Taxonomy and phylogeny of Cryphonectria and allied genera

This thesis represents a critical taxonomical review of the fungal genus Cryphonectria sensu lato. An appropriate taxonomy for this group is of great importance because it includes many well known tree pathogens such as the chestnut blight fungus Cryphonectria parasitica and the Eucalyptus canker pathogen Cryphonectria cubensis. The many taxonomic changes introduced in studies presented in this thesis have largely arisen as a result of DNA sequence comparisons for Cryphonectria spp. that show that Cryphonectria sensu lato is comprised of different lineages, strongly supported by robust morphological characteristics. New taxa, of which many are pathogenic, have also been discovered. The expanded number of species of Cryphonectria and related genera as well as the consideration of large numbers of isolates has furthermore made it possible to establish a broad view of the group at the super-generic level. The first part of the thesis deals with studies on Cryphonectria cubensis. A new genus Chrysoporthe is described for C. cubensis sensu lato. Two additional species are also described for phylogenetic sub-clades previously known as C. cubensis. These include Chrysoporthe austroafricana, representing all isolates from South Africa, and an anamorphic species described in the new genus Chrysoporthella as Chrysop. hodgesiana, which is currently only known from Colombia on native Tibouchina spp. Isolate collections from several new host genera for Chr. cubensis are also characterized. Collections from Eucalyptus in Cuba, now representing the epitype of Chr. cubensis, also define the type of Chr. cubensis as residing in the South American sub-clade. Another new species, Chrysoporthe inopima from Tibouchina lepidota in Colombia is described as well as a new species Chrysoporthe doradensis for isolates from Eucalyptus spp. in Ecuador. A new family Cryphonectriaceae is described in this thesis for Cryphonectria, Chrysoporthe and Endothia. Genera in this family are united by orange stromatic tissue, with the pigments colouring purple in 3% KOH and yellow in lactic acid. The existence of this new family confirms the close relationship of Cryphonectria and morphologically similar genera. A proposal to conserve the name Cryphonectria against the new type C. parasitica is presented. This is required because Cryphonectria gyrosa, the currently accepted type, was erroneously used as type. The conservation of Cryphonectria against C. parasitica made it possible to describe the new genus Amphilogia for C. gyrosa. Amphilogia also includes a second species from New Zealand described as Amphilogia major, although no isolates currently exist for this species. New genera for existing Cryphonectria spp., as well as newly discovered fungi are presented in this thesis. The new genus Rostraureum is established for a fungus pathogenic on Terminalia ivorensis in Ecuador. This fungus also represents a new species, Rostraureum tropicale. Cryphonectria longirostris, originating from Puerto Rico, Trinidad and Tabago, is also transferred to Rostraureum. A fungus morphologically similar to Chrysoporthe on native Tibouchina, Miconia and exotic Eucalyptus spp. in Colombia, is described as Aurapex penicillata gen. sp. nov. Cryphonectria havanensis is transferred to the new genus Microthia. Cryphonectria coccolobae also resides in this genus based on morphology, although its phylogenetic relationship to C. havanensis could not be confirmed due the absence of isolates. A new fungus was discovered during surveys for C. coccolobae on Coccoloba uvifera in Florida, which is described in the new genus Ursicollum as U. fallax. Phylogenetic analyses in this study also clearly distinguish Cryphonectria eucalypti from Cryphonectria, and this fungus is thus transferred to the new genus Holocryphia. A minireview is presented at the end of the thesis and discusses the new taxonomic concepts developed for Cryphonectria during this thesis, and recent studies by other authors. The review describes how this new taxonomic scheme has changed our view and understanding of the distribution and ecology of Cryphonectria sensu stricto from what it has traditionally been seen. The final part of the thesis is written in the form of a monograph. It contains background information of all the species, including many pathogens, currently known in Cryphonectria and allied genera. The majority of these have recently been described, some in this thesis, and this chapter thus contains all recent information pertaining to them. It is intended that this monograph should be useful as a manual, enabling users to work with and isolate these fungi and to identify the different taxa based on morphology and phylogenetic relationships. The studies presented in this thesis greatly change the taxonomy of Cryphonectria sensu lato, which is now seen as representing a large number of genera and species in a new family. Many would argue that Cryphonectria is still monophyletic, but the different lineages shown by DNA sequence comparisons are morphologically inordinately diverse, and clearly represent different genera. Studies presented in this thesis further suggest that additional genera await description from diverse geographical areas and ecological niches. The studies presented in this thesis will hopefully provide a foundation against which these new taxa can be compared and will improve our understanding of tree diseases.Thesis (PhD)--University of Pretoria, 2009.Microbiology and Plant PathologyUnrestricte

