Redisposition of phoma-like anamorphs in Pleosporales.

The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and Mycosphaerella, suggesting the polyphyly of the genus. Recent molecular, phylogenetic studies led to the conclusion that Phoma should be restricted to Didymellaceae. The present study focuses on the taxonomy of excluded Phoma species, currently classified in Phoma sections Plenodomus, Heterospora and Pilosa. Species of Leptosphaeria and Phoma section Plenodomus are reclassified in Plenodomus, Subplenodomus gen. nov., Leptosphaeria and Paraleptosphaeria gen. nov., based on the phylogeny determined by analysis of sequence data of the large subunit 28S nrDNA (LSU) and Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS). Phoma heteromorphospora, type species of Phoma section Heterospora, and its allied species Phoma dimorphospora, are transferred to the genus Heterospora stat. nov. The Phoma acuta complex (teleomorph Leptosphaeria doliolum), is revised based on a multilocus sequence analysis of the LSU, ITS, small subunit 18S nrDNA (SSU), ß-tubulin (TUB), and chitin synthase 1 (CHS-1) regions. Species of Phoma section Pilosa and allied Ascochyta species were determined to belong to Pleosporaceae based on analysis of actin (ACT) sequence data. Anamorphs that are similar morphologically to Phoma and described in Ascochyta, Asteromella, Coniothyrium, Plectophomella, Pleurophoma and Pyrenochaeta are included in this study. Phoma-like species, which grouped outside the Pleosporineae based on a LSU sequence analysis, are transferred to the genera Aposphaeria, Paraconiothyrium and Westerdykella. The genera Medicopsis gen. nov. and Nigrograna gen. nov. are introduced to accommodate the medically important species formerly known as Pyrenochaeta romeroi and Pyrenochaeta mackinnonii, respectively. TAXONOMIC NOVELTIES: New genera: Medicopsis Gruyter, Verkley & Crous, Nigrograna Gruyter, Verkley & Crous, Paraleptosphaeria Gruyter, Verkley & Crous, Subplenodomus Gruyter, Verkley & Crous. New species: Aposphaeria corallinolutea Gruyter, Aveskamp & Verkley, Paraconiothyrium maculicutis Verkley & Gruyter. New combinations: Coniothyrium carteri (Gruyter & Boerema) Verkley & Gruyter, C. dolichi (Mohanty) Verkley & Gruyter, C. glycines (R.B. Stewart) Verkley & Gruyter, C. multiporum (V.H. Pawar, P.N. Mathur & Thirum.) Verkley & Gruyter, C. telephii (Allesch.) Verkley & Gruyter, Heterospora (Boerema, Gruyter & Noordel.) Gruyter, Verkley & Crous, H. chenopodii (Westend.) Gruyter, Aveskamp & Verkley, H. dimorphospora (Speg.) Gruyter, Aveskamp & Verkley, Leptosphaeria errabunda (Desm.) Gruyter, Aveskamp & Verkley, L. etheridgei (L.J. Hutchison & Y. Hirats.) Gruyter, Aveskamp & Verkley, L. macrocapsa (Trail) Gruyter, Aveskamp & Verkley, L. pedicularis (Fuckel) Gruyter, Aveskamp & Verkley, L. rubefaciens (Togliani) Gruyter, Aveskamp & Verkley, L. sclerotioides (Sacc.) Gruyter, Aveskamp & Verkley, L. sydowii (Boerema, Kesteren & Loer.) Gruyter, Aveskamp & Verkley, L. veronicae (Hollós) Gruyter, Aveskamp & Verkley, Medicopsis romeroi (Borelli) Gruyter, Verkley & Crous, Nigrograna mackinnonii (Borelli) Gruyter, Verkley & Crous, Paraconiothyrium flavescens (Gruyter, Noordel. & Boerema) Verkley & Gruyter, Paracon. fuckelii (Sacc.) Verkley & Gruyter, Paracon. fusco-maculans (Sacc.) Verkley & Gruyter, Paracon. lini (Pass.) Verkley & Gruyter, Paracon. tiliae (F. Rudolphi) Verkley & Gruyter, Paraleptosphaeria dryadis (Johanson) Gruyter, Aveskamp & Verkley, Paralept. macrospora (Thüm.) Gruyter, Aveskamp & Verkley, Paralept. nitschkei (Rehm ex G. Winter) Gruyter, Aveskamp & Verkley, Paralept. orobanches (Schweinitz: Fr.) Gruyter, Aveskamp & Verkley, Paralept. praetermissa (P. Karst.) Gruyter, Aveskamp & Verkley, Plenodomus agnitus (Desm.) Gruyter, Aveskamp & Verkley, Plen. biglobosus (Shoemaker & H. Brun) Gruyter, Aveskamp & Verkley, Plen. chrysanthemi (Zachos, Constantinou & Panag.) Gruyter, Aveskamp & Verkley, Plen. collinsoniae (Dearn. & House) Gruyter, Aveskamp & Verkley, Plen. confertus (Niessl ex Sacc.) Gruyter, Aveskamp & Verkley, Plen. congestus (M.T. Lucas) Gruyter, Aveskamp & Verkley, Plen. enteroleucus (Sacc.) Gruyter, Aveskamp & Verkley, Plen. fallaciosus (Berl.) Gruyter, Aveskamp & Verkley, Plen. hendersoniae (Fuckel) Gruyter, Aveskamp & Verkley, Plen. influorescens (Boerema & Loer.) Gruyter, Aveskamp & Verkley, Plen. libanotidis (Fuckel) Gruyter, Aveskamp & Verkley, Plen. lindquistii (Frezzi) Gruyter, Aveskamp & Verkley, Plen. lupini (Ellis & Everh.) Gruyter, Aveskamp & Verkley, Plen. pimpinellae (Lowen & Sivan.) Gruyter, Aveskamp & Verkley, Plen. tracheiphilus (Petri) Gruyter, Aveskamp & Verkley, Plen. visci (Moesz) Gruyter, Aveskamp & Verkley, Pleospora fallens (Sacc.) Gruyter & Verkley, Pleo. flavigena (Constantinou & Aa) Gruyter & Verkley, Pleo. incompta (Sacc. & Martelli) Gruyter & Verkley, Pyrenochaetopsis pratorum (P.R. Johnst. & Boerema) Gruyter, Aveskamp & Verkley, Subplenodomus apiicola (Kleb.) Gruyter, Aveskamp & Verkley, Subplen. drobnjacensis (Bubák) Gruyter, Aveskamp & Verkley, Subplen. valerianae (Henn.) Gruyter, Aveskamp & Verkley, Subplen. violicola (P. Syd.) Gruyter, Aveskamp & Verkley, Westerdykella capitulum (V.H. Pawar, P.N. Mathur & Thirum.) de Gruyter, Aveskamp & Verkley, W. minutispora (P.N. Mathur ex Gruyter & Noordel.) Gruyter, Aveskamp & Verkley. New names: Pleospora angustis Gruyter & Verkley, Pleospora halimiones Gruyter & Verkley.

