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Anthracoidea species are highly host-specific smut fungi. Their host range is restricted to a single sedge species or sedge species belonging to the same or closely related sections. The species on Carex obtusata was referred to as Anthracoidea caryophylleae. However, the hosts of A. caryophylleae were reduced to carices in Carex sect. Mitratae, in its traditional circumscription. In the most recently proposed classification of Carex, C. obtusata has been placed within the Capitata Clade of C. subgen. Euthyceras. In order to clarify the taxonomic status of the Anthracoidea species on C. obtusata, we conducted a molecular study of specimens on C. obtusata and C. caryophyllea, using LSU rDNA sequences. It was found that the Anthracoidea species on C. obtusata is distinct from A. caryophylleae. A new species, Anthracoidea obtusatae on C. obtusata, is described and illustrated from Russia, based on a specimen from the Altay Mts. Its phylogenetic placement and affinities in Anthracoidea are analyzed. Anthracoidea obtusatae is distributed in Central Asia—the Northern Tian Shan Range (Zailiysky Alatau Range and Ketmen Ridge) and the Russian and Mongolian Altay Mts. A morphological examination of a specimen of Anthracoidea on C. obtusata from Canada found that its spore morphology did not match that of A. obtusatae. Additional collections and molecular study are required to clarify the taxonomic status of the North American Anthracoidea species on C. obtusata.

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

A new smut fungus, Entyloma eranthidis on Eranthis longistipitata from Uzbekistan, revealed by molecular, morphological, and ecological evidence, is described and illustrated. It differs from all other species of Entyloma by host specialization on Eranthis and by having longer (≤35(–38) μm) spores and thicker (≤10(–12) μm) spore walls. ITS rDNA sequence analysis indicates that the new species does not cluster with other species of Entyloma on Ranunculaceae.

Species delimitation is one of the most fundamental processes in biology. Biodiversity undertakings, for instance, require explicit species concepts and criteria for species delimitation in order to be relevant and translatable. However, a perfect species concept does not exist for Fungi. Here, we review the species concepts commonly used in Basidiomycota, the second largest phylum of Fungi that contains some of the best known species of mushrooms, rusts, smuts, and jelly fungi. In general, best practice is to delimitate species, publish new taxa, and conduct taxonomic revisions based on as many independent lines of evidence as possible, that is, by applying a so-called unifying (or integrative) conceptual framework. However, the types of data used vary considerably from group to group. For this reason we discuss the different classes of Basidiomycota, and for each provide: (i) a general introduction with difficulties faced in species recognition, (ii) species concepts and methods for species delimitation, and (iii) community recommendations and conclusions.

Patterns and drivers of succession provide insight into the mechanisms that govern community assembly and are indicators of community resilience and stability but are still poorly understood in microbial communities. We assessed whether the successional trends of woody vegetation are mirrored by foliar fungal endophyte communities of three tree species that are abundant across the woody successional gradient using a total amplicon sequencing approach. Additionally, we test the relative contribution of host identity, abiotic predictors, biotic factors, and spatial distance between sites in predicting community composition and species richness of endophyte communities. Unlike the woody community, endophyte communities showed no consistent evidence of deterministic successional trends. Host identity was the most important factor structuring fungal endophyte community composition. Spatial distance played some role in explaining differences in community composition, but the effects of this and other environmental variables were small and not consistent between different host species. Much of the variation in endophyte composition remained unexplained. Host identity was most important in predicting endophyte richness. Although endophyte communities showed no deterministic succession, community assembly was most strongly influenced by host identity and spatial distance.

Kálmán Vánky (15th of June 1930–18th of October 2021) was arguably the most prolific researcher of smut fungi so far. He published more than 1000 taxonomic novelties, and crowned his outstanding oeuvre with the most comprehensive monograph of the smut fungi (Smut Fungi of the World) written to date.

