Publications by authors named "Jolanda Roux"

40 Publications

A new species in the Mycosphaerellaceae from Cecidomyiidae leaf galls on Avicennia marina in South Africa.

Antonie Van Leeuwenhoek 2021 May 28;114(5):515-526. Epub 2021 Feb 28.

Department of Plant and Soil Sciences, DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.

During studies to investigate the health of mangrove trees in South Africa, high numbers of Avicennia marina were found with leaf galls caused by unidentified adults and larvae of midges (Cecidomyiidae). Fungal fruiting structures were commonly observed on the abaxial areas of the galls. To determine the identity of the fungi associated with the gall midges, phylogenetic analyses using multigene sequence data were used. The nuclear large subunit (LSU), internal transcribed spacer (ITS), and a portion of the actin gene region (ACT), were amplified and analyzed. The results revealed that the fungal fruiting structures represent a new taxon in the Mycosphaerellaceae described here as Zasmidium mangrovei sp. nov. This is the first report of a species in the Mycosphaerellaceae associated with cecidomyiid leaf galls on A. marina.
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http://dx.doi.org/10.1007/s10482-021-01537-3DOI Listing
May 2021

Cryphonectriaceae associated with rust-infected in Hawaii.

MycoKeys 2020 31;76:49-79. Epub 2020 Dec 31.

Department of Biochemistry, Genetics and Microbiology, FABI, University of Pretoria, Pretoria 0028, South Africa University of Hawaii at Manoa Honolulu United States of America.

(Myrtales, Myrtaceae) trees in Hawaii are severely affected by a rust disease caused by (Pucciniales, Sphaerophragmiaceae), but they are commonly co-infected with species of Cryphonectriaceae (Diaporthales). In this study, and other trees in the Myrtales were examined on three Hawaiian Islands for the presence of Cryphonectriaceae. Bark samples with fruiting bodies were collected from infected trees and fungi were isolated directly from these structures. Pure cultures were produced and the fungi were identified using DNA sequence data for the internal transcribed spacer (ITS) region, part of the β-tubulin () gene and the transcription elongation factor-1α () gene. Five species in three genera of Cryphonectriaceae were identified from Myrtaceae tree samples. These included , and three previously-unknown taxa described here as sp. nov., sp. nov. and sp. nov. Representative isolates of , , , and were used in artificial inoculation studies to consider their pathogenicity on . , and produced lesions on young trees in inoculation trials, suggesting that, together with , they may contribute to the death of trees. Microsatellite markers were subsequently used to consider the diversity of on the Islands and thus to gain insights into its possible origin in Hawaii. Isolates of this important Myrtaceae and particularly pathogen were found to be clonal. This provides evidence that was introduced to the Hawaiian Islands as a single introduction, from a currently unknown source.
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http://dx.doi.org/10.3897/mycokeys.76.58406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7790811PMC
December 2020

Phytophthora Species Associated with Roots of Native and Non-native Trees in Natural and Managed Forests.

Microb Ecol 2021 Jan 2;81(1):122-133. Epub 2020 Aug 2.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.

Roots act as a biological filter that exclusively allows only a portion of the soil-associated microbial diversity to infect the plant. This microbial diversity includes organisms both beneficial and detrimental to plants. Phytophthora species are among the most important groups of detrimental microbes that cause various soil-borne plant diseases. We used a metabarcoding approach with Phytophthora-specific primers to compare the diversity and richness of Phytophthora species associated with roots of native and non-native trees, using different types of soil inocula collected from native and managed forests. Specifically, we analysed (1) roots of two non-native tree species (Eucalyptus grandis and Acacia mearnsii) and native trees, (2) roots of two non-native tree species from an in vivo plant baiting trial, (3) roots collected from the field versus those from the baiting trial, and (4) roots and soil samples collected from the field. The origin of the soil and the interaction between root and soil significantly influenced Phytophthora species richness. Moreover, species richness and community composition were significantly different between the field root samples and field soil samples with a higher number of Phytophthora species in the soil than in the roots. The results also revealed a substantial and previously undetected diversity of Phytophthora species from South Africa.
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http://dx.doi.org/10.1007/s00248-020-01563-0DOI Listing
January 2021

Poroid Hymenochaetaceae associated with trees showing wood-rot symptoms in the Garden Route National Park of South Africa.

Mycologia 2020 Jul-Aug;112(4):722-741. Epub 2020 Jun 23.

Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria , Pretoria, 0028, South Africa.

Poroid Hymenochaetaceae associated with wood rots of trees in three timber-harvesting compartments of the Garden Route National Park (GRNP), South Africa, were investigated using multilocus phylogenetic analyses and morphology of the basidiomes. Results revealed the presence of 10 species belonging to five genera. Six of the species are known, but four are described as new. The known species include , and . The new species are described as , and .
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http://dx.doi.org/10.1080/00275514.2020.1753160DOI Listing
May 2021

Quantification of Outcrossing Events in Haploid Fungi Using Microsatellite Markers.

J Fungi (Basel) 2020 Apr 14;6(2). Epub 2020 Apr 14.

Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa.

Species in genera of the fungal family Ceratocystidaceae are known to have different mating strategies, including heterothallism and homothallism. Of these, species of , typified by the pathogen all undergo unidirectional mating-type switching. This implies that the pathogens possess the ability to self, but also to undergo sexual outcrossing between isolates of different mating types. In this study, we extended the recently developed microsatellite-based technique to determine the extent to which outcrossing occurs in ascospore masses of haploid fungi to two field collections of . In this way, the role of reproductive strategies in shaping population structure and diversity could be better understood. Results showed that a high frequency of outcrossing occurs in isolates of the pathogen from both non-native and native areas. This explains the high level of genetic diversity previously observed in this population despite the fact that this pathogen has the ability to self.
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http://dx.doi.org/10.3390/jof6020048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7345254PMC
April 2020

Taxonomy and species diversity of species in the Garden Route National Park of South Africa inferred from morphology and multilocus phylogenies.

Mycologia 2019 Sep-Oct;111(5):730-747. Epub 2019 Aug 26.

Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria , Pretoria , 0028 , South Africa.

is a cosmopolitan genus that encompasses species with cultural, economic, and pathogenic importance. Despite the importance of this genus, knowledge pertaining to the species diversity of in South Africa is limited. This study aimed at elucidating the identity and phylogenetic placements of samples obtained during a survey of wood-rotting fungi in the Garden Route National Park (GRNP) of South Africa, supplemented with isolates obtained from other localities across the country. Identification was achieved by means of multilocus phylogenetic inference combined with morphological evaluation. In total, eight distinct species of were recovered from different hosts and localities across the country. Of these, cf. and cf. represent possible new records for South Africa. Two novel species are described, namely, . and , sp. nov., is characterized by a triquetrous and broadly attached basidiome, a sulcate or zonate yellowish brown to brown pilear surface, and ovoid to ellipsoid basidiospores. is distinguished by an applanate to ungulate, sometimes convex, dimidiate to broadly attached basidiome, a chocolate-brown pilear surface covered with a hard woody-like crust and ellipsoid, broadly ellipsoid to ovoid basidiospores. The discovery of two new species in this study raises the known species in South Africa to 13.
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http://dx.doi.org/10.1080/00275514.2019.1635387DOI Listing
March 2020

Nine novel species of Huntiella from southern China with three distinct mating strategies and variable levels of pathogenicity.

Mycologia 2018 Nov-Dec;110(6):1145-1171. Epub 2018 Nov 15.

b China Eucalypt Research Centre , Chinese Academy of Forestry , Zhanjiang 524022, Guangdong Province , China.

The ascomycete genus Huntiella (Microascales) has a cosmopolitan distribution and occurs on a wide range of woody plants. Little is known regarding the identity, diversity, origin, or impact of these fungi in China. Recently, isolates of Huntiella spp. were collected from stumps of freshly felled trees or wounds on plantation-grown Eucalyptus in Guangdong, Guangxi, Fujian, and Hainan provinces of southern China. Additional isolates were obtained from stumps of Acacia confusa near Eucalyptus plantations in Hainan Province. The aim of this study was to identify these Huntiella species and to test their pathogenicity on Eucalyptus seedlings. Morphology and multigene phylogenies of the nuclear rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) region and partial β-tubulin (BT1) and translation elongation factor 1α (TEF1α) genes revealed nine previously unknown Huntiella species, eight from Eucalyptus and one from A. confusa. The mating types of these species were determined, showing that seven are heterothallic, one is homothallic, and one is unisexual (MAT1-2-1 gene). Pathogenicity tests showed that the nine Huntiella species can produce lesions on Eucalyptus seedlings, larger than wounds caused by controls on these plants. This study provides a basic understanding of the distribution, diversity, and pathogenicity of Huntiella species in southern China.
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http://dx.doi.org/10.1080/00275514.2018.1515450DOI Listing
April 2019

Non-Mendelian segregation influences the infection biology and genetic structure of the African tree pathogen Ceratocystis albifundus.

Fungal Biol 2018 04 21;122(4):222-230. Epub 2017 Dec 21.

Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.

The African fungal tree pathogen, Ceratocystis albifundus, undergoes uni-directional mating type switching, giving rise to either self-fertile or self-sterile progeny. Self-sterile isolates lack the MAT1-2-1 gene and have reduced fitness such as slower growth and reduced pathogenicity, relative to self-fertile isolates. While it has been hypothesized that there is a 1:1 ratio of self-fertile to self-sterile ascospore progeny in relatives of C. albifundus, some studies have reported a significant bias in this ratio. This could be due to the fact that either fewer self-sterile ascospores are produced or that self-sterile ascospores have low viability. We quantified the percentage of self-sterile and self-fertile ascospores from ascospore masses in C. albifundus using real-time PCR. Primers were designed to distinguish between spores that contained the MAT1-2-1 gene and those where this gene had been deleted. A significant bias towards the self-fertile mating type was observed in all single ascospore masses taken from sexual structures produced in haploid-selfed cultures. The same result was observed from a disease outbreak situation in an intensively managed field of cultivated native trees, and this was coupled with very low population diversity in the pathogen. This was in contrast to the results obtained from ascospore masses taken from the crosses performed under laboratory conditions or ascomata on native trees in a non-disease situation, where either self-fertile or self-sterile ascospores were dominant. The results suggest that reproductive strategies play a significant role in the infection biology and genetic structure of C. albifundus populations.
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http://dx.doi.org/10.1016/j.funbio.2017.12.008DOI Listing
April 2018

species isolated from plantations and nurseries in South China.