A framework to bridge scales in distribution modeling of soil microbiota.

Creating accurate habitat suitability and distribution models (HSDMs) for soil microbiota is far more challenging than for aboveground organism groups. In this perspective paper, we propose a conceptual framework that addresses several of the critical issues holding back further applications. Most importantly, we tackle the mismatch between the broadscale, long-term averages of environmental variables traditionally used, and the environment as experienced by soil microbiota themselves. We suggest using nested sampling designs across environmental gradients and objectively integrating spatially hierarchic heterogeneity as covariates in HSDMs. Second, to incorporate the crucial role of taxa co-occurrence as driver of soil microbial distributions, we promote the use of joint species distribution models, a class of models that jointly analyze multiple species' distributions, quantifying both species-specific environmental responses (i.e. the environmental niche) and covariance among species (i.e. biotic interactions). Our approach allows incorporating the environmental niche and its associated distribution across multiple spatial scales. The proposed framework facilitates the inclusion of the true relationships between soil organisms and their abiotic and biotic environments in distribution models, which is crucial to improve predictions of soil microbial redistributions as a result of global change.

Fusarium foetens, a new species pathogenic to begonia elatior hybrids (Begonia x hiemalis) and the sister taxon of the Fusarium oxysporum species complex.

A new disease recently was discovered in begonia elatior hybrid (Begonia × hiemalis) nurseries in The Netherlands. Diseased plants showed a combination of basal rot, vein yellowing and wilting and the base of collapsing plants was covered by unusually large masses of Fusarium macroconidia. A species of Fusarium was isolated consistently from the discolored veins of leaves and stems. It differed morphologically from F. begoniae, a known agent of begonia flower, leaf and stem blight. The Fusarium species resembled members of the F. oxysporum species complex in producing short monophialides on the aerial mycelium and abundant chlamydospores. Other phenotypic characters such as polyphialides formed occasionally in at least some strains, relatively long monophialides intermingled with the short monophialides formed on the aerial mycelium, distinct sporodochial conidiomata, and distinct pungent colony odor distinguished it from the F. oxysporum species complex. Phylogenetic analyses of partial sequences of the mitochondrial small subunit of the ribosomal DNA (mtSSU rDNA), nuclear translation elongation factor 1α (EF-1α) and ß-tubulin gene exons and introns indicate that the Fusarium species represents a sister group of the F. oxysporum species complex. Begonia × hiemalis cultivars Bazan, Bellona and Netja Dark proved to be highly susceptible to the new species. Inoculated plants developed tracheomycosis within 4 wk, and most died within 8 wk. The new taxon was not pathogenic to Euphorbia pulcherrima, Impatiens walleriana and Saintpaulia ionantha that commonly are grown in nurseries along with B. × hiemalis. Inoculated plants of Cyclamen persicum did not develop the disease but had discolored vessels from which the inoculated fungus was isolated. Given that the newly discovered begonia pathogen is distinct in pathogenicity, morphology and phylogeny from other fusaria, it is described here as a new species, Fusarium foetens.

First Occurrence of Alternaria alternata on Gypsophila paniculata in Bulgaria.

During late summer 1996 to 1997, 27 to 30% of Gypsophila paniculata (baby's-breath) plants were noted as diseased in an experimental field (Kazanlak, Bulgaria). Symptoms on lower and middle leaves consisted of small circular spots, with light brown centers and reddish purple margins. Development of numerous spots (which grew larger) and, especially, damage to the midrib led to withering of leaflets. Conidiophores of the isolated fungus were dark, formed singly or in clusters, were unbranched with three to eight septa, and were 40 to 120 µm long. Conidia, produced in branched chains (four to six conidia or longer), were brown, globose, and ovate to pyriform with short beaks, contained four to five transverse and zero to two longitudinal septa, and were 36.6 to 46.6 × 10.0 to 13.3 µm. The fungus was identified as Alternaria alternata. Pathogenicity was confirmed by artificial inoculation of potted G. paniculata and Dianthus caryophyllus plants. Conidia (2 weeks old) produced on potato dextrose agar were sprayed on plants in a 5 × 103 suspension, and plants were incubated at 20 to 24°C in a moist chamber for 2 days. Lesion development in both plant species was observed and recorded at 4 to 5 and 6 to 7 days after inoculation, respectively. Lesions were most numerous on G. paniculata. This is the first report of A. alternata on baby's-breath in Bulgaria. References: (1) M. B. Ellis. 1971. Dematiaceous Hyphomycetes. Commonwealth Mycological Institute, Kew, U.K. (2) E. G. Simmons. Alternaria themes and variations. Mycotaxon 37:79, 1990.

First Report of Cercospora traversiana on Trigonella coerulea in Bulgaria.

In the spring of 1996, diseased plants of Trigonella coerulea were noted in an experimental area at Kazanlak, Bulgaria. The primary symptoms were leaf spots 8 to 2 mm in diameter, light brown then becoming gray and slightly zonate, and surrounded by a diffuse chlorotic margin. When single lesions occur the disease normally develops as a typical leaf spot. However, the development of more than one spot is followed rapidly by yellowing and withering of entire leaflets. Stem lesions usually begin at the point of leaf attachment, extend both directions about 15 to 20 mm, and often encircle the stems. Isolations on potato dextrose agar (PDA) yielded a slow-growing, gray fungus. Conidia from the isolated fungus when inoculated at 3.104 spores per ml on potted T. coerulea seedlings and kept in a moisture chamber for 48 h caused foliar spots in 5 to 8 days and sporulating structures similar to those seen in field observations. Simultaneous inoculation of T. foenum-graecum (fenugreek) plants produced similar symptoms, but the percentage of successfully inoculated leaves (3.6%) was lower than in T. coerulea (27.6%). Conidiophores of the fungus are dark, arising in clusters, unbranched, septate (1 to 3), and have small conidial scars. Conidia are hyaline, straight, multicelled (1 to 17), tapering at the base, and measured 30 to 212 × 4 to 6 µm. The pathogen was identified as Cercospora traversiana Sacc. and this is the first report of its occurrence in Bulgaria.

