Safety and efficacy of a feed additive consisting of endo-1,4-β xylanase, endo-1,4-β-glucanase and xyloglucan-specific-endo-β-1,4-glucanase produced by Trichoderma citrinoviride DSM 33578 (Huvezym® neXo) for all Suidae (Huvepharma EOOD)

Following a request from the European Commission, the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of Huvezym® neXo 100 G/L, a product containing endo-1,4-β-xylanase, endo-1,4-β-glucanase and xyloglucan-specific-endo-β-1,4-glucanase activities produced by a non-genetically modified strain of Trichoderma citrinoviride (DSM 33578), as a zootechnical additive for all Suidae. The applicant provided information confirming the taxonomic identification of the production strain. The batches used for the characterisation of the final formulations showed compliance with the minimum specifications of the additive in terms of enzyme activities (> 15,000 EPU, > 1000 CU, > 1000 XGU per g) but not for the ratio of the enzymes, which is lower (ca. 7:1:1) than the ones specified (15:1:1). The Panel could not conclude on the representativeness of the test item used in the toxicological and tolerance studies with respect to the final formulations. Therefore, the conclusions are limited to the product with a minimum enzyme activity of 15,000 EPU, 1000 CU, 1000 XGU per g and a xylanase:glucanase:xyloglucanase ratio of 15:1:1. The Panel concluded that the additive is safe for the target species, consumers and the environment. Huvezym® neXo 100 G is not an irritant to the skin and eyes but should be considered a skin sensitiser. Huvezym® neXo 100 L is neither an irritant to the skin and eyes nor a skin sensitiser. Due to the proteinaceous nature of the active substances, the additive is considered a respiratory sensitiser. The additive has the potential to be efficacious in all reproductive Suidae at the minimum proposed use level. Owing to the lack of sufficient data, the Panel could not conclude on the efficacy of the additive for Suidae for fattening or reared for reproduction.

Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of Microbotryomycetes

Mycoparasites in Basidiomycota comprise a diverse group of fungi, both morphologically and phylogenetically. They interact with their hosts through either fusion-interaction or colacosome-interaction. Colacosomes are subcellular structures formed by the mycoparasite at the host-parasite interface, which penetrate the parasite and host cell walls. Previously, these structures were detected in 19 fungal species, usually by means of transmission electron microscopy. Most colacosome-forming species have been assigned to Microbotryomycetes (Pucciniomycotina, Basidiomycota), a highly diverse class, comprising saprobic yeasts, mycoparasites, and phytoparasites. In general, these myco- and phytoparasites are dimorphic organisms, with a parasitic filamentous morph and saprobic yeast morph. We investigated colacosome-forming mycoparasites based on fungarium material, freshly collected specimens, and cultures of yeast morphs. We characterised the micromorphology of filamentous morphs, the physiological characteristics of yeast morphs, and inferred phylogenetic relationships based on DNA sequence data from seven loci. We outline and employ an epifluorescence-based microscopic method to assess the presence and organisation of colacosomes. We describe five new species in the genus Colacogloea, the novel dimorphic mycoparasite Mycogloiocolax gerardii, and provide the first report of a sexual, mycoparasitic morph in Colacogloea philyla and in the genus Slooffia. We detected colacosomes in eight fungal species, which brings the total number of known colacosome-forming fungi to 27. Finally, we revealed three distinct types of colacosome organisation in Microbotryomycetes. Taxonomic novelties and typifications: New family: Mycogloiocolacaeae Schoutteten & Yurkov; New genus: Mycogloiocolax Schoutteten & Rödel; New species: Colacogloea bettinae Schoutteten & Begerow, C. biconidiata Schoutteten, C. fennica Schoutteten & Miettinen, C. microspora Schoutteten, C. universitatis-gandavensis Schoutteten & Verbeken, Mycogloiocolax gerardii Schoutteten & Rödel; New combinations: Slooffia micra (Bourdot & Galzin) Schoutteten, Fellozyma cerberi (A.M. Yurkov et al.) Schoutteten & Yurkov, Fellozyma telluris (A.M. Yurkov et al.) Schoutteten & Yurkov; Epitypifications (basionyms): Achroomyces insignis Hauerslev, Platygloea micra Bourdot & Galzin, Platygloea peniophorae Bourdot & Galzin; Lectotypification (basionym): Platygloea peniophorae Bourdot & Galzin Citation: Schoutteten N, Yurkov A, Leroux O, Haelewaters D, Van Der Straeten D, Miettinen O, Boekhout T, Begerow D, Verbeken A (2023). Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of Microbotryomycetes. Studies in Mycology 106: 41-94. doi: 10.3114/sim.2022.106.02.

