Papers by Gwynneth Matcher
Amplicon sequencing dataset of microbial eukaryotes (18S ssh rRNA); bacteria (16S) and Archaea (1... more Amplicon sequencing dataset of microbial eukaryotes (18S ssh rRNA); bacteria (16S) and Archaea (16S) from coastal seawater near the shore of the Prince Edward Islands (Indian Ocean, Sub-Antarctica); sampled from a single location (37.58 degrees South 46.36 degrees East) in 2012, 2013, 2014 and 2015.
African Journal of Marine Science, 2021
The occurrence of harmful algal blooms (HABs) is increasing in frequency and intensity in South A... more The occurrence of harmful algal blooms (HABs) is increasing in frequency and intensity in South African estuaries because of eutrophication. This study used DNA metabarcoding to identify the benthic diatom community structure in the eutrophic Sundays Estuary. The recurrent HAB phytoplankton species Heterosigma akashiwo was recorded at bloom concentrations (∼100 µg Chl a l−1) in the brackish, vertically stratified middle reaches of the estuary. In contrast, microphytobenthos biomass increased towards the upper reaches in response to elevated availability of total oxidised nitrogen (NOx) and increased sediment stability. A total of 76 diatom species were identified using the molecular technique. Seven known nutrient-tolerant diatom species indicate a preference for either ammonium or NOx enrichment. Benthic diatom community diversity (H′ < 1) and evenness (J′ < 0.25) were low in the brackish middle reaches of the estuary, where the HABs decreased available light. Heterosigma akashiwo has been found in previous studies to suppress the growth of co-occurring taxa. Future research efforts should focus on verifying this relationship over seasonal timescales given the dominance of H. akashiwo in spring/summer. As the persistently nutrient-enriched state and stable flow conditions of the Sundays Estuary is the key driver of change, management efforts should be geared towards re-establishing the estuary’s natural flow variations and to measures that can mitigate nutrient pollution.
Aquatic Microbial Ecology, 2021
Phytoplankton bloom events result in distinct changes in the composition and availability of nutr... more Phytoplankton bloom events result in distinct changes in the composition and availability of nutrients as well as physical conditions within aquatic ecosystems, resulting in significant effects on bacterial communities. Using a metabarcoding approach, this study investigated the effect of a harmful algal bloom (HAB) of Heterosigma akashiwo in the Sundays Estuary, South Africa, on bacterial community structures in this estuarine ecosystem over an entire bloom event. The occurrence of bacterial lineages occurring in both the oxygen-rich surface water and hypoxic bottom waters in this study reflects the respiratory flexibility and potential for both aerobic and anaerobic metabolism across a wide range of bacterial phylogenetic lineages. A close correlation between the bacterial community profiles and the physiological state of the bloom was observed, with Flavobacteria found in increased relative abundances during the H. akashiwo HAB. Flavobacteria are commonly reported in the literatu...
Polar Biology, 2019
Soils of continental Antarctic nunataks represent unusual ecosystems with concomitant unique bact... more Soils of continental Antarctic nunataks represent unusual ecosystems with concomitant unique bacterial community profiles which have not been assessed for the vast majority of Antarctic nunataks. This study focussed on the previously uncharacterised inland nunataks of the Jutulsessen and Ahlmannryggen ranges in Dronning Maud Land. As with many oligotrophic soils in Antarctica, bacteria from the phyla Acidobacteria, Actinobacteria and Proteobacteria were prevalent. High relative abundances of Bacteroidetes and Chloroflexi were also observed in these soils. Potential phototrophic capabilities of these bacterial populations were indicated by the presence of genes involved in the Calvin-Benson reductive pentose phosphate cycle as well as that of aerobic phototrophic bacteriochlorophyll. Clear spatial patterns of bacterial biodiversity between nunataks in this study were observed, particularly between the Jutulsessen and Ahlmannryggen nunataks which are geographically separated by the Jutulstraumen glacier. Not unexpectedly, the bacterial community profiles found in these nunataks were distinct from those found in alternate biogeographic regions (e.g. Dry Valleys, Peninsula and Larsemann Hills). Despite belonging to the same bioregion (i.e. Dronning Maud Land), however, the clear differentiation of bacterial communities between the Jutulsessen/Ahlmannryggen and that of Sør Rondane suggests that, based on bacterial phylogeography, the Dronning Maud Land bioregion can be divided into sub-bioregions.
