Emma Steenkamp

University of Pretoria | UP · Department of Microbiology and Plant Pathology

The molecular mechanisms influencing Fusarium circinatum , an important pine tree pathogen, remain partially understood. We recently reported a biofilm-mediated response in this fungus, which supports its adaptation to harsh conditions including heat stress. Herein, we report that biofilm extracellular vesicles (EVs) play a key role in this adaptiv...

South Africa has a small but growing olive industry. Until now, no virological research has been carried out on this crop locally. Seventeen samples were collected from various olive cultivars from a single producer in the Stellenbosch growing area of South Africa. RNAseq was performed on total RNA, and the compositions of the metaviromes were dete...

The mitochondrial genome of Dematophora necatrix is 121,350 base pairs in length with a G + C content of 30.19%. Phylogenetic analysis showed that D. necatrix grouped with other members of the Xylariaceae, with which its mitogenome also shares a broadly similar architecture and gene content. The D. necatrix mitogenome contains 14 protein-coding and...

Fusarium circinatum is an important fungal pathogen of Pinus species utilized in commercial forestry worldwide. In Colombia, it was first found on nursery plants and later in plantations associated with basal cankers on young trees. In this study, we explored the population diversity of the pathogen in Colombia by analyzing 136 isolates collected f...

In ascomycetous fungi, sexual mate recognition requires interaction of the Ste2 receptor protein produced by one partner with the α-factor peptide pheromone produced by the other partner. In some fungi, Ste2 is further needed for chemotropism towards plant roots to allow for subsequent infection and colonization. Here, we investigated whether this...

In the original publication [...]

The African fungus Ceratocystis albifundus does not cause disease symptoms on its wide range of native woody hosts. However, on non-native Acacia mearnsii and orchard-grown Protea cynaroides , it represents an economically significant pathogen. Because previous studies exploring the biological fitness of C. albifundus were constrained by small samp...

South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nome...

The capacity to form biofilms is a common trait among many microorganisms present on Earth. In this study, we demonstrate for the first time that the fatal pine pitch canker agent, Fusarium circinatum , can lead a biofilm‐like lifestyle with aggregated hyphal bundles wrapped in extracellular matrix (ECM). Our research shows F. circinatum 's ability...

The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. ci...

The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threads to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. ci...

Extracellular vesicles (EVs) are tiny messengers that convey bioactive molecules from donor to recipient cells, leading to changes in their physiology and function. We investigated the role of EVs in shaping growth and the biofilm biology of the tree pathogen Fusarium circinatum and its interaction with the susceptible host, Pinus patula . Vesicles...

The capacity to form biofilms is a common trait among many microorganisms present on Earth. In this study, we demonstrate for the first time that the fatal pine pitch canker agent, Fusarium circinatum, can lead a biofilm-like lifestyle with aggregated hyphal bundles wrapped in extracellular matrix (ECM). Our study suggests that F. circinatum biofil...

Organisms from all kingdoms of life release membrane vesicles, which are tiny and spherical structures made of a lipid bilayer. Membrane vesicles carry out a number of functions, such as forming new cell membranes, removing waste products from the cell, and transporting lipids and other substances from parent to recipient cells. The payloads often...

Bradyrhizobium comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of sub...

A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates rep...

Hybridization is recognized as a notable driver of evolution and adaptation, which closely related species may exploit in the form of incomplete reproductive barriers. Three closely related species of Ceratocystis (i.e., C. fimbriata, C. manginecans and C. eucalypticola) have previously been shown to hybridize. In such studies, naturally occurring...

The aggregation of fungal cells embedded in a matrix of extracellular matrix (ECM) results in a biofilm— a microbial community of sessile cells attached to biotic and/or abiotic surfaces. In this study, we demonstrate for the first time that the fatal pine pitch canker agent, Fusarium circinatum , can lead a biofilm-like lifestyle with aggregated h...

The capacity to form biofilms forms part of the life history traits of nearly all microorganisms present on earth. In this study, we demonstrate for the first time that the fatal pine pitch canker agent, Fusarium circinatum , can lead a biofilm-like lifestyle with aggregated hyphal bundles wrapped in extracellular matrix (ECM). Our study suggests t...

The capacity to form biofilms is a common trait among many microorganisms present on Earth. In this study, we demonstrate for the first time that the fatal pine pitch canker agent, Fusarium circinatum , can lead a biofilm-like lifestyle with aggregated hyphal bundles wrapped in extracellular matrix (ECM). Our study suggests that F. circinatum biofi...

The capacity to form biofilms is a common trait among many microorganisms present on Earth. In this study, we demonstrate for the first time that the fatal pine pitch canker agent, Fusarium circinatum , can lead a biofilm-like lifestyle with aggregated hyphal bundles wrapped in extracellular matrix (ECM). Our research shows F. circinatum 's ability...

Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some...

