Bronwyn Kirby - Academia.edu (original) (raw)

Papers by Bronwyn Kirby

Actinobacterial diversity associated with rooibos plants. GenBank accessions KY857826-KY857837

Frontiers in microbiology, 2017

Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodologic... more Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation. Using simulated viromes that mimic environmental data challenges we assessed the performance of five assemblers (CLC-Workbench, IDBA-UD, SPAdes, RayMeta, ABySS). Individual analyses of relevant scaffold length fractions revealed shortcomings of some programs in reconstruction of viral genomes with excessive read coverage (IDBA-UD, RayMeta), and in accurate assembly of scaffolds ≥50 kb (SPAdes, RayMeta, ABySS). The CLC-Workbench assembler performed best in terms of genome recovery (including highly covered genomes) and correct reconstruction of large scaffolds; and was used to assemble a virome from ...

Genome Announcements, 2016

The rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with an... more The rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with antimicrobial activity. This brief report describes the genome sequence of threeBacillusspecies isolates from South African marine sponges, which produce compounds with antimicrobial activity. A search for secondary metabolite clusters revealed several secondary metabolite pathways in these genomes, which may hold promise as novel antibiotics.

Journal of Applied Phycology, 2015

Marine macroalgae host diverse bacterial communities with which they share a complex array of che... more Marine macroalgae host diverse bacterial communities with which they share a complex array of chemical interactions based on the exchange of nutrients, minerals and secondary metabolites. The brown alga Splachnidium rugosum is a rich source of a valuable fucose-containing sulphated polysaccharide (fucoidan). It grows exclusively in the Southern Hemisphere along temperate shores. While growth and development are dependent on specific microbial interactions, the microbiome of S. rugosum has not been characterized. This study reports on the composition and uniqueness of epiphytic bacterial communities associated with S. rugosum. Sporophytes were collected during winter (July 2012) from the Western Cape (−34° 18′ 5.0004″, +18° 48′ 59.0004″), South Africa. Culture-based methods relied on a range of selective marine media including marine agar, nutrient sea water agar, nutrient agar and thiosulfate-citrate-bile-salts-sucrose agar. Epiphytic isolates were identified to species level by 16S rRNA gene sequence analysis and encompassed 39 Gram-negative and 2 Gram-positive bacteria. Isolates were classified as Gamma-Proteobacteria, Alpha-Proteobacteria, Firmicutes or Bacteriodetes. Gamma-Proteobacteria were the most abundant, dominated by Vibrio and Pseudoalteromonas species. Three isolates displayed low sequence identity (˂97 %) with their closest relatives and were grouped into the genera Shewanella, Sphingomonas and Sulfitobacter. All bacterial isolates (41) were screened for anti-microbial activity against indicator strains of Bacillus cereus, Staphylococcus epidermidis, Mycobacterium smegmatis, Micrococcus luteus and Pseudomonas putida. Fifteen isolates (36 %) displayed antimicrobial activity against one or more of the indicator strains. One isolate (Pseudomonas sp.) was active against all strains tested. Splachnidium rugosum is a valuable source for the discovery of bioactive compounds of bacterial origin active against human pathogens.

Journal of Molecular Catalysis B: Enzymatic, 2015

Journal of environmental management, 2014

There is a global need for the implementation of more cost-effective green technologies for the t... more There is a global need for the implementation of more cost-effective green technologies for the treatment of effluent from wineries. However, systems reliant on microbial biodegradation may be adversely affected by the highly seasonal character of cellar waste. In this study, the biodegradation of two different formulations of winery effluent in sand bioreactors was compared. The degradation of organic substrates and formation of metabolites was monitored by physicochemical analyses of pore water and final effluent samples. Changes in the bacterial community structures were detected using molecular fingerprinting. In wastewater with an overall COD of 2027 mg/L, a formulation with a high concentration of acetate (800 mg COD/L) was more recalcitrant to degradation than a formulation with a high concentration of glucose (800 mg COD/L). Ethanol, glucose and phenolics were degraded preferentially in the deeper layers of the sand bioreactors (average Eh 25 mV) than in the superficial laye...

