UWCScholar :: Browsing by Author "Trindade, Marla"

Browsing by Author "Trindade, Marla"

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Antibacterial activities of bacteria isolated from the marine sponges Isodictya compressa and Higginsia bidentifera collected from Algoa Bay, South Africa
(MDPI AG, 2017) Matobole, Relebohile Matthew; van Zyl, Leonardo Joaquim; Parker-Nance, Shirley; Davies-Coleman, Michael T.; Trindade, Marla
Due to the rise inmulti-drug resistant pathogens and other diseases, there is renewed interest in marine sponge endosymbionts as a rich source of natural products (NPs). The South African marine environment is rich in marine biota that remains largely unexplored and may represent an important source for the discovery of novel NPs.We first investigated the bacterial diversity associated with five South African marine sponges, whose microbial populations had not previously been investigated, and select the two sponges (Isodictya compressa and Higginsia bidentifera) with highest species richness to culture bacteria. By employing 33 different growth conditions 415 sponge-associated bacterial isolates were cultured and screened for antibacterial activity. Thirty-five isolates showed antibacterial activity, twelve of which exhibited activity against the multi-drug resistant Escherichia coli 1699, implying that some of the bioactive compounds could be novel. Genome sequencing of two of these isolates confirmed that they harbour uncharacterized biosynthetic pathways that may encode novel chemical structures.
Bioactivity and genome guided isolation of a novel antimicrobial protein from Thalassomonas viridans
(University of the Western Cape, 2019) Adams, Shanice Raquel; Trindade, Marla
The continued emergence of bacterial resistance to the antibiotics currently employed to treat several diseases has added to the urgency to discover and develop novel antibiotics. It is well established that natural products have been the source of the most effective antibiotics that are currently being used to treat infectious diseases and they remain a major source for drug production. Natural products derived from marine microorganisms have received much attention in recent years due to their applications in human health. One of the biggest bottlenecks in the drug discovery pipeline is the rediscovery of known compounds. Hence, dereplication strategies such as genome sequencing, genome mining and LCMS/MS among others, are essential for unlocking novel chemistry as it directs compound discovery away from previously described compounds. In this study, the genome of a marine microorganism, Thalassomonas viridans XOM25T was mined and its antimicrobial activity was assessed against a range of microorganisms. Genome sequencing data revealed that T. viridans is a novel bacterium with an average nucleotide identity of 81% to its closest relative T. actiniarum. Furthermore, genome mining data revealed that 20% of the genome was committed to secondary metabolisms and that the pathways were highly novel at a sequence level. To our knowledge, this species has not previously been exploited for its antimicrobial activity. Hence, the aim of this study was to screen for bioactivity and identify the biosynthetic gene/s responsible for the observed bioactivity in T. viridans using a bioassay-and-genome- guided isolation approach to assess the bioactive agent. The bioassay-guided fractionation approach coupled to LCMS/MS led to the identification of a novel antimicrobial protein, TVP1. Bioinformatic analyses showed that TVP1 is a novel antimicrobial protein that is found in the tail region of a prophage in the T. viridans genome. Phage-derived proteins have previously been shown to induce larval settlement in some marine invertebrates. Since the mechanism of action of TVP1 remains unknown, it remains a speculation whether it may offer a similar function. More research is required to determine the biotechnological application and the role of TVP1 in its host and natural environment.