Fungi under Modified Atmosphere-The Effects of CO2 Stress on Cell Membranes and Description of New Yeast Stenotrophomyces fumitolerans gen. nov., sp. nov

High levels of carbon dioxide are known to inhibit the growth of microorganisms. A total of twenty strains of filamentous fungi and yeasts were isolated from habitats with enriched carbon dioxide concentration. Most strains were derived from modified atmosphere packed (MAP) food products or mofettes and were cultivated under an atmosphere of 20% CO2 and 80% O2. The influence of CO2 on fungal cell membrane fatty acid profiles was examined in this study. Major changes were the increase in linolenic acid (C18:3 cis 9, 12, 15) and, additionally in most strains, linoleic acid (C18:2 cis 9, 12) with a maximum of 24.8%, at the expense of oleic (C18:1 cis 9), palmitic (C16:0), palmitoleic (C16:1 cis 9) and stearic acid (C18:0). The degree of fatty acid unsaturation increased for all of the strains in the study, which consequently led to lower melting temperatures of the cell membranes after incubation with elevated levels of CO2, indicating fluidization of the membrane and a potential membrane malfunction. Growth was reduced in 18 out of 20 strains in laboratory experiments and a change in pigmentation was observed in several strains. Two of the isolated strains, strain WT5 and strain WR1, were found to represent a hitherto undescribed yeast for which the new genus and species Stenotrophomyces fumitolerans (MB# 849906) is proposed.

Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities

During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3T, isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1T, isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3T = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1T = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.

Species and temperature-dependent fermentative aptitudes of Mrakia genus for innovative brewing

The use of non-conventional brewing yeasts as alternative starters is a very promising approach which received increasing attention from worldwide scientists and brewers. Despite the feasible application of non-conventional yeasts in brewing processes, their regulations and safety assessment by the European Food Safety Authority still represent a bottlenecked hampering their commercial release, at least into EU market. Thus, research on yeast physiology, accurate taxonomic species identification and safety concerns associated with the use of non-conventional yeasts in food chains is needed to develop novel healthier and safer beers. Currently, most of the documented brewing applications catalysed by non-conventional yeasts are associated to ascomycetous yeasts, while little is known about analogous uses of basidiomycetous taxa. Therefore, in order to extend the phenotypic diversity of basidiomycetous brewing yeasts the aim of this investigation is to check the fermentation aptitudes of thirteen Mrakia species in relation to their taxonomic position within the genus Mrakia. The volatile profile, ethanol content and sugar consumption were compared with that produced by a commercial starter for low alcohol beers, namely Saccharomycodes ludwigii WSL 17. The phylogeny of Mrakia genus showed three clusters that clearly exhibited different fermentation aptitudes. Members of M. gelida cluster showed a superior aptitude to produce ethanol, higher alcohols, esters and sugars conversion compared to the members of M. cryoconiti and M. aquatica clusters. Among M. gelida cluster, the strain M. blollopis DBVPG 4974 exhibited a medium flocculation profile, a high tolerance to ethanol and to iso-α-acids, and a considerable production of lactic and acetic acids, and glycerol. In addition, an inverse relationship between fermentative performances and incubation temperature is also displayed by this strain. Possible speculations on the association between the cold adaptation exhibited by M. blollopis DBVPG 4974 and the release of ethanol in the intracellular matrix and in the bordering environment are presented.