IMA Fungus 2017 Dec 17;8(2):259-286. Epub 2017 Oct 17.

China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), ZhanJiang 524022, GuangDong Province, China.

Diseases caused by species of () represent a serious threat to the growth and sustainability of plantations in China. Symptoms caused by these fungi mainly include leaf blight on trees in plantations and rotting of stems and leaves in nurseries. Extensive surveys have recently been conducted where species were collected in plantations and nurseries in the FuJian, GuangDong, GuangXi, and YunNan Provinces of South China. Additional isolates were baited from soil samples in the Hong Kong Region. The aim of this study was to identify the 115 isolates obtained using comparisons of DNA sequence data for the β-tubulin (), calmodulin (), histone H3 () and partial translation elongation factor-1α () gene regions as well as their morphological features. Seven known species were identified, including , , , , , and . In addition, six novel taxa were collected and are described here as , , , , and spp. nov. Overall, the results reflect a high diversity of species in China.
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http://dx.doi.org/10.5598/imafungus.2017.08.02.04DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729712PMC
December 2017

Phylogenetic species recognition and hybridisation in Lasiodiplodia: A case study on species from baobabs.

Fungal Biol 2017 04 3;121(4):420-436. Epub 2016 Aug 3.

Department of Plant and Soil Sciences, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0083, South Africa. Electronic address:

Lasiodiplodia species (Botryosphaeriaceae, Ascomycota) infect a wide range of typically woody plants on which they are associated with many different disease symptoms. In this study, we determined the identity of Lasiodiplodia isolates obtained from baobab (Adansonia species) trees in Africa and reviewed the molecular markers used to describe Lasiodiplodia species. Publicly available and newly produced sequence data for some of the type strains of Lasiodiplodia species showed incongruence amongst phylogenies of five nuclear loci. We conclude that several of the previously described Lasiodiplodia species are hybrids of other species. Isolates from baobab trees in Africa included nine species of Lasiodiplodia and two hybrid species. Inoculation trials with the most common Lasiodiplodia species collected from these trees produced significant lesions on young baobab trees. There was also variation in aggressiveness amongst isolates from the same species. The apparently widespread tendency of Lasiodiplodia species to hybridise demands that phylogenies from multiple loci (more than two and preferably four or more) are compared for congruence prior to new species being described. This will avoid hybrids being incorrectly described as new taxa, as has clearly occurred in the past.
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http://dx.doi.org/10.1016/j.funbio.2016.07.014DOI Listing
April 2017

Overlap of latent pathogens in the Botryosphaeriaceae on a native and agricultural host.

Fungal Biol 2017 04 6;121(4):405-419. Epub 2016 Aug 6.

Department of Microbiology and Plant Pathology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.

Some species of the Botryosphaeriaceae are capable of infecting a broad range of host plants. We studied the species diversity of Botryosphaeriaceae associated with marula (Sclerocarya birrea subsp. caffra, Anacardiaceae) trees in South Africa over two seasons, as well as species common to both S. birrea and adjacent mango (Mangifera indica, Anacardiaceae) trees in a subset of sites. Gene flow amongst populations of Botryosphaeriaceae shared on these tree species was tested using microsatellite markers. Twelve species were identified from S. birrea and eleven species were found on M. indica trees. From isolations done in 2006, the dominant species on S. birrea was Neofusicoccum vitifusiforme, while N. parvum was the dominant species isolated from M. indica. Neofusicoccum parvum was dominant in isolations from both hosts in 2012. Isolates of Botryosphaeria fabicerciana, Lasiodiplodia mahajangana, L. pseudotheobromae, L. theobromae, N. mediterraneum, and N. umdonicola were also collected from both hosts. Population genetic analyses on isolates of N. parvum suggested that three populations were present, each comprising isolates from both hosts. There was significant gene flow between N. parvum populations on these hosts. This ability to infect multiple hosts and to migrate amongst them facilitates the establishment and spread of species and genotypes of the Botryosphaeriaceae, such as N. parvum, in new areas.
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http://dx.doi.org/10.1016/j.funbio.2016.07.015DOI Listing
April 2017

Endophytic Botryosphaeriaceae, including five new species, associated with mangrove trees in South Africa.

Fungal Biol 2017 04 21;121(4):361-393. Epub 2016 Sep 21.