Biochemical characterisation of an alpha-amylase with pullulan hydrolase type III characteristics derived from a hot spring metagenomics library
(University of the Western Cape, 2024) Boersma, Bianca; Trindade, Marla
The field of metagenomics has provided biotechnological researchers with new enzymes and insight into previously unknown enzyme families with potential for novel modes of action and being able to function under extreme conditions, such as extremes of temperature, acidity or alkalinity. The enzymes can also often act on multiple substrates and show increased affinity for certain substrates. In this study, the aim was to biochemically characterise a putative type III pullulan hydrolase (PHTIII). A sequence-based metagenomic screen from previous performed by Xiao Ping Hu (2010) was used to identify novel glycosyl hydrolase enzymes in shotgun metagenomic sequence data from the Mphizi hot spring in Malawi. An identified ORF, named Pull3.1, displayed low sequence identity to a characterised α-amylase (62.71%) and 61.66% to a characterised pullulan hydrolase type III, and was, therefore, hypothesized to be an α-amylase (EC 3.2.1.1) with pullulan hydrolase type III (EC 3.2.1.x) characteristics. Further sequence analysis indicated that Pull3.1 had a glycogen binding site and that it belongs to the GH13_20 family as well as having a family 48 carbohydrate-binding module. Pull3.1 displayed the highest substrate conversion rates for starch, pullulan and glycogen. The products released were of the following degrees of polymerisation 3, 2 or 1, in accordance with the products released from the PHTIII from Thermococcus aggregans. Pull3.1 is a thermozyme that shows maximum activity at 75°C and an optimum pH of 7. It was thermostable up to 80°C and had a half-life of 11.6 min at 50°C. Further kinetic characterisation showed that Pull3.1 had a high affinity for starch. The KM value of 0.048 mg/ml is within the range reported for other α-amylase enzymes, and Pull3.1 had a Vmaxof 0,729 (μmol mL−1). All of this data indicates that Pull3.1 is a good candidate for a starch conversion process that requires thermozymes.
Biochemical characterization of β-xylosidase and β-glucosidase isolated from a thermophilic horse manure metagenomic library
(University of the Western Cape, 2020) Ndata, Kanyisa; Trindade, Marla
The complete degradation of recalcitrant lignocellulose biomass into value-added products requires the efficient and synergistic action of lignocellulose degrading enzymes. This has resulted in a need for the discovery of new hydrolytic enzymes which are more effective than commonly used ones. β-xylosidases and β-glucosidases are key glycoside hydrolases (GHs) that catalyse the final hydrolytic steps of xylan and cellulose degradation, essential for the complete degradation of lignocellulose. Functional-based metagenomics has been employed successfully for the identification and discovery of novel GH genes from a metagenome library. Therefore, this approach was used in this study to increase the chances of discovering novel glycoside hydrolase genes from a horse manure metagenomic DNA library constructed in a previous study. Three fosmid clones P55E4, P81G1, and P89A4 exhibiting β-xylosidase activity were found to encode putative glycosyl hydrolases designated XylP55, XylP81, and BglP89. Amino acid sequence analysis revealed that XylP55, XylP81, and BglP89 are members of the GH43, GH39, and GH3 glycoside hydrolase families, respectively. Phylogenetic analysis of XylP81 and BglP89 indicated that these showed relatively low sequence similarities to other homologues in the respective GH families. The enzymes were expressed and purified, and only XylP81 and BglP89 were biochemically characterized. XylP81 (~58 kDa) and BglP89 (~84 kDa) both showed optimum activity at pH 6 and 50℃ and retained 100% residual activity at 55℃ after 1-hour indicating that they are moderately thermostable. XylP81 had high specific activity against 4-nitrophenyl-β-D-xylopyranoside (pNPX; 122 U/mg) with a KM value of 5.3 mM, kcat/KM of 20.3 s-1mM-1, and it showed enzyme activity against α-L-arabinofuranosidase, β-galactosidase, and β-glucosidase activity. BglP89 had a high specific activity for 4-nitrophenyl-β-D-glucopyranoside (pNPG; 133.5 U/mg) with a KM value of 8.4 mM, kcat/KM of 22 s-1mM-1 and also showed α-L-arabinofuranosidase, β-galactosidase, β-glucosidase, and low β-xylosidase activity. BglP89 also showed low hydrolytic activity on cellobiose, β-glucan, and lichenan indicating that it is a broad specificity β-glucosidase. XylP81 retained ~40% activity in the presence of 3 M xylose whilst BglP89 showed considerable glucose tolerance at 150 mM glucose and retained ~46% residual activity. This study reveals two metagenomic derived enzymes (β-xylosidase and β-glucosidase) showing characteristics that could make them potential candidates for lignocellulose biomass degradation in biotechnological and industrial applications.
Biodiscovery of Novel Bioactivities from the South African Marine Environment
(University of the Western Cape, 2016) Hoosen, Reyghana; Trindade, Marla
There is currently a global health crisis taking place, which is the increasing occurrence of drug-resistant pathogens within clinical microorganisms. Drugresistant pathogens are increasingly becoming more difficult to treat; whereas novel drug discovery has declined, therefore there is an urgency to develop novel drug candidates that are able to combat these infections. The marine environment is an important source of biodiversity resulting from the various environmental niches that have formed due to a multitude of conditions such as, low temperatures, high pressure, various pH as well as salinity. These niches are potentially able to harbour diverse bacterial communities therefore making the marine environment a good source for the bioprospecting of novel microorganisms and antimicrobial compounds.