Safety and efficacy of a feed additive consisting of endo-1,4-beta xylanase, endo-1,4-beta-glucanase and xyloglucan-specific-endo-beta-1,4-glucanase produced by Trichoderma citrinovirideDSM 33578 (Huvezym® neXo 100 G/L) for all poultry species, ornamental birds and piglets (weaned and suckling) (Huvepharma EOOD)

Following a request from the European Commission, the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of the product Huvezym® neXo 100 G/L containing an endo-1,4-beta xylanase, an endo-1,4-beta-glucanase and a xyloglucan-specific-endo-beta-1,4-glucanase produced by a non-genetically modified strain of Trichoderma citrinoviride (DSM 33578) as a zootechnical additive for feed in all poultry species, ornamental birds and piglets (weaned and suckling). The information regarding the production strain did not allow to confirm its taxonomic identification. The batches used for the characterisation of the final formulations showed compliance with the minimum specifications of the additive in terms of enzyme activities but showed ratios between the enzymes lower than the ones specified for the additive. The FEEDAP Panel considered that the below-described conclusions would apply to the final formulations of the additive as per specifications with xylanase:glucanase, xylanase:xyloglucanase and glucanase:xyloglucanase ratios of 15, 15 and 1, respectively. Based on the data available, the Panel concluded that the additive is safe for the target species, consumers and the environment. Huvezym® neXo 100 G (granulated form) is neither skin corrosive nor eye irritant but should be considered a potential skin sensitiser. Huvezym® neXo 100 L (liquid) is neither skin corrosive nor sensitising and it is not an eye irritant. Due to lack of data, no conclusions can be drawn on the skin irritation of the final formulations of the additive. Due to the proteinaceous nature of the active substances, the additive is considered a respiratory sensitiser. The FEEDAP Panel concluded that the additive has the potential to be efficacious in chickens for fattening, chickens reared for laying and breeding, and all growing poultry and ornamental birds at the minimum intended level of 1,500 EPU, 100 CU and 100 XGU/kg complete feed. Owing to the lack of sufficient data, the Panel could not conclude on the efficacy of the additive for laying hens and weaned piglets.

Yeasts from temperate forests

Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.

Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

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.

Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).

AM-Induced Alteration in the Expression of Genes, Encoding Phosphorus Transporters and Enzymes of Carbohydrate Metabolism in Medicago lupulina

Plant-microbe interactions, including those of arbuscular mycorrhiza (AM), have been investigated for a wide spectrum of model plants. The present study focuses on an analysis of gene expression that encodes phosphate and sugar transporters and carbohydrate metabolic enzymes in a new model plant, the highly mycotrophic Medicago lupulina MLS-1 line under conditions of phosphorus deficiency and inoculation with Rhizophagus irregularis. Expression profiles were detected by RT-PCR at six plant stages of development (second leaf, third leaf, shooting, axillary shoot branching initiation, axillary shoot branching, flowering initiation). In comparison to control (without AM), the variant with AM inoculation exhibited a significant elevation of transcription levels of carbohydrate metabolic enzymes (MlSUS, MlHXK1) and sucrose transporters (MlSUC4) in M. lupulina leaves at the shooting stage. We suggest that this leads to a significant increase in the frequency of AM infection, an abundance of mycelium in roots and an increase in AM efficiency (which is calculated by the fresh weight of aerial parts and roots at the axillary shoot branching initiation stage). In roots, the specificity of MlPT4 and MlATP1 gene expressions were revealed for effective AM symbiosis. The level of MlPT4 transcripts in AM roots increased more than tenfold in comparison to that of non-specific MlPT1 and MlPT2. For the first time, MlPT1 expression was shown to increase sharply against MlPT2 in M. lupulina roots without AM at the shooting initiation stage. A significant increase in MlRUB expression was revealed at late stages in the host plant's development, during axillary shoot branching and flowering initiation. The opposite changes characterized MlHXK1 expression. Alteration in MlHXK1 gene transcription was the same, but was more pronounced in roots. The obtained results indicate the importance of genes that encode phosphate transporters and the enzymes of carbohydrate metabolism for effective AM development at the shooting stage in the host plant.

A complete digitization of German herbaria is possible, sensible and should be started now

Plants, fungi and algae are important components of global biodiversity and are fundamental to all ecosystems. They are the basis for human well-being, providing food, materials and medicines. Specimens of all three groups of organisms are accommodated in herbaria, where they are commonly referred to as botanical specimens.

The large number of specimens in herbaria provides an ample, permanent and continuously improving knowledge base on these organisms and an indispensable source for the analysis of the distribution of species in space and time critical for current and future research relating to global biodiversity. In order to make full use of this resource, a research infrastructure has to be built that grants comprehensive and free access to the information in herbaria and botanical collections in general. This can be achieved through digitization of the botanical objects and associated data.

