Genera of phytopathogenic fungi: GOPHY 4.

This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including Ascochyta, Cadophora, Celoporthe, Cercospora, Coleophoma, Cytospora, Dendrostoma, Didymella, Endothia, Heterophaeomoniella, Leptosphaerulina, Melampsora, Nigrospora, Pezicula, Phaeomoniella, Pseudocercospora, Pteridopassalora, Zymoseptoria, and one genus of oomycetes, Phytophthora. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names. Taxonomic novelties: New genera: Heterophaeomoniella L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pteridopassalora C. Nakash. & Crous; New species: Ascochyta flava Qian Chen & L. Cai, Cadophora domestica L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora rotunda L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora vinacea J.R. Úrbez-Torres, D.T. O'Gorman & Gramaje, Cadophora vivarii L. Mostert, Havenga, Halleen & Gramaje, Celoporthe foliorum H. Suzuki, Marinc. & M.J. Wingf., Cercospora alyssopsidis M. Bakhshi, Zare & Crous, Dendrostoma elaeocarpi C.M. Tian & Q. Yang, Didymella chlamydospora Qian Chen & L. Cai, Didymella gei Qian Chen & L. Cai, Didymella ligulariae Qian Chen & L. Cai, Didymella qilianensis Qian Chen & L. Cai, Didymella uniseptata Qian Chen & L. Cai, Endothia cerciana W. Wang. & S.F. Chen, Leptosphaerulina miscanthi Qian Chen & L. Cai, Nigrospora covidalis M. Raza, Qian Chen & L. Cai, Nigrospora globospora M. Raza, Qian Chen & L. Cai, Nigrospora philosophiae-doctoris M. Raza, Qian Chen & L. Cai, Phytophthora transitoria I. Milenkovic, T. Májek & T. Jung, Phytophthora panamensis T. Jung, Y. Balci, K. Broders & I. Milenkovic, Phytophthora variabilis T. Jung, M. Horta Jung & I. Milenkovic, Pseudocercospora delonicicola C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora farfugii C. Nakash., I. Araki, & Ai Ito, Pseudocercospora hardenbergiae Crous & C. Nakash., Pseudocercospora kenyirana C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora perrottetiae Crous, C. Nakash. & C.Y. Chen, Pseudocercospora platyceriicola C. Nakash., Y. Hatt, L. Suhaizan & I. Nurul Faziha, Pseudocercospora stemonicola C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora terengganuensis C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora xenopunicae Crous & C. Nakash.; New combinations: Heterophaeomoniella pinifoliorum (Hyang B. Lee et al.) L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pseudocercospora pruni-grayanae (Sawada) C. Nakash. & Motohashi., Pseudocercospora togashiana (K. Ito & Tak. Kobay.) C. Nakash. & Tak. Kobay., Pteridopassalora nephrolepidicola (Crous & R.G. Shivas) C. Nakash. & Crous, Pteridopassalora lygodii (Goh & W.H. Hsieh) C. Nakash. & Crous; Typification: Epitypification: Botrytis infestans Mont., Cercospora abeliae Katsuki, Cercospora ceratoniae Pat. & Trab., Cercospora cladrastidis Jacz., Cercospora cryptomeriicola Sawada, Cercospora dalbergiae S.H. Sun, Cercospora ebulicola W. Yamam., Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora ixorana J.M. Yen & Lim, Cercospora liquidambaricola J.M. Yen, Cercospora pancratii Ellis & Everh., Cercospora pini-densiflorae Hori & Nambu, Cercospora profusa Syd. & P. Syd., Cercospora pyracanthae Katsuki, Cercospora horiana Togashi & Katsuki, Cercospora tabernaemontanae Syd. & P. Syd., Cercospora trinidadensis F. Stevens & Solheim, Melampsora laricis-urbanianae Tak. Matsumoto, Melampsora salicis-cupularis Wang, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora angiopteridis Goh & W.H. Hsieh, Pseudocercospora basitruncata Crous, Pseudocercospora boehmeriigena U. Braun, Pseudocercospora coprosmae U. Braun & C.F. Hill, Pseudocercospora cratevicola C. Nakash. & U. Braun, Pseudocercospora cymbidiicola U. Braun & C.F. Hill, Pseudocercospora dodonaeae Boesew., Pseudocercospora euphorbiacearum U. Braun, Pseudocercospora lygodii Goh & W.H. Hsieh, Pseudocercospora metrosideri U. Braun, Pseudocercospora paraexosporioides C. Nakash. & U. Braun, Pseudocercospora symploci Katsuki & Tak. Kobay. ex U. Braun & Crous, Septogloeum punctatum Wakef.; Neotypification: Cercospora aleuritis I. Miyake; Lectotypification: Cercospora dalbergiae S.H. Sun, Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora profusa Syd. & P. Syd., Melampsora laricis-urbanianae Tak. Matsumoto, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora symploci Katsuki & Tak. Kobay. ex U. Braun & Crous. Citation: Chen Q, Bakhshi M, Balci Y, Broders KD, Cheewangkoon R, Chen SF, Fan XL, Gramaje D, Halleen F, Horta Jung M, Jiang N, Jung T, Májek T, Marincowitz S, Milenkovic T, Mostert L, Nakashima C, Nurul Faziha I, Pan M, Raza M, Scanu B, Spies CFJ, Suhaizan L, Suzuki H, Tian CM, Tomsovský M, Úrbez-Torres JR, Wang W, Wingfield BD, Wingfield MJ, Yang Q, Yang X, Zare R, Zhao P, Groenewald JZ, Cai L, Crous PW (2022). Genera of phytopathogenic fungi: GOPHY 4. Studies in Mycology 101: 417-564. doi: 10.3114/sim.2022.101.06.

