Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds
- Waterworth, Samantha C, Isemonger, Eric W, Rees, Evan R, Dorrington, Rosemary A
- Authors: Waterworth, Samantha C , Isemonger, Eric W , Rees, Evan R , Dorrington, Rosemary A
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/429411 , vital:72608 , xlink:href="https://doi.org/10.1111/1758-2229.12916"
- Description: Stromatolites are complex microbial mats that form lithified layers. Fossilized stromatolites are the oldest evidence of cellular life on Earth, dating back over3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline, the former being morphologically and structurally similar to fossilized phosphatic stromatolites formations. Using assembled shotgun metagenomic analysis, we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteria phylum. We identified functional gene sets in genomic bins conserved across two geographically isolated stromatolite formations, which included relatively high copy numbers of genes involved in the reduction of nitrates and phosphatic compounds. Additionally, we found little evidence of Archaeal species in these stromatolites, suggesting that they may not play an important role in peritidal stromatolite formations, as proposed for hypersaline formations.
- Full Text:
- Date Issued: 2020
- Authors: Waterworth, Samantha C , Isemonger, Eric W , Rees, Evan R , Dorrington, Rosemary A
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/429411 , vital:72608 , xlink:href="https://doi.org/10.1111/1758-2229.12916"
- Description: Stromatolites are complex microbial mats that form lithified layers. Fossilized stromatolites are the oldest evidence of cellular life on Earth, dating back over3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline, the former being morphologically and structurally similar to fossilized phosphatic stromatolites formations. Using assembled shotgun metagenomic analysis, we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteria phylum. We identified functional gene sets in genomic bins conserved across two geographically isolated stromatolite formations, which included relatively high copy numbers of genes involved in the reduction of nitrates and phosphatic compounds. Additionally, we found little evidence of Archaeal species in these stromatolites, suggesting that they may not play an important role in peritidal stromatolite formations, as proposed for hypersaline formations.
- Full Text:
- Date Issued: 2020
Distinct responses of bacterial communities to agricultural and urban impacts in temperate southern African estuaries
- Matcher, Gwynneth F, Froneman, P William, Meiklejohn, Ian, Dorrington, Rosemary A
- Authors: Matcher, Gwynneth F , Froneman, P William , Meiklejohn, Ian , Dorrington, Rosemary A
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/479218 , vital:78271 , https://doi.org/10.1016/j.ecss.2017.11.015
- Description: Worldwide, estuaries are regarded as amongst the most ecologically threatened ecosystems and are increasingly being impacted by urban development, agricultural activities and reduced freshwater inflow. In this study, we examined the influence of different human activities on the diversity and structure of bacterial communities in the water column and sediment in three distinct, temperate permanently open estuarine systems within the same geographic region of southern Africa. The Kariega system is freshwater-deprived and is considered to be relatively pristine; the Kowie estuary is marine-dominated and impacted by urban development, while the Sundays system is fresh-water dominated and impacted by agricultural activity in its catchment. The bacterial communities in all three systems comprise predominantly heterotrophic species belonging to the Bacteroidetes and Proteobacteria phyla with little overlap between bacterioplankton and benthic bacterial communities at the species level. There was overlap between the operational taxonomic units (OTUs) of the Kowie and Kariega, both marine-influenced estuaries. However, lower species richness in the Kowie, likely reflects the impact of human settlements along the estuary. The dominant OTUs in the Sundays River system were distinct from those of the Kariega and Kowie estuaries with an overall decrease in species richness and evenness. This study provides an important snapshot into the microbial population structures of permanently open temperate estuarine systems and the influence of anthropogenic impacts on bacterial diversity and community structure.
