The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered.

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

Disturbance alters the forest soil microbiome.

Billions of microorganisms perform critical below-ground functions in all terrestrial ecosystems. While largely invisible to the naked eye, they support all higher lifeforms, form symbiotic relationships with ~90% of terrestrial plant species, stabilize soils, and facilitate biogeochemical cycles. Global increases in the frequency of disturbances are driving major changes in the structure and function of forests. However, despite their functional significance, the disturbance responses of forest microbial communities are poorly understood. Here, we explore the influence of disturbance on the soil microbiome (archaea, fungi and bacteria) of some of the world's tallest and most carbon-dense forests, the Mountain Ash forests of south-eastern Australia. From 80 sites, we identified 23,277 and 19,056 microbial operational taxonomic units from the 0-10 cm and 20-30 cm depths of soil respectively. From this extensive data set, we found the diversity and composition of these often cryptic communities has been altered by human and natural disturbance events. For instance, the diversity of ectomycorrhizal fungi declined with clearcut logging, the diversity of archaea declined with salvage logging, and bacterial diversity and overall microbial diversity declined with the number of fires. Moreover, we identified key associations between edaphic (soil properties), environmental (slope, elevation) and spatial variables and the composition of all microbial communities. Specifically, we found that soil pH, manganese, magnesium, phosphorus, iron and nitrate were associated with the composition of all microbial communities. In a period of widespread degradation of global forest ecosystems, our findings provide an important and timely insight into the disturbance responses of soil microbial communities, which may influence key ecological functions.

Direct and indirect disturbance impacts in forests.

Human and natural disturbances are key drivers of change in forest ecosystems. Yet, the direct and indirect mechanisms which underpin these changes remain poorly understood at the ecosystem level. Here, using structural equation modelling across a 150+ year chronosequence, we disentangle the direct and indirect effects of major disturbances in a temperate forest ecosystem. We show that wildfires, logging and post-fire (salvage) logging can affect plant and microbial communities and abiotic soil properties both directly and indirectly through plant-soil-microbial interactions. We quantified 68 direct and indirect disturbance effects across these components, with the majority resulting in ecosystem-wide adverse effects. Indirect disturbance effects accounted for 43% of total disturbance effects, with some amplifying or partially mitigating direct disturbance effects. Overall, human disturbances were associated with more negative effects than natural disturbances. Our analyses provide novel insights into the multifaceted dynamics of forest disturbances and the mechanisms which underpin their relative impacts.

Naming names: the first women taxonomists in mycology.

The transition from amateur to professional in natural history is generally regarded as having taken place in the nineteenth century, but landmark events such as the 1917 appointment of mycologist Johanna Westerdijk (1883-1961) as the first female professor in the Netherlands indicate that the pattern of change for women was more varied and delayed than for men. We investigate this transition in mycology, and identify only 43 women in the Western World who published scientific mycological literature pre-1900, of whom twelve published new fungal taxa. By charting the emergence of these women over time, and comparing the output of self-taught amateurs and university graduates, we establish the key role of access to higher education in female participation in mycology. Using a suite of strategies, six of the self-taught amateurs managed to overcome their educational disadvantages and name names - Catharina Dörrien (the first to name a fungal taxon), Marie-Anne Libert, Mary Elizabeth Banning, Élise-Caroline Bommer, Mariette Rousseau, and Annie Lorrain Smith. By 1900, the professional era for women in mycology was underway, and increasing numbers published new taxa. Parity with male colleagues in recognition and promotion, however, remains an ongoing issue.

Biophysical characterization and structural determination of the potent cytotoxic Psathyrella asperospora lectin.

A lectin with strong cytotoxic effect on human colon cancer HT29 and monkey kidney VERO cells was recently identified from the Australian indigenous mushroom Psathyrella asperospora and named PAL. We herein present its biochemical and structural analysis using a multidisciplinary approach. Glycan arrays revealed binding preference towards N-acetylglucosamine (GlcNAc) and, to a lesser extent, towards sialic acid (Neu5Ac). Submicromolar and millimolar affinity was measured by surface plasmon resonance for GlcNAc and NeuAc, respectively. The structure of PAL was resolved by X-ray crystallography, elucidating both the protein's amino acid sequence as well as the molecular basis rationalizing its binding specificity. Proteins 2017; 85:969-975. © 2016 Wiley Periodicals, Inc.

Mushroom lectins: specificity, structure and bioactivity relevant to human disease.