Department of Plant and Soil Sciences, DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa. Electronic address:

Little is known regarding the fungi, especially fungal pathogens, associated with mangroves in Africa. This includes fungi in the Botryosphaeriaceae that comprise numerous opportunistic, stress-associated pathogens often associated with trees affected by environmental and anthropogenically generated stresses, such as those affecting mangroves. We investigated the occurrence of endophytic Botryosphaeriaceae along the entire distribution of mangroves in South Africa. Asymptomatic branches were collected from ten localities and six mangrove species. Isolates resembling species of Botryosphaeriaceae were identified based on multi-gene sequence data of the internal transcribed spacer regions (ITS), including the 5.8S nrRNA, the beta-tubulin (tub2), partial translation elongation factor 1-alpha (tef1-α), and DNA-directed RNA polymerase II second largest subunit (rpb2) gene regions. Inoculation trials were conducted on healthy branches of Avicennia marina and Bruguiera gymnorrhiza to evaluate the potential pathogenicity of the collected species. Fourteen species in the Botryosphaeriaceae belonging to four genera, Botryosphaeria, Diplodia, Lasiodiplodia, and Neofusicoccum were collected, including five new species. Neofusicoccum was the most prevalent genus followed by Lasiodiplodia, with species of Diplodia and Botryosphaeria being the least frequent. The inoculation studies revealed that one of the new species, Lasiodiplodia avicenniae is highly pathogenic to A. marina and could pose a threat to the health of these trees.
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http://dx.doi.org/10.1016/j.funbio.2016.09.004DOI Listing
April 2017

Ecology and population structure of a tree wound-infecting fungus in a native South African forest environment.

Fungal Biol 2017 01 16;121(1):69-81. Epub 2016 Sep 16.

Department of Plant and Soil Sciences, FABI, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa. Electronic address:

Ceratocystis tsitsikammensis was first isolated from bark harvesting wounds on two indigenous tree species in the Afromontane forests of the Western Cape Province of South Africa. Inoculation studies indicated that it is a potential pathogen of native Rapanea melanophloeos trees. In this study, we investigated the distribution, ecology and biology of C. tsitsikammensis in the Garden Route National Park of South Africa. Isolates were obtained from wounds on R. melanophloeos, three non-native hosts as well as from nitidulid and staphylinid beetles visiting wounds on these trees. The genetic diversity and population biology of the fungus was examined using microsatellite markers. Its mating strategy was also determined by amplifying its mating type genes and the fungus was shown to be homothallic. Despite the homothallic nature of the fungus, high levels of random mating and absence of genetic structure was found in the investigated population, suggesting a strong effect of gene flow, probably linked to insect dispersal. The gene diversity of C. tsitsikammensis was similar to that of a related fungus, Ceratocystis albifundus, that is known to be native in Africa. This, together with the fact that C. tsitiskamensis is not known elsewhere, within or outside South Africa, suggests that it is native and endemic to the Cape Afromontane region.
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http://dx.doi.org/10.1016/j.funbio.2016.09.002DOI Listing
January 2017

Ophiostomatoid fungi associated with mangroves in South Africa, including Ophiostoma palustre sp. nov.

Antonie Van Leeuwenhoek 2016 Dec 25;109(12):1555-1571. Epub 2016 Aug 25.

Department of Plant and Soil Sciences, DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, Gauteng, South Africa.

Mangrove trees are continuously under stress due to environmental and/or anthropogenic pressures, which expose them to attack by pathogens, compromising their survival. Ophiostomatoid fungi cause sap stain and diseases of a wide spectrum of tree species globally. These fungi infect trees through natural, insect, animal and/or human made wounds. During routine surveys of mangrove trees in South Africa, wounds on branches and stems of Avicennia marina were regularly monitored for the presence of ophiostomatoid fungi at ten study sites in the country. The stems of four mangrove species, A. marina, Bruguiera gymnorrhiza, Rhizophora mucronata and Barringtonia racemosa were also wounded and evaluated for the appearance of these fungi. Ophiostomatoid fungi were obtained from the mangrove associate B. racemosa, but not from any of the true mangroves. Analyses of DNA sequence data for the internal transcribed spacer, β-tubulin, calmodulin and translation elongation factor gene regions revealed that the fungi isolated from the wounds on B. racemosa belong to three species in the Ophiostomataceae, including a new taxon described here as Ophiostoma palustre sp. nov. These results suggest that the mangrove associate B. racemosa is more prone to colonization by ophiostomatoid fungi than the true mangroves.
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http://dx.doi.org/10.1007/s10482-016-0757-7DOI Listing
December 2016

Endophytic Cryphonectriaceae on native Myrtales: Possible origin of Chrysoporthe canker on plantation-grown Eucalyptus.

Fungal Biol 2016 Jun-Jul;120(6-7):827-35. Epub 2016 Mar 22.

Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa. Electronic address:

Chrysoporthe austroafricana (Cryphonectriaceae) is a damaging canker pathogen on Eucalyptus species in Southern Africa. Recent studies have shown that the fungus occurs on native Syzygium species and that it has apparently undergone a host range expansion from these native trees to infect non-native Eucalyptus. The aim of this study was to consider whether Chr. austroafricana and other Cryphonectriaceae might exist as endophytes in native Myrtaceae, providing a source of inoculum to infect non-native Myrtales. Healthy branches were collected from Myrtaceae in Mozambique, incubated in florist foam, allowed to dry gradually and monitored for the appearance of fruiting bodies resembling species in the Cryphonectriaceae. Isolates were identified based on DNA sequence data. Two species in the Cryphonectriaceae were obtained, representing the first evidence that species in the Cryphonectriaceae occur as endophytes on native Myrtales, thus providing a source of inoculum to infect non-native and susceptible trees. This has important implications regarding the movement of planting stock used by ornamental tree and forestry enterprises.
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http://dx.doi.org/10.1016/j.funbio.2016.03.005DOI Listing
September 2017

Fungal Genomics Challenges the Dogma of Name-Based Biosecurity.

PLoS Pathog 2016 05 5;12(5):e1005475. Epub 2016 May 5.

Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Brisbane, Queensland, Australia.

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http://dx.doi.org/10.1371/journal.ppat.1005475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858198PMC
May 2016

The genetic landscape of Ceratocystis albifundus populations in South Africa reveals a recent fungal introduction event.

Fungal Biol 2016 05 11;120(5):690-700. Epub 2016 Mar 11.

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa. Electronic address:

Geographical range expansion or host shifts is amongst the various evolutionary forces that underlie numerous emerging diseases caused by fungal pathogens. In this regard, Ceratocystis albifundus, the causal agent of a serious wilt disease of Acacia mearnsii trees in Africa, was recently identified killing cultivated Protea cynaroides in the Western Cape (WC) Province of South Africa. Protea cynaroides is an important native plant in the area and a key component of the Cape Floristic Region. The appearance of this new disease outbreak, together with isolates of C. albifundus from natural ecosystems as well as plantations of nonnative trees, provided an opportunity to consider questions relating to the possible origin and movement of the pathogen in South Africa. Ten microsatellite markers were used to determine the genetic diversity, population structure, and possible gene flow in a collection of 193 C. albifundus isolates. All populations, other than those from the WC, showed high levels of genetic diversity. An intermediate level of gene flow was found amongst populations of the pathogen. The results suggest that a limited number of individuals have recently been introduced into the WC, resulting in a novel disease problem in the area.
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http://dx.doi.org/10.1016/j.funbio.2016.03.001DOI Listing
May 2016

Novel ophiostomatalean fungi from galleries of Cyrtogenius africus (Scolytinae) infesting dying Euphorbia ingens.

Antonie Van Leeuwenhoek 2016 Apr 3;109(4):589-601. Epub 2016 Feb 3.

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.

Euphorbia ingens trees have been dying in large numbers in the Limpopo Province of South Africa for approximately 15 years. The ambrosia beetle Cyrtogenius africus is often found infesting diseased and dying trees. The aim of this study was to identify the ophiostomatoid fungi occurring in the galleries of C. africus. Logs infested with this beetle were collected from the KwaZulu-Natal, Limpopo, Mpumalanga, and North West Provinces of South Africa. Fungi belonging to the Ophiostomatales were identified based on morphology and comparison of sequence data for the β-tubulin, ITS1-5.8S-ITS2 and LSU gene regions. A novel species of Ophiostoma and a novel genus in the Ophiostomatales were identified. Inoculation studies with these fungi produced lesions in the branches of healthy E. ingens trees.
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http://dx.doi.org/10.1007/s10482-016-0661-1DOI Listing
April 2016

Three genetic groups of the Eucalyptus stem canker pathogen Teratosphaeria zuluensis introduced into Africa from an unknown source.

Antonie Van Leeuwenhoek 2016 Jan 24;109(1):21-33. Epub 2015 Oct 24.

Department of Microbiology and Plant Pathology, FABI, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.

The Eucalyptus stem canker pathogen Teratosphaeria zuluensis was discovered in South Africa in 1988 and it has subsequently been found in several other African countries as well as globally. In this study, the population structure, genetic diversity and evolutionary history of T. z uluensis were analysed using microsatellite markers to gain an enhanced understanding of its movement in Africa. Isolates were collected from several sites in Malawi, Mozambique, Uganda and Zambia. Data obtained were compared with those previously published for a South African population. The data obtained from 334 isolates, amplified across eight microsatellite loci, were used for assignment, differentiation and genetic diversity tests. STRUCTURE analyses, θ st and genetic distances revealed the existence of two clusters, one dominated by isolates from South Africa and the other by isolates from the Zambezi basin including Malawi, Mozambique and Zambia. High levels of admixture were found within and among populations, dominated by the Mulanje population in Malawi. Moderate to low genetic diversity of the populations supports the previously held view that the pathogen was introduced into Africa. The clonal nature of the Ugandan population suggests a very recent introduction, most likely from southern Africa.
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http://dx.doi.org/10.1007/s10482-015-0606-0DOI Listing
January 2016

Independent origins and incipient speciation among host-associated populations of Thielaviopsis ethacetica in Cameroon.

Fungal Biol 2015 Nov 16;119(11):957-972. Epub 2015 Jun 16.