PLOS ONE, 2019
Introduction Emerging viral diseases, most of which are zoonotic, pose a significant threat to gl... more Introduction Emerging viral diseases, most of which are zoonotic, pose a significant threat to global health. There is a critical need to identify potential new viral pathogens and the challenge is to identify the reservoirs from which these viruses might emerge. Deep sequencing of invertebrate transcriptomes has revealed a plethora of viruses, many of which represent novel lineages representing both plant and animal viruses and little is known about the potential threat that these viruses pose. Methods Providence virus, an insect virus, was used to establish a productive infection in Vigna unguiculata (cowpea) plants. Providence virus particles purified from these cowpea plants were used to infect two mammalian cell lines. Findings Here, we present evidence that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal cells. The observation that Providence virus can readily infect both plants and mammalian cell culture lines demonstrates the ability of an insect RNA virus to establish productive infections across two kingdoms, in plants and invertebrate and vertebrate animal cell lines. Conclusions The study highlights the potential of phytophagous insects as reservoirs for viral re-assortment and that plants should be considered as reservoirs for emerging viruses that may be potentially pathogenic to humans.
Transactions of the Royal Society of South Africa, 2019
The increasing incidence of cyanobacterial blooms in Southern African aquatic systems is raising ... more The increasing incidence of cyanobacterial blooms in Southern African aquatic systems is raising concern about the potential for these microorganisms to contaminate potable water with toxic secondary metabolites. This study focused on two lakes, an estuary and the sea in a small catchment in Maputaland, northern KwaZulu Natal, South Africa, fed by groundwater impacted by sewage effluent discharged from houses and residential complexes. The important effluents identified were nitrate, nitrite, ammonium-N and ortho-phosphate at concentrations above that which might be expected in a sandy catchment where all the water emanates from rainfall averaging about 1000 mm per annum. Analyses of the microalgae in two freshwater lakes showed that cyanophytes made up over 88% of the phytoplankton in the larger Lake Mgobezeleni and over 50% in the smaller Lake Shazibe. This raises concerns about the potential health risk to communities using this water for domestic, agricultural and recreational purposes. Microscope images showed the cyanophytes to be embedded in mucus. Next Generation Sequencing analysis of bacterial 16S rRNA genes showed a persistent cyanobacterial bloom in Lake Mgobezeleni, including cyanobacterial taxa closely related to species that are known to produce cyanotoxins, including Microcystis aeruginosa, which produces the hepatotoxin microcystin. Other less dominant potential cyanotoxin producers were detected in all the water bodies sampled. These results highlight the importance of identifying water systems at risk of experiencing cytotoxic cyanobacterial blooms and, most importantly, the need to monitor such vulnerable systems to ensure the safety of surrounding communities. Where the groundwater is being used by householders with boreholes, the nitrogen and phosphate concentrations were within South African drinking water quality standards but the presence of cyanophytes appears to indicate that the target environmental water quality standards published by the government are too high for this area.
Estuarine, Coastal and Shelf Science, 2018
Worldwide, estuaries are regarded as amongst the most ecologically threatened ecosystems and are ... more 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 marinedominated and impacted by urban development, while the Sundays system is freshwater 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.