Dieback and decline pathogens of olive trees in South Africa.

Trunk disease fungal pathogens reduce olive production globally by causing cankers, dieback, and other decline-related symptoms on olive trees. Very few fungi have been reported in association with olive dieback and decline in South Africa. Many of the fungal species reported from symptomatic olive trees in other countries have broad host ranges and are known to occur on other woody host plants in the Western Cape province, the main olive production region of South Africa. This survey investigated the diversity of fungi and symptoms associated with olive dieback and decline in South Africa. Isolations were made from internal wood symptoms of 145 European and 42 wild olive trees sampled in 10 and 9 districts, respectively. A total of 99 taxa were identified among 440 fungal isolates using combinations of morphological and molecular techniques. A new species of Pseudophaeomoniella, P. globosa, had the highest incidence, being recovered from 42.8 % of European and 54.8 % of wild olive samples. This species was recovered from 9 of the 10 districts where European olive trees were sampled and from all districts where wild olive trees were sampled. Members of the Phaeomoniellales (mainly P. globosa) were the most prevalent fungi in five of the seven symptom types considered, the only exceptions being twig dieback, where members of the Botryosphaeriaceae were more common, and soft/white rot where only Basidiomycota were recovered. Several of the species identified are known as pathogens of olives or other woody crops either in South Africa or elsewhere in the world, including species of Neofusicoccum, Phaeoacremonium, and Pleurostoma richardsiae. However, 81 of the 99 taxa identified have not previously been recorded on olive trees and have unknown interactions with this host. These taxa include one new genus and several putative new species, of which four are formally described as Celerioriella umnquma sp. nov., Pseudophaeomoniella globosa sp. nov., Vredendaliella oleae gen. & sp. nov., and Xenocylindrosporium margaritarum sp. nov.

Genera of phytopathogenic fungi: GOPHY 2.

This paper represents the second contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information regarding the pathology, distribution, hosts and disease symptoms for the treated genera. In addition, primary and secondary DNA barcodes for the currently accepted species are included. This second paper in the GOPHY series treats 20 genera of phytopathogenic fungi and their relatives including: Allantophomopsiella, Apoharknessia, Cylindrocladiella, Diaporthe, Dichotomophthora, Gaeumannomyces, Harknessia, Huntiella, Macgarvieomyces, Metulocladosporiella, Microdochium, Oculimacula, Paraphoma, Phaeoacremonium, Phyllosticta, Proxypiricularia, Pyricularia, Stenocarpella, Utrechtiana and Wojnowiciella. This study includes the new genus Pyriculariomyces, 20 new species, five new combinations, and six typifications for older names.

