Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera

Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the ß-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa

Systematic reappraisal of species in Phoma section Paraphoma, Pyrenochaeta and Pleurophoma

Sequence data from the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of isolates of Phoma section Paraphoma were compared with those of representative isolates of the morphologically similar anamorph genera Pleurophoma and Pyrenochaeta and of the type species of Phoma sections Phoma, Pilosa and Plenodomus. Phoma section Paraphoma was found to be highly polyphyletic within the Pleosporales and only distantly related to Phoma section Phoma. The genus Paraphoma, which is based on Paraphoma radicina, is reintroduced in the Phaeosphaeriaceae with two additional taxa. The new genera Setophoma and Neosetophoma, type species Setophoma terrestris comb. nov. and Neosetophoma samarorum comb. nov., are introduced and represent species that are closely related to Paraphoma but differ based on morphological characters and molecular phylogeny. Phoma coonsii is transferred to genus Chaetosphaeronema that also belongs to the Phaeosphaeriaceae. Pyrenochaetopsis gen. nov. is introduced to accommodate the type species Pyrenochaetopsis leptospora comb. nov., as well as several other species formerly accommodated in Phoma and Pyrenochaeta. Pyrenochaetopsis is closely related to Pyrenochaeta and classified in the Cucurbitariaceae. Pleurophoma cava is transferred to genus Pyrenochaeta. The new genera elucidate the confusing taxonomy of species in genera Phoma, Pyrenochaeta and Pleurophoma and recognize monophyletic genera with distinct teleomorph affinities

Phyllosticta citriasiana sp. nov., the cause of Citrus tan spot of Citrus maxima in Asia

Guignardia citricarpa, the causal agent of Citrus Black Spot, is subject to phytosanitary legislation in the European Union and the U.S.A. This species is frequently confused with G. mangiferae, which is a non-pathogenic, and is commonly isolated as an endophyte from citrus fruits and a wide range of other hosts. Recently, necrotic spots similar to those caused by G. citricarpa were observed on fruit of Citrus maxima intercepted in consignments exported from Asia. In these spots, pycnidia and conidia of a Guignardia species closely resembling G. citricarpa were observed, and therefore measures were taken for the consignments in line with the European Union legislation for G. citricarpa. To determine the identity of the causal organism on this new host, fungal isolates were subjected to DNA sequence analysis of the internal transcribed spacer region (ITS1, 5.8S, ITS2), translation elongation factor 1-alpha (TEF1) and actin genes. A combined phylogenetic tree resolved three species correlating to G. citricarpa, G. mangiferae and a previously undescribed species, Phyllosticta citriasiana sp. nov., closely related to G. citricarpa. Morphologically P. citriasiana can be distinguished from G. citricarpa by having larger conidia, longer conidial appendages, and in not producing any diffuse yellow pigment when cultivated on oatmeal agar (OA). Furthermore, it is distinguishable from G. mangiferae by having smaller conidia, with a narrower mucoid sheath. In culture, colonies of P. citriasiana can also be distinguished from G. citricarpa and G. mangiferae by being darker shades of grey and black on OA, malt extract agar (MEA), potato-dextrose agar, and cornmeal agar. Furthermore, cultures of P. citriasiana achieved optimal growth after 2 weeks at 21-27°C, and ceased to grow at 30-33°C. In contrast, colonies of G. citricarpa and G. mangiferae achieved optimal growth at 27-30°C, and ceased to grow at 30-36°C Colonies of P. citriasiana also grew faster than those of G. citricarpa and G. mangiferae on OA and MEA. Phyllosticta citriasiana appears to be a harmful pathogen of Citrus maxima, causing a tan spot on fruit, underlining the need for further surveys and research to determine its distribution and host range

Multiple Didymella teleomorphs are linked to the Phoma clematidina morphotype

The fungal pathogen Phoma clematidina is used as a biological agent to control the invasive plant species Clematis vitalba in New Zealand. Research conducted on P. clematidina as a potential biocontrol agent against C. vitalba, led to the discovery of two perithecial-forming strains. To assess the diversity of P. clematidina and to clarify the teleomorph-anamorph relationship, phylogenetic analyses of 18 P. clematidina strains, reference strains representing the Phoma sections in the Didymellaceae and strains of related species associated with Clematis were conducted. Partial sequences of the ITS1, ITS2 and 5.8S rRNA gene, the ß-tubulin gene and 28S rRNA gene were used to clarify intra- and inter-species relationships. These analyses revealed that P. clematidina resolves into three well-supported clades which appear to be linked to differences in host specificity. Based on these findings, Didymella clematidis is newly described and the descriptions of P. clematidina and D. vitalbina are amended

Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation

Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic

Biologische melkveehouderij heeft toekomst met weerbare koe

In 2007 is onderzoek gedaan naar de visie van de biologische sector op diergezondheid en dierenwelzijn. Veehouders uit vier sectoren (melkvee, geiten, varkens en pluimvee) zijn geïnterviewd over hun visie en ideeën rond diergezondheid en dierenwelzijn. Voor de biologische melkveesector zijn 31 melkveehouders individueel ondervraagd. Daarna zijn tijdens een bijeenkomst van Natuurweide nog eens 25 veehouders aan het woord geweest. De uitkomsten van het onderzoek geven onderzoekers en beleidsmakers een beeld van de aspecten die de sector belangrijk vindt. Dit kan als basis dienen voor nieuw onderzoek of beleid. Daarnaast heeft u nu als melkveehouder de mogelijkheid om uw eigen visie te toetsen aan wat er leeft bij uw collega’s. Samengevat vinden de biologische melkveehouders dat zij een veilig en gezond product moeten leveren op een maatschappelijk en economisch verantwoorde manier met gezonde koeie

Bloedingsziekte in paardenkastanje

Samenvatting van de voordracht te houden op 30 november 2005 tijdens de Najaarsvergadering van de KNPV (Koninklijke Nederlandse Plantenziektekundige Vereniging). Onderzoek naar oorzaak en distributie van de paardenkastanjeziekt

Taxonomie van plant-pathogene schimmels als basis voor identificatie en detectie: resultaten van het Uitvoeringsconsortium Schimmels

Plant-pathogene schimmels worden traditioneel geïdentificeerd op basis van morfologische karakteristieken. Dit is over het algemeen tijdrovend, veel expertise en leidt vaak tot misidentificatie. Het doel van het werk uitgevoerd door het Uitvoeringsconsortium Schimmels was dan ook gericht op de verbetering van detectie- en identificatietechnieken van plant pathogene schimmels met de nadruk op quarantaineorganismen. Op grond van het economische, wetenschappelijke, en ecologische belang, de aanwezigheid van Q-organismen, en de wetenschappelijke startpositie binnen Nederland is in eerste instantie de keuze gevallen op de geslachten Colletotrichum, Phoma, en Phytophthora. De gegenereerde dat zijn opgenomen in de Q-bank