- Full Text:
- Date Issued: 2018
- Authors: Matcher, Gwynneth F , Froneman, P William , Meiklejohn, Ian , Dorrington, Rosemary A
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/479218 , vital:78271 , https://doi.org/10.1016/j.ecss.2017.11.015
- Description: Worldwide, estuaries are regarded as amongst the most ecologically threatened ecosystems and are increasingly being impacted by urban development, agricultural activities and reduced freshwater inflow. In this study, we examined the influence of different human activities on the diversity and structure of bacterial communities in the water column and sediment in three distinct, temperate permanently open estuarine systems within the same geographic region of southern Africa. The Kariega system is freshwater-deprived and is considered to be relatively pristine; the Kowie estuary is marine-dominated and impacted by urban development, while the Sundays system is fresh-water dominated and impacted by agricultural activity in its catchment. The bacterial communities in all three systems comprise predominantly heterotrophic species belonging to the Bacteroidetes and Proteobacteria phyla with little overlap between bacterioplankton and benthic bacterial communities at the species level. There was overlap between the operational taxonomic units (OTUs) of the Kowie and Kariega, both marine-influenced estuaries. However, lower species richness in the Kowie, likely reflects the impact of human settlements along the estuary. The dominant OTUs in the Sundays River system were distinct from those of the Kariega and Kowie estuaries with an overall decrease in species richness and evenness. This study provides an important snapshot into the microbial population structures of permanently open temperate estuarine systems and the influence of anthropogenic impacts on bacterial diversity and community structure.
- Full Text:
- Date Issued: 2018
Living phosphatic stromatolites in a low-phosphorus environment: Implications for the use of phosphorus as a proxy for phosphate levels in paleosystems
- Buttner, Steffen H, Isemonger, Eric W, Isaacs, Michelle, van Niekerk, Deon, Sipler, Rachel E, Dorrington, Rosemary A
- Authors: Buttner, Steffen H , Isemonger, Eric W , Isaacs, Michelle , van Niekerk, Deon , Sipler, Rachel E , Dorrington, Rosemary A
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/429450 , vital:72611 , xlink:href="https://doi.org/10.1111/gbi.12415"
- Description: In the geological record, fossil phosphatic stromatolites date back to the Great Oxidation Event in the Paleoproterozoic, but living phosphatic stromatolites have not been described previously. Here, we report on cyanobacterial stromatolites in a supratidal freshwater environment at Cape Recife, South African southern coast, precipitating Ca carbonate alternating with episodes of Ca phosphate deposition. In their structure and composition, the living stromatolites from Cape Recife closely resemble their fossilized analogues, showing phosphatic zonation, microbial casts, tunnel structures and phosphatic crusts of biogenic origin. The microbial communities appear to be also similar to those proposed to have formed fossil phosphatic stromatolites. Phosphatic domains in the material from Cape Recife are spatially and texturally associated with carbonate precipitates, but form distinct entities separated by sharp boundaries. Electron Probe Micro-Analysis shows that Ca/P ratios and the overall chemical compositions of phosphatic precipitates are in the range of octacalcium phosphate, amorphous tricalcium phosphate and apatite. The coincidence in time of the emergence of phosphatic stromatolites in the fossil record with a major episode of atmospheric oxidation led to the assumption that at times of increased oxygen release the underlying increased biological production may have been linked to elevated phosphorus availability. The stromatolites at Cape Recife, however, form in an environment where ambient phosphorus concentrations do not exceed 0.28μM, one to two orders of magnitude below the previously predicted minimum thresh-old of >5 μM for biogenic phosphate precipitation in paleo-systems. Accordingly, we contest the previously proposed suitability of phosphatic stromatolites as a proxy for high ambient phosphate concentrations in supratidal to shallow ocean settings in earth history.
- Full Text:
- Date Issued: 2020
- Authors: Buttner, Steffen H , Isemonger, Eric W , Isaacs, Michelle , van Niekerk, Deon , Sipler, Rachel E , Dorrington, Rosemary A
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/429450 , vital:72611 , xlink:href="https://doi.org/10.1111/gbi.12415"
- Description: In the geological record, fossil phosphatic stromatolites date back to the Great Oxidation Event in the Paleoproterozoic, but living phosphatic stromatolites have not been described previously. Here, we report on cyanobacterial stromatolites in a supratidal freshwater environment at Cape Recife, South African southern coast, precipitating Ca carbonate alternating with episodes of Ca phosphate deposition. In their structure and composition, the living stromatolites from Cape Recife closely resemble their fossilized analogues, showing phosphatic zonation, microbial casts, tunnel structures and phosphatic crusts of biogenic origin. The microbial communities appear to be also similar to those proposed to have formed fossil phosphatic stromatolites. Phosphatic domains in the material from Cape Recife are spatially and texturally associated with carbonate precipitates, but form distinct entities separated by sharp boundaries. Electron Probe Micro-Analysis shows that Ca/P ratios and the overall chemical compositions of phosphatic precipitates are in the range of octacalcium phosphate, amorphous tricalcium phosphate and apatite. The coincidence in time of the emergence of phosphatic stromatolites in the fossil record with a major episode of atmospheric oxidation led to the assumption that at times of increased oxygen release the underlying increased biological production may have been linked to elevated phosphorus availability. The stromatolites at Cape Recife, however, form in an environment where ambient phosphorus concentrations do not exceed 0.28μM, one to two orders of magnitude below the previously predicted minimum thresh-old of >5 μM for biogenic phosphate precipitation in paleo-systems. Accordingly, we contest the previously proposed suitability of phosphatic stromatolites as a proxy for high ambient phosphate concentrations in supratidal to shallow ocean settings in earth history.
