Publications by authors named "Tom W May"

36 Publications

Re-Evaluation of the Species Complex in Australia.

J Fungi (Basel) 2021 Feb 26;7(3). Epub 2021 Feb 26.

Agriculture Victoria, Department of Jobs, Precincts and Regions, AgriBio Centre, Bundoora 3083, Victoria, Australia.

The species complex is highly variable morphologically and causes powdery mildew on a wide range of species, including stone fruit. A taxonomic revision of the species complex in 2020 identified 12 species, seven of which were newly characterised. In order to clarify which species of this complex are present in Australia, next generation sequencing was used to isolate the fungal ITS+28S and host chloroplast gene regions from 56 powdery mildew specimens of stone fruit and ornamental species accessioned as or sp. in Australian reference collections. The specimens were collected in Australia, Switzerland, Italy and Korea and were collected from 1953 to 2018. Host species were confirmed using phylogenetic analysis, which identified that four had been misidentified as but were actually . species were identified using ITS+28S phylogenetic analysis, recognising three species on stone fruit and related ornamental hosts in Australia. These were , the rose powdery mildew, and two species in the . species complex: o. , which was the predominant species, and a previously unidentified species from peach, which we describe here as .
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http://dx.doi.org/10.3390/jof7030171DOI Listing
February 2021

Setting scientific names at all taxonomic ranks in italics facilitates their quick recognition in scientific papers.

IMA Fungus 2020 Nov 17;11(1):25. Epub 2020 Nov 17.

Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.

It is common practice in scientific journals to print genus and species names in italics. This is not only historical as species names were traditionally derived from Greek or Latin. Importantly, it also facilitates the rapid recognition of genus and species names when skimming through manuscripts. However, names above the genus level are not always italicized, except in some journals which have adopted this practice for all scientific names. Since scientific names treated under the various Codes of nomenclature are without exception treated as Latin, there is no reason why names above genus level should be handled differently, particularly as higher taxon names are becoming increasingly relevant in systematic and evolutionary studies and their italicization would aid the unambiguous recognition of formal scientific names distinguishing them from colloquial names. Several leading mycological and botanical journals have already adopted italics for names of all taxa regardless of rank over recent decades, as is the practice in the International Code of Nomenclature for algae, fungi, and plants, and we hereby recommend that this practice be taken up broadly in scientific journals and textbooks.
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http://dx.doi.org/10.1186/s43008-020-00048-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7670697PMC
November 2020

The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa.

Microorganisms 2020 Nov 30;8(12). Epub 2020 Nov 30.

Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia.

Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.
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http://dx.doi.org/10.3390/microorganisms8121910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7760934PMC
November 2020

New species of associated with Australian terrestrial orchids in the Cryptostylidinae and Drakaeinae.

Mycologia 2021 Jan-Feb;113(1):212-230. Epub 2020 Nov 4.

Ecology and Evolution, Research School of Biology, The Australian National University , Canberra, ACT 2601, Australia.

Many orchids have an obligate relationship with mycorrhizal fungi for seed germination and support into adulthood. Despite the importance of as mycorrhizal partners, many species remain undescribed. Here, we use multiple sequence locus phylogenetic analyses to delimit and describe six new species associated with Australian terrestrial orchids from the subtribes Cryptostylidinae and Drakaeinae. Five of the new species, , and , all associate with (Cryptostylidinae), whereas associates with (Drakaeinae). Isolates representing were previously also reported in association with (Drakaeinae). All newly described species were delimited by phylogenetic analyses of four loci (nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 [ITS], [ATP synthase], [glutamate synthase], and mt 16S rDNA [mtLSU]). The pairwise sequence divergence between species for the ITS region ranged from 5.6% to 25.2%, and the maximum sequence divergence within the newly described species ranged from 1.64% to 4.97%. There was a gap in the distribution of within- and between-species pairwise divergences in the region of 4-6%, with only one within-species value of 4.97% (for two isolates) and one between-species value of 5.6% (involving an isolate of ) falling within this region. Based on fluorescence staining, all six new species are binucleate and have septate, cylindrical hyphae. There was some subtle variation in culture morphology, but colony diameter as measured on 3MN+vitamin medium after 6 wk of growth did not differ among species. However, grew significantly ( < 0.02) slower than others on ½ FIM and ¼ potato dextrose agar (PDA) media. Formal description of these species contributes significantly to documentation of diversity and provides names and delimitations to underpin further research on the fungi and their relationships with orchids.
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http://dx.doi.org/10.1080/00275514.2020.1813473DOI Listing
November 2020

Procedures and timetable for proposals to amend of the .

Authors:
Tom W May

IMA Fungus 2020 24;11:21. Epub 2020 Sep 24.

Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia.

Procedures for preparing and submitting proposals to amend or enhance of the are provided. Such proposals will be considered by the Fungal Nomenclature Session of the XII International Mycological Congress to he held in Amsterdam in 2022. A timetable is laid out for the submission of proposals, due by 31 December 2021, their publication in , the appearance of the 'Synopsis of proposals" and the conduct of the pre-Congress guiding vote.
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http://dx.doi.org/10.1186/s43008-020-00044-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513284PMC
September 2020

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus 2020 10;11:14. Epub 2020 Jul 10.

International Commission on the Taxonomy of Fungi, Champaign, IL USA.

True fungi () and fungus-like organisms (e.g. , ) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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http://dx.doi.org/10.1186/s43008-020-00033-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7353689PMC
July 2020

Chapter F of the as approved by the 11th International Mycological Congress, San Juan, Puerto Rico, July 2018.

IMA Fungus 2019 27;10:21. Epub 2019 Dec 27.

Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany.

A revised version of of the is presented, incorporating amendments approved by the Fungal Nomenclature Session of the 11th International Mycological Congress held in San Juan, Puerto Rico in July 2018. The process leading to the amendments is outlined. Key changes in the are (1) removal of option to use a colon to indicate the sanctioned status of a name, (2) introduction of correctability for incorrectly cited identifiers of names and typifications, and (3) introduction of option to use name identifiers in place of author citations. Examples have been added to aid the interpretation of new Articles and Recommendations, and Examples have also been added to the existing Art. F.3.7 concerning the protection extended to new combinations based on sanctioned names or basionyms of sanctioned names (which has been re-worded), and to Art. F.3.9 concerning typification of names accepted in the sanctioning works.
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http://dx.doi.org/10.1186/s43008-019-0019-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325661PMC
December 2019

Rediscovering an old foe: Optimised molecular methods for DNA extraction and sequencing applications for fungarium specimens of powdery mildew (Erysiphales).

PLoS One 2020 13;15(5):e0232535. Epub 2020 May 13.

Department of Jobs, Agriculture Victoria Research, Regions and Precincts, Bundoora, Australia.

The purpose of this study was to identify a reliable DNA extraction protocol to use on 25-year-old powdery mildew specimens from the reference collection VPRI in order to produce high quality sequences suitable to address taxonomic phylogenetic questions. We tested 13 extraction protocols and two library preparation kits and found the combination of the E.Z.N.A.® Forensic DNA kit for DNA extraction and the NuGen Ovation® Ultralow System library preparation kit was the most suitable for this purpose.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232535PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219758PMC
July 2020

Phylogeny and diversity of (Polyporaceae, Basidiomycota).

MycoKeys 2019 12;54:77-98. Epub 2019 Jun 12.

Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.

Four species of , , , and are described as new and is proposed as a new combination, based on morphological characteristics and molecular phylogenetic analyses inferred from internal transcribed spacer (ITS) and large subunit nuclear ribosomal RNA gene (nLSU) sequences. , and occur in China, occurs in the USA, and the distribution of is extended from New Zealand to Australia. is characterized by the distinct narrow oblong basidiospores measuring 10.5-13.5 × 3.9-5 µm. is characterized by the presence of ventricose cystidioles occasionally with a simple septum, dissepimental hyphae usually with a simple septum, unique thick-walled basidia and distinctly wide oblong basidiospores measuring 13.5-16.5 × 7.5-9.5 µm. is characterized by its large pores (2-3 per mm), a dimitic hyphal structure with non-dextrinoid skeletal hyphae and wide oblong basidiospores measuring 12-15 × 6-8 µm. is characterized by distinctly small pores (7-9 per mm), the presence of dendrohyphidia, and distinctly small ellipsoid basidiospores measuring 5.3-6.7 × 3-4.1 µm. is proposed as a new combination. is shown to be a synonym of and is considered a synonym of .
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http://dx.doi.org/10.3897/mycokeys.54.34362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584150PMC
June 2019

Solving the taxonomic identity of s.l. (Thelephorales, Basidiomycota) - a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data.

MycoKeys 2019 4;50:1-77. Epub 2019 Apr 4.

Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden.

is an ectomycorrhizal, corticioid fungus whose name is frequently assigned to collections of basidiomata as well as root tip and soil samples from a wide range of habitats and hosts across the northern hemisphere. Despite this, its identity is unclear; eight heterotypic taxa have in major reviews of the species been considered synonymous with or morphologically similar to , but no sequence data from type specimens have been available. With the aim to clarify the taxonomy, systematics, morphology, ecology and geographical distribution of and its morphologically similar species, we studied their type specimens as well as 147 basidiomata collections of mostly North European material. We used gene trees generated in BEAST 2 and PhyML and species trees estimated in STACEY and ASTRAL to delimit species based on the ITS, LSU, Tef1α and mtSSU regions. We enriched our sampling with environmental ITS sequences from the UNITE database. We found the group to contain 13 molecularly and morphologically distinct species. Three of these, , and , are already known to science, while ten species are here described as new: , , , , , , , , and . We discovered and to form a sister clade to all other species in s.l. These two species, unlike all other species in the complex, are dimitic. In this study, we designate epitypes for , and and lectotypes for and . We show that the holotype of and the lectotype of are conspecific with , but in the absence of molecular information we regard and as doubtful taxa due to their aberrant morphology. We confirm , and as excluded taxa, since their morphology clearly show that they belong to other genera. A key to the species of the group is provided. We found to be a common species with a wide, Holarctic distribution, forming ectomycorrhiza with a large number of host species in habitats ranging from tropical forests to the Arctic tundra. The other species in the group were found to be less common and have narrower ecological niches.
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http://dx.doi.org/10.3897/mycokeys.50.32432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477855PMC
April 2019

Recognition of the discipline of conservation mycology.

Conserv Biol 2019 06 26;33(3):733-736. Epub 2018 Nov 26.

Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.

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http://dx.doi.org/10.1111/cobi.13228DOI Listing
June 2019

Naming names: the first women taxonomists in mycology.

Stud Mycol 2018 Mar 19;89:63-84. Epub 2017 Dec 19.

Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004, Australia.

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.
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http://dx.doi.org/10.1016/j.simyco.2017.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002341PMC
March 2018

Fungal nomenclature evolving: changes adopted by the 19 International Botanical Congress in Shenzhen 2017, and procedures for the Fungal Nomenclature Session at the 11 International Mycological Congress in Puerto Rico 2018.

IMA Fungus 2017 Dec 28;8(2):211-218. Epub 2017 Sep 28.

Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, 960 Carling Avenue, K.W Neatby Building, Ottawa, Ontario K1A 0C6, Canada.

This article summarizes the key changes in the rules relating to the nomenclature of fungi made at the XIX International Botanical Congress in Shenzhen, China, in July 2017. Most significant was the decision to transfer decision-making on matters related only to the naming of fungi from International Botanical to International Mycological Congresses (IMCs). The rules relating to fungi are to be grouped together in a separate section of the (ICN). The way in which the Fungal Nomenclature Session will operate at the upcoming IMC in Puerto Rico in 2018 is summarized and the timetable for new proposals is presented. In addition, approval for names included on lists of protected names to be protected against unlisted as well as known competing names were passed, as were some simplifications relating to the naming of pleomorphic fungi. From 1 January 2019, it will also be necessary to deposit details of lecto-, neo-, and epitypifications in one of the recognized repositories of fungal names in order for them to be validly published and to establish their priority. Various aspects relating to typifications were referred to a new Special Committee, with a separate Special Subcommittee charged with addressing the issue of using DNA sequences as types for all groups covered by the ICN. It is anticipated that the Shenzhen Code will be published in the first half of 2018.
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http://dx.doi.org/10.5598/imafungus.2017.08.02.01DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729709PMC
December 2017

Report of the Nomenclature Committee for Fungi - 21: Lists from working groups.

Authors:
Tom W May

IMA Fungus 2017 Jun 1;8(1):205-210. Epub 2017 Jun 1.

Royal Botanic Gardens Victoria, 100 Birdwood Avenue, Melbourne, Victoria 3004, Australia.

Six lists of names from working groups set up under Art. 14.13 are approved, consisting of three names of families, 43 names of genera and five names of species, to be treated as conserved against the listed synonymous or homonymous names. Lists were compiled by working groups approved by the International Commission on the Taxonomy of Fungi and the Nomenclature Committee for Fungi: on , , , , , and and . Issues around interpretation of Art. 14.13 and 56.3 and implementation of Art. 57.2 are discussed.
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http://dx.doi.org/10.5598/imafungus.2017.08.01.13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493535PMC
June 2017

Report of the Nomenclature Committee for Fungi - 20.

Authors:
Tom W May

IMA Fungus 2017 Jun 1;8(1):189-203. Epub 2017 Jun 1.

Royal Botanic Gardens Victoria, 100 Birdwood Avenue, Melbourne, Victoria 3004, Australia.