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20 Hatfield, University of Pretoria, Pretoria 0028, South Africa. Electronic address:

Thielaviopsis ethacetica was recently reinstated as a distinct taxon using DNA phylogenies. It is widespread affecting several crop plants of global economic importance. In this study, microsatellite markers were developed and used in conjunction with sequence data to investigate the genetic diversity and structure of Th. ethacetica in Cameroon. A collection of 71 isolates from cacao, oil palm, and pineapple, supplemented with nine isolates from other countries were analysed. Four genetic groups were identified. Two of these were associated with oil palm in Cameroon and showed high genetic diversity, suggesting that they might represent an indigenous population of the pathogen. In contrast, the remaining two groups, associated with cacao and pineapple, had low genetic diversity and, most likely, represent introduced populations. There was no evidence of gene flow between these groups. Phylogenetic analyses based on sequences of the tef1-α as well as the combined flanking regions of six microsatellite loci were consistent with population genetic analyses and suggested that Th. ethacetica is comprised of two divergent genetic lineages.
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http://dx.doi.org/10.1016/j.funbio.2015.05.009DOI Listing
November 2015

Host jumps shaped the diversity of extant rust fungi (Pucciniales).

New Phytol 2016 Feb 13;209(3):1149-58. Epub 2015 Oct 13.

Department of Microbiology and Plant Pathology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.

The aim of this study was to determine the evolutionary time line for rust fungi and date key speciation events using a molecular clock. Evidence is provided that supports a contemporary view for a recent origin of rust fungi, with a common ancestor on a flowering plant. Divergence times for > 20 genera of rust fungi were studied with Bayesian evolutionary analyses. A relaxed molecular clock was applied to ribosomal and mitochondrial genes, calibrated against estimated divergence times for the hosts of rust fungi, such as Acacia (Fabaceae), angiosperms and the cupressophytes. Results showed that rust fungi shared a most recent common ancestor with a mean age between 113 and 115 million yr. This dates rust fungi to the Cretaceous period, which is much younger than previous estimations. Host jumps, whether taxonomically large or between host genera in the same family, most probably shaped the diversity of rust genera. Likewise, species diversified by host shifts (through coevolution) or via subsequent host jumps. This is in contrast to strict coevolution with their hosts. Puccinia psidii was recovered in Sphaerophragmiaceae, a family distinct from Raveneliaceae, which were regarded as confamilial in previous studies.
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http://dx.doi.org/10.1111/nph.13686DOI Listing
February 2016

Fungi associated with black mould on baobab trees in southern Africa.

Antonie Van Leeuwenhoek 2015 Jul 3;108(1):85-95. Epub 2015 May 3.

Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Sciences, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa,

There have been numerous reports in the scientific and popular literature suggesting that African baobab (Adansonia digitata) trees are dying, with symptoms including a black mould on their bark. The aim of this study was to determine the identity of the fungi causing this black mould and to consider whether they might be affecting the health of trees. The fungi were identified by sequencing directly from mycelium on the infected tissue as well as from cultures on agar. Sequence data for the ITS region of the rDNA resulted in the identification of four fungi including Aureobasidium pullulans, Toxicocladosporium irritans and a new species of Rachicladosporium described here as Rachicladosporium africanum. A single isolate of an unknown Cladosporium sp. was also found. These fungi, referred to here as black mould, are not true sooty mould fungi and they were shown to penetrate below the bark of infected tissue, causing a distinct host reaction. Although infections can lead to dieback of small twigs on severely infected branches, the mould was not found to kill trees.
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http://dx.doi.org/10.1007/s10482-015-0466-7DOI Listing
July 2015

New Ceratocystis species from Eucalyptus and Cunninghamia in South China.

Antonie Van Leeuwenhoek 2015 Jun 4;107(6):1451-73. Epub 2015 Apr 4.

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.

During routine surveys for possible fungal pathogens in the rapidly expanding plantations of Eucalyptus and Cunninghamia lanceolata in China, numerous isolates of unknown species in the genus Ceratocystis (Microascales) were obtained from tree wounds. In this study we identified the Ceratocystis isolates from Eucalyptus and Cunninghamia in the GuangDong, GuangXi, FuJian and HaiNan Provinces of South China based on morphology and through comparisons of DNA sequence data for the ITS, partial β-tubulin and TEF-1α gene regions. Morphological and DNA sequence comparisons revealed two previously unknown species residing in the Indo-Pacific Clade. These are described here as Ceratocystis cercfabiensis sp. nov. and Ceratocystis collisensis sp. nov. Isolates of Ceratocystis cercfabiensis showed intragenomic variation in their ITS sequences and four strains were selected for cloning of the ITS gene region. Twelve ITS haplotypes were obtained from 17 clones selected for sequencing, differing in up to seven base positions and representing two separate phylogenetic groups. This is the first evidence of multiple ITS types in isolates of Ceratocystis residing in the Indo-Pacific Clade. Caution should thus be exercised when using the ITS gene region as a barcoding marker for Ceratocystis species in this clade. This study also represents the first record of a species of Ceratocystis from Cunninghamia.
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http://dx.doi.org/10.1007/s10482-015-0441-3DOI Listing
June 2015

Reconsidering species boundaries in the Ceratocystis paradoxa complex, including a new species from oil palm and cacao in Cameroon.

