Donald A. Cowan

Donald A. Cowan
University of Pretoria | UP · Department of Biochemistry Genetics and Microbiology

PhD (Waikato)

About

868
Publications
144,732
Reads
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16,632
Citations
Introduction
I lead the University of Pretoria Centre for Microbial Ecology and Genomics, a 30-strong research team which includes 4 Research Fellows and 10 postdocs. Our research interests are broad, and include the microbial ecology of various hot and cold desert soil environments, and of agricultural soils and the plant rhizospheric zone. We are also active functional metagenomics and gene discovery, with an emphasis of various classes of biocatalysts and on the genes for stress response and adaptation.
Additional affiliations
April 2009 - September 2020
University of Pretoria
Position
  • Landscape scale study of Namib Desert microbial ecology and metagenomics
Description
  • A multi-faceted international collaborative research program investigating the form and function of microbial communities in the west African Namib Desert region.
July 2001 - May 2012
University of the Western Cape
Position
  • Extremophile metagenomics
January 2000 - present
University of Pretoria
Position
  • Microbial ecology of Antarctic Dry Valley soils
Description
  • A wide-ranging study of the ecology, structure and function of microbial communities in the Dry Valley soils of eastern Antarctica
Education
February 1978 - December 1980
The University of Waikato
Field of study
  • Biochemistry
March 1976 - November 1977
The University of Waikato
Field of study
  • Biochemistry
March 1973 - November 1975
The University of Waikato
Field of study
  • Biology and Chemistry (double major)