First Report of Phoma strasseri as a Pathogen of Stachys officinalis in Bulgaria.

For several years, a leaf spot disease has been observed on Betony, Stachys officinalis (synonym Betonica officinalis), in an experimental field in Kazanlak, Bulgaria. The round to somewhat angular spots (6 to 8 mm diameter) are dark brown with a pale center and have a chlorotic halo. A Phoma species isolated from the lesions formed regular to irregular, light brown colonies on potato dextrose agar (PDA). The isolate was studied as described by de Gruyter and Noordeloos (2). After 7 days, the growth rate was 43 mm on oatmeal agar and 33 mm on malt agar; the colonies were olivaceous gray-to-glauceous gray with a regular outline and with finely floccose, white-to-olivaceous gray aerial mycelium. Pycnidia, produced after 2 weeks, were ostiolate, globose to subglobose, 120 to 280 µm in diameter, citrine or honey, and later olivaceous to olivaceous black. The conidiogenous cells were globose to bottle shaped, 2 to 6 × 3 to 5 µm. The conidia were hyaline and unicellular, 5 to 7.5 × 2.5 to 4.2 µm, cylindrical to ellipsoidal with several small, scattered guttules. Chlamydospores were absent. According to these in vitro characters and after comparing the isolate with several Phoma isolates present in the culture collection of the Dutch Plant Protection Service, Wageningen, the Netherlands, the fungus has been identified as Phoma strasseri Moesz. The pathogenicity of the isolate was confirmed by artificial leaf inoculation of potted S. officinalis plants with a spore suspension (8 × 106 spores per ml) kept in a moist chamber for 48 h at a mean average temperature of 16°C. Leaf spots observed 4 to 5 days after inoculation were similar to those observed in the field. P. strasseri was subsequently reisolated from the spots. P. strasseri (synonym Phoma mentae Strasser) has been recorded as the cause of rhizome and stem rot on mint, Mentha spp., in Europe, Japan, and North America (3). In addition, this fungus has been found in New Zealand (strain identified at the Dutch Plant Protection Service, unpublished data). To our knowledge, this is the first report of P. strasseri on S. officinalis in Bulgaria. P. strasseri may produce septate conidia and, therefore, can be classified in Phoma section Phyllostictoides Zherbele ex Boerema (1). P. strasseri clearly differs from other Phoma species described on Lamiaceae: Phoma leonuri Letendre (Phoma section Plenodomus (Preuss) Boerema et al., pycnidia scleroplectenchymatous, conidia aseptate, 3.5 to 5.5 × 1.5 to 2.5 µm), Phoma dorenboschii Noordel. & de Gruyter (Phoma Sacc. section Phoma, conidia aseptate, 3 to 5.5 × 2 to 2.5 µm, producing dendritic crystals in vitro), and Phoma valerianae Henn. (Phoma Sacc. section Phoma, conidia aseptate, 2.5 to 4 × 1.5 to 2 µm). Occasionally P. strasseri has been isolated from other Lamiaceae, namely Monarda didyma (Dutch Plant Protection Service, unpublished data). There is also a report from Valeriana sp. (3). References: (1) G. H. Boerema. Mycotaxon 64:321, 1998. (2) J. de Gruyter and M. E. Noordeloos. Persoonia 15(1):71, 1992. (3) C. E. Horner. Plant Dis. Rep. 55:814, 1971.

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 beta-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.

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 Lophiostomataceaes. 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.

A class-wide phylogenetic assessment of Dothideomycetes.

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.