Fungal communities in above-ground tree tissues are hyperdiverse and are influenced by biotic interactions with other organisms living in or on these tissues. These biotic interactions are, however, still poorly understood. In this study, we aimed to understand how insect-associated gall formation on

Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

The species of Anthracoidea on Carex are host-specific smut fungi restricted to sedges belonging to the same or closely related sections. They are characterized by sori that form black, hard bodies around aborted nuts of their hosts. In Carex sect. Hallerianae, only one species, C. halleriana, is known as a host of Anthracoidea. The taxonomic status of this smut fungus was problematic due to a lack of molecular data. It has been reported under different names, mainly as “A. caricis” or “A. irregularis”. A comparative morphological study and molecular phylogenetic analysis, using LSU (large subunit) nuclear rDNA sequences, supported the recognition of a distinct species, A. hallerianae. The new species is described and illustrated based on material from Central Europe, the Iberian Peninsula, the Balkan Peninsula, the Mediterranean area and Transcaucasia. Citation: Denchev T. T., Denchev C. M., Koopman J., Begerow D. & Kemler M. 2021: Host specialization and molecular evidence support a distinct species of smut fungus, Anthracoidea hallerianae (Anthracoideaceae), on Carex halleriana (Cyperaceae). – Willdenowia 51: 57–67. Version of record first published online on 9 March 2021 ahead of inclusion in April 2021 issue.

Foliar fungi, especially endophytic fungi, constitute an important part of the microbiome of plants. Yet little is known about the composition of these communities. In this study, we isolated fungi from leaf tissues of the desert plant Welwitschia mirabilis to determine the culturable diversity of the foliar fungal community. The isolated fungal taxa, which grouped into 17 distinct lineages, were identified by sequencing elongation factor 1 alpha, beta-tubulin 1, beta-tubulin 2 and the internal transcribed spacer region. The culturable community was mainly composed of cosmopolitan fungal genera despite the unique taxonomic position of the plant and its geographic isolation. To test for endemism in two of the common fungal genera, Alternaria and Aureobasidium, we built haplotype networks using a global data set. Even this broad data set showed little evidence for specialisation within this unique host or its geographical location. The data suggest that the culturable members of communities of leaf-associated fungi in habitats with little plant coverage, such as the Namib Desert, are mainly established by long-distance aerially distributed fungal inocula and few of these taxa co-evolve with the host within the habitat.Significance: The culturable members of fungal communities associated with an ecological and evolutionary isolated plant have not co-speciated with their hosts, but to a large extent are composed of globally distributed fungal species. Harsh environmental conditions and the geographic isolation of host plants seem to favour ubiquitous fungal species over more specialist fungal species. Open data sets*: https://www.ncbi.nlm.nih.gov/genbank *see accession numbers in text

