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Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Impact of a novel protein meal on the gastrointesinal microbiota and host transciptome of larval zebrafish Danio rerio
Rurangwa, E. ; Sipkema, D. ; Kals, J. ; Veld, M. ter; Forlenza, M. ; Bacanu, G.M. ; Smidt, H. ; Palstra, A.P. - \ 2015
Frontiers in Physiology 6 (2015). - ISSN 1664-042X - 27 p.
large gene lists - intestinal microbiota - gut microbiota - digestive physiology - solea-senegalensis - metal uptake - sp-nov - fish - expression - iron
Larval zebrafish was subjected to a methodological exploration of the gastrointestinal microbiota and transcriptome. Assessed was the impact of two dietary inclusion levels of a novel protein meal (NPM) of animal origin (ragworm Nereis virens) on the gastrointestinal tract (GIT). Microbial development was assessed over the first 21 days post egg fertilisation (dpf) through 16S rRNA gene-based microbial composition profiling by pyrosequencing. Differentially expressed genes in the GIT were demonstrated at 21 dpf by whole transcriptome sequencing (mRNAseq). Larval zebrafish showed rapid temporal changes in microbial colonization but domination occurred by one to three bacterial species generally belonging to Proteobacteria and Firmicutes. The high iron content of NPM may have led to an increased relative abundance of bacteria that were related to potential pathogens and bacteria with an increased iron metabolism. Functional classification of the 328 differentially expressed genes indicated that the GIT of larvae fed at higher NPM level was more active in transmembrane ion transport and protein synthesis. mRNAseq analysis did not reveal a major activation of genes involved in the immune response or indicating differences in iron uptake and homeostasis in zebrafish fed at the high inclusion level of NPM
The Colletotrichum gigasporum species complex
Liu, F. ; Cai, L. ; Crous, P.W. ; Damm, U. - \ 2014
Persoonia 33 (2014). - ISSN 0031-5850 - p. 83 - 97.
sp-nov - primer sets - endophytes - pathogens - china - gloeosporioides - anthracnose - diversity - sequences - acutatum
In a preliminary analysis, 21 Colletotrichum strains with large conidia preserved in the CBS culture collection clustered with a recently described species, C. gigasporum, forming a clade distinct from other currently known Colletotrichum species complexes. Multi-locus phylogenetic analyses (ITS, ACT, TUB2, CHS-1, GAPDH) as well as each of the single-locus analyses resolved seven distinct species, one of them being C. gigasporum. Colletotrichum gigasporum and its close allies thus constitute a previously unknown species complex with shared morphological features. Five of the seven species accepted in the C. gigasporum species complex are described here as novel species, namely C. arxii, C. magnisporum, C. pseudomajus, C. radicis and C. vietnamense. A species represented by a single sterile strain, namely CBS 159.50, was not described as novel species, and is treated as Colletotrichum sp. CBS 159.50. Furthermore, C. thailandicum is reduced to synonymy with C. gigasporum.
Pestalotiopsis revisited
Maharachchikumbura, S.S.N. ; Hyde, K.D. ; Groenewald, J.Z. ; Xu, J. ; Crous, P.W. - \ 2014
Studies in Mycology 79 (2014). - ISSN 0166-0616 - p. 121 - 186.
ribosomal dna-sequences - sp-nov - morphological characters - conidial structure - camellia-sinensis - natural-products - twig blight - primer sets - leaf-spot - disease
Species of Pestalotiopsis occur commonly as plant pathogens, and represent a fungal group known to produce a wide range of chemically novel, diverse metabolites. In the present study, we investigated 91 Pestalotiopsis isolates from the CBS-KNAW Fungal Biodiversity Centre (CBS) culture collection. The phylogeny of the Amphisphaeriaceae was constructed based on analysis of 28S nrRNA gene (LSU) sequence data, and taxonomic changes are proposed to reflect more natural groupings. We combined morphological and DNA data, and segregated two novel genera from Pestalotiopsis, namely Neopestalotiopsis and Pseudopestalotiopsis. The three genera are easily distinguishable on the basis of their conidiogenous cells and colour of their median conidial cells. We coupled morphological and combined sequence data of internal transcribed spacer (ITS), partial ß-tubulin (TUB) and partial translation elongation factor 1-alpha (TEF) gene regions, which revealed 30 clades in Neopestalotiopsis and 43 clades in Pestalotiopsis. Based on these data, 11 new species are introduced in Neopestalotiopsis, 24 in Pestalotiopsis, and two in Pseudopestalotiopsis. Several new combinations are proposed to emend monophyly of Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis.