New and rare coelomycetes with appendage-bearing conidia from Pondoland, South Africa

During a mycological excursion to the Pondoland region of South Africa in 2008, six interesting anamorphic fungi with appendage-bearing conidia were isolated. They are Bartalinia pondoensis, Crucellisporium umtamvunae, and Mycohypallage margaretae, all of which are new to science, Mycohypallage congesta with a new observation of gelatinous basal appendage, Mycotribulus mirabilis on a new host plant, Apodytes, and Chaetospermum camelliae. Morphological characters are described and notes provided. The teleomorphic affinity of C. umtamvunae to the Helotiales is proposed based on DNA sequence data.http://www.mycotaxon.com

Five new species of the Botryosphaeriaceae from Acacia karroo in South Africa

The Botryosphaeriaceae represents an important, cosmopolitan family of latent pathogens infecting woody plants. Recent studies on native trees in southern Africa have revealed an extensive diversity of species of Botryosphaeriaceae, about half of which have not been previously described. This study adds to this growing body of knowledge, by discovering five new species of the Botryosphaeriaceae on Acacia karroo, a commonly occurring native tree in southern Africa. These species were isolated from both healthy and diseased tissues, suggesting they could be latent pathogens. The isolates were characterized based on their morphology and compared to other species for which DNA sequence data are available, in phylogenetic analyses based on the ITS, TEF-1α, β-tubulin and LSU gene regions. The five new species were described as Diplodia allocellula, Dothiorella dulcispinae, Do. brevicollis, Spencermartinsia pretoriensis and Tiarosporella urbis-rosarum. Evidence emerging from this study suggests that many more species of the Botryosphaeriaceae remain to be discovered in the southern Africa.Members of the Tree Protection Cooperative Programme (TPCP), the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and the University of Pretoria, South Africa.http://www.cryptogamie.com/pagint_en/recherche/affich_sommaire.php?cnumero=65hb201

Celoporthe dispersa gen. et sp. nov. from native Myrtales in South Africa

In a survey for Cryphonectria and Chrysoporthe species on Myrtales in South Africa, a fungus resembling the stem canker pathogen Chrysoporthe austroafricana was collected from native Syzygium cordatum near Tzaneen (Limpopo Province), Heteropyxis canescens near Lydenburg (Mpumalanga Province) and exotic Tibouchina granulosa in Durban (KwaZulu-Natal Province). The fungus was associated with dying branches and stems on S. cordatum, H. canescens and T. granulosa. However, morphological differences were detected between the unknown fungus from these three hosts and known species of Chrysoporthe. The aim of this study was to characterise the fungus using DNA sequence comparisons and morphological features. Pathogenicity tests were also conducted to assess its virulence on Eucalyptus (ZG 14 clones), H. natalensis and T. granulosa. Plants of H. canescens were not available for inoculation. Results showed distinct morphological differences between the unknown fungus and Chrysoporthe spp. Phylogenetic analysis showed that isolates reside in a clade separate from Chrysoporthe and other related genera. Celoporthe dispersa gen. et sp. nov. is, therefore, described to accommodate this fungus. Pathogenicity tests showed that C. dispersa is not pathogenic to H. natalensis, but that it is a potential pathogen of Eucalyptus and Tibouchina spp

Population structure of Chrysoporthe austroafricana in southern Africa determined using Vegetative Compatibility Groups (VCGs)