After examination of specimens, mainly from the herbarium (MA) and the mycological collection (MA-Fungi) of the Royal Botanic Garden of Madrid, we report several novelties on smut fungi within Europe. Two species of smut fungi, Sporisorium egyptiacum and Tilletia viennotii, are reported for the first time from Europe. A finding of Sphacelotheca polygoni-serrulati represents a second record for Europe. Six species of smut fungi, Moreaua kochiana, Schizonella elynae, Sporisorium egyptiacum, Thecaphora thlaspeos, Tilletia viennotii, and Ustanciosporium majus, are recorded for the first time from the Iberian Peninsula. Five species of smut fungi, Moreaua kochiana, Schizonella elynae, Sporisorium egyptiacum, Thecaphora thlaspeos, and Ustanciosporium majus, are newly recorded from Spain. Three species, Moreaua kochiana, Sphacelotheca polygoni-serrulati, and Tilletia viennotii, are new for Portugal. A specimen of Moreaua kochiana represents a new record for France. Arabis serpillifolia is reported as a new host of The-caphora thlaspeos. New distribution records from the Iberian Peninsula are given for Anthracoidea arenariae, Microbotryum minuartiae, M. silenes-saxifragae, and Tranzscheliella sparti. We also include a phylogenetic analysis of DNA sequences of Moreaua kochiana, generated in this study, to understand this species’ relationships within its genus., Tras examinar especímenes principalmente del herbario (MA) y de la colección de hongos (MA-Fungi) del Real Jardín Botánico de Madrid reportamos varias novedades de carboneros dentro de Europa.Dos especies de carbones, Sporisorium egyptiacum y Tilletia viennotii, se citan por primera vez para Europa. Reportamos también la segunda cita de Sphacelotheca polygoni-serrulati para Europa. Seis especies, Moreaua kochiana, Schizonella elynae, Sporisorium egyptiacum, Thecaphora thlaspeos, Tilletia viennotii, y Ustanciosporium majus, se citan por primera vez para la Península Ibérica; cinco especies, Moreaua kochiana, Schizonella elynae, Sporisorium egyptiacum, Thecaphora thlaspeos, y Ustanciosporium majus, son nuevas citas para España; tres especies, Moreaua kochiana, Sphacelotheca polygoni-serrulati, y Tilletia viennotii, son nuevas citas para Portugal. Una colección de Moreaua kochiana representa una nueva cita para Francia. Arabis serpillifolia se menciona por primera vez como un hospedante para Thecaphora thlaspeos. Se registran nuevas localidades en la Península Ibérica para Anthracoidea arenariae, Microbotryum minuartiae, M. silenes-saxifragae y Tranzscheliella sparti. Incluimos también un análisis filogenético de secuencias de ADN de dos especímenes de Moreaua kochiana, generadas en este estudio, para entender las relaciones filogenéticas de esta especie dentro su género.

Pilze wachsen entweder als einzellige Hefen oder mit mehrzelligen Hyphen. Bei Hyphen handelt es sich um lange, haufig septierte Zellschlauche. Um Nahrstofftransport und Zellplasmabewegungen zwischen den Zellen zu gewahrleiste sind die Septen mit einem Septenporus versehen, dessen Aufbau charakteristisch fur bestimmte pilzliche Untergruppen ist. Eine Besonderheit der Hyphen ist, dass sie nur apikal wachsen und unter gunstigen Nahrstoffbedingungen theoretisch unendlich wachsen konnen. So stammt zum Beispiel der groste bekannte Organismus (bekannt als humongous fungus) aus der Wurzelfaule erzeugenden Gattung Armillaria (Hallimasch), besiedelt mehrere Hektar Waldboden in Oregon und wiegt mehrere Tonnen. Auch die Bildung von Hexenringen, bei denen die Fruchtkorper einer Art in einem Kreis stehen, basiert auf dieser Form des stetigen apikalen Hyphenwachstums: ausgehend von einer Spore, wachsen und verzweigen sich die Hyphen in alle Richtungen. Da alle Hyphen bei entsprechendem Nahrungsangebot mit derselben Geschwindigkeit wachsen, sind sie an der Spitze gleich alt und bilden die Fruchtkorper auch zum gleichen Zeitpunkt.

Pilze vereinen sowohl Merkmale von Tieren, wie die heterotrophe Ernahrungsweise oder das Vorhandensein von Chitin, als auch von Pflanzen, wie die Immobilitat oder das Vorhandensein von Zellwanden. Nicht nur diese Mischung aus Merkmalen, sondern auch ihre okologische Bedeutung und ihre grose Diversitat machen deutlich, dass Pilze eine eigene wichtige Grosgruppe der Eukaryoten bilden. Die Kombination verschiedener Merkmale, die auch in anderen Gruppen vorkommen, macht ihre Abgrenzung nicht immer einfach. Fruher wurden verschiedene Gruppen als „Pilze“ zusammengefasst. Die Myxomyceten, die Dictyostelida und die Peronosporomycetes (Oomycota/Oophyta) werden hier an anderer Stelle behandelt, da detaillierte morphologische Untersuchungen sowie molekulare Daten gezeigt haben, dass es sich bei der ursprunglichen Zusammenfassung der „Pilze“ um eine kunstliche Gruppierung handelte. Die Gruppe der „Fungi“ – auch als „echte Pilze“ oder „Chitinpilze“ bezeichnet – umfasst die Schwestergruppe der Holozoa (Metazoa und Choanoflagellaten) – also pilzliche Gruppen, die Chitin als ein Baustein der Zellwand nutzen und ursprunglich opisthokont begeiselt waren. Im Laufe der Evolution wurden die begeiselten Stadien offensichtlich in Anpassung an das Landleben reduziert. Im Vergleich zu Tieren und Pflanzen haben Pilze keine echten Gewebe entwickelt. Neben einzelligen Formen und Stadien ist die Hyphe das grundlegende Strukturelement, das in Pseudoparenchymen komplexe Strukturen aufbauen kann und die morphologische Differenzierung ermoglichet. Dabei sind sowohl auf zellularer als auch auf anatomisch-morphologischer Ebene Strukturen entstanden, die nur bei den echten Pilzen zu finden sind. Dabei sind vor allem die Fruchtkorper sehr formenreich.