Introducing the Consolidated Species Concept to resolve species in the Teratosphaeriaceae
Quaedvlieg, W. ; Binder, M. ; Groenewald, J.Z. ; Summerell, B.A. ; Carnegie, A.J. ; Burgess, T.I. ; Crous, P.W. - \ 2014
Persoonia 33 (2014). - ISSN 0031-5850 - p. 1 - 40.
internal transcribed spacer - mycosphaerella-spp. - sp-nov - eucalyptus leaves - gene genealogies - south-africa - leaf spots - phylogenetic reassessment - reproductive isolation - multigene phylogeny
The Teratosphaeriaceae represents a recently established family that includes numerous saprobic, extremophilic, human opportunistic, and plant pathogenic fungi. Partial DNA sequence data of the 28S rRNA and RPB2 genes strongly support a separation of the Mycosphaerellaceae from the Teratosphaeriaceae, and also provide support for the Extremaceae and Neodevriesiaceae, two novel families including many extremophilic fungi that occur on a diversity of substrates. In addition, a multi-locus DNA sequence dataset was generated (ITS, LSU, Btub, Act, RPB2, EF-1a and Cal) to distinguish taxa in Mycosphaerella and Teratosphaeria associated with leaf disease of Eucalyptus, leading to the introduction of 23 novel genera, five species and 48 new combinations. Species are distinguished based on a polyphasic approach, combining morphological, ecological and phylogenetic species concepts, named here as the Consolidated Species Concept (CSC). From the DNA sequence data generated, we show that each one of the five coding genes tested, reliably identify most of the species present in this dataset (except species of Pseudocercospora). The ITS gene serves as a primary barcode locus as it is easily generated and has the most extensive dataset available, while either Btub, EF-1a or RPB2 provide a useful secondary barcode locus.
Fungal Planet description sheets: 214–280
Crous, P.W. ; Shivas, R.G. ; Quaedvlieg, W. ; Bank, M. van der; Zhang, Y. ; Summerell, B.A. ; Guarro, J. ; Wingfield, M.J. ; Wood, A.R. ; Alfenas, A.C. ; Braun, U. ; Cano-Lira, J.F. ; Garcia, D. ; Marin-Felix, Y. ; Alvarado, P. ; Andrade, J.P. ; Armengol, J. ; Assefa, A. ; Breeÿen, A. den; Camele, I. ; Cheewangkoon, R. ; Souza, J.T. De; Duong, T.A. ; Esteve-Raventós, F. ; Fournier, J. ; Frisullo, S. ; García-Jiménez, J. ; Gardiennet, A. ; Gené, J. ; Hernández-Restrepo, M. ; Hirooka, Y. ; Hospenthal, D.R. ; King, A. ; Lechat, C. ; Lombard, L. ; Mang, S.M. ; Marbach, P.A.S. ; Marincowitz, S. ; Montaño-Mata, N.J. ; Moreno, G. ; Perez, C.A. ; Pérez Sierra, A.M. ; Robertson, J.L. ; Roux, J. ; Rubio, E. ; Schumacher, R.K. ; Stchigel, A.M. ; Sutton, D.A. ; Tan, Y.P. ; Thompson, E.H. ; Vanderlinde, E. ; Walker, A.K. ; Walker, D.M. ; Wickes, B.L. ; Wong, P.T.W. ; Groenewald, J.Z. - \ 2014
Persoonia 32 (2014). - ISSN 0031-5850 - p. 184 - 306.
sp-nov - phylogeny reveals - eucalyptus-microfungi - host-associations - gene phylogeny - sequence data - diaporthales - morphology - gnomoniaceae - conioscypha
Novel species of microfungi described in the present study include the following from South Africa: Cercosporella dolichandrae from Dolichandra unguiscati, Seiridium podocarpi from Podocarpus latifolius, Pseudocercospora parapseudarthriae from Pseudarthria hookeri, Neodevriesia coryneliae from Corynelia uberata on leaves of Afrocarpus falcatus, Ramichloridium eucleae from Euclea undulata and Stachybotrys aloeticola from Aloe sp. (South Africa), as novel member of the Stachybotriaceae fam. nov. Several species were also described from Zambia, and these include Chaetomella zambiensis on unknown Fabaceae, Schizoparme pseudogranati from Terminalia stuhlmannii, Diaporthe isoberliniae from Isoberlinia angolensis, Peyronellaea combreti from Combretum mossambiciensis, Zasmidium rothmanniae and Phaeococcomyces rothmanniae from Rothmannia engleriana, Diaporthe vangueriae from Vangueria infausta and Diaporthe parapterocarpi from Pterocarpus brenanii. Novel species from the Netherlands include: Stagonospora trichophoricola, Keissleriella trichophoricola and Dinemasporium trichophoricola from Trichophorum cespitosum, Phaeosphaeria poae, Keissleriella poagena, Phaeosphaeria poagena, Parastagonospora poagena and Pyrenochaetopsis poae from Poa sp., Septoriella oudemansii from Phragmites australis and Dendryphion europaeum from Hedera helix (Germany) and Heracleum sphondylium (the Netherlands). Novel species from Australia include: Anungitea eucalyptorum from Eucalyptus leaf litter, Beltraniopsis neolitseae and Acrodontium neolitseae from Neolitsea australiensis, Beltraniella endiandrae from Endiandra introrsa, Phaeophleospora parsoniae from Parsonia straminea, Penicillifer martinii from Cynodon dactylon, Ochroconis macrozamiae from Macrozamia leaf litter, Triposporium cycadicola, Circinotrichum cycadis, Cladosporium cycadicola and Acrocalymma cycadis from Cycas spp. Furthermore, Vermiculariopsiella dichapetali is described from Dichapetalum rhodesicum (Botswana), Marasmius vladimirii from leaf litter (India), Ophiognomonia acadiensis from Picea rubens (Canada), Setophoma vernoniae from Vernonia polyanthes and Penicillium restingae from soil (Brazil), Pseudolachnella guaviyunis from Myrcianthes pungens (Uruguay) and Pseudocercospora neriicola from Nerium oleander (Italy). Novelties from Spain include: Dendryphiella eucalyptorum