Publications

Publications (868)
Article
Full-text available
Background Top-soil microbiomes make a vital contribution to the Earth’s ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these...
Article
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An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces). New genera: Haudseptori...
Article
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Human activities such as agriculture and mining are leading causes of water pollution worldwide. Individual contaminants are known to negatively affect microbial communities. However, the effect of multifaceted pollution on these communities is less well understood. We investigated, using next-generation sequencing of the 16S rRNA genes, the effect...
Article
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Significance Changes in the extent of ice sheets through evolutionary timescales have influenced the connectivity of soil invertebrate populations across the Antarctic landscape. We use genetic divergences to estimate isolation times for soil invertebrates along the Transantarctic Mountains. Four species of Collembola (Arthropoda) each showed genet...
Article
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Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to repre...
Preprint
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1 A surprising diversity and abundance of microorganisms resides in the cold desert 2 soils of Antarctica. The metabolic processes that sustain them, however, are poorly 3 understood. In this study, we used metagenomic and biogeochemical approaches to 4 study the microbial communities in 16 physicochemically diverse mountainous and 5 glacial soils...
Preprint
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The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, there is insufficient evidence for ancient human-pathogen interactions in the region...
Article
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Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic thermophile belonging to the family Bacillaceae. Previous studies have shown that this bacterium harbours co-localised genes coding for a carbon monoxide (CO) dehydrogenase (CODH) and Ni-Fe hydrogenase (Phc) complex and oxidises CO and produces hydrogen (H2) g...
Article
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Background: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. Methods: Following...
Article
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In Antarctic environments, the combination of both abiotic and biotic stressors results in simple trophic levels dominated by microbiomes. Although the past two decades have revealed substantial insights regarding the diversity and structure of microbiomes, we lack mechanistic insights regarding community interactions and how phages may affect thes...
Article
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Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic...
Article
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The effects of temperature on microorganisms in high latitude regions, and their possible feedbacks in response to change, are unclear. Here, we assess microbial functionality and composition in response to a substantial temperature change. Total soil biomass, amoA gene sequencing, extracellular activity assays and soil physicochemistry were measur...
Article
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Rare biosphere represents the majority of Earth's biodiversity and performs vital ecological functions, yet little is known about its biogeographical patterns and community assembly processes in terrestrial ecosystems. Herein, we investigated the community composition and phylogeny of rare (relative abundance <0.1%) and abundant (>1%) bacteria in d...
Article
Background Peritoneal dialysis (PD) peritonitis is a feared complication of PD, with significant sequelae for the patient. The cause of PD peritonitis is largely due to a single organism (≥75% of cases) and rarely due to multiple organisms. Methods In this pilot study, we investigated 25 cases of PD peritonitis with 16S ribosomal RNA (rRNA) next-g...
Article
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In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and me...
Preprint
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The balance of nutrients in soil is critical for microbial growth and function, and stoichiometric values below the Redfield ratio for C:N:P can negatively affect microbial ecosystem services. However, few studies have assessed the relationships between nutrient balance and biological productivity in extremely nutrient-poor habitats. The Mackay Gla...
Article
The exhaustive use of antibiotics in humans, animal farming and other agricultural practices has resulted in the frequent appearance of antibiotic resistant bacteria in human-impacted habitats. However, antibiotic resistance in natural (less-impacted) habitats is less understood. Using shotgun metagenomics we analysed soils from relatively low anth...
Preprint
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By modulating the structure, diversity and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients and low water availability are known to limit microbial activity. Although phages may substantially govern trophic interactions in cold de...
Article
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Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are relatively simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial commun...
Article
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The Namib Desert is one of the world’s only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was...
Article
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Hydrogen gas represents a promising alternative energy source to dwindling fossil fuel reserves, as it carries the highest energy per unit mass and its combustion results in the release of water vapour as only byproduct. The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius is able to produce hydrogen via the water-gas shift r...
Article
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Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicat...
Preprint
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Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. Our results indicate that the distal IM of the Neolithic ‘Middle Iron Age’ (c. AD 1485) Bantu-speaking individual exhibits features indicative of a largely mixe...
Article
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Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons...
Preprint
Full-text available
Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are exceptionally simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial com...
Article
The fungal rhizosphere communities associated with soil surrounding Aizoaceae plants in the Namaqua National Park in the Succulent Karoo biodiversity hotspot, South Africa, were analysed by culture-dependent and culture-independent methods. The keratinophilic fungal Order, Onygenales, was the most abundant Order observed in the total fungal populat...
Article
Les entrées de grottes et les abris sous roche sont des lieux fréquentés depuis le début du Pléistocène par les homininés anciens puis par les premiers Homo sapiens. Les découvertes archéologiques provenant de plusieurs grottes d'Afrique subsaharienne témoignent de l ' évolution technologique et comportementale des Hommes Anatomiquement Modernes, d...
Article
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Dispersal is a critical yet poorly understood factor underlying macroecological patterns in microbial communities ¹ . Airborne microbial transport is assumed to occupy a central role in determining dispersal outcomes 2,3 , and extra-range dispersal has important implications for predicting ecosystem resilience and response to environmental change ⁴...
Article
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The blood that flows perpetually through our veins and arteries performs numerous functions essential to our survival. Besides distributing oxygen, this vast circulatory system facilitates nutrient transport, deters infection and dispenses heat throughout our bodies. Since human blood has traditionally been considered to be an entirely sterile envi...
Article
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Land-use change from natural to managed agricultural ecosystems significantly impacts soil bacterial diversity and function. The Eastern Free State (EFS) is one of the most productive agricultural regions in South Africa. However, no studies aiming to understand the changes in bacterial diversity, composition and function due to land-use change in...
Article
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Aim To assess spatial patterns of genetic and species‐level diversity for Namib Desert Collembola using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene sequences. Location Namib Desert gravel plains. Taxon Collembola (springtails). Methods A total of 77 soil samples were collected along NE‐SW (60 km) and E‐W (160 km) transects from w...
Article
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Abiotic and biotic factors control ecosystem biodiversity, but their relative contributions remain unclear. The ultraoligotrophic ecosystem of the Antarctic Dry Valleys, a simple yet highly heterogeneous ecosystem, is a natural laboratory well-suited for resolving the abiotic and biotic controls of community structure. We undertook a multidisciplin...
Article
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Plant-microbe interactions mediate both the invasiveness of introduced plant species and the impacts that they have in invaded ecosystems. Although the phylogenetic composition of the rhizospheric microbiome of Acacia dealbata (an invasive Australian tree species) has been investigated, little is known about the functional potential of the constitu...
Chapter
Cyanobacteria are the dominant living features of Antarctic terrestrial environments. They have the capacity to directly influence components of the cryosphere including nutrient acquisition, soil stabilisation and driving soil community structure. This book chapter incorporates recent literature to discuss how gradients of cyanobacterial abundance...
Chapter
Alkalinicity presents a challenge for life due to a “reversed” proton gradient that is unfavourable to many bioenergetic processes across the membranes of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great scientific and biotechnological...
Chapter
In this book chapter, we focus on the research performed to date on the microbiology and microbial ecology of the Namib Desert, one of the oldest hyperarid deserts on Earth. Microbial communities consist of complex assemblages of interacting microorganisms, ranging from viruses to small eukaryotes (such as nematodes and springtails) and these micro...
Preprint
Dispersal is a critical yet poorly understood factor underlying macroecological patterns in microbial communities. Airborne microbial transport is assumed to occupy a central role in determining dispersal outcomes and extra-range dispersal has important implications for predicting ecosystem resilience and response to environmental change. One of th...
Article
Full-text available
Background The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H2) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehydrogenase–hydrogenase enzyme complex. Although little is known about the hydrogenogenic capacities of different strains of this...
Article
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Background The rhizosheath-root system is an adaptive trait of sandy-desert speargrasses in response to unfavourable moisture and nutritional conditions. Under the deserts’ polyextreme conditions, plants interact with edaphic microorganisms that positively affect their fitness and resistance. However, the trophic simplicity and environmental harshn...
Article
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Background: Geobacillus and Parageobacillus are two ecologically diverse thermophilic genera within the phylum Firmicutes. These taxa have long been of biotechnological interest du