Chrysoporthe austroafricana is one of the most damaging pathogens of Eucalyptus trees in southern Africa. It also occurs on non-native Tibouchina granulosa trees and native Syzygium species. Additional isolates of the pathogen from previously unstudied countries in the region have become available from survey studies. The aim of this study was to use VCGs to consider the diversity in populations of isolates collected in various countries in southern Africa (Malawi, Mozambique, Namibia, South Africa and Zambia) and from different hosts. We also wanted to determine whether there are shared VCGs among these countries and hosts in southern Africa and establish a VCG tester strain data base. Results showed a high diversity amongst isolates from different countries and hosts, but suggested little movement of VCGs among countries or hosts based on the available isolates. A total of 108 VCG tester strains were identified for southern Africa.The University of Pretoria (UP), National Research Foundation (NRF), Forestry and Agricultural Biotechnology Institute (FABI) and Tree Protection Cooperative Program (TPCP).http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1439-0329hb2016Microbiology and Plant Patholog

Botryosphaeriaceae species overlap on four unrelated, native South African hosts

Botryosphaeriaceae represents an important and diverse family of latent fungal pathogens of woody plants. We address the question of host range of these fungi by sampling leaves and branches of four native South African trees, including Acacia karroo (Fabaceae), Celtis africana (Cannabaceae), Searsia lancea (Anacardiaceae), and Gymnosporia buxifolia (Celastraceae).Twonew species of the Botryosphaeriaceae, namely Tiarosporella africana sp. nov. and Aplosporella javeedii sp. nov. were identified, together with fiveknown species, including Neofusicoccum parvum, Neofusicoccum kwambonambiense, Spencermartinsia viticola, Diplodia pseudoseriata, and Botryosphaeria dothidea. Most Botryosphaeriaceae occurred on more than one host. With the exception of S. lancea, which was infected by A. javeedii all the hosts were infected by more than one Botryosphaeriaceae species. Collectively, the results suggest that some intrinsic host factors, possibly combined with local environmental conditions, affect the distribution and co-infectivity of various hosts by the Botryosphaeriaceae. This would counteract the general ability of a species in the Botryosphaeriaceae to infect a broad range of plants. The combination of host and environmental factors might also explain why some Botryosphaeriaceae with apparently broad host ranges, are found on different suites of hosts in different areas of the world.Tree Protection Cooperative Programme (TPCP), the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and the University of Pretoria, South Africa.http://www.elsevier.com/locate/funbiohb201

Microthia, Holocryphia and Ursicollum, three new genera on Eucalyptus and Coccoloba for fungi previously known as Cryphonectria

Cryphonectria havanensis is a fungus associated with Eucalyptus species in Cuba and Florida (U.S.A.). Until recently, there have been no living cultures of C. havanensis and it has thus not been possible to assess its taxonomic status. Isolates thought to represent this fungus have, however, emerged from surveys of Eucalyptus in Mexico and Hawaii (U.S.A.). Results of this study showed that these isolates represent C. havanensis but reside in a genus distinct from Cryphonectria sensu stricto, which is described here as Microthia. Isolates of an unidentified fungus occurring on Myrica faya in the Azores and Madeira also grouped in Microthia and were identical to other M. havanensis isolates. Cryphonectria coccolobae, a fungus occurring on sea grape (Coccoloba uvifera) in Bermuda and Florida, was found to be morphologically identical to Microthia and is transferred to this genus, but as a distinct species. Surveys for M. coccolobae on sea grape in Florida, yielded a second diaporthalean fungus from this host. This fungus is morphologically and phylogenetically distinct from M. coccolobae and other closely related taxa and is described as Ursicollum fallax gen. et sp. nov. Phylogenetic analyses in this study have also shown that isolates of C. eucalypti, a pathogen of Eucalyptus in South Africa and Australia, group in a clade separate from all other groups including that representing Cryphonectria sensu stricto. This difference is supported by the fact that Cryphonectria eucalypti has ascospore septation different to that of all other Cryphonectria species. A new genus, Holocryphia, is thus erected for C. eucalypti