from Eucalyptus globulus, Conioscypha minutispora from dead wood, Diplogelasinospora moalensis and Pseudoneurospora canariensis from soil and Inocybe lanatopurpurea from reforested woodland of Pinus spp. Novelties from France include: Kellermania triseptata from Agave angustifolia, Zetiasplozna acaciae from Acacia melanoxylon, Pyrenochaeta pinicola from Pinus sp. and Pseudonectria rusci from Ruscus aculeatus. New species from China include: Dematiocladium celtidicola from Celtis bungeana, Beltrania pseudorhombica, Chaetopsina beijingensis and Toxicocladosporium pini from Pinus spp. and Setophaeosphaeria badalingensis from Hemerocallis fulva. Novel genera of Ascomycetes include Alfaria from Cyperus esculentus (Spain), Rinaldiella from a contaminated human lesion (Georgia), Hyalocladosporiella from Tectona grandis (Brazil), Pseudoacremonium from Saccharum spontaneum and Melnikomyces from leaf litter (Vietnam), Annellosympodiella from Juniperus procera (Ethiopia), Neoceratosperma from Eucalyptus leaves (Thailand), Ramopenidiella from Cycas calcicola (Australia), Cephalotrichiella from air in the Netherlands, Neocamarosporium from Mesembryanthemum sp. and Acervuloseptoria from Ziziphus mucronata (South Africa) and Setophaeosphaeria from Hemerocallis fulva (China). Several novel combinations are also introduced, namely for Phaeosphaeria setosa as Setophaeosphaeria setosa, Phoma heteroderae as Peyronellaea heteroderae and Phyllosticta maydis as Peyronellaea maydis. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Phylogenetic circumscription of Arthrographis (Eremomycetaceae, Dothideomycetes)
Giraldo, A. ; Gené, J. ; Sutton, D.A. ; Madrid, H. ; Cano, J. ; Crous, P.W. ; Guarro, J. - \ 2014
Persoonia 32 (2014). - ISSN 0031-5850 - p. 102 - 114.
keratinophilic fungi - molecular-data - ribosomal dna - sp-nov - ascomycota - tubeufiaceae - systematics - arthropsis - evolution - revision
Numerous members of Ascomycota and Basidiomycota produce only poorly differentiated arthroconidial asexual morphs in culture. These arthroconidial fungi are grouped in genera where the asexual-sexual connections and their taxonomic circumscription are poorly known. In the present study we explored the phylogenetic relationships of two of these ascomycetous genera, Arthrographis and Arthropsis. Analysis of D1/D2 sequences of all species of both genera revealed that both are polyphyletic, with species being accommodated in different orders and classes. Because genetic variability was detected among reference strains and fresh isolates resembling the genus Arthrographis, we carried out a detailed phenotypic and phylogenetic analysis based on sequence data of the ITS region, actin and chitin synthase genes. Based on these results, four new species are recognised, namely Arthrographis chlamydospora, A. curvata, A. globosa and A. longispora. Arthrographis chlamydospora is distinguished by its cerebriform colonies, branched conidiophores, cuboid arthroconidia and terminal or intercalary globose to subglobose chlamydospores. Arthrographis curvata produced both sexual and asexual morphs, and is characterised by navicular ascospores and dimorphic conidia, namely cylindrical arthroconidia and curved, cashew-nut-shaped conidia formed laterally on vegetative hyphae. Arthrographis globosa produced membranous colonies, but is mainly characterised by doliiform to globose arthroconidia. Arthrographis longispora also produces membranous colonies, but has poorly differentiated conidiophores and long arthroconidia. Morphological variants are described for A. kalrae and our results also revealed that Eremomyces langeronii and A. kalrae, traditionally considered the sexual and asexual morphs of the same species, are not conspecific.
Sulfate Reduction at Low Ph To Remediate Acid Mine Drainage
Sánchez-Andrea, I. ; Sanz, J.L. ; Bijmans, M.F.M. ; Stams, A.J.M. - \ 2014
Journal of Hazardous Materials 269 (2014). - ISSN 0304-3894 - p. 98 - 109.
fluidized-bed reactor - metal-contaminated water - rate-determining step - reducing bacteria - waste-water - microbial community - sp-nov - biological treatment - constructed wetland - passive treatment
Industrial activities and the natural oxidation of metallic sulfide-ores produce sulfate-rich waters with low pH and high heavy metals content, generally termed acid mine drainage (AMD). This is of great environmental concern as some heavy metals are highly toxic. Within a number of possibilities, biological treatment applying sulfate-reducing bacteria (SRB) is an attractive option to treat AMD and to recover metals. The process produces alkalinity, neutralizing the AMD. Simultaneously. The sulfide that is produced react with the metal in solution and precipitates them as metal sulfides. Here, important factors for biotechnological application of SRB such as the inocula, the pH of the process, the substrates and the reactor design are discussed. Microbial communities of sulfidogenic reactors treating AMD which comprise fermentative-, acetogenic- and SRB as well as methanogenic archaea are reviewed
Species of the Colletotrichum gloeosporioides complex associated with anthracnose diseases of Proteaceae
Liu, F. ; Damm, U. ; Cai, L. ; Crous, P.W. - \ 2013
Fungal Diversity 61 (2013)1. - ISSN 1560-2745 - p. 89 - 105.