Lectins are non-immunoglobulin proteins that bind diverse sugar structures with a high degree of selectivity. Lectins play crucial role in various biological processes such as cellular signaling, scavenging of glycoproteins from the circulatory system, cell-cell interactions in the immune system, differentiation and protein targeting to cellular compartments, as well as in host defence mechanisms, inflammation, and cancer. Among all the sources of lectins, plants have been most extensively studied. However, more recently fungal lectins have attracted considerable attention due to their antitumor, antiproliferative and immunomodulatory activities. Given that only 10% of mushroom species are known and have been taxonomically classified, mushrooms represent an enormous unexplored source of potentially useful and novel lectins. In this review we provide an up-to-date summary on the biochemical, molecular and structural properties of mushroom lectins, as well as their versatile applications specifically focusing on mushroom lectin bioactivity.

Concordance of seven gene genealogies compared to phenotypic data reveals multiple cryptic species in Australian dermocyboid Cortinarius (Agaricales).

This study aims to delimit species of Australian dermocyboid fungi (Cortinarius, Agaricales) using genealogical concordance on well-characterised phenotypic species and to assess the utility of seven loci for DNA barcoding Australian Cortinarius taxa. Eighty-six collections of dermocyboid Cortinarius were sampled from across southern Australia. Phenotypic species were first recognised by performing clustering analyses on a comprehensive phenotypic dataset including morphological, colour and pigment data. Then phylogenetic species were delimited from the concordance of seven locus genealogies (ITS, nLSU, gpd, mcm7, rpb1, rpb2 and tef1). Seventeen phenotypic species were recognised while the concordance of gene genealogies recovered 35 phylogenetic species. All loci except for LSU recovered most phylogenetic species, although only rpb1 correctly identified all phylogenetic species. The ITS region is confirmed as an effective barcode for Cortinarius and a standard pairwise distance threshold of 2.0% is proposed to DNA barcode Australian Cortinarius taxa. Australian dermocyboid fungi belong in separate clades to the boreal clade Dermocybe, mostly in the clade Splendidi. This study provides a solid foundation for future ecological, taxonomic and systematic research on one of the most diverse genera of mushrooms worldwide.

G2/M cell cycle arrest by an N-acetyl-D-glucosamine specific lectin from Psathyrella asperospora.

A new N-acetyl-D-glucosamine (GlcNAc) specific lectin was identified and purified from the fruiting body of the Australian indigenous mushroom Psathyrella asperospora. The functional lectin, named PAL, showed hemagglutination activity against neuraminidase treated rabbit and human blood types A, B and O, and exhibited high binding specificity towards GlcNAc, as well as mucin and fetuin, but not against asialofetuin. PAL purified to homogeneity by a combination of ammonium sulfate precipitation, chitin affinity chromatography and size exclusion chromatography, was monomeric with a molecular mass of 41.8 kDa, was stable at temperatures up to 55 °C and between pH 6-10, and did not require divalent cations for optimal activity. De novo sequencing of PAL using LC-MS/MS, identified 10 tryptic peptides that revealed substantial sequence similarity to the GlcNAc recognizing lectins from Psathyrella velutina (PVL) and Agrocybe aegerita (AAL-II) in both the carbohydrate binding and calcium binding sites. Significantly, PAL was also found to exert a potent anti-proliferative effect on HT29 cells (IC50 0.48 µM) that was approximately 3-fold greater than that observed on VERO cells; a difference found to be due to the differential expression of cell surface GlcNAc on HT29 and VERO cells. Further characterization of this activity using propidium iodine staining revealed that PAL induced cell cycle arrest at G2/M phase in a manner dependent on its ability to bind GlcNAc.

Proposals for consideration at IMC12 to modify provisions related solely to fungi in Chapter F of the International Code of Nomenclature for algae, fungi, and plants.

Seven proposals or sets of proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) have been received. These proposals are formally presented together here. The topics addressed relate to: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. In addition, a suggestion is included to update the mention of the World Directory of Culture Collections in Article 40.7 Note 4. A Synopsis of the formal proposals will be provided in early July 2024, and the mycological community will be invited to provide a guiding vote on the proposals with a closing date of 2 August 2024. Final decisions on the proposals will be made following debate at the Fungal Nomenclature Session of IMC12 in August 2024.

Synopsis of proposals on fungal nomenclature: a review of the proposals concerning Chapter F of the International Code of Nomenclature for algae, fungi, and plants submitted to the XII International Mycological Congress, 2024.

A commentary is provided on the seven formally published proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) that will be dealt with by the Fungal Nomenclature Session (FNS) of the 12th International Mycological Congress (IMC12) in August 2024. The proposals deal with: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. Information is also provided on the composition and role of the Fungal Nomenclature Bureau, the operation of the FNS and the pre-Congress Guiding vote.

On the trail of a critically endangered fungus: A world-first application of wildlife detection dogs to fungal conservation.