The increasing number and duration of inundations is reported to be a consequence of climate change and may severely compromise non-adapted macroorganisms. The effect of flooding events on terrestrial and aquatic microbial communities is, however, less well understood. They may respond to the changed abiotic properties of their native habitat, and the native community may change due to the introduction of alien species. We designed an experiment to investigate the effect of five different flooding durations on the terrestrial and aquatic communities of eukaryotic microorganism, using the AquaFlow mesocosms. With amplicon sequencing of the small subunit (SSU) and internal transcribed spacer (ITS) rRNA gene regions, we analyzed community compositions directly before and after flooding. Subsequently, they were monitored for another 28 days, to determine the sustainability of community changes. Our results revealed a temporary increase in similarity between terrestrial and aquatic communities according to OTU composition (operational taxonomic unit, serves as a proxy for species). Increased similarity was mainly caused by the transmission of OTUs from water to soil. A minority of these were able to persist in soil until the end of the experiment. By contrast, the vast majority of soil OTUs was not transmitted to water. Flooding duration affected the community structure (abundance) more than composition (occurrence). Terrestrial communities responded immediately to flooding and the flooding duration influenced the community changes. Independent from flooding duration, all terrestrial communities recovered largely after flooding, indicating a remarkable resilience to the applied disturbances. Aquatic communities responded immediately to the applied inundations too. At the end of the experiment, they grouped according to the applied flooding duration and the amount of ammonium and chloride that leached from the soil. This indicates a sustained long-term response of the aquatic communities to flooding events.

The Claude Leon Foundation, University of Pretoria, the Tree Protection Co-operative Programme, and the Genome Research Institute at the University of Pretoria.

Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal&ndash, host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal&ndash, plant and fungal&ndash, microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant&ndash, microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant&ndash, microbe interactions.

Author(s): Valent, Barbara; Farman, Mark; Tosa, Yukio; Begerow, Dominik; Fournier, Elisabeth; Gladieux, Pierre; Islam, M Tofazzal; Kamoun, Sophien; Kemler, Martin; Kohn, Linda M; Lebrun, Marc-Henri; Stajich, Jason E; Talbot, Nicholas J; Terauchi, Ryohei; Tharreau, Didier; Zhang, Ning

National Research Foundation of South Africa (Grant specific unique reference number (UID83924).Tree Protection Co-operative Program (TPCP), the THRIP initiative of the Department of Trade and Industry and the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) based in the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa.