Mycologia 2014 Jul-Aug;106(4):757-84. Epub 2014 Jul 1.

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20, University of Pretoria, Pretoria, 0028, South Africa

The Ceratocystis paradoxa complex accommodates a group of fungal pathogens that have become specialized to infect mostly monocotyledonous plants. Four species currently are recognized in this group, including C. paradoxa, which has a widespread distribution and broad host range. In this study, multigene phylogenetic analyses involving sequences of the ITS, β-tubulin and TEF-1α gene loci, in combination with phenotypic and mating studies, were used to characterize purported C. paradoxa isolates from Cameroon and to compare them with isolates from elsewhere, including protologs and type specimens of known species. We show that the C. paradoxa complex comprises substantially greater species diversity than previously recognized. One new species in this group is described from Cameroon as Ceratocystis cerberus, while C. paradoxa sensu stricto (s. str.) and four other species are redefined. Lectotypes are designated for C. ethacetica and Endoconidium fragrans (synonym of C. ethacetica), while epitypes are designated for C. paradoxa s. str., C. ethacetica and C. musarum. A neotype is designated for Catenularia echinata (synonym of C. ethacetica) and two species, previously treated in Thielaviopsis, are transferred to Ceratocystis.
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http://dx.doi.org/10.3852/13-298DOI Listing
October 2014

Bark and ambrosia beetles (Curculionidae: Scolytinae), their phoretic mites (Acari) and associated Geosmithia species (Ascomycota: Hypocreales) from Virgilia trees in South Africa.

Fungal Biol 2014 May-Jun;118(5-6):472-83. Epub 2014 Apr 3.

DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), Forestry and Agricultural Biotechnology Institute (FABI), Department of Microbiology and Plant Pathology, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa; Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa. Electronic address:

Bark and ambrosia beetles are ecologically and economically important phloeophagous insects that often have complex symbiotic relationships with fungi and mites. These systems are greatly understudied in Africa. In the present study we identified bark and ambrosia beetles, their phoretic mites and their main fungal associates from native Virgilia trees in the Cape Floristic Region (CFR) of South Africa. In addition, we tested the ability of mites to feed on the associated fungi. Four species of scolytine beetles were collected from various Virgilia hosts and from across the CFR. All were consistently associated with various Geosmithia species, fungi known from phloeophagous beetles in many parts of the world, but not yet reported as Scolytinae associates in South Africa. Four beetle species, a single mite species and five Geosmithia species were recovered. The beetles, Hapalogenius fuscipennis, Cryphalini sp. 1, and Scolytoplatypus fasciatus were associated with a single species of Elattoma phoretic mite that commonly carried spores of Geosmithia species. Liparthrum sp. 1 did not carry phoretic mites. Similar to European studies, Geosmithia associates of beetles from Virgilia were constant over extended geographic ranges, and species that share the same host plant individual had similar Geosmithia communities. Phoretic mites were unable to feed on their Geosmithia associates, but were observed to feed on bark beetle larvae within tunnels. This study forms the first African-centred base for ongoing global studies on the associations between arthropods and Geosmithia species. It strengthens hypotheses that the association between Scolytinae beetles and dry-spored Geosmithia species may be more ubiquitous than commonly recognised.
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http://dx.doi.org/10.1016/j.funbio.2014.03.006DOI Listing
January 2015

The Myrtle rust pathogen, Puccinia psidii, discovered in Africa.

IMA Fungus 2013 Jul 24;4(1):155-9. Epub 2013 Jun 24.

Forestry and Agricultural Biotechnology Institute (FABI), Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa.

Puccinia psidii, the cause of a disease today commonly referred to as Myrtle rust, is considered a high priority quarantine threat globally. It has a wide host range in the Myrtaceae and it is feared that it may result in significant damage to native ecosystems where these plants occur. The fungus is also of considerable concern to plantation forestry industries that propagate Australian Eucalyptus species. In May 2013, symptoms of a rust disease resembling those of P. psidii were observed on an ornamental Myrtaceous shrub in a garden in South Africa. The fungus was identified based on DNA sequence data of the ITS and 5.8S nrRNA gene regions and here we report, for the first time, the presence of P. psidii in Africa.
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http://dx.doi.org/10.5598/imafungus.2013.04.01.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719202PMC
July 2013

Diversimorbus metrosiderotis gen. et sp. nov. and three new species of Holocryphia (Cryphonectriaceae) associated with cankers on native Metrosideros angustifolia trees in South Africa.

Fungal Biol 2013 May 22;117(5):289-310. Epub 2013 Mar 22.

DST/NRF Centre of Excellence in Tree Health Biotechnology-CTHB, Forestry and Agricultural Biotechnology Institute-FABI, Department of Microbiology and Plant Pathology, Private Bag X20, University of Pretoria, Pretoria 0028, South Africa.