- Full Text:
- Date Issued: 2020
South African research in the Southern Ocean: New opportunities but serious challenges
- Treasure, Anne M, Moloney, Coleen, Bester, Marthán N, Findlay, Ken P, Best, Peter B, Cowan, Don A, De Bruyn, P J Nico, Dorrington, Rosemary A, Fagereng, Ake, Froneman, P William, Grantham, Geoff H, Hunt, Brian P V, Meiklejohn, Ian, Pakhomov, Evgeny A, Roychoudhury, Alakendra N, Ryan, Peter G, Smith, Valdon R, Chown, Steven L, Ansorge, Isabelle J
- Authors: Treasure, Anne M , Moloney, Coleen , Bester, Marthán N , Findlay, Ken P , Best, Peter B , Cowan, Don A , De Bruyn, P J Nico , Dorrington, Rosemary A , Fagereng, Ake , Froneman, P William , Grantham, Geoff H , Hunt, Brian P V , Meiklejohn, Ian , Pakhomov, Evgeny A , Roychoudhury, Alakendra N , Ryan, Peter G , Smith, Valdon R , Chown, Steven L , Ansorge, Isabelle J
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/480584 , vital:78457 , https://hdl.handle.net/10520/EJC133146
- Description: South Africa has a long track record in Southern Ocean and Antarctic research and has recently invested considerable funds in acquiring new infrastructure for ongoing support of this research. This infrastructure includes a new base at Marion Island and a purpose-built ice capable research vessel, which greatly expand research opportunities. Despite this investment, South Africa's standing as a participant in this critical field is threatened by confusion, lack of funding, lack of consultation and lack of transparency. The research endeavour is presently bedevilled by political manoeuvring among groups with divergent interests that too often have little to do with science, while past and present contributors of research are excluded from discussions that aim to formulate research strategy. This state of affairs is detrimental to the country's aims of developing a leadership role in climate change and Antarctic research and squanders both financial and human capital.
- Full Text:
- Date Issued: 2013
- Authors: Treasure, Anne M , Moloney, Coleen , Bester, Marthán N , Findlay, Ken P , Best, Peter B , Cowan, Don A , De Bruyn, P J Nico , Dorrington, Rosemary A , Fagereng, Ake , Froneman, P William , Grantham, Geoff H , Hunt, Brian P V , Meiklejohn, Ian , Pakhomov, Evgeny A , Roychoudhury, Alakendra N , Ryan, Peter G , Smith, Valdon R , Chown, Steven L , Ansorge, Isabelle J
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/480584 , vital:78457 , https://hdl.handle.net/10520/EJC133146
- Description: South Africa has a long track record in Southern Ocean and Antarctic research and has recently invested considerable funds in acquiring new infrastructure for ongoing support of this research. This infrastructure includes a new base at Marion Island and a purpose-built ice capable research vessel, which greatly expand research opportunities. Despite this investment, South Africa's standing as a participant in this critical field is threatened by confusion, lack of funding, lack of consultation and lack of transparency. The research endeavour is presently bedevilled by political manoeuvring among groups with divergent interests that too often have little to do with science, while past and present contributors of research are excluded from discussions that aim to formulate research strategy. This state of affairs is detrimental to the country's aims of developing a leadership role in climate change and Antarctic research and squanders both financial and human capital.