Plants release extracellular vesicles (EVs) for various reasons, such as unconventional protein secretion, RNA transport, and defence against pathogens. However, very little is known about plant EV biosynthesis and diverse and bioactive luminal contents, including how they alter recipient cell biology and function. To study EVs, researchers often i...

Plants release extracellular vesicles (EVs) for various reasons, such as unconventional protein secretion, RNA transport, and defence against pathogens. However, very little is known about plant EV biosynthesis and diverse and bioactive luminal contents, including how they alter recipient cell biology and function. To study EVs, researchers often i...

Hybridization is recognized as a notable driver of evolution and adaptation, which closely related species may exploit in the form incomplete reproductive barriers. Three closely related species of Ceratocystis (i.e., C. fimbriata, C. manginecans and C. eucalypticola) previously have been shown to hybridize by mating naturally occurring self-steril...

Transcriptional regulation controls gene expression through regulatory promoter regions that contain conserved sequence motifs. These motifs, also known as regulatory elements, are critically important to expression, which is driving research efforts to identify and characterize them. Yeasts have been the focus of such studies in fungi, including i...

The pine pitch canker pathogen Fusarium circinatum is endemic in the Southeast United States and Central America and represents an invasive threat globally. This ecologically adaptable fungus readily infects all parts of its pine hosts, leading to widespread mortality of nursery seedlings and decline in the health and productivity of forest stands....

The complete RNA genome sequence of a novel member of the genus Potyvirus infecting Barleria repens has been determined. A plant showing symptoms of virus-like leaf mosaic was sampled in the Western Cape province of South Africa, and the associated virus has been tentatively named "Barleria repens mottle virus" (BaRMoV). The genome of BaRMoV consis...

Pigeonpea (Cajanus cajan (L.) Millsp.) is an important grain legume, which, like several other legumes, depends on the process of biological nitrogen fixation for its nitrogen (N2) requirement by forming a symbiotic association with rhizobia. Compared to other tropical legumes, however, the productivity of pigeonpea in South Africa is low, despite...

Study of the diversity of indigenous rhizobia associated with pigeonpea to screen elite nitrogen fixing rhizobial strains for development as inoculants to enhance South African pigeonpea production

The cultivation of chickpea (Cicer arietinum L.) in South Africa is dependent on the application of suitable Mesorhizobium inoculants. Therefore, we evaluated the symbiotic effectiveness of several Mesorhizobium strains with different chickpea genotypes under controlled conditions. The tested parameters included shoot dry weight (SDW), nodule fresh...

Nearly all microbes, including fungal pathogens, form biofilms, which are structured communities of microbial aggregates enclosed in self-produced extracellular polymeric substances (EPS) and attached to a surface. Studying plant-associated fungal biofilms can enhance understanding of fungal biology and knowledge of the links between fungal disease...

Fusarium circinatum is an economically important pathogen of pine and resides in the Fusarium fujikuroi species complex. Here we investigated the molecular processes underlying growth in F. circinatum by exploring the association between growth and the nutritional environment provided by the pine host. For this purpose, we subjected a mapping popul...

Abstract Pitch canker on plantation‐grown Pinus species, caused by the fungal pathogen Fusarium circinatum, first appeared in the western and southern Cape regions of South Africa. However, outbreaks have subsequently been reported from the major plantation growing regions of KwaZulu‐Natal and Limpopo in the eastern, summer rainfall regions of the...

This is the first report of chrysanthemum virus B (CVB) and chrysanthemum chlorotic mottle viroid (CChMVd) on Chrysanthemum × morifolium cultivars, in South Africa. Samples were collected from plants showing vein clearing, mosaic and chlorosis, in the Western Cape province. RNAtag-seq was applied and indicated the presence of CVB in all four sample...

The availability of multiple gene sequences, and in particular full genome sequence data, for microbial strains has changed how taxonomists delineate subspecies belonging to the Archaea and Bacteria. Well-defined phylogenetic lineages that share higher genome similarity values compared to the widely used species thresholds are often described as su...

The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC s...

Samples showing blotchy mottle symptoms were collected from soybeans in NorthWest province, South Africa. The assembly of high-throughput sequencing data from three samples yielded contigs of 13,426 to 13,435nt, which represent the first complete genome sequences of soybean blotchy mosaic virus (SbBMV). SbBMV shows a typical cytorhabdovirus gene or...

The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease and/or mycotoxin contamination on numerous crops. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. W...

Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genome...

Mix'ta. L. fem. n. Mixta the mixed one, referring to the mixed lifestyles of species in the genus. Proteobacteria / Gammaproteobacteria / Enterobacterales / Enterobacteriaceae / Mixta Mixta forms part of the Enterobacteriaceae and contains species of agricultural and clinical importance. The members of this genus exhibit mixed lifestyles and have b...

Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genome...

The mating-type (MAT1) locus encodes transcription factors essential for the onset of the sexual cycle in ascomycete fungi. This locus has been characterised in only a few heterothallic, plant pathogenic Mycosphaerellaceae and Teratosphaeriaceae. We used available genome sequences for Mycosphaerellales species to investigate the presence of two uni...