The botanical research community can count on a long-standing tradition of collaboration among institutions and individuals. It agreed on data standards and standard services even before the advent of computerization and information networking, an example being the Index Herbariorum as a global registry of herbaria helping towards the unique identification of specimens cited in the literature.

In the spirit of this collaborative history, 51 representatives from 30 institutions advocate to start the digitization of botanical collections with the overall wall-to-wall digitization of the flat objects stored in German herbaria. Germany has 70 herbaria holding almost 23 million specimens according to a national survey carried out in 2019. 87% of these specimens are not yet digitized. Experiences from other countries like France, the Netherlands, Finland, the US and Australia show that herbaria can be comprehensively and cost-efficiently digitized in a relatively short time due to established workflows and protocols for the high-throughput digitization of flat objects.

Most of the herbaria are part of a university (34), fewer belong to municipal museums (10) or state museums (8), six herbaria belong to institutions also supported by federal funds such as Leibniz institutes, and four belong to non-governmental organizations. A common data infrastructure must therefore integrate different kinds of institutions.

Making full use of the data gained by digitization requires the set-up of a digital infrastructure for storage, archiving, content indexing and networking as well as standardized access for the scientific use of digital objects. A standards-based portfolio of technical components has already been developed and successfully tested by the Biodiversity Informatics Community over the last two decades, comprising among others access protocols, collection databases, portals, tools for semantic enrichment and annotation, international networking, storage and archiving in accordance with international standards. This was achieved through the funding by national and international programs and initiatives, which also paved the road for the German contribution to the Global Biodiversity Information Facility (GBIF).

Herbaria constitute a large part of the German botanical collections that also comprise living collections in botanical gardens and seed banks, DNA- and tissue samples, specimens preserved in fluids or on microscope slides and more. Once the herbaria are digitized, these resources can be integrated, adding to the value of the overall research infrastructure. The community has agreed on tasks that are shared between the herbaria, as the German GBIF model already successfully demonstrates.

We have compiled nine scientific use cases of immediate societal relevance for an integrated infrastructure of botanical collections. They address accelerated biodiversity discovery and research, biomonitoring and conservation planning, biodiversity modelling, the generation of trait information, automated image recognition by artificial intelligence, automated pathogen detection, contextualization by interlinking objects, enabling provenance research, as well as education, outreach and citizen science.

We propose to start this initiative now in order to valorize German botanical collections as a vital part of a worldwide biodiversity data pool.

Notes, outline and divergence times of Basidiomycota

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.

Saccharomycopsis oxydans sp. nov., a new non-fermentative member in the genus Saccharomycopsis isolated from a traditional dairy product of Iran

A total of 21 yeast isolates were recovered as part of a research project on biodiversity of yeasts in traditional dairy products in Alborz province, Iran. Standard protocols were used to carry out phenotypic, biochemical, physiological characterization and the phylogenetic analysis of combined the D1/D2 domain of the large ribosomal subunit (26S or LSU) and ITS region sequences. Five strains represented a potential new ascomycetous yeast species. Ascospore formation was not observed in these strains, and they did not ferment the examined carbon sources. Phylogenetic analysis placed these isolates in a well-supported sub-clade in the genus Saccharomycopsis. Here, we describe this novel yeast as Saccharomycopsis oxydans sp. nov.

DSMZ: the European Union’s first Registered Collection under the Nagoya Protocol

The Convention on Biological Diversity and the Nagoya Protocol have created new challenges for international microbiological research. With the implementation of the Nagoya Protocol in 2014, the European Union created a new voluntary legal mechanism, the Register of Collections, to help users of collections, including culture collections, have an easier path to Nagoya Protocol compliance by using a so-called ‘registered collection'. The Leibniz Institute DSMZ is the first, and so far only, collection to successfully be entered into the Register. The challenges and lessons learned during this process can be informative for culture collections and users of microbial resources beyond the EU and indeed around the world.