Biological approach to improving the evaporation rates of mine wastewater desalination brine treated in evaporation ponds
(University of the Western Cape, 2021) Moyo, Anesu Conrad; Trindade, Marla
The disposal of brine effluent from inland wastewater desalination plants is a growing global problem with adverse economic and environmental implications because of the substantial cost associated with its disposal and the potential for polluting groundwater resources. Currently, the best and most economical option for brine disposal from inland desalination plants is the use of evaporation ponds, which concentrate the liquid until getting a solid waste that can be valued or directly managed by an authorized company. The effectiveness of these ponds is therefore dependent on the evaporation rate, which has previously been improved by the addition of dyes such as methylene blue. However, the addition of chemical dyes to the evaporation ponds poses a threat to the environment, wildlife, and humans.
Biosurfactant screening through metagenomic and culture-based approaches
(University of the Western Cape, 2022) Sithole, Nombuso Slindile; Trindade, Marla
The biosurfactant market is still predominantly represented by the three main products: surfactin, sophorolipids, and rhamnolipids, mainly as a result of the high cost and low yield associated with biosurfactant production. Moreover, only a few novel structures have been discovered in the last decade, due to a lack of interest, low hit rate, and high redundancy, in which the predominant microorganisms producing the same group of biosurfactants are isolated. Hence, there is the obvious need to open up the market with structurally and functionally diverse compounds that have the potential to tailor to specific needs or applications in different industries.
Comparison of plasmids from clinical Lactobacillus strains
(University of the Western Cape, 2018) Harris, Lyle Keenan; Trindade, Marla
The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy and BV infected women Lactobacillus crispatus and Lactobacillus jensennii has been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. However, no study has evaluated the impact of plasmids on the vaginal lactobacilli. In the present study two plasmids, pLc17 and pLc4, isolated from vaginal Lactobacillus species of both healthy and BV infected women were characterized. pLc4 was present in both Lactobacillus crispatus and Lactobacillus jensennii while pLc17 was only present in Lactobacillus crispatus. pLc17 (16663 bp in size) encoded a ribonucleotide diphosphate reductase (RNR), a filamentation induced by cAMP-like (FIC-like) protein and numerous mobile elements.
Comparison of plasmids from clinical Lactobacillus strains
(University of the Western Cape, 2018) Lyle Keenan , Harris; Trindade, Marla
The vaginal mucosa is dominated by Gram positive, rod shaped lactobacilli which serve as a natural barrier against infection. In both healthy and BV infected women Lactobacillus crispatus and Lactobacillus jensennii has been found to be the predominant Lactobacillus species. Many studies have been conducted to assess factors influencing lactobacilli dominance in the vaginal microbiome. However, no study has evaluated the impact of plasmids on the vaginal lactobacilli. In the present study two plasmids, pLc17 and pLc4, isolated from vaginal Lactobacillus species of both healthy and BV infected women were characterized. pLc4 was present in both Lactobacillus crispatus and Lactobacillus jensennii while pLc17 was only present in Lactobacillus crispatus. pLc17 (16663 bp in size) encoded a ribonucleotide diphosphate reductase (RNR), a filamentation induced by cAMP-like (FIC-like) protein and numerous mobile elements. The FIC-like protein may assist pLc17 to persist within the bacterial population, while RNR is commonly associated with phages and may indicate phage infection. pLc4 (4224 bp in size) encodes for a replication initiator protein and a plasmid partitioning protein. The replication protein on pLc4 shows 44% identity with the replication initiation protein of pSMQ173b_03. On further phylogenetic and sequence analysis with other Rolling Circle Replication (RCR) plasmids, pLc4 appears to be novel as the plasmid shows a low degree of similarity to these RCR plasmids. pLc17 appears to carry both a RCR replicon as well as a theta replicon, similar to pIP501, the broad-host-range plasmid from Bacillus subtilis. The relative Plasmid Copy Number (PCN) for pLc4 and pLc17 was analysed using quantitative polymerase chain reaction (qPCR) for the healthy state relative to the disease state from twentyeight vaginal swab samples obtained from the National Institute for Communicable Diseases (NICD). The relative PCN for pLc4 and pLc17 had a fold increase of ~2.803 and ~1.693, respectively in the healthy patient samples relative to BV infected patient samples. However, there were not found to be significant differences when taking the standard error into account Due to the novelty of these plasmids further analysis and characterisation is required for both plasmids, to establish what role they may play in the health of the vaginal milieu.