Manual of Industrial Microbiology and Biotechnology, Third Edition

This chapter presents a number of methods that have been successfully applied in the screening fo... more This chapter presents a number of methods that have been successfully applied in the screening for enzymes from extremophilic microorganisms and their communities. Parameters such as temperature, pH, percentage of relative humidity, salinity, dO2, redox state, moisture content, light, local geology, weather (cloud, precipitation, wind speed), and so on, may be critical or irrelevant. Thermophilic samples, psychrophilic samples, halophilic samples, acidophilic samples, superficial sea- and freshwater samples are the issues for consideration in the sampling of various specific extreme environments. Two major extraction protocols may be used: (i) phenol extraction, where the gentle hydrophobicity of phenol makes it a good solvent for DNA extraction, and (ii) the use of commercial kits. Extremophiles are an obvious source of novel enzymes that may revolutionize the biofuels industry. Several bacterial and fungal species produce ligninases, with the enzymes produced by brown- and white-rot fungi being studied the most extensively. A report by Tuncer and his coworkers found that the ratio of carbon (C)/nitrogen (N) affected enzyme production and that a C/N ratio of 4:1 to 5.3:1 resulted in maximal enzyme production. This report also highlighted the need to grow all test strains on a range of different carbon sources, because the amount of extracellular enzymes produced varies depending on the carbon source, and it is essential to find the best medium for enzyme production. There is certainly a need for standardized methods for performing metagenomics projects, from physical-chemical description of sampling sites and sampling procedures down to the data interpretation and integration.

Extremophiles Handbook, 2011

Polar Microbiology: Life in a Deep Freeze

This chapter talks about the development of culture-independent, molecular methods that have revo... more This chapter talks about the development of culture-independent, molecular methods that have revolutionized the field and the understanding of molecular ecology. Through the use of these techniques, it is now apparent that the earlier culture-based studies were not a representative reflection of the dominant microorganisms in many psychrophilic habitats. Cyanobacteria present in Dry Valleys mineral soils are considered to be the major primary producers and contribute significantly to microbial diversity. Lithic communities are classified by the specific environmental niche they reside in, and hypoliths, chasmoliths, and cryptoendoliths are further discussed in this chapter. The majority of bacteria isolated from permafrost are aerobic and include a number of coryneforms, endospore formers, sulfate reducers, nitrifying and denitrifying bacteria, and cellulose degraders. The microbial mat bacterial diversity of 10 Dry Valleys lakes was assessed by culturing techniques (heterotrophic growth conditions and fatty acid analysis). Microbial mats from Markham and Ward Hunt Ice Shelves showed species homogeneity in the vertical profile, which has not been seen previously in Antarctic mats, possibly due to differences in mat thickness. The stratified Antarctic mats from the McMurdo Ice Shelf were up to 8 cm thick in places, while the Arctic mats in this study were approximately 2 cm. Using metagenomic methods researchers can assess the diversity of culturable and uncultured organisms, including rare taxa.

The Dry Valleys Desert of Eastern Antarctica is an ice-free region of 4800 km2, which accounts fo... more The Dry Valleys Desert of Eastern Antarctica is an ice-free region of 4800 km2, which accounts for less than 2% of the total Antarctic landmass. Previously, it was thought that the prevailing environmental conditions of these hyper-arid cold deserts, such as strong katabatic winds, low temperatures, and low humidity, would severely limit the ability of microorganisms to survive in this habitat, and the Dry Valleys could only support low microbial populations [Wynn-Williams, 1990]. However, recent culture-independent ...

Journal of Clinical Virology, 2015

Enzyme and microbial technology, 2015

Bacterial laccases show low activities but can be of biotechnological interest due to industriall... more Bacterial laccases show low activities but can be of biotechnological interest due to industrially suitable characteristics such as thermostability and tolerance to alkaline pH. In this study, three separate mutations (M298F, V290N and V290A) were introduced at or near the T1 copper site of the small laccase (SLAC) from Streptomyces coelicolor A3(2) and biochemical properties were assessed in comparison with the native enzyme. The mutation, V290N showed approximately double the activity of SLAC when ABTS was used as substrate while the specific activity of SLAC-M298F was 4-5 times higher than that of SLAC when the assays were performed at ≥70°C. There was no significant difference in activity with 2,6-dimethoxyphenol (2,6-DMP); however, there was a significant shift in the optimal pH from pH 9.5 (SLAC) to 7.5 (SLAC-V290N). Optimal temperature for activity was not significantly altered but thermostability was reduced in all three mutants. The substrate range of the mutant variants re...

Journal of Applied Microbiology, 2007

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2006

Two novel nocardioform actinomycetes, strains Q41T and HMC25T, were isolated from soil samples co... more Two novel nocardioform actinomycetes, strains Q41T and HMC25T, were isolated from soil samples collected in the Western Cape province, South Africa. Rapid genus identification revealed that the isolates belonged to the genus Kribbella (based on single-digestion restriction analysis of the 16S rRNA gene sequences with MboI, VspI, SphI, SnaBI, SalI and AgeI). Both isolates had ll-diaminopimelic acid and glycine in their cell-wall peptidoglycan, and contained mannose and ribose as whole-cell sugars. Strain HMC25T is able to grow at 45 °C and in the presence of NaCl (3 %), cephaloridine (10 μg ml−1) and gentamicin sulphate (10 μg ml−1). Strain Q41T grows in the presence of NaCl (2 %). Neither strain was able to grow under anaerobic conditions, whereas Kribbella flavida KACC 20248T, Kribbella jejuensis HD9T, Kribbella koreensis KACC 20250T and Kribbella sandramycini KACC 20249T exhibited weak but distinct growth under anaerobic conditions. Physiological test results and 16S rRNA gene seq...