Arthroderma chiloniense sp. nov. isolated from human stratum corneum: Description of a new Arthroderma species

A 68-year-old woman was submitted to our hospital because of erythematous and scaly skin lesions. To exclude tinea samples of stratum corneum were collected and used for mycological investigations. In this material, no fungal elements were detected microscopically, but inoculation on Sabouraud agar with cycloheximide yielded a presumptive dermatophyte fungus. Subsequent detailed investigations with conventional morphological and physiological methods and a phylogenetic analysis of the combined LSU rRNA gene (D1/D2 domains) and ITS region sequences suggested that the fungus represents a hitherto undescribed species of the genus Arthroderma. Here, we describe this species as Arthroderma chiloniense sp. nov., EMBL accession no. LT992885. This new species can be distinguished from phylogenetically related Arthroderma species using ribosomal ITS and LSU genes, and 60S L10 protein sequences; specific macroscopic, microscopic and physiological features are lacking. Our attempts to re-isolate this fungus from the patient's skin failed although her skin lesions persisted. Most likely A. chiloniense is a geophilic species that incidentally contaminated or transiently colonised the patient's skin. To avoid diagnostic misinterpretations, it is necessary to distinguish A. chiloniense from truly pathogenic dermatophytes like Trichophyton (T.) rubrum and T. interdigitale which can easily be confused with A. chiloniense based on similar mycelium morphology.

A unique fungal strain collection from Vietnam characterized for high performance degraders of bioecological important biopolymers and lipids

Fungal strains are abundantly used throughout all areas of biotechnology and many of them are adapted to degrade complex biopolymers like chitin or lignocellulose. We therefore assembled a collection of 295 fungi from nine different habitats in Vietnam, known for its rich biodiversity, and investigated their cellulase, chitinase, xylanase and lipase activity. The collection consists of 70 isolates from wood, 55 from soil, 44 from rice straw, 3 found on fruits, 24 from oil environments (butchery), 12 from hot springs, 47 from insects as well as 27 from shrimp shells and 13 strains from crab shells. These strains were cultivated and selected by growth differences to enrich phenotypes, resulting in 211 visually different fungi. DNA isolation of 183 isolates and phylogenetic analysis was performed and 164 species were identified. All were subjected to enzyme activity assays, yielding high activities for every investigated enzyme set. In general, enzyme activity corresponded with the environment of which the strain was isolated from. Therefore, highest cellulase activity strains were isolated from wood substrates, rice straw and soil and similar substrate effects were observed for chitinase and lipase activity. Xylanase activity was similarly distributed as cellulase activity, but substantial activity was also found from fungi isolated from insects and shrimp shells. Seven strains displayed significant activities against three of the four tested substrates, while three degraded all four investigated carbon sources. The collection will be an important source for further studies. Therefore representative strains were made available to the scientific community and deposited in the public collection of the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig.

Extremophilic yeasts: the toughest yeasts around?

Microorganisms are widely distributed in a multitude of environments including ecosystems that show challenging features to most life forms. The combination of extreme physical and chemical factors contributes to the definition of extreme habitats although the definition of extreme environments changes depending on one's point of view: anthropocentric, microbial-centric or zymo-centric. Microorganisms that live under conditions that cause hard survival are called extremophiles. In particular organisms that require extreme conditions are called true extremophiles while organisms that tolerate them to some extent are termed extremotolerant. Deviation of temperature, pH, osmotic stress, pressure and radiation from the common range delineates extreme environments. Yeasts are versatile eukaryotic organisms that are not frequently considered the toughest microorganisms in comparison with prokaryotes. Nevertheless extremophilic or extremotolerant species are present also within this group. Here a brief description is provided of the main extreme habitats and the metabolic and physiological modifications adopted by yeasts depending on their adverse conditions. Additionally the main extremophilic and extremotolerant yeast species associated with a few extreme habitats are listed.

Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK)

Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.