- Full Text:
- Date Issued: 2013
Unlocking the Diversity of Pyrroloiminoquinones Produced by Latrunculid Sponge Species
- Kalinski, Jarmo-Charles J, Krause, Rui W M, Parker-Nance, Shirley, Waterworth, Samantha C, Dorrington, Rosemary A
- Authors: Kalinski, Jarmo-Charles J , Krause, Rui W M , Parker-Nance, Shirley , Waterworth, Samantha C , Dorrington, Rosemary A
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/191802 , vital:45165 , xlink:href="https://doi.org/10.3390/md19020068"
- Description: Sponges of the Latrunculiidae family produce bioactive pyrroloiminoquinone alkaloids including makaluvamines, discorhabdins, and tsitsikammamines. The aim of this study was to use LC-ESI-MS/MS-driven molecular networking to characterize the pyrroloiminoquinone secondary metabolites produced by six latrunculid species. These are Tsitsikamma favus, Tsitsikamma pedunculata, Cyclacanthia bellae, and Latrunculia apicalis as well as the recently discovered species, Tsitsikamma nguni and Tsitsikamma michaeli. Organic extracts of 43 sponges were analyzed, revealing distinct species-specific chemical profiles. More than 200 known and unknown putative pyrroloiminoquinones and related compounds were detected, including unprecedented makaluvamine-discorhabdin adducts and hydroxylated discorhabdin I derivatives. The chemical profiles of the new species T. nguni closely resembled those of the known T. favus (chemotype I), but with a higher abundance of tsitsikammamines vs. discorhabdins. T. michaeli sponges displayed two distinct chemical profiles, either producing mostly the same discorhabdins as T. favus (chemotype I) or non- or monobrominated, hydroxylated discorhabdins. C. bellae and L. apicalis produced similar pyrroloiminoquinone chemistry to one another, characterized by sulfur-containing discorhabdins and related adducts and oligomers. This study highlights the variability of pyrroloiminoquinone production by latrunculid species, identifies novel isolation targets, and offers fundamental insights into the collision-induced dissociation of pyrroloiminoquinones.
- Full Text:
- Date Issued: 2021
- Authors: Kalinski, Jarmo-Charles J , Krause, Rui W M , Parker-Nance, Shirley , Waterworth, Samantha C , Dorrington, Rosemary A
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/191802 , vital:45165 , xlink:href="https://doi.org/10.3390/md19020068"
- Description: Sponges of the Latrunculiidae family produce bioactive pyrroloiminoquinone alkaloids including makaluvamines, discorhabdins, and tsitsikammamines. The aim of this study was to use LC-ESI-MS/MS-driven molecular networking to characterize the pyrroloiminoquinone secondary metabolites produced by six latrunculid species. These are Tsitsikamma favus, Tsitsikamma pedunculata, Cyclacanthia bellae, and Latrunculia apicalis as well as the recently discovered species, Tsitsikamma nguni and Tsitsikamma michaeli. Organic extracts of 43 sponges were analyzed, revealing distinct species-specific chemical profiles. More than 200 known and unknown putative pyrroloiminoquinones and related compounds were detected, including unprecedented makaluvamine-discorhabdin adducts and hydroxylated discorhabdin I derivatives. The chemical profiles of the new species T. nguni closely resembled those of the known T. favus (chemotype I), but with a higher abundance of tsitsikammamines vs. discorhabdins. T. michaeli sponges displayed two distinct chemical profiles, either producing mostly the same discorhabdins as T. favus (chemotype I) or non- or monobrominated, hydroxylated discorhabdins. C. bellae and L. apicalis produced similar pyrroloiminoquinone chemistry to one another, characterized by sulfur-containing discorhabdins and related adducts and oligomers. This study highlights the variability of pyrroloiminoquinone production by latrunculid species, identifies novel isolation targets, and offers fundamental insights into the collision-induced dissociation of pyrroloiminoquinones.