Development of a high throughput cell-free metagenomic screening platform
(University of the Western Cape, 2016) Nevondo, Walter; Trindade, Marla
The estimated 5 × 10³⁰ prokaryotic cells inhabiting our planet sequester some 350–550 Petagrams (1 Pg = 1015 g) of carbon, 85–130 Pg of nitrogen, and 9–14 Pg of phosphorous, making them the largest reservoir of those nutrients on Earth (Whitman et al. 1998). However, reports suggest that only less than 1% of these microscopic organisms are cultivable (Torsvik et al. 1990; Sleator et al. 2008). Until recently with the development of metagenomic techniques, the knowledge of microbial diversity and their metabolic capabilities has been limited to this small fraction of cultivable organisms (Handelsman et al. 1998). While metagenomics has undoubtedly revolutionised the field of microbiology and biotechnology it has been generally acknowledged that the current approaches for metagenomic bio- rospecting / screening have limitations which hinder this approach to fully access the metabolic potentials and genetic variations contained in microbial genomes (Beloqui et al. 2008). In particular, the construction of metagenomic libraries and heterologous expression are amongst the major obstacles. The aim of this study was to develop an ultra-high throughput approach for screening enzyme activities using uncloned metagenomic DNA, thereby eliminating cloning steps, and employing in vitro heterologous expression. To achieve this, three widely used techniques: cell-free transcription-translation, in vitro compartmentalisation (IVC) and Fluorescence Activated Cell Sorting (FACS) were combined to develop this robust technique called metagenomic in vitro compartmentalisation (mIVC-FACS). Moreover, the E. coli commercial cell-free system was used in parallel to a novel, in-house Rhodococcus erythropolis based cell-free system. The versatility of this technique was tested by identifying novel beta-xylosidase encoding genes derived from a thermophilic compost metagenome. In addition, the efficiency of mIVC-FACS was compared to the traditional metagenomic approaches; function-based (clone library screening) and sequence-based (shotgun sequencing and PCR screening). The results obtained here show that the R. erythropolis cell-free system was over thirty-fold more effective than the E. coli based system based on the number of hits obtained per million double emulsions (dE) droplets screened. Six beta-xylosidase encoding genes were isolated and confirmed from twenty-eight positive dE droplets. Most of the droplets that were isolated from the same gate encoded the same enzyme, indicating that this technique is highly selective. A comparison of the hit rate of this screening approach with the traditional E. coli based fosmid library method shows that mIVC-FACS is at least 2.5 times more sensitive. Although only a few hits from the mIVC-FACS screening were selected for confirmation of beta-xylosidase activity, the proposed hit rate suggests that a significant number of positive hits are left un-accessed through the traditional clone library screening system. In addition, these results also suggest that E. coli expression system might be intrinsically sub-optimal for screening for hemicellulases from environmental genomes compared to R. erythropolis system. The workflow required for screening one million clones in a fosmid library was estimated to be about 320 hours compared to 144 hours required via the mIVC-FACS screening platform. Some of the gene products obtained in both screening platforms show multiple substrate activities, suggesting that the microbial consortia of composting material consist of microorganisms that produce enzymes with multiple lignocellulytic activities. While this platform still requires optimisation, we have demonstrated that this technique can be used to isolate genes encoding enzymes from mixed microbial genomes. mIVC-FACS is a promising technology with the potential to take metagenomic studies to the second generation of novel natural products bio-prospecting. The astonishing sensitivity and ultra-high throughput capacity of this technology offer numerous advantages in metagenomic bio-prospecting.