Interspecies-cooperations of abutilon theophrasti with root colonizing microorganisms disarm BOA-OH allelochemicals

A facultative, microbial micro-community colonizing roots of Abutilon theophrasti Medik. supports the plant in detoxifying hydroxylated benzoxazolinones. The root micro-community is composed of several fungi and bacteria with Actinomucor elegans as a dominant species. The yeast Papiliotrema baii and the bacterium Pantoea ananatis are actively involved in the detoxification of hydroxylated benzoxazolinones by generating H₂O₂. At the root surface, laccases, peroxidases and polyphenol oxidases cooperate for initiating polymerization reactions, whereby enzyme combinations seem to differ depending on the hydroxylation position of BOA-OHs. A glucosyltransferase, able to glucosylate the natural benzoxazolinone detoxification intermediates BOA-5- and BOA-6-OH, is thought to reduce oxidative overshoots by damping BOA-OH induced H₂O₂ generation. Due to this detoxification network, growth of Abutilon theophrasti seedlings is not suppressed by BOA-OHs. Polymer coats have no negative influence. Alternatively, quickly degradable 6-hydroxy-5-nitrobenzo[d]oxazol-2(3H)-one can be produced by the micro-community member Pantoea ananatis at the root surfaces. The results indicate that Abutilon theophrasti has evolved an efficient strategy by recruiting soil microorganisms with special abilities for different detoxification reactions which are variable and may be triggered by the allelochemical´s structure and by environmental conditions.

Physically Triggered Morphology Changes in a Novel Acremonium Isolate Cultivated in Precisely Engineered Microfabricated Environments

Fungi are strongly affected by their physical environment. Microfabrication offers the possibility of creating new culture environments and ecosystems with defined characteristics. Here, we report the isolation of a novel member of the fungal genus Acremonium using a microengineered cultivation chip. This isolate was unusual in that it organizes into macroscopic structures when initially cultivated within microwells with a porous aluminum oxide (PAO) base. These “templated mycelial bundles” (TMB) were formed from masses of parallel hyphae with side branching suppressed. TMB were highly hydrated, facilitating the passive movement of solutes along the bundle. By using a range of culture chips, it was deduced that the critical factors in triggering the TMB were growth in microwells from 50 to 300 μm in diameter with a PAO base. Cultivation experiments, using spores and pigments as tracking agents, indicate that bulk growth of the TMB occurs at the base. TMB morphology is highly coherent and is maintained after growing out of the microwells. TMB can explore their environment by developing unbundled lateral hyphae; TMB only followed if nutrients were available. Because of the ease of fabricating numerous microstructures, we suggest this is a productive approach for exploring morphology and growth in multicellular microorganisms and microbial communities.

Xanthothecium peruvianum isolated from human stratum corneum: A case report, characterisation and short review that suggest emendation of Arachnomyces peruvianus

From stratum corneum samples of a palmar eczema, a fungus was isolated that developed white colonies with a yellowish dark reverse, suggestive of dermatophytes. The isolate produced numerous chlamydospores and sparse aleuroconidia, was resistant to cycloheximide, grew well on human stratum corneum samples and was positive in tests for urease production and hair perforation, but no dermatophyte could be identified. After several weeks, cleistothecia with delicate asci and disc-shaped ascospores were formed, suggesting Arachnomyces spp. The analyses of the ribosomal ITS and LSU (D1/D2 domains) nucleotide sequences proved a good match with the ex-type strain of Xanthothecium peruvianum (family Onygenaceae, order Onygenales), and LSU sequence showed 99% similarity with Arachnomyces glareosus. This is the first report of X. peruvianum isolated from human skin. The description of our isolate provides new information about this species and proposes its transfer to the genus Arachnomyces with the subsequent emendation of the description of Arachnomyces peruvianus. Morphologically and physiologically it mimics dermatophytes and other species of the genus Arachnomyces. Although the clinical situation did not suggest any relevance for A. peruvianus as a primary pathogen, this fungus may act as a secondary pathogen under suitable conditions due to its keratinolytic capacity.

Yeast culture collections in the twenty-first century: new opportunities and challenges