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009

A novel actinomycete, strain TVU1T, was isolated from leaves of the indigenous South African plan... more A novel actinomycete, strain TVU1T, was isolated from leaves of the indigenous South African plant Tulbaghia violacea. Applying a polyphasic approach, the isolate was identified as a member of the genus Micromonospora. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain TVU1T was most closely related to Micromonospora echinospora DSM 43816T. However, phylogenetic analysis based on gyrB gene sequences showed that strain TVU1T was most closely related to the type strains of Micromonospora aurantiaca and Micromonospora chalcea. DNA–DNA relatedness values between strain TVU1T and the type strains of M. echinospora, M. aurantiaca and M. chalcea were 7.6±4.5, 45.9±2.0 and 60.9±4.5 %, respectively. Strain TVU1T could be distinguished from the type strains of all three of these species by several physiological characteristics, such as colony colour, NaCl tolerance, growth temperature range and sole carbon source utilization pattern. Strain TVU1T (=DSM 45142T=NRRL B-24576T...

Environmental Microbiology, 2009

Despite the apparent severity of the environmental conditions in the McMurdo Dry Valleys, Eastern... more Despite the apparent severity of the environmental conditions in the McMurdo Dry Valleys, Eastern Antarctica, recent phylogenetic studies conducted on mineral soil samples have revealed the presence of a wide diversity of microorganisms, with actinobacteria representing one of the largest phylotypic groups. Previous metagenomic studies have shown that the majority of Antarctic actinobacterial populations are classified as 'uncultured'. In this study, we assessed the diversity of actinobacteria in Antarctic cold desert soils by complementing traditional culture-based techniques with a metagenomic study. Phylogenetic analysis of clones generated with actinobacteriumand streptomycete-specific PCR primers revealed that the majority of the phylotypes were most closely related to uncultured Pseudonocardia and Nocardioides species. Phylotypes most closely related to a number of rarer actinobacteria genera, including Geodermatophilus, Modestobacter and Sporichthya, were also identified. While complementary culturedependent studies isolated a number of Nocardia and Pseudonocardia species, the majority of the cultured isolates (> 80%) were Streptomyces species-although phylotypes affiliated to the genus Streptomyces were detected at a low frequency in the metagenomic study. This study confirms that Antarctic Dry Valley desert soil harbours highly diverse actinobacterial communities and suggests that many of the phylotypes identified may represent novel, uncultured species.

Antonie van Leeuwenhoek, 2009

Given the advances in molecular biology, many microbial taxonomists feel that a sequencing based ... more Given the advances in molecular biology, many microbial taxonomists feel that a sequencing based method should be developed that can replace DNA-DNA hybridisation for species delineation. The potential of the gyrB gene to be used for phylogenetic studies has been investigated within a number of actinobacterial genera, including Gordonia, Micromonospora and the whorl-forming Streptomyces species. This study aimed to determine whether the gyrB gene can discriminate between type strains of the genus Kribbella. Previous studies, in the genus Micromonospora, have found that a gyrB-based genetic distance of 0.014 correlates to a DNA relatedness of 70% and that those strains with a genetic distance of greater than 0.014 are likely to be distinct species. In this study, the gyrB-based genetic distances between Kribbella type strains were found to range from 0.0164 to 0.1495, supporting the use of the 0.014 genetic-distance value as the threshold for species delineation within this genus. Phylogenetic analysis based on the gyrB gene had improved resolution (longer branch lengths) compared to that based on the 16S rRNA gene sequence. Based on this study, the gyrB gene can be used to distinguish between Kribbella type strains. Furthermore, it is proposed that a 390-nucleotide sequence of the gyrB gene of a Kribbella isolate is sufficient to assess whether it is likely to represent a new species, before time and effort is invested in polyphasic taxonomic characterisation of the isolate. Keywords Kribbella Á Nocardioidaceae Á gyrB Á Actinobacteria Á Phylogeny Á Genetic distance Á Horizontal gene transfer The GenBank accession numbers for the gyrB gene sequences obtained in this study are shown in Fig. 3.