Botryosphaeria dothidea is the type species of Botryosphaeria (Botryosphaeriaceae, Botryosphaeriales). Fungi residing in this order are amongst the most widespread and important canker and dieback pathogens of trees worldwide, with B. dothidea one of the most common species on a large number of hosts. Its taxonomic circumscription has undergone substantial change in the past decade, making it difficult to interpret the large volume of literature linked to the name B. dothidea. This pathogen profile synthesizes the current understanding of B. dothidea pertaining to its distribution, host associations and role as a pathogen in managed and natural woody environments. The prolonged latent infection or endophytic phase is of particular importance, as it implies that the fungus can easily pass undetected by quarantine systems in traded living plants, fruits and other plant parts. Infections typically become obvious only under conditions of host stress, when disease symptoms develop. This study also considers the knowledge emerging from the recently sequenced B. dothidea genome, elucidating previously unknown aspects of the species, including mating and host infection strategies. Despite more than 150 years of research on B. dothidea, there is clearly much to be learned regarding this global tree pathogen. This is increasingly important given the stresses imposed on various woody hosts as a result of climate change. TAXONOMY: Botryosphaeria dothidea (Moug. ex Fr) Ces. & De Not, 1863. Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Botryosphaeriales, Family Botryosphaeriaceae, Genus Botryosphaeria, Species dothidea. HOST RANGE: Confirmed on more than 24 host genera, including woody plants, such as Acacia (= Vachellia), Eucalyptus, Vitis and Pistachio. DISEASE SYMPTOMS: Associated with twig, branch and stem cankers, tip and branch dieback, fruit rot, blue stain and plant death. USEFUL WEBSITES: The Botryosphaeria site for detailed morphological descriptions (http://www.crem.fct.unl.pt/botryosphaeria_site/); Systematic Mycology and Microbiology Laboratory Fungal Database for all literature and associated hosts (https://nt.ars-grin.gov/fungaldatabases/); TreeBASE link for the combined ITS and TEF‐1α tree (http://purl.org/phylo/treebase/phylows/study/TB2:S18906); DOE Joint Genome Institute, JGI Mycocosm for the Botryosphaeria dothidea genome (http://genome.jgi.doe.gov/Botdo1_1/Botdo1_1.home.html).

Yeasts are common in all habitats and interact with dead and living substrates such as plants, animals, and fungi. Besides their saprobic capabilities, parasitic interactions of yeasts and yeast-like organisms were brought into focus through enhanced/new species discovery that expanded our knowledge about phylogenetic relationships of yeasts and parasitic fungal lineages. Especially common dimorphism of many Basidiomycota goes along with an alternating saprobic yeast stage and parasitic filamentous stage. Interestingly, this seems to be a common feature not only for plant parasites but also for animal and fungal parasites. Even some Ascomycota share this character.

Yeasts are integral parts of phylloplane communities of temperate regions, where ecosystems are not only influenced by short-term fluctuations in abiotic conditions, but additionally by cyclic seasonal changes. Phylloplane yeasts possess physiological adaptations, such as pigmentation and extracellular polysaccharides that enable them to resist harsh conditions encountered in these environments. Additionally, through production of plant hormone-like metabolites, they also might influence the behavior, fitness, and growth of their plant host. Here we review how the understanding of yeasts in this environment has improved in the last years due to discoveries in new habitats, new developments in taxonomy, but also the application of environmental sequencing and genomics. These new technologies, as well as traditional approaches, have made it clear that yeasts are not only occupying this environment to gain nutrients, but they are active participants that shape the structure of microbial communities by diverse interactions with other community members.

The group of the anthericolous Microbotryum species on Silene consists of narrowly host-specialized fungi. Despite intensive taxonomic and phylogenetic studies in this group over the past two decades, the actual species richness has not yet been fully uncovered. Thirteen of these species cause typical anther infection, with soral development restricted to the anthers. Three other species cause atypical infection, with soral development resulting in swollen and deformed flowers (completely filled with spores) and affecting both the anthers and the filaments. A comparative morphological study and molecular phylogenetic analyses, using ITS and LSU rDNA sequences, revealed a new species, Microbotryum arcticum, causing anther infection of Silene uralensis subsp. arctica. Microbotryum arcticum is described and illustrated on the basis of material from Greenland and the eastern Canadian Arctic. An emended description of M. savilei, which causes atypical infection of the same host plant in the eastern Canadian Arctic, is also given. Morphological characters of healthy flowers of S. uralensis subsp. arctica are compared with those of flowers with anther infection and with those of flowers with atypical infection.