Endophyte isolations from Syzygium cordatum and a Eucalyptus clone (Myrtaceae) reveal new host and geographical reports for the Mycosphaerellaceae and Teratosphaeriaceae

Speci e s of Mycosphaerellaceae and Teratosphaeriaceae (Ascomycetes) cause important leaf, shoot and canker diseases globally on a broad range of hosts, including Eucalyptus and other Myrtaceae. Recently, species of the Mycosphaerellaceae and Teratosphaeriaceae have been isolated as asymptomatic endophytes. In this study, endophytic species of Mycosphaerellaceae and Teratosphaeriaceae were isolated from samples taken from healthy native Syzygium cordatum (Myrtaceae) and related non-native Eucalyptus grandis x E. camaldulensis (hybrid clone) growing in Mtubatuba, KwaZulu Natal, South Africa. Multi-locus sequence analysis (MLSA) using the Internal Transcribed Spacer (ITS) region, the partial Large Subunit (LSU; 28S nrDNA) of the nuclear ribosomal DNA operon and Translation Elongation Factor-1α (TEF-1α) genes were used to correctly identify the 22 resulting isolates. The isolates grouped in five clades representing Readeriella considenianae that was isolated only from the Eucalyptus hybrid clone, Mycosphaerella marksii and M. vietnamensis from S. cordatum and Pseudocercospora crystallina from both S. cordatum and the Eucalyptus hybrid clone. Interestingly, the serious canker pathogen T. zuluensis was isolated from Eucalyptus leaves, although it is known only from stem and branch cankers. Of the species found, R. considenianae and M. vietnamensis were found in South Africa for the first time, while M. marksii, M. vietnamensis and P. crystallina were shown to naturally infect native S. cordatum for the first time. Despite the limited number of trees sampled, the new host and distribution reports show that more intensive sampling, especially following an endophyte approach, will reveal more complete patterns of host preference and geographical distribution for these fungi.Thutuka Funding programme of the National Research Foundation (NRF), members of the Tree Protection Co-operative Programme (TPCP) and the Department of Science and Technology (DST)/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa.http://link.springer.com/journal/13313hb201

Species delineation in the tree pathogen genus Celoporthe (Cryphonectriaceae) in southern 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, TEF1a gene and two areas of the b-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.We thank the University of Pretoria (UP), National Research Foundation (NRF), Forestry and Agricultural Biotechnology Institute (FABI) and Tree Protection Cooperative Program (TPCP) for financial support.http://www.mycologia.org/am201

Multiple Phytophthora species associated with a single riparian ecosystem in South Africa

The diversity of Phytophthora spp. in rivers and riparian ecosystems has received considerable international attention, although little such research has been conducted in South Africa. This study determined the diversity of Phytophthora spp. within a single river in Gauteng province of South Africa. Samples were collected over 1 y including biweekly river baiting with Rhododendron indicum leaves. Phytophthora isolates were identified with phylogenetic analyses of sequences for the internal transcribed spacer (ITS) region of the ribosomal DNA and the mitochondrial cytochrome oxidase c subunit I (coxI) gene. Eight Phytophthora spp. were identified, including a new taxon, P. taxon Sisulu-river, and two hybrid species from Cooke’s ITS clade 6. Of these, species from Clade 6 were the most abundant, including P. chlamydospora and P. lacustris. Species residing in Clade 2 also were encountered, including P. multivora, P. plurivora and P. citrophthora. The detection of eight species in this investigation of Phytophthora diversity in a single riparian river ecosystem in northern South Africa adds to the known diversity of this genus in South Africa and globally.We further acknowledge financial support from the National Research Foundation (NRF), the Department of Science and Technology/National Research Foundation (DST/NRF) Centre of Excellence in Tree Health Biotechnology (CTHB) and the University of Pretoria, South Africa.http://www.mycologia.orgam2016Forestry and Agricultural Biotechnology Institute (FABI)Genetic