- Full Text:
- Date Issued: 2021
Working together for our oceans: a marine spatial plan for Algoa Bay, South Africa
- Dorrington, Rosemary A, Lombard, Amanda T, Bornman, Thomas G, Adams, Janine B, Cawthra, Hayley C, Deyzel, Shaun H P, Goschen, Wayne S, Liu, Kenneth, Mahler-Coetzee, Jacques, Matcher, Gwynneth F, McQuaid, Christopher D, Parker-Nance, Shirley, Paterson, Angus W, Perissinotto, Renzo, Porri, Francesca, Roberts, Michael J, Snow, Bernadette, Vrancken, Patrick
- Authors: Dorrington, Rosemary A , Lombard, Amanda T , Bornman, Thomas G , Adams, Janine B , Cawthra, Hayley C , Deyzel, Shaun H P , Goschen, Wayne S , Liu, Kenneth , Mahler-Coetzee, Jacques , Matcher, Gwynneth F , McQuaid, Christopher D , Parker-Nance, Shirley , Paterson, Angus W , Perissinotto, Renzo , Porri, Francesca , Roberts, Michael J , Snow, Bernadette , Vrancken, Patrick
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/480806 , vital:78478 , https://hdl.handle.net/10520/EJC-df3d267ab
- Description: Southern Africa occupies a critical position within the southern hemisphere for the study of broadscale global change and the three oceans around South Africa (the Atlantic, Indian and Southern Oceans) play a vital role in determining local and regional climate and weather patterns. Oceans and coasts also provide various resources and services (e.g. food and carbon sequestration), but these services are threatened by human activities. Uncertainty of the impact and consequences of these anthropogenic activities makes it problematic to manage marine resources. Given the recent global emphasis on the development of ‘ocean economies’, the exploitation of living (fisheries, aquaculture and tourism) and non-living (oil and gas, minerals, energy) marine resources should be on a scale that is socially and economically justifiable and ecologically sustainable. In 2014, ‘Operation Phakisa’ was launched in South Africa as an initiative to accelerate execution of the National Development Plan. The primary focus of Phakisa is to unlock the economic potential of South Africa’s oceans. This will be achieved through the ‘implementation of an overarching, integrated ocean governance framework for sustainable growth of the ocean economy that will maximise socio-economic benefits while ensuring adequate ocean environmental protection’ by 2019. Marine spatial planning (MSP) is a key component of this integrated governance framework, and the development of MSP legislation during 2016 was prioritised as ‘critical’ to achieving the Operation Phakisa objectives. Accordingly, the Department of Environmental Affairs (DEA) published the Marine Spatial Planning Bill (2017) ‘to provide a framework for marine spatial planning in South Africa’s waters; to provide for the development of the marine spatial plan; to provide for institutional arrangements for the implementation of the marine spatial plan and governance of the use of the ocean by multiple sectors; and to provide for matters connected therewith’.
- Full Text:
- Date Issued: 2018
- Authors: Dorrington, Rosemary A , Lombard, Amanda T , Bornman, Thomas G , Adams, Janine B , Cawthra, Hayley C , Deyzel, Shaun H P , Goschen, Wayne S , Liu, Kenneth , Mahler-Coetzee, Jacques , Matcher, Gwynneth F , McQuaid, Christopher D , Parker-Nance, Shirley , Paterson, Angus W , Perissinotto, Renzo , Porri, Francesca , Roberts, Michael J , Snow, Bernadette , Vrancken, Patrick
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/480806 , vital:78478 , https://hdl.handle.net/10520/EJC-df3d267ab
- Description: Southern Africa occupies a critical position within the southern hemisphere for the study of broadscale global change and the three oceans around South Africa (the Atlantic, Indian and Southern Oceans) play a vital role in determining local and regional climate and weather patterns. Oceans and coasts also provide various resources and services (e.g. food and carbon sequestration), but these services are threatened by human activities. Uncertainty of the impact and consequences of these anthropogenic activities makes it problematic to manage marine resources. Given the recent global emphasis on the development of ‘ocean economies’, the exploitation of living (fisheries, aquaculture and tourism) and non-living (oil and gas, minerals, energy) marine resources should be on a scale that is socially and economically justifiable and ecologically sustainable. In 2014, ‘Operation Phakisa’ was launched in South Africa as an initiative to accelerate execution of the National Development Plan. The primary focus of Phakisa is to unlock the economic potential of South Africa’s oceans. This will be achieved through the ‘implementation of an overarching, integrated ocean governance framework for sustainable growth of the ocean economy that will maximise socio-economic benefits while ensuring adequate ocean environmental protection’ by 2019. Marine spatial planning (MSP) is a key component of this integrated governance framework, and the development of MSP legislation during 2016 was prioritised as ‘critical’ to achieving the Operation Phakisa objectives. Accordingly, the Department of Environmental Affairs (DEA) published the Marine Spatial Planning Bill (2017) ‘to provide a framework for marine spatial planning in South Africa’s waters; to provide for the development of the marine spatial plan; to provide for institutional arrangements for the implementation of the marine spatial plan and governance of the use of the ocean by multiple sectors; and to provide for matters connected therewith’.
- Full Text:
- Date Issued: 2018
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