Currently, the monophyletic lineage of anther smuts on Caryophyllaceae includes 22 species classified in the genus Microbotryum. They are model organisms studied in many disciplines of fungal biology. A molecular phylogenetic approach was used to resolve species boundaries within the caryophyllaceous anther smuts, as species delimitation based solely on phenotypic characters was problematic. Several cryptic species were found amongst the anther smuts on Caryophyllaceae, although some morphologically distinct species were discernible, and most species were characterized by high host-specificity. In this study, anther smut specimens infecting Silene saxifraga were analysed using rDNA sequences (ITS and LSU) and morphology to resolve their specific status and to discuss their phylogenetic position within the lineage of caryophyllaceous anther smuts. The molecular phylogeny revealed that all specimens form a monophyletic lineage that is supported by the morphological trait of reticulate spores with tuberculate interspaces (observed in certain spores). This lineage cannot be attributed to any of the previously described species, and the anther smut on Silene saxifraga is described and illustrated here as a new species, Microbotryum silenes-saxifragae. This species clusters in a clade that includes Microbotryum species, which infect both closely and distantly related host plants growing in diverse ecological habitats. It appears possible that host shifts combined with changes to ecological host niches drove the evolution of Microbotryum species within this clade.

Anther smuts in the genus Microbotryum often show very high host specificity toward their caryophyllaceous hosts, but some of the larger host groups such as Dianthus are crucially undersampled for these parasites so that the question of host specificity cannot be answered conclusively. In this study we sequenced the internal transcribed spacer (ITS) region of members of the Microbotryum dianthorum species complex as well as their Dianthus hosts. We compared phy- logenetictreesoftheseparasitesincludingsequencesofanther smuts from other Caryophyllaceae, mainly Silene ,w ith phy- logenies of Caryophyllaceae that are known to harbor anther smuts. Additionally we tested whether observed patterns in parasitesareduetosharedancestryorifgeographic separation is a factor that should be taken into consideration in delimitat- ing species. Parasites on Dianthus showed mainly an arbitrary distribution on Dianthus hosts, whereas parasites on other Caryophyllaceae formed well-supported monophyletic clades that corresponded to restricted host groups. The same pattern was observed in the Caryophyllaceae studied: morphological- ly described Dianthus species did not correspond well with monophyletic clades based on molecular data, whereas other Caryophyllaceae mainly did. We suggest that these different patterns primarily result from different breeding systems and speciation times between different host groups as well as difficulties in species delimitations in the genus Dianthus.

The members of the smut genus Microbotryum are pathogens of a wide range of host plant species from nine dicotyledonous families. Within the genus, the species sporulating in anthers of Caryophyllaceae form a monophyletic group that in recent years attracted much interest in various biological studies. The phylogenetic framework developed for species delimitation within Microbotryum revealed that high level host-specificity is a major feature of most caryophyllaceous anther smuts. However, the great number of anther smut specimens on diverse host plant species reported worldwide has still not been included in phylogenetic analyses due to the inaccessibility of recently collected specimens, and thus many species remain still undiscovered. In this study, anther smut specimens on Heliosperma pusillum originating from all main mountain ranges of the European Alpine System were examined using partial rDNA sequence and/or morphological analyses. The investigation revealed that all specimens are morphologically uniform and phylogenetically represent a monophyletic lineage, sister to Microbotryum lagerheimii complex on Atocion rupestre/Silene lacera/Silene vulgaris/Viscaria vulgaris. This lineage cannot be attributed to any of the previously described species, and therefore the smut in anthers of H. pusillum is described and illustrated here as a new species, Microbotryum heliospermae. The species is known from subalpine zone of the Alps, the Carpathians, the Dinaric Alps, and the Pyrenees, inhabiting host plants growing in open spring communities or semihumid mountain meadows.