yunnan provinces - fungal pathogens - primer sets - sp-nov - china - guizhou - hosts
Anthracnose disease of Proteaceae has in the past chiefly been attributed to infections by C. acutatum, C. boninense and C. gloeosporioides. In the present study, a multi-locus phylogenetic analysis (ACT, CAL, CHS-1, GAPDH, GS, ITS, TUB2) revealed that strains of the C. gloeosporioides complex associated with Proteaceae belong to at least six species. These include C. alienum, C. aotearoa, C. kahawae (subsp. ciggaro), C. siamense, and two new taxa, C. proteae and C. grevilleae. The most economically important pathogen of Proteaceae seems to be C. alienum, and not C. gloeosporioides as previously reported. All taxa associated with Proteaceae are morphologically described on different media in culture, except strains of C. siamense, which proved to be sterile. Furthermore, C. populi is synonymised with C. aenigma.
Families of Dothideomycetes
Hyde, K.D. ; Gareth Jones, E.B. ; Liu, J.K. ; Ariyawansa, H. ; Boehm, E. ; Boonmee, S. ; Braun, U. ; Chomnunti, P. ; Crous, P.W. ; Dai, D.Q. ; Diederich, P. ; Dissanayake, A. ; Doilom, M. ; Doveri, F. ; Hongsanan, S. ; Jayawardena, R. ; Lawrey, J.D. ; Li, Y.M. ; Liu, Y.X. ; Lücking, R. ; Monkai, J. ; Muggia, L. ; Nelsen, M.P. ; Pang, K.L. ; Phookamsak, R. ; Senanayake, I.C. ; Shearer, C.A. ; Suetrong, S. ; Tanaka, K. ; Thambugala, K.M. ; Wijayawardene, N.N. ; Wikee, S. ; Wu, H.X. ; Zhang, Y. ; Aguirre-Hudson, B. ; Alias, S.A. ; Aptroot, A. ; Bahkali, A.H. ; Berezza, J.L. ; Bhat, D.J. ; Camporesi, E. ; Chukeatirote, E. ; Gueidan, C. ; Hawksworth, D.L. ; Hirayama, K. ; Hoog, S. de; Kang, J.C. ; Knudsen, K. ; Li, W.J. ; Li, X.H. ; Liu, Z.Y. ; Mapook, A. ; McKenzie, E.H.C. ; Miller, A.N. ; Mortimer, P.E. ; Phillips, A.J.L. ; Raja, H.A. ; Scheuer, C. ; Schumm, F. ; Taylor, J.E. ; Tian, Q. ; Tibpromma, S. ; Wanasinghe, D.N. ; Wang, Y. ; Xu, J.C. ; Yacharoen, S. ; Yan, J.Y. ; Zhang, M. - \ 2013
Fungal Diversity 63 (2013)1. - ISSN 1560-2745 - p. 1 - 313.
ribosomal dna-sequences - morphologically similar genera - foliicolous lichenized fungi - intertidal mangrove wood - leaf-inhabiting fungi - fresh-water habitats - new-zealand fungi - russian far-east - papua-new-guinea - sp-nov
Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.
The Botryosphaeriaceae: genera and species known from culture
Phillips, A.J.L. ; Alves, A. ; Abdollahzadeh, J. ; Slippers, B. ; Wingfield, M.J. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
Studies in Mycology 76 (2013)1. - ISSN 0166-0616 - p. 51 - 167.
native syzygium-cordatum - grapevine trunk diseases - dna-sequence data - castilla-y-leon - new-south-wales - 1st report - sp-nov - neofusicoccum-parvum - sphaeropsis-sapinea - western-australia
In this paper we give an account of the genera and species in the Botryosphaeriaceae. We consider morphological characters alone as inadequate to define genera or identify species, given the confusion it has repeatedly introduced in the past, their variation during development, and inevitable overlap as representation grows. Thus it seems likely that all of the older taxa linked to the Botryosphaeriaceae, and for which cultures or DNA sequence data are not available, cannot be linked to the species in this family that are known from culture. Such older taxa will have to be disregarded for future use unless they are epitypified. We therefore focus this paper on the 17 genera that can now be recognised phylogenetically, which concentrates on the species that are presently known from culture. Included is a historical overview of the family, the morphological features that define the genera and species and detailed descriptions of the 17 genera and 110 species. Keys to the genera and species are also provided. Phylogenetic relationships of the genera are given in a multi-locus tree based on combined SSU, ITS, LSU, EF1-a and ß-tubulin sequences. The morphological descriptions are supplemented by phylogenetic trees (ITS alone or ITS + EF1-a) for the species in each genus.
Characterisation of Neofusicoccum species causing mango dieback in Italy
Ismail, A.M. ; Cirvilleri, G. ; Lombard, L. ; Crous, P.W. ; Groenewald, J.Z. ; Polizzi, G. - \ 2013
Journal of plant pathology - Formerly Rivista di patologia vegetale 95 (2013)3. - ISSN 1125-4653 - p. 549 - 557.
mangifera-indica - phylogenetic analysis - south-africa - 1st report - sp-nov - botryosphaeria - pathogenicity - lasiodiplodia - morphology - grapevine
Species of Botryosphaeriaceae are important fungal pathogens of mango worldwide. A survey of 11 mango orchards located in the provinces of Catania, Messina, Palermo and Ragusa (Sicily, southern Italy), resulted in the isolation of a large number (76) of Neofusicoccum isolates associated with decline and dieback symptoms. Isolates were identified based on morphology and DNA sequence data analyses of the internal transcribed spacer region of the nrDNA and partial translation of the elongation factor 1-alpha gene regions. Two species of Neofusicoccum were identified, which included N. parvum and N. australe, the former of which was the dominant species. The high incidence in local orchards and the pathogenicity results indicate that N. parvum and N. australe are important pathogens of mango in Sicily where they may significantly limit mango production.