Ta.tum.el'la N.L. fem. dim. n. Tatumella , named to honor Harvey Tatum, an American bacteriologist who made many contributions to our understanding of the classification and identification of fermentative and nonfermentative bacteria of medical importance. Pseudomonadota / Gammaproteobacteria / Enterobacterales / Enterobacteriaceae / Tatumella The...

Since the discovery of Paraburkholderia tuberum, an indigenous South African species and one of the first beta-rhizobia described, several other South African rhizobial Paraburkholderia species have been recognized. Here, we investigate the taxonomic status of 31 rhizobial isolates from the root nodules of diverse South African legume hosts in the...

Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta

Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were Calobota sericea, Lessertia diffusa, Vachellia karroo, and Wiborgia monoptera, of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos...

Syzygium cordatum (Myrtacease) is one of the most common encountered and widely distributed tree species indigenous to South Africa. This tree is often affected by a malformation disease characterized by grossly misshapen inflorescences that do not bear fruit. Because such symptoms have previously been attributed to Fusarium species in other plants...

Genomic sequence of Fusarium pilosicola

Africa is known for its rich legume diversity with a significant number of endemic species originating in South Africa. Many of these legumes associate with rhizobial symbionts of the genus Bradyrhizobium, of which most represent new species. Yet, none of the Bradyrhizobium species from South Africa have been described. In this study, phylogenetic...

Escherichia coli comprises diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and ass...

Extracellular vesicles (EVs) are subcellular carriers of bioactive compounds with a complex array of functional effects on target cells. In mammals, circulating bodily fluid microbiota EVs (mbEVs) deliver cargo from source cells and adversely or favorably alter the physiology of the same source, neighboring, and distant recipient cells in an autocr...

The isolation of rhizobial strains from the root and stem nodules remains a commonly used method despite its limitations as it enables the identification of mainly dominant symbiotic groups within rhizobial communities. To overcome these limitations, we used genus-specific nifD primers in a culture-independent assessment of Bradyrhizobium communiti...

Fusarium circinatum is an important pathogen of pine trees globally. Despite its economic importance, little is known regarding the molecular processes underlying its pathogenicity and virulence. In this study we explored the potential role of fusaric acid (FA), a known phytotoxin, in the pathogenicity of the fungus. FA is a polyketide secondary me...

erpenes represent the biggest group of natural compounds on earth. This large class of organic hydrocarbons is distributed among all cellular organisms, including fungi. The different classes of terpenes produced by fungi are mono, sesqui, di- and triterpenes, although triterpene ergosterol is the main sterol identified in cell membranes of these o...

Draft genomes of Penicillium roqueforti, Fusarium sororula, Chalaropsis populi, and Chrysoporthe puriensis are presented. Penicillium roqueforti is a model fungus for genetics, physiological and metabolic studies, as well as for biotechnological applications. Fusarium sororula and Chrysoporthe puriensis are important tree pathogens, and Chalaropsis...

Legumes in the Fynbos vegetation of the Western Cape of South Africa have emerged as candidates for domestication, particularly for their adaptation to acidic and infertile soils. However, South African rhizobia have been shown to be very diverse and unique, and a detailed understanding of them is essential to success in forage breeding programs th...

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a slid...

In this study, we investigated to possible role of Ras2 in Fusarium circinatum- a fungus that causes pine pitch canker disease on many different pine species and has a wide geographic distribution. This protein is encoded by the RAS2 gene and has been shown to control growth and pathogenicity in a number of fungi in a mitogen-activated protein kina...

Sexual reproduction is ubiquitous in nature, and nowhere is this more so than in the fungi. Heterothallic behaviour is observed when there is a strict requirement of contact between two individuals of opposite mating-type for sexual reproduction to occur. In contrast, a homothallic species can complete the entire sexual cycle in isolation, although...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Repeat-Induced Point mutations (RIP) serves as a genome defence mechanism that impedes the deleterious consequences of repeated motifs such as transposable elements in fungi. Genomic regions with RIP are biased for adenosine and thymine transitions and the cumulative influence of RIP is thought to have a considerable impact on genome composition. W...

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agr...

Forest pathogens are a major cause of forest disturbances and they have a significant economic impact on commercial forestry. Genomics is an important technology now available for studies concerning tree health, enabling researchers to better understand pathosystems and potentially to prevent future epidemics from occurring. Comparative genomics at...

Nearly all microbes including fungi grow firmly attached to surfaces as a biofilm. Yet, attention towards fungal interactions with plants and the environment is dedicated to free-floating (planktonic) cells. Fungal biofilms are generally thought to configure interactions across and among plant populations. Despite this, plant fungal biofilm researc...

Paraburkholderia youngii sp. nov. and 'Paraburkholderia atlantica'-Brazilian and Mexican Mimosa-associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae, Systematic and Applied Microbiology (2020), Abstract Previous studies have recognized South and Central/Latin American mimosoid legumes in the genera Mimosa, Piptaden...