Aquaculture Research, 2019
An understanding of copepod feeding behaviour is not only critical for understanding the ecology ... more An understanding of copepod feeding behaviour is not only critical for understanding the ecology of the species, but also to develop a suitable dietary and culture system for intensive cultivation of the species for marine hatcheries. Copepods are an essential prey item that promotes survival for early stage larval fish with small mouth gape under culture conditions (Mckinnon et al., 2003; Shields et al., 1999). The utilization of copepods in aquaculture still remains sporadic, due to low productivity in mass culture which is related to difficulties in mass culture of the species. Research is needed to identify an optimal feeding practice that would maximize productivity for any copepod species of aquaculture interest. In estuaries, copepods are exposed to a diversity of food items where they select suitable prey to maintain their nutritional and energetic needs (Kiørboe & Jiang, 2013). Certain copepods change their feeding mode from herbivorous to omnivorous depending on phytoplankton size composition which may differ between seasons
Limnology and Oceanography, 2018
The Prince Edward Islands (PEIs) lie within the Antarctic Circumpolar Current (ACC), in a transit... more The Prince Edward Islands (PEIs) lie within the Antarctic Circumpolar Current (ACC), in a transition zone bordered by the sub-Antarctic Front (SAF) to the north and the Antarctic Polar Front (APF) in the south. A climate-driven southward shift of the ACC and its frontal systems, the SAF and APF, in the vicinity of the PEIs is associated with a long-term decline in the frequency of island-associated phytoplankton blooms. These oceanographic perturbations coincide with significant declines in top predator populations attributed to shifts in the distribution and availability of prey, illustrating the interconnectedness between the marine and terrestrial ecosystems of the PEIs. This study investigated the influence of oceanographic variability on the marine ecosystem of the PEIs. A shift in phytoplankton and bacterial communities was observed that coincides with the position of the southern branch of the SAF, which was located to the north of the PEIs during 2014 and to the south during 2012, 2013, and 2015. These shifts in the diversity and structure of marine microbial communities correlate with significant perturbations in the position of the SAF relative to the islands leading us to conlclude that bacterial and phytoplankton communities in the PEI region are strongly influenced by shifts in the position of the SAF relative to the PEIs. This study highlights the critical need to link ongoing physical time series measurements with biological observations to provide a better understanding of the direct role that the upstream dynamics has on the near-shore island environment and its productivity.
South African Journal of Science, 2018
Southern Africa occupies a critical position within the southern hemisphere for the study of broa... more 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. 1 The primary focus of Phakisa is to unlock the economic potential of South Africa's oceans. 2 This will be achieved through the 'implementation of an overarching, integrated ocean governance framework for sustainable growth of the ocean economy that will maximise socioeconomic 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) 3 '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'.
MicrobiologyOpen, 2016
The Latrunculiidae are a family of cold water sponges known for their production of bioactive pyr... more The Latrunculiidae are a family of cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids. Previously it was shown that the bacterial community associated with a Tsitsikamma sponge species comprises unusual bacterial taxa and is dominated by a novel Betaproteobacterium. Here, we have characterized the bacterial communities associated with six latrunculid species representing three genera (Tsitsikamma, Cyclacanthia, and Latrunculia) as well as a Mycale species, collected from Algoa Bay on the South African southeast coast. The bacterial communities of all seven sponge species were dominated by a single Betaproteobacterium operational taxonomic unit (OTU 0.03), while a second OTU 0.03 was dominant in the Mycale sp. The Betaproteobacteria OTUs from the different latrunculid sponges are closely related and their phylogenetic relationship follows that of their hosts. We propose that the latrunculid Betaproteobacteria OTUs are members of a specialized group of sponge symbionts that may have coevolved with their hosts. A single dominant Spirochaetae OTU 0.03 was present in the Tsitsikamma and Cyclacanthia sponge species, but absent from the Latrunculia and Mycale sponges. This study sheds new light on the interactions between latrunculid sponges and their bacterial communities and may point to the potential involvement of dominant symbionts in the biosynthesis of the bioactive secondary metabolites.