Phaeoacremonium species diversity on woody hosts in the Western Cape Province of South Africa.

Nineteen Phaeoacremonium species are currently known in South Africa. These have been reported from grapevines, fruit trees, fynbos twig litter and arthropods. In other countries some of these Phaeoacremonium species are also known from hosts such as European olive, quince and willow that commonly occur in the Western Cape Province of South Africa, where most South African records of Phaeoacremonium have been made. The aim of this study was to investigate the species diversity and host-range of Phaeoacremonium in the Western Cape Province of South Africa by characterising 156 isolates collected from 29 woody hosts. Phylogenetic analyses of combined actin and beta-tubulin datasets allowed for the identification of 31 species among the 156 isolates, including 13 new species and 3 known species that had not been recorded in South Africa previously. The new Phaeoacremonium species include P. album, P. aureum, P. bibendum, P. gamsii, P. geminum, P. junior, P. longicollarum, P. meliae, P. oleae, P. paululum, P. proliferatum, P. rosicola and P. spadicum. All previous records of P. alvesii in South Africa were re-identified as P. italicum, but both species were recovered during this survey. A total of 35 described Phaeoacremonium species are now known from South Africa, more than double the number reported from any other country. This high diversity reflects the high diversity of indigenous flora of the Cape Floral Region, a biodiversity hotspot mainly situated in the Western Cape Province. Paraphyly and incongruence between individual phylogenies of the actin and beta-tubulin regions complicated species delimitation in some cases indicating that additional phylogenetic markers should be investigated for use in Phaeoacremonium phylogenies to prevent misidentifications and the introduction of vague species boundaries.

Response of Vitis vinifera cell cultures to Eutypa lata and Trichoderma atroviride culture filtrates: expression of defence-related genes and phenotypes.

Cell suspension cultures of Vitis vinifera cv. Dauphine berries were used to study the response to the vascular pathogen, Eutypa lata, in comparison with a biological control agent, Trichoderma atroviride, that was previously shown to be effective in pruning wound protection. The expression of genes coding for enzymes of the phenylpropanoid pathway and pathogenesis-related (PR) proteins was profiled over a 48-h period using quantitative reverse transcriptase PCR. The cell cultures responded to elicitors of both fungi with a hypersensitive-like response that lead to a decrease in cell viability. Similar genes were triggered by both the pathogen and biocontrol agent, but the timing patterns and magnitude of expression was dependent on the specific fungal elicitor. Culture filtrates of both fungi caused upregulation of phenylalanine ammonia-lyase (PAL), 4-coumaroyl Co-A ligase (CCo-A) and stilbene synthase (STS), and a downregulation of chalcone synthase (CHS) genes. The pathogen filtrate caused a biphasic pattern in the upregulation of PAL and STS genes which was not observed in cells treated with filtrates of the biocontrol agent. Analytical assays showed significantly higher total phenolic content and chitinolytic enzyme activity in the cell cultures treated with the T. atroviride filtrate compared to the pathogen filtrate. These results corresponded well to the higher expression of PAL and chitinase class IV genes. The response of the cell cultures to T. atroviride filtrate provides support for the notion that the wound protection by the biocontrol agent at least partially relies on the induction of grapevine resistance mechanisms.

Trunk Disease Fungi Associated With Diospyros kaki in South Africa.

Persimmon trees with dieback symptoms and cankers were observed in three production areas in Western Cape Province in South Africa. Isolations were made from diseased branches, cankers, and pruning wounds as well as fungal fruiting bodies on dead branches and old pruning wounds. Several trunk disease pathogens were identified based on morphological characteristics and by molecular methods, including Diaporthe eres, D. infecunda, Eutypella citricola, E. microtheca, Phaeoacremonium parasiticum, P. scolyti, P. australiense, P. minimum, Fomitiporia capensis, Fomitiporia sp., Fomitiporella sp., and Inocutis sp., which were isolated from persimmon for the first time in the world. Other first reports from persimmon in South Africa include D. foeniculina, D. ambigua, D. mutila, Diaporthe sp., Neofusicoccum australe, N. parvum, Diplodia seriata, and Eutypa lata. Pathogenicity tests conducted with all species, except the basidiomycetes, confirmed their status as possible persimmon pathogens. This is the first study to determine and identify fungi associated with diseased persimmon in South Africa. The knowledge gained in this study forms the basis for further research to determine the impact of these fungi on persimmon productivity.