Development of a novel high throughput method for identifying phage-host pairs in an extreme environment
(University of the Western Cape, 2017) Olonade, Israel Temiloluwa; Trindade, Marla
There are approximately 10³¹ bacteriophages in the biosphere, outnumbering bacteria 10:1, hence, the dynamic and specific nature of phage-host interactions exerts significant influence on microbial communities. Bacteriophages also represent the reservoir of the highest known genetic diversity making them a potential source of novel biotechnological products. However, the isolation of novel bacteriophages is limited by the observation that less than 1% of bacterial hosts have been cultured. This study aimed to bypass this problem by developing novel culture independent approaches to improve our ability to isolate novel phage-host pairs. Samples were collected from an abandoned copper prospecting site near the Gobabeb Desert Research and Training Station and a Salt lake located in the Swakopmund region of the Namibian desert. Two approaches were explored in this study namely viral tagging and reverse metaviromics. For viral tagging, fluorescently labelling the environmental phage fraction before challenging the environmental bacterial fraction with tagged phages proved difficult. This was most likely due to the complex interaction of the labelling agent with phages and requires further studies. For the reverse metaviromics approach, total DNA from the environmental phage fractions was extracted, sequenced and analyzed for novel phages. Analysis of the phage diversity showed that the copper site was dominated by tailed viruses as has been shown for other extreme arid environments. However, the saline site was atypical of marine environments, with tailed viruses being the most abundant, suggesting that the diversity present is not only driven by salinity. Using the metaviromic sequence data to guide the selection of potential bacterial hosts, two strategies were employed. In the first, putative hosts were predicted based on similarity of phage sequences to those identified in databases. Media targeting these specific genera were employed, 8 bacterial species were isolated and based on 16S rRNA similarity to the closest known species were identified as Halomonas caseinilytica, Halomonas eurihalina, Halomonas sinaiensis, Idiomarina loihiensis, Marinobacter xestospongiae, Virgibacillus salarius and two Salinivibrio species. The 16S rRNA analysis also suggested that H. sinaiensis, V. salarius and both Salinivibrio species are novel. All 8 isolates were challenged with the environmental phage fraction. A novel phage, SMHB1, was isolated on one of the Salinivibrio spp. and is only the second characterized phage ever described for this genus. SMHB1 is a 32 kb myovirus, with a head diameter of 56 nm, and a tail length of 106 nm. The second approach involved the design of fluorescently labelled probes targeting phages identified from the metaviromic sequence data. In a control E. coli system to detect cloned phage DNA fragments, 87% of the interrogated cells showed significant hybridization of the phage specific probe to the target. The optimized method was applied to a simulated environmental bacterial fraction and a detection limit of 1:100 was observed for the bacteria containing the phage DNA fragment of interest. This study demonstrates the possibility of improving the specificity of isolating phage-host pairs in a culture-independent manner by incorporating sequence data in the experimental design; and contributes to our knowledge of the phage diversity of an understudied extreme environment.
Discovery of antibacterial lead compounds from marine organisms
(University of the Western Cape, 2020) Afolayan, Omolola; Beukes, Denzil R; Trindade, Marla
Marine organisms including algae and bacteria are known to produce chemically diverse secondary metabolites for survival purposes in the marine environment. Scientists have identified some of these natural products as therapeutic agents including some antibiotics. Given the increase in the resistance of pathogenic microorganisms especially methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium tuberculosis to commonly prescribed antibiotics, researchers have turned towards exploiting marine natural products for new antibacterial compounds. Due to the proven success of finding bioactive compounds in the marine environment this study therefore aims to discover lead compounds against MRSA and Mycobacterium tuberculosis from two marine sources, the marine algae and the bacteria associated with marine invertebrates referred to as bacterial isolates.
Discovery of biomolecules from South African marine sponge symbionts through Metagenomic studies
(University of the Western Cape, 2018) Mapatha, Matlakala Reginah; Trindade, Marla
Marine sponges are known to harbour diverse microorganisms which have been proposed to be involved in the synthesis of most of the natural compounds derived from sponges. However, only about 1% of these microorganisms can currently be identified through culturebased approaches, limiting the discovery of novel natural compounds. To overcome this limitation, a metagenomics approach has been introduced for the discovery of natural compounds from symbiotic bacterial metagenomic DNA.