Plant and animal conservation have benefited from the assistance of wildlife detection dogs (WDDs) since 1890, but their application to fungal conservation has not been trialed. In a world-first, we tested the effectiveness of WDDs and human surveyors when searching for experimentally outplanted fungi in natural habitat. We focused on a critically endangered fungus from Australia, Hypocreopsis amplectens, and showed that a WDD outperformed a human surveyor: our WDD detected a greater proportion of targets, had a faster time to first discovery, and had fewer false negatives. Our study highlights the tremendous potential for WDDs to enhance fungal conservation by demonstrating their utility in one of the most challenging fungal systems: a rare species with low population densities and low volatility. Our findings suggest that the application of WDDs to fungal conservation should enhance continuing efforts to document and conserve an understudied kingdom that is threatened by habitat loss and climate change.

Taxonomic revision of fleshy species of Hydnellum, Neosarcodon, and Sarcodon (Thelephorales) from Australasia.

Stipitate Thelephorales are basidiomycetous, mostly hydnoid, ectomycorrhizal fungi. Some species have declined considerably, and some are threat-listed as vulnerable or endangered. These ecological concerns require a well-resolved taxonomy to understand diversity in this group of fungi and facilitate conservation. However, phylogenetic studies have mostly neglected Southern Hemisphere representatives. This study examines the fleshy species of stipitate Thelephorales from native forests in Australia and New Zealand, using morphological analyses and phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and D1-D2 domains at the 5' end of nuc 28S rDNA (28S) sequences amplified from DNA isolated from fungarium collections and environmental DNA (eDNA) sequences from the Australian Microbiome initiative. Five new species, Sarcodon austrofibulatus, Hydnellum gatesiae, H. nothofagacearum, H. pseudoioeides, and H. variisporum, are described, Sarcodon carbonarius is transferred to Neosarcodon, and a key is provided for the six named species in the region. Boletopsis and Neosarcodon are reported from Australia for the first time based on detections from eDNA in soil samples taken from native forests. The Australasian species of Hydnellum occupy a highly derived position with the phylogeny of the genus, the members of which are otherwise all from the Northern Hemisphere, suggestive of a long-distance dispersal origin for the Australasian species.

Cultures as types and the utility of viable specimens for fungal nomenclature.

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.

Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia.

Laccaria (Hydnangiaceae, Agaricales, Basidiomycota) is one of the more intensively studied ectomycorrhizal genera; however, species boundaries within Laccaria and the closely related Hydnangium and Podohydnangium in Australia have not yet been examined with molecular sequence data. Based on morphological characters, eight native species of Laccaria are currently recognized in Australia, as well as three Hydnangium species and the monotypic Podohydnangium australe. Sequences of the internal transcribed spacer region of nuclear rDNA (ITS), RNA polymerase beta subunit II (rpb2) and translation elongation factor 1 alpha (tef-1α) were generated from 77 collections of Laccaria, Hydnangium and Podohydnangium from Australia. Ten phylogenetic species and a further 11 potential species (represented by singletons) of Laccaria in Australia are delimited from sequence analyses. Most of the morphological species contained cryptic phylogenetic species, but these species were always nested entirely within a given morphological species, although not always as sister taxa. The rpb2 locus performed best as a species barcode with pairwise and patristic distance measures. The ITS sequence region returned the least resolved gene tree of the three regions examined and was the least useful as a barcode region. Based on the phylogenetic topology, there appears to have been multiple gains and/or losses of the ectomycorrhizal association of some species with the myrtle beech, Nothofagus cunninghamii as well as of sequestrate basidiocarps and two-spored basidia.

Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era.

Fungal taxonomy is a fundamental discipline that aims to recognise all fungi and their kinships. Approximately 5% of a practical estimate of 2.2-3.8 million species globally are currently known, and consequently the Fungal Tree of Life (FTOL) is very incompletely reconstructed. With the advances of new technologies, mycology is marching into the interdisciplinary and globalisation era. To make fungal taxonomy relevant, innovative sampling methods and phylogenomics analyses should be performed to reconstruct a much more comprehensive FTOL. In association with this densely sampled FTOL, multiomics will reveal what drives fungal species diversification and how fungal traits evolve to adapt to various environments, while metagenomics will facilitate the understanding and protection of the ecological functions of fungi. A coordinated approach to pursuing these research agendas that includes conceiving of and costing a mission to describe all the fungi on the planet will unlock potential of fungi to support sustainable development of our society.

A comparison of the accuracy of mushroom identification applications using digital photographs.