Frontiers in Microbiology, 2016
South African Journal of Science
Although many vectors exist for Escherichia coli and closely related species, there are few broad... more Although many vectors exist for Escherichia coli and closely related species, there are few broad host range vectors that can be conjugated into a large variety of Gram-negative bacteria. We have constructed a broad host range vector, pMJ445, that facilitates the analysis of divergent promoters in Gram-negative bacteria. The vector was validated using two intergenic regions derived from gene clusters involved in hydantoin hydrolysis, from the environmental isolates Pseudomonas putida and Agrobacterium tumefaciens. The DNA sequences analysed were capable of activating expression of the reporter enzymes, β-glucuronidase and β-galactosidase, present on pMJ445, indicating the presence of divergent promoters in the sequences selected. In addition, we demonstrated that pMJ445 can be applied to gene regulation studies.
Microbial ecology, 2015
As part of a larger investigation, the effect of apex predation on estuarine bacterial community ... more As part of a larger investigation, the effect of apex predation on estuarine bacterial community structure, through trophic cascading, was investigated using experimental in situ mesocosms. Through either the removal (filtration) or addition of specific size classes of planktonic groups, four different trophic scenarios were established using estuarine water and its associated plankton. One such treatment represented a "natural" scenario in which stable apex predatory pressure was qualified. Water samples were collected over time from each of the treatments for bacterial community evaluation. These samples were assessed through pyrosequencing of the variable regions 4 and 5 of the bacterial 16S rRNA gene and analysed at the species operational taxonomic unit (OTU) level using a community procedure. The blue-green group dominated the samples, followed by Proteobacteria and Bacteroidetes. Samples were the most similar among treatments at the commencement of the experiment. W...
Methods in Molecular Biology, 2011
Biocatalytic conversion of 5-substituted hydantoin derivatives is an efficient method for the pro... more Biocatalytic conversion of 5-substituted hydantoin derivatives is an efficient method for the production of unnatural enantiomerically pure amino acids. The enzymes required to carry out this hydrolysis occur in a wide variety of eubacterial species each of which exhibit variations in substrate selectivity, enantiospecificity, and catalytic efficiency. Screening of the natural environment for bacterial strains capable of utilizing hydantoin as a nutrient source (as opposed to rational protein design of known enzymes) is a cost-effective and valuable approach for isolating microbial species with novel hydantoin-hydrolysing enzyme systems. Once candidate microbial isolates have been identified, characterization and optimization of the activity of target enzyme systems can be achieved by subjecting the hydantoin-hydrolysing system to physicochemical manipulations aimed at the enzymes activity within the natural host cells, expressed in a heterologous host, or as purified enzymes. The latter two options require knowledge of the genes encoding for the hydantoin-hydrolysing enzymes. This chapter describes the methods that can be used in conducting such development of hydantoinase-based biocatalytic routes for production of target amino acids.
South African Journal of Science, 2014
Following the first description of living marine stromatolites along the South African east coast... more Following the first description of living marine stromatolites along the South African east coast, new investigations along the south coast have revealed the occurrence of extensive fields of actively calcifying stromatolites. These stromatolites have been recorded at regular distances along a 200-km stretch of coastline, from Cape Recife in the east to the Storms River mouth in the west, with the highest density found between Schoenmakerskop and the Maitland River mouth. All active stromatolites are associated with freshwater seepage streams flowing from the dune cordon, which form rimstone dams and other accretions capable of retaining water in the supratidal platform. Resulting pools can reach a maximum depth of about 1 m and constitute a unique ecosystem in which freshwater and marine organisms alternate their dominance in response to vertical mixing and the balance between freshwater versus marine inflow. Although the factors controlling stromatolite growth are yet to be determ...