Diversity of dsDNA viruses in a South African hot spring assessed by metagenomics and microscopy
(MDPI, 2017) Zablocki, Olivier; van Zyl, Leonardo Joaquim; Kirby, Bronwyn; Trindade, Marla
The current view of virus diversity in terrestrial hot springs is limited to a few sampling sites. To expand our current understanding of hot spring viral community diversity, this study aimed to investigate the first African hot spring (Brandvlei hot spring; 60 C, pH 5.7) by means of electron microscopy and sequencing of the virus fraction. Microscopy analysis revealed a mixture of regular- and ‘jumbo’-sized tailed morphotypes (Caudovirales), lemon-shaped virions (Fuselloviridae-like; salterprovirus-like) and pleiomorphic virus-like particles. Metavirome analysis corroborated the presence of His1-like viruses and has expanded the current clade of salterproviruses using a polymerase B gene phylogeny. The most represented viral contig was to a cyanophage genome fragment, which may underline basic ecosystem functioning provided by these viruses. Furthermore, a putative Gemmata-related phage was assembled with high coverage, a previously undocumented phage-host association. This study demonstrated that a moderately thermophilic spring environment contained a highly novel pool of viruses and should encourage future characterization of a wider temperature range of hot springs throughout the world.
Engineering Parageobacillus thermoglucosidans as a robust platform for bioethanol production
(University of the Western Cape, 2018) van Zyl, Leonardo Joaquim; Trindade, Marla; Cowan, Donald; Ludidi, Ndiko
Parageobacillus thermoglucosidans is a promising “platform” organism to use in the production ofa range of useful metabolites with demonstrated ability to produce ethanol, isobutanol and polylactic acid for bio-degradable plastics. Extensive work has been done in engineering the organism for enhanced ethanol production. However, an often used and highly effective alternative pathway (pyruvate decarboxylase mediated) for ethanol production has not yet been demonstrated in P. thermoglucosidans. We first characterize two novel bacterial pyruvate decarboxylase enzymes (PDC’s) then attempt to express the more thermostable of these enzymes from Gluconobacter oxydans in P. thermoglucosidans to improve ethanol yields. Initial expression was unsuccessful. Analysis of the codon usage pattern for the gene revealed that the codon usage was suboptimal in the heterologous host P. thermoglucosidans. After codon harmonization, we could demonstrate successful expression of the enzyme at 45°C, however not at the bacterium’s optimum growth temperature of 60°C. This was concomitant with enhanced ethanol production close to the theoretical yield possible (0.5g/l).
Factors influencing pigment production by halophilic bacteria and its effect on brine evaporation rates
(Wiley, 2018) Silva-Castro, Gloria Andrea; Moyo, Anesu Conrad; Khumalo, Londiwe; van Zyl, Leonardo Joaquim; Petrik, Leslie F.; Trindade, Marla
The disposal of reject brine, a highly concentrated waste by-product generated by various industrial processes, represents a major economic and environmental challenge. The common practice in dealing with the large amounts of brine generated is to dispose of it in a pond and allow it to evaporate. The rate of evaporation is therefore a key factor in the effectiveness of the management of these ponds. The addition of various dyes has previously been used as a method to increase the evaporation rate. In this study, a biological approach, using pigmented halophilic bacteria (as opposed to chemical dyes), was assessed. Two bacteria, an Arthrobacter sp. and a Planococcus sp. were selected due to their ability to increase the evaporation of synthetic brine. When using industrial brine, supplementation of the brine with an iron source was required to maintain the pigment production. Under these conditions, the Planococcus sp. CP5-4 produced a carotenoid-like pigment, which resulted in a 20% increase in the evaporation rate of the brine. Thus, the pigment production capability of halophilic bacteria could potentially be exploited as an effective step in the management of industrial reject brines, analogous to the crystallizer ponds used to mine salt from sea water.