Human activities, land management and climate change all have great impact on soil biology, but our knowledge of biodiversity of soil organisms is still very limited. Therefore, we assessed responses of soil yeasts to land management, and analysed 57 soils showing different land use from three distinct localities. We isolated and identified molecularly a total of 40 yeasts including several new species. Overall, species composition of different localities was very heterogeneous and nearly half of the species were found in a single site only. The analysis of species abundance and community composition revealed a strong long-term effect of forest replacement by grassland vegetation. Unlike forests, grasslands harbour predominantly ascomycetous yeasts and their proportion increases with management intensity. In forests, evenness of yeast communities followed the gradient of land management intensity and natural beech forests harboured the most unevenly structured community, thereby mirroring the evenness of plant communities.

The plant-parasitic genus Microbotryum (Pucciniomycotina) has been used as a model for various biological studies, but fundamental aspects of its life history have not been documented in detail. The smut fungus is characterized by a dimorphic life cycle with a haploid saprophytic yeast-like stage and a dikaryotic plant-parasitic stage, which bears the teliospores as dispersal agents. In this study, seedlings and flowers of Silene latifolia Poir. (Caryophyllaceae) were inoculated with teliospores or sporidial cells of Microbotryum lychnidis-dioicae (DC. ex Liro) G. Deml & Oberw. and the germination of teliospores, the infection process, and the proliferation in the host tissue were documented in vivo using light and electron microscopy. Although germination of the teliospore is crucial for the establishment of Microbotryum, basidium development is variable under natural conditions. In flowers, where the amount of nutrients is thought to be high, the fungus propagates as sporidia, and mating of compatible cells takes place only when flowers are withering and nutrients are decreasing. On cotyledons (i.e., nutrient-depleted conditions), conjugation occurs shortly after teliospore germination, often via intrapromycelial mating. After formation of an infectious hypha with an appressorium, the invasion of the host occurs by direct penetration of the epidermis. While the growth in the plant is typically intercellular, long distance proliferation seems mediated through xylem tracheary elements. At the beginning of the vegetation period, fungal cells were found between meristematic shoot host cells, indicating a dormant phase inside the plant. By using different microscopy techniques, many life stages of Microbotryum are illustrated for the first time, thereby allowing new interpretations of laboratory data.

Members of the fungal genus Microbotryum are well‐known parasites on eudicotyledonous plant hosts. However, recent studies focused exclusively on Microbotryum species being parasites in the anthers of Caryophyllaceae in which strong host‐specificity was confirmed by molecular analyses. Consequently, species numbers have risen considerably as multi‐host parasites were split up in so‐called cryptic species. We subjected three non‐caryophyllaceous Microbotryum groups to molecular phylogenetic analyses to see whether we would confirm multi‐host morphospecies or if host‐specific cryptic species in these selected groups could be revealed as well (i.e. a group of non‐caryophyllaceous anther smuts, parasites on different Fallopia species, and parasites on Polygonum bistorta and Polygonum vi‐viparum). We applied a multiple analysis strategy to correct for varying alignment effects on a two‐locus dataset (ITS and LSU rDNA). The results obtained by the different approaches are uniform; high host‐specificity...

Recent collections of Microbotryum (Pucciniomycotina, Basidiomycota) specimens inhabiting anthers of different caryophyllaceous host plants were analysed using LM and electron microscopy, as well as molecular phylogenetic analyses using rDNA (ITS and LSU) sequences. The phylogenetic relationships of caryophyllaceous anther parasites are discussed. Three new species, Microbotryum adenopetalae, M. minuartiae, and M. silenes-acaulis, are described based on morphological, ecological, and molecular characteristics. New host plants are reported for Microbotryum dianthorum (Dianthus jacquemontii and Petrorhagia saxifraga) and M. lychnidis-dioicae (Cucubalus baccifer and Silene zawadskii). For Microbotryum violaceum, a neotype is selected.

