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Abstract The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.

A rare smut fungus, Anthracoidea pseudofoetidae, is reported for the first time from Russia, based on a specimen from the Altai Republic. Carex enervis is a new host record for A. pseudofoetidae. Two new records for Greece, Microbotryum duriaeanum and M. moenchiae-manticae, and a new record for Morocco, Microbotryum moehringiae, are also presented. Microbotryum moehringiae is recorded for the first time from Africa. Cerastium brachypetalum subsp. roeseri is a new host record for Microbotryum duriaeanum. New molecular data are provided for these smut fungi. Updated phylogenetic trees for Anthracoidea and Microbotryum are also given.

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 Eucalyptus foliage correlates with the diversity of foliar fungal communities in surrounding healthy leaf tissue, as well as the co-occurrence patterns among the members of the fungal community. We used ITS metabarcoding to characterise the foliar fungal communities of 179 individual E. grandis trees. These trees were assigned to infestation levels of the wasp Leptocybe invasa (Eulophidae: Hymenoptera), which causes gall formation on shoot tips and leaves of its host. Fungal community networks were calculated using a Pearson correlation coefficient. The composition and diversity of fungal communities were influenced by the severity of L. invasa infestations. We identified potential Eucalyptus pathogens with high sequence abundance at all disease severity levels, but network analysis indicated that the co-occurrence of potential pathogens between no to mild and medium to heavy infestation differed significantly. A better understanding of microbial interactions, especially the role of pathogens, can be useful for controlling disease- and beneficial host-associated microbial communities.

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 Thecaphora 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.

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

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−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−plant and fungal−microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant−microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant−microbe interactions.

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.

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. 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. 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.