Fungal Planet description sheets: 154–213
Crous, P.W. ; Wingfield, M.J. ; Guarro, J. ; Cheewangkoon, R. ; Bank, M. van der; Swart, W.J. ; Stchigel, A.M. ; Cano-Lira, J.F. ; Roux, J. ; Madrid, H. ; Damm, U. ; Wood, A.R. ; Shuttleworth, L.A. ; Hodges, C.S. ; Munster, M. ; Jesús Yáñez-Morales, M. de; Zúñiga-Estrada, L. ; Cruywagen, E.M. ; Hoog, G.S. de; Silvera, C. ; Najafzadeh, J. ; Davison, E.M. ; Davison, P.J.N. ; Barrett, M.D. ; Barrett, R.L. ; Manamgoda, D.S. ; Minnis, A.M. ; Kleczewski, N.M. ; Flory, S.L. ; Castlebury, L.A. ; Clay, K. ; Hyde, K.D. ; Maússe-Sitoe, S.N.D. ; Chen, S. ; Lechat, C. ; Hairaud, M. ; Lesage-Meessen, L. ; Pawlowska, J. ; Wilk, M. ; Sliwinska-Wyrzychowska, A. ; Metrak, M. ; Wrzosek, M. ; Pavlic-Zupanc, D. ; Maleme, H.M. ; Slippers, B. ; Mac Cormack, W.P. ; Archuby, D.I. ; Grünwald, N.J. ; Tellería, M.T. ; Dueñas, M. ; Martín, M.P. ; Marincowitz, S. ; Beer, Z.W. de; Perez, C.A. ; Gené, J. ; Marin-Felix, Y. ; Groenewald, J.Z. - \ 2013
Persoonia 31 (2013). - ISSN 0031-5850 - p. 188 - 296.
sp-nov - colletotrichum-sansevieriae - anamorph genus - south-africa - 1st report - phytophthora-ipomoeae - leaf-blight - genera - phylogeny - botryosphaeriaceae
Novel species of microfungi described in the present study include the following from South Africa: Camarosporium aloes, Phaeococcomyces aloes and Phoma aloes from Aloe, C. psoraleae, Diaporthe psoraleae and D. psoraleae-pinnatae from Psoralea, Colletotrichum euphorbiae from Euphorbia, Coniothyrium prosopidis and Peyronellaea prosopidis from Prosopis, Diaporthe cassines from Cassine, D. diospyricola from Diospyros, Diaporthe maytenicola from Maytenus, Harknessia proteae from Protea, Neofusicoccum ursorum and N. cryptoaustrale from Eucalyptus, Ochrocladosporium adansoniae from Adansonia, Pilidium pseudoconcavum from Greyia radlkoferi, Stagonospora pseudopaludosa from Phragmites and Toxicocladosporium ficiniae from Ficinia. Several species were also described from Thailand, namely: Chaetopsina pini and C. pinicola from Pinus spp., Myrmecridium thailandicum from reed litter, Passalora pseudotithoniae from Tithonia, Pallidocercospora ventilago from Ventilago, Pyricularia bothriochloae from Bothriochloa and Sphaerulina rhododendricola from Rhododendron. Novelties from Spain include Cladophialophora multiseptata, Knufia tsunedae and Pleuroascus rectipilus from soil and Cyphellophora catalaunica from river sediments. Species from the USA include Bipolaris drechsleri from Microstegium, Calonectria blephiliae from Blephilia, Kellermania macrospora (epitype) and K. pseudoyuccigena from Yucca. Three new species are described from Mexico, namely Neophaeosphaeria agaves and K. agaves from Agave and Phytophthora ipomoeae from Ipomoea. Other African species include Calonectria mossambicensis from Eucalyptus (Mozambique), Harzia cameroonensis from an unknown creeper (Cameroon), Mastigosporella anisophylleae from Anisophyllea (Zambia) and Teratosphaeria terminaliae from Terminalia (Zimbabwe). Species from Europe include Auxarthron longisporum from forest soil (Portugal), Discosia pseudoartocreas from Tilia (Austria), Paraconiothyrium polonense and P. lycopodinum from Lycopodium (Poland) and Stachybotrys oleronensis from Iris (France). Two species of Chrysosporium are described from Antarctica, namely C. magnasporum and C. oceanitesii. Finally, Licea xanthospora is described from Australia, Hypochnicium huinayensis from Chile and Custingophora blanchettei from Uruguay. Novel genera of Ascomycetes include Neomycosphaerella from Pseudopentameris macrantha (South Africa), and Paramycosphaerella from Brachystegia sp. (Zimbabwe). Novel hyphomycete genera include Pseudocatenomycopsis from Rothmannia (Zambia), Neopseudocercospora from Terminalia (Zambia) and Neodeightoniella from Phragmites (South Africa), while Dimorphiopsis from Brachystegia (Zambia) represents a novel coelomycetous genus. Furthermore, Alanphillipsia is introduced as a new genus in the Botryosphaeriaceae with four species, A. aloes, A. aloeigena and A. aloetica from Aloe spp. and A. euphorbiae from Euphorbia sp. (South Africa). A new combination is also proposed for Brachysporium torulosum (Deightoniella black tip of banana) as Corynespora torulosa. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Circumscription of the anthracnose pathogens Colletotrichum lindemuthianum and C. nigrum
Liu, F. ; Cai, L. ; Crous, P.W. ; Damm, U. - \ 2013
Mycologia 105 (2013)4. - ISSN 0027-5514 - p. 844 - 860.