OBJECTIVE: To compare the accuracy of three popular mushroom identification software applications in identifying mushrooms involved in exposures reported to the Victorian Poisons Information Centre and Royal Botanic Gardens Victoria. BACKGROUND: Over the past 10 years, an increasing number of software applications have been developed for use on smart phones and tablet devices to identify mushrooms. We have observed an increase in poisonings after incorrect identification of poisonous species as edible, using these applications. DESIGN: We compared the accuracy of three iPhone™ and Android™ mushroom identification applications: Picture Mushroom (Next Vision Limited©), Mushroom Identificator (Pierre Semedard©), and iNaturalist (iNaturalist, California Academy of Sciences©). Each app was tested independently by three researchers using digital photographs of 78 specimens sent to the Victorian Poisons Information Centre and Royal Botanic Gardens Victoria over a two-year period, 2020-2021. Mushroom identification was confirmed by an expert mycologist. For each app, individual and combined results were compared. RESULTS: Picture Mushroom was the most accurate of the three apps and correctly identified 49% (95% CI [0-100]) of specimens, compared with Mushroom Identificator (35% [15-56]) and iNaturalist (35% [0-76]). Picture Mushroom correctly identified 44% of poisonous mushrooms [0-95], compared with Mushroom Identificator (30% [1-58]) and iNaturalist (40% [0-84), but Mushroom Identificator identified more specimens of Amanita phalloides correctly (67%), compared to Picture Mushroom (60%) and iNaturalist (27%). Amanita phalloides was falsely identified, twice by Picture Mushroom and once by iNaturalist. CONCLUSIONS: Mushroom identification applications may be useful future tools to assist clinical toxicologists and the general public in the accurate identification of mushrooms species but, at present, are not reliable enough to exclude exposure to potentially poisonous mushrooms when used alone.

New species of Tulasnella associated with Australian terrestrial orchids in the subtribes Megastylidinae and Thelymitrinae.

Tulasnella (Tulasnellaceae) is a genus of fungus that can form mycorrhizal associations with orchids (Orchidaceae). Here we used molecular phylogenetic analyses and morphological characteristics of pure cultures across four different media to support the description of five new Tulasnella species associated with commonly occurring and endangered Australian orchids. Tulasnella nerrigaensis associates with Calochilus; T. subasymmetrica and T. kiataensis with Thelymitra; and T. korungensis and T. multinucleata with Pyrorchis and Rimacola respectively. The newly described species were primarily delimited by analyses of five loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), C14436 (adenosine triphosphate [ATP] synthase), C4102 (glutamate synthase), C3304 (ATP helicase), and mt large subunit 16S rDNA (mtLSU). Tulasnella subasymmetrica is introduced for some isolates previously identified as T. asymmetrica, and this latter species is characterized from multilocus sequencing of a new isolate that matches ITS sequences from the ex-type culture. Morphological differences between the new species are slight. Tulasnella multinucleata has 6-12 nuclei per hyphal compartment which is the first instance of multinucleate rather than binucleate or trinucleate hyphal compartments in Tulasnella. The formal description of these species of Tulasnella will aid in future evolutionary and ecological studies of orchid-fungal interactions.

Redelimitation of Heteroradulum (Auriculariales, Basidiomycota) with H.australiense sp. nov.

Auriculariales accommodates species with diverse basidiomes and hymenophores. From morphological and phylogenetic perspectives, we perform a taxonomic study on Heteroradulum, a recently validated genus within the Auriculariales. The genus Grammatus is merged into Heteroradulum, and thus its generic type G.labyrinthinus is combined with Heteroradulum and G.semis is reaccepted as a member of Heteroradulum. Heteroradulumaustraliense is newly described on the basis of three Australian specimens. Heteroradulumyunnanense is excluded from this genus and its taxonomic position at the generic level is considered uncertain. Accordingly, the circumscription of Heteroradulum is re-delimited and the concept of this genus is adjusted by including irpicoid to poroid hymenophores and a hyphal system with clamp connections or simple septa. A key to all nine accepted species of Heteroradulum is presented.

Ethanolic and aqueous extracts derived from Australian fungi inhibit cancer cell growth in vitro.

Fifteen Australian macrofungi were investigated for cytotoxic activity. Ethanol, cold and hot water extracts of each species were screened for cytotoxic activity against normal mouse fibroblast cells (NIH/3T3), healthy human epithelial kidney cells (HEK-293), four cancer cell lines, gastric adenocarcinoma cells (AGS), two mammary gland adenocarcinoma cells (MDA-MB-231, MCF7) and colorectal adenocarcinoma cells (HT-29) with a validated MTT assay. Most extracts derived from Omphalotus nidiformis, Cordyceps cranstounii and Cordyceps gunnii demonstrated significant cytotoxic activity toward a variety of cancer cell lines. In contrast only some extracts from Coprinus comatus, Cordyceps hawkesii, Hypholoma fasciculare, Lepista nuda, Leratiomyces ceres and Ophiocordyceps robertsii displayed significant cytotoxic activity, which was usually selective for only one or two cancer cell lines tested. The least cytotoxic species evaluated in this study were Agaricus bitorquis, Coprinopsis atrametaria, Psathyrella asperospora, Russula clelandii, Tricholoma sp. AU2 and Xerula mundroola.