further sequencing is required to accurately resolve the genome for functional characterization. Several biosynthetic gene clusters were identified and demonstrated the bioactive potential of Tsitsikamma favus-associated bacteria. A biosynthetic gene cluster was identified on an unclustered contig that included several genetic features that were indicative of possible pyrroloiminoquinone production.
- Full Text:
- Date Issued: 2018
- Authors: Waterworth, Samantha Che
- Date: 2018
- Subjects: Marine biodiversity , Metagenomics , Sponges Biotechnology , Spirochetes , Natural products Biotechnology
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61826 , vital:28065
- Description: Several pyrroloiminoquinone alkaloids exhibiting cytotoxic, anti-tumour activity have been isolated from sponges within the Latrunculiidae family that are endemic to the South African coastline. Other, structurally similar pyrroloiminoquinone compounds have been isolated from geographically distant and phylogenetically distinct marine sponges, as well as terrestrial myxomycetes which suggested that sponge-associated bacteria may be the true biosynthetic origin of pyrroloiminoquinone compounds. Previous studies have shown that there is conservation of spirochete and betaproteobacterial species in the bacterial communities associated with South African Latrunculiidae sponges and it was proposed that these conserved bacteria represented candidate pyrroloiminoquinone-producers. This study aimed to confirm the conserved dominance of betaproteobacteria and spirochetes within bacterial communities associated with South African latrunculid sponges and employed a shotgun metagenomic approach to assess the functional and biosynthetic potential of associated microbiota in Tsitsikamma favus sponges. Clustering of assembled contigs revealed twenty-three putative bacterial genomes, of which, two were identified as representatives of the conserved betaproteobacteria and spirochete species previously identified in Tsitsikamma sponges. It was shown that the spirochete was most likely an obligate symbiont that benefitted the host sponge through possible defence against pathogenic bacteria and/or nutrient acquisition. The putative genome representing the conserved betaproteobacteria was found to be heavily contaminated and further sequencing is required to accurately resolve the genome for functional characterization. Several biosynthetic gene clusters were identified and demonstrated the bioactive potential of Tsitsikamma favus-associated bacteria. A biosynthetic gene cluster was identified on an unclustered contig that included several genetic features that were indicative of possible pyrroloiminoquinone production.
- Full Text:
- Date Issued: 2018
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