molecular diversity - differential cultivars - genetic-variability - sequence-analysis - host-specificity - primer sets - sp-nov - glomerella - resistance - identification
The anthracnose pathogen of common bean (Phaseolus vulgaris) is usually identified as Colletotrichum lindemuthianum, while anthracnose of potato (Solanum tuberosum), peppers (Capsicum annuum), tomato (S. lycopersicum) and several other crop plants is often attributed to C. coccodes. In order to study the phylogenetic relationships of these important pathogens, we conducted a multigene analysis (ITS, ACT, TUB2, CHS-1, GAPDH) of strains previously identified as C. lindemuthianum, C. coccodes and other related species, as well as representative species of the major Colletotrichum species complexes. Strains of C. lindemuthianum belonged to a single clade; we selected an authentic specimen as lectotype, and an appropriate specimen and culture from the CBS collection to serve as epitype. Two clades were resolved within C. coccodes s. lat. One clade included the ex-neotype strain of C. coccodes on Solanum, while an epitype was selected for C. nigrum, which represents the oldest name of the second clade, which occurs on Capsicum, Solanum, as well as several other host plants. Furthermore, we recognized C. lycopersici as a synonym of C. nigrum, and C. biologicum as a synonym of C. coccodes.
Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi
Gomes, R.R. ; Glienke, C. ; Videira, S.I.R. ; Lombard, L. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
Persoonia 31 (2013). - ISSN 0031-5850 - p. 1 - 41.
internal transcribed spacer - south-africa - species concepts - sp-nov - coelomycete phomopsis - foeniculum-vulgare - multigene analysis - north-america - ribosomal dna - twig dieback
Diaporthe (Phomopsis) species have often been reported as plant pathogens, non-pathogenic endophytes or saprobes, commonly isolated from a wide range of hosts. The primary aim of the present study was to resolve the taxonomy and phylogeny of a large collection of Diaporthe species occurring on diverse hosts, either as pathogens, saprobes, or as harmless endophytes. In the present study we investigated 243 isolates using multilocus DNA sequence data. Analyses of the rDNA internal transcribed spacer (ITS1, 5.8S, ITS2) region, and partial translation elongation factor 1-alpha (TEF1), beta-tubulin (TUB), histone H3 (HIS) and calmodulin (CAL) genes resolved 95 clades. Fifteen new species are described, namely Diaporthe arengae, D. brasiliensis, D. endophytica, D. hongkongensis, D. inconspicua, D. infecunda, D. mayteni, D. neoarctii, D. oxe, D. paranensis, D. pseudomangiferae, D. pseudophoenicicola, D. raonikayaporum, D. schini and D. terebinthifolii. A further 14 new combinations are introduced in Diaporthe, and D. anacardii is epitypified. Although species of Diaporthe have in the past chiefly been distinguished based on host association, results of this study confirm several taxa to have wide host ranges, suggesting that they move freely among hosts, frequently co-colonising diseased or dead tissue. In contrast, some plant pathogenic and endophytic taxa appear to be strictly host specific. Given this diverse ecological behaviour among members of Diaporthe, future species descriptions lacking molecular data (at least ITS and HIS or TUB) should be strongly discouraged.
Glycerol fermentation to hydrogen by Thermotoga maritima: Proposed pathway and bioenergetic considerations
Maru, B.T. ; Bielen, A.A.M. ; Constanti, M. ; Medina, F. ; Kengen, S.W.M. - \ 2013
International Journal of Hydrogen Energy 38 (2013)14. - ISSN 0360-3199 - p. 5563 - 5572.
biohydrogen production - escherichia-coli - caldicellulosiruptor-saccharolyticus - 3-phosphate dehydrogenase - anaerobic fermentation - nucleotide-sequence - dark fermentation - embden-meyerhof - sp-nov - bacteria
The production of biohydrogen from glycerol, by the hyperthermophilic bacterium Thermotoga maritima DSM 3109, was investigated in batch and chemostat systems. T. maritima converted glycerol to mainly acetate, CO2 and H2. Maximal hydrogen yields of 2.84 and 2.41 hydrogen per glycerol were observed for batch and chemostat cultivations, respectively. For batch cultivations: i) hydrogen production rates decreased with increasing initial glycerol concentration, ii) growth and hydrogen production was optimal in the pH range of 7–7.5, and iii) a yeast extract concentration of 2 g/l led to optimal hydrogen production. Stable growth could be maintained in a chemostat, however, when dilution rates exceeded 0.025 h-1 glycerol conversion was incomplete. A detailed overview of the catabolic pathway involved in glycerol fermentation to hydrogen by T. maritima is given. Based on comparative genomics the ability to grow on glycerol can be considered as a general trait of Thermotoga species. The exceptional bioenergetics of hydrogen formation from glycerol is discussed
Molecular typing of Dutch isolates of Xanthomonas arboricola pathovar pruni isolated from ornamental cherry laurel
Bergsma-Vlami, M. ; Martin, W. ; Koenraadt, H. ; Teunissen, H. ; Pothier, J.F. ; Duffy, B. ; Doorn, J. van - \ 2012
Journal of plant pathology - Formerly Rivista di patologia vegetale 94 (2012)Supp.1. - ISSN 1125-4653 - p. S29 - S35.