Genomic characterization of a prophage, Smhb1, that Infects Salinivibrio kushneri BNH isolated from a Namib Desert saline spring
(MDPI, 2021) Olonade, Israel; van Zyl, Leonardo Joaquim; Trindade, Marla
Recent years have seen the classification and reclassification of many viruses related to the model enterobacterial phage P2. Here, we report the identification of a prophage (Smhb1) that infects Salinivibrio kushneri BNH isolated from a Namib Desert salt pan (playa). Analysis of the genome revealed that it showed the greatest similarity to P2-like phages that infect Vibrio species and showed no relation to any of the previously described Salinivibrio-infecting phages. Despite being distantly related to these Vibrio infecting phages and sharing the same modular gene arrangement as seen in most P2-like viruses, the nucleotide identity to its closest relatives suggest that, for now, Smhb1 is the lone member of the Peduovirus genus Playavirus. Although host range testing was not extensive and no secondary host could be identified for Smhb1, genomic evidence suggests that the phage is capable of infecting other Salinivibrio species, including Salinivibrio proteolyticus DV isolated from the same playa. Taken together, the analysis presented here demonstrates how adaptable the P2 phage model can be. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)
(Elsevier, 2015) Maropola, Mapula Kgomotso Annah; Ramond, Jean-Baptiste; Trindade, Marla
Culture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic content must be representative of the total microbial diversity. In this study, we evaluated the endophytic bacterial diversity retrieved using different mDNA extraction procedures. Metagenomic DNA from sorghum (Sorghum bicolor L. Moench) stem and root tissues were extracted using two classical DNA extraction protocols (CTAB- and SDS-based) and five commercial kits. The mDNA yields and quality as well as the reproducibility were compared. 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) was used to assess the impact on endophytic bacterial community structures observed. Generally, the classical protocols obtained high mDNA yields from sorghum tissues; however, they were less reproducible than the commercial kits. Commercial kits retrieved higher quality mDNA, but with lower endophytic bacterial diversities compared to classical protocols.
Improving Evaporation Rate of Mine Wastewater
(University of the Western Cape, 2018) Khumalo, Londiwe Thandeka Precious; Trindade, Marla; Petrik, Leslie
The treatment of mine water at the eMalahleni Water Reclamation Plant (EWRP) results in the production of large volumes of brine. Different brine management methods have been applied to dispose the brine but the evaporation pond method is regarded as the cheaper, most effective and less laborious method for brine disposal. Brine wastewater is pumped into the pond where it evaporates resulting in the mixture of salts. The rate at which evaporation occurs is influenced by many factors such as temperature, salinity, humidity and wind. Due to high salinities in brine the EWRP is currently experiencing a challenge with low evaporation rate. Here, a comparative study was done to determine the efficiency of using a chemical and a biological approach to enhance the evaporation rate of reject brine. The chemical approach involved the addition of various concentrations of methylene blue dye (100 to 300 ppm with 50 ppm increments) to 1L volumes of brine, and measuring the evaporation rate. On the other hand, the biological approach involved the isolation of pigmented halophilic bacteria from eMalahleni brine and Cerebos salt samples. Isolated bacterial strains were characterised based on their morphology, biochemical and salt tolerance characteristics. Furthermore, the strains were identified using 16S rRNA gene sequence analysis. Among the isolated halophilic bacterial strains, EP-3, an Arthobacter agilis isolated from the eMalahleni brine produced a darker pigment compared to the other strains. Therefore, EP-3 was evaluated for its effect on the evaporation of brine using a culture inoculum or the addition pigment extracted from an EP-3 culture. The addition of MB above 100 ppm overcame the effect of salt precipitation and resulted in higher evaporation (41%) rate. Addition of pigmented bacteria or bacterial extracted pigment to the brine respectively resulted in 18% and 24% increase in the evaporation rate.
Investigating the antimicrobial potential of Thalassomonas actiniarum
(University of Western Cape, 2020) Pheiffer, Fazlin; Trindade, Marla; van Zyl, Leonardo
The World Health Organisation predicts that by the year 2050, 10 million people could die annually as a result of infections caused by multidrug resistant bacteria. Individuals with compromised immune systems, caused by underlying disease such as HIV, MTB and COVID-19, are at a greater risk. Antibacterial resistance is a global concern that demands the discovery of novel drugs. Natural products, used since ancient times to treat diseases, are the most successful source of new drug candidates with bioactivities including antibiotic, antifungal, anticancer, antiviral, immunosuppressive, anti-inflammatory and biofilm inhibition. Marine bioprospecting has contributed significantly to the discovery of novel bioactive NPs with unique structures and biological activities, superior to that of compounds from terrestrial origin. Marine invertebrate symbionts are particularly promising sources of marine NPs as the competition between microorganisms associated with invertebrates for space and nutrients is the driving force behind the production of antibiotics, which also constitute pharmaceutically relevant natural products.

Browsing by Author "Trindade, Marla"

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