The twenty-first century has brought new opportunities and challenges to yeast culture collections, whether they are long-standing or recently established. Basic functions such as archiving, characterizing and distributing yeasts continue, but with expanded responsibilities and emerging opportunities. In addition to a number of well-known, large public repositories, there are dozens of smaller public collections that differ in the range of species and strains preserved, field of emphasis and services offered. Several collections have converted their catalogues to comprehensive databases and synchronize them continuously through public services, making it easier for users worldwide to locate a suitable source for specific yeast strains and the data associated with these yeasts. In-house research such as yeast taxonomy continues to be important at culture collections. Because yeast culture collections preserve a broad diversity of species and strains within a species, they are able to make discoveries in many other areas as well, such as biotechnology, functional, comparative and evolution genomics, bioprocesses and novel products. Due to the implementation of the Convention of Biological Diversity (CBD) and the Nagoya Protocol (NP), there are new requirements for both depositors and users to ensure that yeasts were collected following proper procedures and to guarantee that the country of origin will be considered if benefits arise from a yeast's utilization. Intellectual property rights (IPRs) are extremely relevant to the current access and benefit-sharing (ABS) mechanisms; most research and development involving genetic resources and associated traditional knowledge will be subject to this topic. Copyright © 2016 John Wiley & Sons, Ltd.

Multigene assessment of the species boundaries and sexual status of the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales)

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful.

General relationships between abiotic soil properties and soil biota across spatial scales and different land-use types

Very few principles have been unraveled that explain the relationship between soil properties and soil biota across large spatial scales and different land-use types. Here, we seek these general relationships using data from 52 differently managed grassland and forest soils in three study regions spanning a latitudinal gradient in Germany. We hypothesize that, after extraction of variation that is explained by location and land-use type, soil properties still explain significant proportions of variation in the abundance and diversity of soil biota. If the relationships between predictors and soil organisms were analyzed individually for each predictor group, soil properties explained the highest amount of variation in soil biota abundance and diversity, followed by land-use type and sampling location. After extraction of variation that originated from location or land-use, abiotic soil properties explained significant amounts of variation in fungal, meso- and macrofauna, but not in yeast or bacterial biomass or diversity. Nitrate or nitrogen concentration and fungal biomass were positively related, but nitrate concentration was negatively related to the abundances of Collembola and mites and to the myriapod species richness across a range of forest and grassland soils. The species richness of earthworms was positively correlated with clay content of soils independent of sample location and land-use type. Our study indicates that after accounting for heterogeneity resulting from large scale differences among sampling locations and land-use types, soil properties still explain significant proportions of variation in fungal and soil fauna abundance or diversity. However, soil biota was also related to processes that act at larger spatial scales and bacteria or soil yeasts only showed weak relationships to soil properties. We therefore argue that more general relationships between soil properties and soil biota can only be derived from future studies that consider larger spatial scales and different land-use types.

Basidiomycetous yeasts from boletales fruiting bodies and their interactions with the mycoparasite Sepedonium chrysospermum and the host fungus Paxillus

Interactions between mushrooms, yeasts, and parasitic fungi are probably common in nature, but are rarely described. Bolete fruiting bodies are associated with a broad spectrum of microorganisms including yeasts, and they are commonly infected with filamentous mycoparasites of the genus Sepedonium (teleomorph Hypomyces). We report the isolation of 17 yeast strains from Paxillus and Xerocomus, 16 of which were obtained from the surface tissue, the primary site of Sepedonium infection. Phylogenetic analyses with the D1/D2 region of the 28S ribosomal gene and the internal transcribed spacers placed the yeasts as Rhodotorula, Rhodosporidium, and Mastigobasidium from the Pucciniomycotina, Cryptococcus, Cystofilobasidium, Holtermanniella, and Trichosporon from the Agaricomycotina, and Kluyveromyces from the Saccharomycotina including the first isolation of Rhodotorula graminis from Europe. To investigate the influence of the yeast strains on the mycoparasite and the host fungus, in vitro assays were conducted with Sepedonium chrysospermum and Paxillus involutus. Both S. chrysospermum growth inhibitory and stimulating yeast strains were detected among the isolates. The number of S. chrysospermum inhibitory yeast strains increased and the number of S. chrysospermum stimulatory yeast strains decreased in the presence of P. involutus in co-cultures. Low nutrient levels in the culture medium also led to an increased number of S. chrysospermum inhibitory yeast strains and ten yeasts inhibited the mycoparasite in spatial separation by a crosswall. Six yeast strains inhibited P. involutus in dual culture, and the inhibitory P. involutus yeast interactions increased to nine in the presence of S. chrysospermum. Our results suggest that the bolete-associated yeasts influence the growth of the mycoparasitic fungus, which may affect the health of the fruiting bodies.

The amsterdam declaration on fungal nomenclature

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.