pectate lyase secretion - acutatum-sensu-lato - colletotrichum-acutatum - c-gloeosporioides - sp-nov - fruit - diversity - infection - susceptibility - pathogenicity
Xanthomonas arboricola pv. pruni (Xap) has been found in several cherry laurel (Prunus laurocerasus) nurseries in the Netherlands, causing leaf spot. As no information is available yet about the epidemiology of this quarantine bacterium in cherry laurel, molecular typing of Xap isolates can considerably improve our understanding of pathogen spread between various cherry laurel production systems in different regions of the Netherlands and pathogen relatedness among different disease outbreaks. In this study, the genotypic diversity within a population of 25 Xap isolates isolated from different cherry laurel cultivars grown in different locations in the Netherlands between 2008-2010, was assessed using Multiple-locus variable-number analysis (MLVA). The identity of these Xap isolates was initially determined based on the EPPO standard PM 7/64. Confirmation of the identity of these Xap isolates was additionally achieved with diverse methodologies, including gyrase subunit B (gyrB) sequence typing, BOXand ERIC-PCR, AFLP, and Xap-specific PCR’s: one based on the previously described Pagani primers (2004) (conventional-PCR and its TaqMan-PCR variant) and one based on the recently described Pothier primers (2011c). Based on the results of the MLVA analysis, the Dutch population of Xap isolates could be divided into two groups; however no correlation with the geographical origin or any other character of these isolates could be established. Additionally, based on colony morphology, a panel of 5 look-a-likes were isolated from symptomatic leaves of P. laurocerasus which reacted in the Xap-specific PCR described by Pagani (2004) but that did not react in the Xap-specific PCR described by Pothier et al. (2011c). Further characterisation of these look-a-like isolates with AFLP, BOXand ERIC-PCR, and gyrB sequencing showed that the Xap-specific PCR described by Pagani does not discriminate between Xap and the look-a-like isolates. Similarly to Pagani PCR, the performance of a pathogenicity test with a pure culture of the isolate was not always discriminative between Xap and the look-a-like isolates, unraveling a complexity in Xanthomonas pathogenicity. Therefore, in routine screening based on the EPPO standard PM 7/64, complementary techniques such as BOX- ERIC-PCR, gyrB sequencing, Xap-specific PCR described by Pothier (2011c), MLVA and AFLP should be used to obtain a reliable diagnosis of Xap and avoid false positive results.
A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species
Maharachchikumbura, S.S.N. ; Guo, L.D. ; Cai, L. ; Chukeatirote, E. ; Wu, W.P. ; Sun, X. ; Crous, P.W. ; Bhat, D.J. ; McKenzie, E.H.C. ; Bahkali, A.H. ; Hyde, K.D. - \ 2012
Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 95 - 129.
dna-sequence database - rna-polymerase-ii - endophytic fungus - beta-tubulin - antifungal metabolites - primer sets - sp-nov - phylogeny - diversity - plant
Pestalotiopsis is a taxonomically confused, pathogenic and chemically creative genus requiring a critical re-examination using a multi-gene phylogeny based on ex-type and ex-epitype cultures. In this study 40 isolates of Pestalotiopsis, comprised of 28 strains collected from living and dead plant material of various host plants from China were studied by means of morphology and analysis of ITS, ß–tubulin and tef1 gene sequence data. Based on molecular and morphological data we describe 14 new species (Pestalotiopsis asiatica, P. chinensis, P. chrysea, P. clavata, P. diversiseta, P. ellipsospora, P. inflexa, P. intermedia, P. linearis, P. rosea, P. saprophyta, P. umberspora, P. unicolor and P. verruculosa) and three species are epitypified (P. adusta, P. clavispora and P. foedans). Of the 10 gene regions (ACT, ß-tubulin, CAL, GPDH, GS, ITS, LSU, RPB 1, SSU and tef1) utilized to resolve cryptic Pestalotiopsis species, ITS, ß–tubulin and tef1 proved to be the better markers. The other gene regions were less useful due to poor success in PCR amplification and/or in their ability to resolve species boundaries. As a single gene tef1 met the requirements for an ideal candidate and functions well for species delimitation due to its better species resolution and PCR success. Although ß-tubulin showed fairly good differences among species, a combination of ITS, ß-tubulin and tef1 gene data gave the best resolution as compared to single gene analysis. This work provides a backbone tree for 22 ex-type/epitypified species of Pestalotiopsis and can be used in future studies of the genus.