The recently described fungal phylum Entorrhizomycota was established solely for the genus Entorrhiza, species of which cause root-galls in Cyperaceae and Juncaceae. Talbotiomyces calosporus (incertae sedis) shares morphological characteristics and an ecological niche with species of Entorrhiza. We investigated the higher classification of T. calosporus to determine whether it belongs in Entorrhizomycota. Ribosomal DNA sequences showed Talbotiomyces to be a close relative of Entorrhiza and both taxa form a highly supported monophyletic group. Based on molecular phylogenetic analyses and in congruence with existing morphological and ecological data, Entorrhiza and Talbotiomyces represent a deep dichotomy within the Entorrhizomycota. While species of Entorrhiza are characterised by dolipores and occur on monocotyledons, members of Talbotiomyces are characterised by simple pores and are associated with eudicotyledons. This expands the host range of the recently described Entorrhizomycota from Poales to other angiosperms. Higher taxa, namely Talbotiomycetales ord. nov. and Talbotiomycetaceae fam. nov., are proposed here to accommodate Talbotiomyces.

The biotic and abiotic environmental experience of plants can influence the offspring without any changes in DNA sequence. These effects can modulate the development of the progeny and their interaction with microorganisms. This interaction includes fungal endophytic communities which have significant effects on trees and their associated ecosystems. In this opinion article, we highlight potential maternal mechanisms through which endophytes could influence the progeny. We argue that a better understanding of these interactions might help to predict the response of trees to stress conditions and enhance the efficiency of tree breeding programs.

The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with incomplete taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.

\(\textit {Background:}\) Yeast-like fungi inhabit soils throughout all climatic zones in a great abundance. While recent estimations predicted a plethora of prokaryotic taxa in one gram of soil, similar data are lacking for fungi, especially yeasts. \(\textit {Methodology/Principal Findings:}\) We assessed the diversity of soil yeasts in different forests of central Germany using cultivation-based techniques with subsequent identification based on rDNA sequence data. Based on experiments using various pre-cultivation sample treatment and different cultivation media we obtained the highest number of yeasts by analysing mixed soil samples with a single nutrient-rich medium. Additionally, several species richness estimators were applied to incidence-based data of 165 samples. All of them predicted a similar range of yeast diversity, namely 14 to 16 species. Randomized species richness curves reached saturation in all applied estimators, thus indicating that the majority of species is detected after approximately 30 to 50 samples analysed. \(\textit {Conclusions/Significance:}\) In this study we demonstrate that robust species identification as well as mathematical approaches are essential to reliably estimate the sampling effort needed to describe soil yeast communities. This approach has great potential for optimisation of cultivation techniques and allows high throughput analysis in the future.

Background Anther smuts of the basidiomycetous genus Microbotryum on Caryophyllaceae are important model organisms for many biological disciplines. Members of Microbotryum are most commonly found parasitizing the anthers of host plants in the family Caryophyllaceae, however they can also be found on the anthers of members of the Dipsacaceae, Lamiaceae, Lentibulariaceae, and Portulacaceae. Additionally, some members of Microbotryum can be found infecting other organs of mainly Polygonaceae hosts. Based on ITS nrDNA sequences of members of almost all genera in Microbotryaceae, this study aims to resolve the phylogeny of the anther smuts and their relationship to the other members of the family of plant parasites. A multiple analysis strategy was used to correct for the effects of different equally possible ITS sequence alignments on the phylogenetic outcome, which appears to have been neglected in previous studies. Results The genera of Microbotryaceae were not clearly resolved, but alignment-independent moderate bootstrap support was achieved for a clade containing the majority of the Microbotryum species. The anther parasites appeared in two different well-supported lineages whose interrelationship remained unresolved. Whereas bootstrap support values for some clades were highly vulnerable to alignment conditions, other clades were more robustly supported. The differences in support between the different alignments were much larger than between the phylogenetic optimality criteria applied (maximum parsimony and maximum likelihood). Conclusion The study confirmed, based on a larger dataset than previous work, that the anther smuts on Caryophyllaceae are monophyletic and that there exists a native North American group that diverged from the European clade before the radiation of the European species. Also a second group of anther smuts was revealed, containing parasites on Dipsacaceae, Lamiaceae, and Lentibulariaceae. At least the majority of the parasites of Asteraceae appeared as a monophylum, but delimitations of some species in this group should be reconsidered. Parasitism on Polygonaceae is likely to be the ancestral state for the Microbotryaceae on Eudicot hosts.