Water SA, 2011
The aim of this study was to conduct an investigation into the bacterial diversity in the freshwa... more The aim of this study was to conduct an investigation into the bacterial diversity in the freshwater-deprived Kariega Estuary, situated along the Eastern Cape coastline, using ribosomal RNA gene sequences obtained by pyrosequencing. Shifts in the microbial diversity were correlated to selected physico-chemical variables along the length of the estuary. More than 27 000 sequences were obtained and rarefaction analyses confirmed a comprehensive appraisal of the microbial diversity present in the Kariega Estuary. Distinct patterns in phylotype distribution from the hypersaline upper reaches to the mouth of the estuary were observed; notably, the importance of the detrital food web within the Kariega Estuary was highlighted by the high occurrence of Bacteroidetes and Actinomycetes. Moreover, while the observed chlorophyll-a concentrations were low (< 0.1 µg•ℓ-1), the presence of Pelagibacter and Flavobacteria amongst the microbial community suggests a potentially important contribution of these microbes towards the total primary productivity of the ecosystem. No human pathogenic microbes were detected within waters of the system. We conclude that pyrosequencing provides a versatile and efficient tool for assessing the microbial diversity in the Kariega Estuary and propose that this technology may provide valuable information on the ecosystem functioning and health of aquatic ecosystems.
The biocatalytic conversion of 5-monosubstituted hydantoin derivatives to optically pure amino ac... more The biocatalytic conversion of 5-monosubstituted hydantoin derivatives to optically pure amino acids involves two reaction steps: the hydrolysis of hydantoin to N-carbamylamino acid by an hydantoinase or dihydropyrimidinase enzyme, followed by conversion of the Ncarbamylamino acid to the corresponding amino acid by an N-carbamoylase enzyme. This biocatalytic process has been successfully applied in several industrial processes for the production of enantiomerically pure amino acids used in the synthesis of pharmaceuticals, insecticides, hormones, and food additives. P. putida RU-KM3 S was selected for study based on inherent high levels of hydantoinase and N-carbamoylase activity. Subsequent biocatalytic analysis of the enzyme activity within this strain revealed unique properties thus prompting further characterization. The main focus of this research was the isolation of the genes encoding the hydantoin-hydrolysing pathway in RU-KM3 S. A genomic library was constructed and screened for heterologous expression of the hydantoin-hydrolysing enzymes. However, this approach was unsuccessful prompting the use of transposon mutagenesis in order to circumvent the drawbacks associated with complementation studies. The enzymes responsible for hydantoin-hydrolysis were identified by insertional inactivation as a dihydropyrimidinase and β-ureidopropionase encoded by dhp and bup respectively. A third open reading frame, encoding a putative transport protein, was identified between the dhp and bup genes and appeared to share a promoter with bup. Analysis of the amino acid sequence deduced from bup and dhp substantiated the distinctive properties and potential industrial application of the L-enantioselective β-ureidopropionase and provided targets for potential optimisation of the substrate-selectivity and activity of the dihydropyrimidinase by site directed mutagenesis. Several transposon-generated mutants with an altered phenotype for growth on minimal medium with hydantoin as the sole source of nitrogen were also isolated. Analysis of the insertion events in these mutants revealed disruptions of genes encoding key elements of the Ntr global regulatory pathway. However, inactivation of these genes had no effect on the dihydropyrimidinase and β-ureidopropionase activity levels. An additional mutant in which the gene coding for the dihydrolipoamide succinyltransferase, which is involved in the TCA cycle, was isolated with reduced levels of both dihydropyrimidinase and β-ureidopropionase activities. These results indicated that the hydantoin-hydrolysis pathway in RU-KM3 S is regulated by carbon rather than nitrogen catabolite repression. This was confirmed by the reduction of hydantoin-hydrolysis in cells grown in excess carbon as opposed to nitrogen. Identification of a putative CRP-binding site within the promoter region of these enzymes further supported the regulatory role of carbon catabolite repression (CCR). As CCR in Pseudomonads is poorly understood, elucidation of the mechanism by which the hydantoinhydrolysing pathway in RU-KM3 S is regulated would provide valuable insight into this complex process. I TABLE OF CONTENTS List of Figures .
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Papers by Gwynneth Matcher