Arthropods vector grapevine trunk disease pathogens.

Arthropod-mediated dispersal of pathogens is known in many cropping systems but has never been demonstrated for grapevine trunk disease pathogens. Arthropods from vineyards were screened for the presence of pathogens associated with Petri disease and esca using cultural and molecular techniques. The ability of the most abundant pathogen-carrying species to inoculate healthy grapevine vascular tissues was also determined. Millipedes and ants were allowed to associate with a DsRed- Express-transformed Phaeomoniella chlamydospora, after which they were exposed to freshly pruned healthy grapevines under controlled conditions and wounds were monitored for subsequent infection. In addition, the possibility of millipede excreta, commonly found on pruning wounds in the field, to act as inoculum source was determined. A diverse arthropod fauna was associated with declining grapevines and many of these carried trunk disease pathogens. However, spiders, the ant Crematogaster peringueyi, and the millipede Ommattoiulus moreleti were the most abundant pathogen carriers. The ant and millipede species fed on pruning wound sap and effectively transmitted trunk disease pathogens. Millipede excreta contained viable spores of Phaeomoniella chlamydospora and may serve as an inoculum source. Numerous arthropods, including beneficial predators, are potential vectors of grapevine trunk disease pathogens. Our results highlight the need for an integrated approach, including targeted management of ants and millipedes at the time of pruning, to limit the spread of grapevine trunk diseases.

First Report of Togninia minima Perithecia on Esca- and Petri-Diseased Grapevines in South Africa.

Esca and petri diseases are important grapevine trunk diseases in South Africa and most other grape-producing countries. The causal pathogens are Phaeomoniella chlamydospora and several species of Phaeoacremonium. In total, 25 species of Phaeoacremonium have been isolated from grapevines of which seven species have been linked to Togninia teleomorphs obtained through in vitro mating studies (3). Of these species, only perithecia of T. minima, T. fraxinopennsylvanica, and T. viticola have been found on grapevines in California (1,2,4). T. minima is heterothallic, and although both mating types are present in South African vineyards, perithecia have never been observed (3). In the current study, grapevine cordons and trunks were collected from vineyards and rootstock mother vines within Western Cape Province for examination in the laboratory under a dissecting microscope. The grapevines displayed general decline symptoms, including reduced vegetative growth, dead or dying shoots and cordons, as well as internal vascular streaking and/or a red/black/brown margin next to decayed wood typically associated with esca and petri disease. Rootstock mother vines were apparently healthy, although many old, cracked pruning wounds were visible. Togninia-like perithecia with distinctive long necks were found along the wood crevices, often on old pruning wounds. The perithecia were removed and placed on microscope slides with sterile water. Structures were measured and slides were washed with 500 µl of sterile water onto potato dextrose agar amended with chloramphenicol (250 mg/liter). Ascospores were allowed to germinate overnight to obtain single ascospore colonies. Perithecia were found on cultivars Muscat d' Alexandrie and Pinotage (Vitis vinifera) at Stellenbosch in May 2011 and on Ramsey (V. champinii) rootstock mother vines at Slanghoek in June 2012. Perithecia were globose to subglobose, black, and often embedded in the wood tissue but also present on the surface of the wood. The length of the necks was 250 to 300 × 47.5 to 55 µm. The asci were hyaline and ranged from 16 to 25 × 3.5 to 5 µm. Ascospores were hyaline, ellipsoid, and ranged from 5 to 6 × 1.5 to 2 µm. These measurements were similar to those reported by Mostert et al. (3) and Rooney et al. (4). Colony growth was typical of T. minima. DNA was extracted from the colonies and the partial betatubulin gene was amplified and sequenced using the primers T1 and Bt2b. Sequences were deposited into GenBank (JX962864 to 67). Based on a megablast search of the NCBI's GenBank nucleotide database, 100% similarity was found with other T. minima sequences (JQ691670.1, HQ605018.1, HQ605014.1; identities = 647/647 [100%], gaps = 0/647 [0%]). To our knowledge, this is the first report on the occurrence of T. minima perithecia on grapevines in Western Cape Province of South Africa. The removal of dead spurs and cordons will be instrumental in lowering the inoculum originating from perithecia, especially in rootstock mother blocks where no control strategies are applied for petri disease or esca. Spore trapping studies are currently in progress to study spore release patterns in order to determine whether pruning wounds are at risk during traditional pruning periods. References: (1) A. Eskalen et al. Plant Dis. 89:528, 2005. (2) A. Eskalen et al. Plant Dis. 89:686, 2005. (3) L. Mostert et al. Stud. Mycol. 54:1, 2006. (4) S. Rooney-Latham et al. Plant Dis. 89:867, 2005.