The Colletotrichum acutatum complex
Damm, U. ; Cannon, P.F. ; Woudenberg, J.H.C. ; Crous, P.W. - \ 2012
Studies in Mycology 73 (2012)1. - ISSN 0166-0616 - p. 37 - 113.
key lime anthracnose - glomerella leaf-spot - f-sp aeschynomene - bitter rot - sp-nov - molecular characterization - olive anthracnose - c-gloeosporioides - endophytic fungi - causal agent
Colletotrichum acutatum is known as an important anthracnose pathogen of a wide range of host plants worldwide. Numerous studies have reported subgroups within the C. acutatum species complex. Multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3) of 331 strains previously identified as C. acutatum and other related taxa, including strains from numerous hosts with wide geographic distributions, confirmed the molecular groups previously recognised and identified a series of novel taxa. Thirty-one species are accepted, of which 21 have not previously been recognised. Colletotrichum orchidophilum clusters basal to the C. acutatum species complex. There is a high phenotypic diversity within this complex, and some of the species appear to have preferences to specific hosts or geographical regions. Others appear to be plurivorous and are present in multiple regions. In this study, only C. salicis and C. rhombiforme formed sexual morphs in culture, although sexual morphs have been described from other taxa (especially as laboratory crosses), and there is evidence of hybridisation between different species. One species with similar morphology to C. acutatum but not belonging to this species complex was also described here as new, namely C. pseudoacutatum.
The Colletotrichum boninense species complex
Damm, U. ; Cannon, P.F. ; Woudenberg, J.H.C. ; Johnston, P.R. ; Weir, B.S. ; Tan, Y.P. ; Shivas, R.G. ; Crous, P.W. - \ 2012
Studies in Mycology 73 (2012). - ISSN 0166-0616 - p. 1 - 36.
1st report - glomerella-acutata - primer sets - sp-nov - anthracnose - identification - diversity - teleomorph - gloeosporioides - compatibility
Although only recently described, Colletotrichum boninense is well established in literature as an anthracnose pathogen or endophyte of a diverse range of host plants worldwide. It is especially prominent on members of Amaryllidaceae, Orchidaceae, Proteaceae and Solanaceae. Reports from literature and preliminary studies using ITS sequence data indicated that C. boninense represents a species complex. A multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3, CAL) of 86 strains previously identified as C. boninense and other related strains revealed 18 clades. These clades are recognised here as separate species, including C. boninense s. str., C. hippeastri, C. karstii and 12 previously undescribed species, C. annellatum, C. beeveri, C. brassicicola, C. brasiliense, C. colombiense, C. constrictum, C. cymbidiicola, C. dacrycarpi, C. novae-zelandiae, C. oncidii, C. parsonsiae and C. torulosum. Seven of the new species are only known from New Zealand, perhaps reflecting a sampling bias. The new combination C. phyllanthi was made, and C. dracaenae Petch was epitypified and the name replaced with C. petchii. Typical for species of the C. boninense species complex are the conidiogenous cells with rather prominent periclinal thickening that also sometimes extend to form a new conidiogenous locus or annellations as well as conidia that have a prominent basal scar. Many species in the C. boninense complex form teleomorphs in culture.
Fungal Planet description sheets: 107-127
Crous, P.W. ; Summerell, B.A. ; Shivas, R.G. ; Burgess, T.I. ; Decock, C.A. ; Dreyer, L.L. ; Granke, L.L. ; Guest, D.I. ; Hardy, G.E.St.J. ; Hausbeck, M.K. ; Hüberli, D. ; Jung, T. ; Koukol, O. ; Lennox, C.L. ; Liew, E.C.Y. ; Lombard, L. ; McTaggart, A.R. ; Pryke, J.S. ; Roets, F. ; Saude, C. ; Shuttleworth, L.A. ; Stukely, M.J.C. ; Vánky, K. ; Webster, B.J. ; Windstam, S.T. ; Groenewald, J.Z. - \ 2012
Persoonia 28 (2012). - ISSN 0031-5850 - p. 138 - 182.
sp-nov - allied genera - south-africa - diaporthales - eucalyptus - genus - cryphonectriaceae - gnomoniaceae - reevaluation - evolutionary
Novel species of microfungi described in the present study include the following from Australia: Phytophthora amnicola from still water, Gnomoniopsis smithogilvyi from Castanea sp., Pseudoplagiostoma corymbiae from Corymbia sp., Diaporthe eucalyptorum from Eucalyptus sp., Sporisorium andrewmitchellii from Enneapogon aff. lindleyanus, Myrmecridium banksiae from Banksia, and Pilidiella wangiensis from Eucalyptus sp. Several species are also described from South Africa, namely: Gondwanamyces wingfieldii from Protea caffra, Montagnula aloes from Aloe sp., Diaporthe canthii from Canthium inerne, Phyllosticta ericarum from Erica gracilis, Coleophoma proteae from Protea caffra, Toxicocladosporium strelitziae from Strelitzia reginae, and Devriesia agapanthi from Agapanthus africanus. Other species include Phytophthora asparagi from Asparagus officinalis (USA), and Diaporthe passiflorae from Passiflora edulis (South America). Furthermore, novel genera of coelomycetes include Chrysocrypta corymbiae from Corymbia sp. (Australia), Trinosporium guianense, isolated as a contaminant (French Guiana), and Xenosonderhenia syzygii, from Syzygium cordatum (South Africa). Pseudopenidiella piceae from Picea abies (Czech Republic), and Phaeocercospora colophospermi from Colophospermum mopane (South Africa) represent novel genera of hyphomycetes. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
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