The Cryphonectriaceae includes important tree pathogens, especially on the Myrtales. During a routine disease survey in the Western Cape Province of South Africa, a fungus resembling the Eucalyptus pathogen Holocryphia eucalypti was observed on native Metrosideros angustifolia (Myrtales). The aims of this study were to identify the fungus and to expand surveys for fungi in the Cryphonectriaceae on M. angustifolia. Fungi were identified based on DNA sequence comparisons and morphological features, and their pathogenicity was tested on M. angustifolia under field conditions. Based on morphology and multigene phylogenetic analyses of DNA sequence data from six gene regions, we describe a new genus including a single species and three new species of Holocryphia (Cryphonectriaceae) from M. angustifolia. These fungi are provided with the names Diversimorbus metrosiderotis gen. et sp. nov., Holocryphia capensis sp. nov., Holocryphia gleniana sp. nov., and Holocryphia mzansi sp. nov. We also revise H. eucalypti, the type of the genus, to include only isolates from Eucalyptus in South Africa. Research results indicated that H. mzansi may undergo host shifts between different tree genera in the Myrtaceae. Inoculation tests showed that isolates of all the newly described species can cause lesions on the branches of M. angustifolia, indicating that they are all pathogens of this tree.
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http://dx.doi.org/10.1016/j.funbio.2013.02.005DOI Listing
May 2013

Species delineation in the tree pathogen genus Celoporthe (Cryphonectriaceae) in southern Africa.

Mycologia 2013 Mar-Apr;105(2):297-311. Epub 2012 Dec 11.

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.

The genus Celoporthe was first described when C. dispersa was discovered in South Africa associated with dieback and cankers on trees in the Myrtales. Four additional species were recently described from Eucalyptus and Syzygium cumini in China as well as S. aromaticum and Eucalyptus in Indonesia. Inoculation trials have shown that all Celoporthe species, including those that have not been found on Eucalyptus species in nature, are pathogenic to Eucalyptus and they are thus potentially threatening to commercial Eucalyptus forestry. New isolates, morphologically similar to Celoporthe, have been collected from S. legatti in South Africa and S. guineense in Zambia. Multigene phylogenetic analyses based on DNA sequences of the ITS region, TEF1α gene and two areas of the β-tubulin gene revealed additional cryptic species in Celoporthe. Phylogenetic data were supported by morphological differences. These resulted in the description of two previously unknown species of Celoporthe, namely C. fontana and C. woodiana, for two of these cryptic groups, while the third group represented C. dispersa. These species all can readily infect Eucalyptus as well as several species of Syzygium, the latter of which are native to Africa.
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http://dx.doi.org/10.3852/12-206DOI Listing
June 2014

Ceratocystis eucalypticola sp. nov. from Eucalyptus in South Africa and comparison to global isolates from this tree.

IMA Fungus 2012 Jun 21;3(1):45-58. Epub 2012 Jun 21.

Department of Genetics, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, Pretoria, South Africa.

Eucalyptus trees, mostly native to Australia, are widely planted in the tropics and Southern Hemisphere for the production of wood and pulp. Worldwide surveys of diseases on these trees have yielded a large collection of Ceratocystis isolates from dying trees or from wounds on their stems. The aim of this study was to characterise these isolates and to consider their relatedness to each other. Culture appearance, morphological features and a distinctive fruity odour in all cultures were typical of species in the Ceratocystis fimbriatasensu lato (s. lat.) complex. Phylogenetic analyses of sequences for the combined ITS, βt-1 and TEF1-α gene regions revealed a genetically diverse group of isolates residing in a single large clade, that were distinct from all other species in the C. fimbriatas. lat. complex. Based on morphology and phylogenetic inference, the Eucalyptus isolates are recognised as closely related. The South African isolates are described here as a new species, C. eucalypticola.
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http://dx.doi.org/10.5598/imafungus.2012.03.01.06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399102PMC
June 2012

High gene flow and outcrossing within populations of two cryptic fungal pathogens on a native and non-native host in Cameroon.

Fungal Biol 2012 Mar 27;116(3):343-53. Epub 2011 Dec 27.

Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa.

In this study, we determined the genetic diversity of 126 isolates representing both Lasiodiplodia theobromae and Lasiodiplodia pseudotheobromae, collected from Theobroma cacao and Terminalia spp. in Cameroon, using simple sequence repeat (SSR) markers. SSR alleles showed clear genetic distinction between L. theobromae and L. pseudotheobromae, supporting their earlier separation as sister species. Both L. theobromae and L. pseudotheobromae populations from Cameroon had high levels of gene diversity, moderate degrees of genotypic diversity, and high levels of gene flow between isolates from T. cacao and Terminalia spp. There was no evidence for geographic substructure in these populations across the region studied, and the SSR alleles were randomly associated in both species, suggesting outcrossing. The significant levels of aggressiveness, evolutionary potential represented by high levels of diversity, outcrossing and gene flow between geographically and host defined populations, identify these fungi as high-risk pathogens for their native and non-native hosts in Cameroon.
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http://dx.doi.org/10.1016/j.funbio.2011.12.001DOI Listing
March 2012