First Report of Lasiodiplodia crassispora as a Pathogen of Grapevine Trunks in South Africa.

In 2003 and 2004, a survey of grapevine (Vitis vinifera L.) trunk pathogens was conducted in 30 vineyards in the Western and Northern Cape and Limpopo provinces of South Africa. In each vineyard, 20 visually healthy plants were sampled randomly by removing the distal part of one cordon arm. Isolations were made onto potato dextrose agar (PDA) from the internal wood decay symptoms observed in the cordon samples. Seven Botryosphaeriaceae spp. were identified, including Lasiodiplodia crassispora (1). Other Botryosphaeriaceae spp. are known grapevine trunk pathogens (2). Species identity was confirmed by DNA sequence data of the partial translation factor 1-α gene (1) and sequences deposited in GenBank (GU233658 and GU233659). The L. crassispora isolates (CBS 125626 and 125627) were associated with brown internal necrosis, a known symptom of grapevine Botryosphaeriaceae spp. infection (3), in the cordon arms of Ruby Cabernet grapevines occurring in two vineyards in the Northern Cape Province. L. crassispora was described from cankered wood of Santalum album in Western Australia and endophytically from Eucalyptus urophylla in Venezuela (1). Its grapevine pathogen status was determined using both isolates in a repeated pathogenicity test that included three isolates each of Botryosphaeria dothidea and Neofusicoccum australe as positive controls (2), Trichoderma harzianum as a nonpathogen treatment, and an uncolonized agar plug as a negative control. The Botryosphaeriaceae spp. and T. harzianum were plated on PDA and incubated at 25°C for 7 days. Lignified, 6-month-old shoots of grapevine cv. Chardonnay were excised from grapevines with internodes 4 to 6 used for inoculations. Before wounding, shoots were disinfected by submersion for 1 min in a 1 ml/liter solution of a quaternary ammonium compound (Sporekill; ICA International Chemicals (Pty) Ltd, Stellenbosch, South Africa). Twelve shoots were used for each isolate or control treatment. Wounds were made 2 mm deep on the fifth internode of the shoots with a 5-mm flame-sterilized cork borer (2,3). Wounds were inoculated with a pathogen colonized agar plug (5 mm in diameter) or an uncolonized agar plug and then covered with Parafilm (2,3). Inoculated shoots were incubated in the dark in moist chambers for 14 days at 25°C. After incubation, the bark of the shoots was peeled from the area around the wound and the lengths of any resultant lesions were measured under sterile conditions. The inoculum effect was assessed by analysis of variance and Student's t-test. Results showed that significantly (P < 0.0001) longer lesions were caused by L. crassispora (13.36 mm) compared with N. australe (9.27 mm) and B. dothidea (5.28 mm) and also significantly longer than lesions caused by the nonpathogen and negative controls (3.23 and 2.90 mm, respectively). To determine if lesions were caused by inoculated fungi, isolations were made from the tissue at the edges of the lesions by aseptically removing five 0.5 × 1 mm pieces of wood and placing them on PDA dishes amended with 0.04 g/liter of streptomycin sulfate. Dishes were incubated under normal fluorescent light at 25°C for 14 days before identifying isolated fungi based on morphological and cultural characteristics (1). To our knowledge, this is the first report of L. crassispora as a grapevine pathogen. References: (1) T. I. Burgess et al. Mycologia 98:423, 2006. (2) J. M. van Niekerk et al. Mycologia 96:781, 2004. (4) J. M. van Niekerk et al. Phytopathol. Mediterr. 45:S43, 2006.