Ratification of appointment of repositories by the International Mycological Congress is reported. The following two family names are recommended for conservation: against ; and the teleomorph-typified against the anamorph-typified . The following family name is not recommended for conservation: against . The following 10 generic names are recommended for conservation: the teleomorph-typified name against the conserved anamorph-typified name ; Sorokīn () against Roussel (); , nom. cons., against an additional name, ; (Fr. : Fr.) P. Kumm. () against (Webb ex Spach) Fourr. () with a conserved type; against ; with a conserved type; with a conserved type; with that spelling; with a conserved type; and against . Conservation of Freng. () against Sacc. () is not opposed. The following generic name is not recommended for conservation: with a conserved type. The proposal to conserve the generic name against was withdrawn. The following 17 species names are recommended for conservation: () against the sanctioned (); against ; () against and ; () against , , and ; with a conserved type; against (); Y. Nisik. & C. Miyake () against Brond. and ; () against ; Schrad. () against Lam. with a conserved type; () with that spelling; (, ) with a conserved type; () with a conserved type; against , and ; Durieu & Lév. against Saut.; with that spelling; with a conserved type; and with a conserved type. The following 22 species names (teleomorph-typified) are recommended for conservation against anamorph-typified names: against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; against ; and against . The following two species names are not recommended for conservation: against ; and () against . It is recommended that the generic name and the species name not be rejected under Art. 56. The following two species names are recommended for rejection under Art. 56: () and . As a result of reference under Art. 53.5, it is recommended that the following two pairs of names are not to be treated as homonyms: De Not. and Planch.; and (Pers.) Bonord. and Sweet.
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http://dx.doi.org/10.5598/imafungus.2017.08.01.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493534PMC
June 2017

New species of associated with terrestrial orchids in Australia.

IMA Fungus 2017 Jun 10;8(1):27-47. Epub 2017 Mar 10.

Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.

Recent studies using sequence data from eight sequence loci and coalescent-based species delimitation methods have revealed several species-level lineages of associated with the orchid genera and in Australia. Here we formally describe three of those species, and spp. nov., as well as an additional species associated with growing in , sp. nov. Species were identified by phylogenetic analyses of the ITS with up to 1.3 % sequence divergence within taxa and a minimum of 7.6 % intraspecific divergence. These new (, ) species are currently only known from orchid hosts, with each fungal species showing a strong relationship with an orchid genus. In this study, and associate with , while associates with and and associates with .
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http://dx.doi.org/10.5598/imafungus.2017.08.01.03DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493536PMC
June 2017

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

Proteins 2017 05 7;85(5):969-975. Epub 2017 Mar 7.

CERMAV, UPR5301, CNRS and Université Grenoble Alpes, Grenoble, 38041, France.

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.
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http://dx.doi.org/10.1002/prot.25265DOI Listing
May 2017

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

Int J Mol Sci 2015 Apr 8;16(4):7802-38. Epub 2015 Apr 8.

Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD 4222, Australia.

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.
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http://dx.doi.org/10.3390/ijms16047802DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425051PMC
April 2015

Fungal biogeography. Global diversity and geography of soil fungi.

Science 2014 Nov;346(6213):1256688

Natural History Museum, University of Tartu, Tartu, Estonia.

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
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http://dx.doi.org/10.1126/science.1256688DOI Listing
November 2014

Mitochondrial microsatellite markers for the Australian ectomycorrhizal fungus Laccaria sp. A (Hydnangiaceae).

Appl Plant Sci 2014 Mar 11;2(3). Epub 2014 Feb 11.

Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, Victoria 3141, Australia.

Unlabelled:

Premise Of The Study: Microsatellite loci were developed for the ectomycorrhizal fungus Laccaria sp. A to investigate the population genetic structure of this fungal symbiont across its fragmented distribution in southeastern Australia. •

Methods And Results: A partial genome sequence from an individual collection of Laccaria sp. A was obtained by 454 genome sequencing. Eight microsatellite markers were selected from 66 loci identified in the genome. The selected markers were highly polymorphic (4-19 alleles per locus, average 13 alleles) and amplified reproducibly from collections made across the distribution of this species. Five of these markers also amplified reproducibly in the sister species Laccaria sp. E (1). All eight of the selected microsatellite loci were from the mitochondrial genome. •

Conclusions: The highly polymorphic markers described here will enable population structure of Laccaria sp. A to be determined, contributing to research on mycorrhizal fungi from a novel distribution.
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http://dx.doi.org/10.3732/apps.1300086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103105PMC
March 2014

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

Mol Phylogenet Evol 2014 Feb 1;71:249-60. Epub 2013 Nov 1.

Royal Botanic Gardens Melbourne, Birdwood Ave, South Yarra, Victoria 3141, Australia. Electronic address:

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.
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http://dx.doi.org/10.1016/j.ympev.2013.10.019DOI Listing
February 2014

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

Glycoconj J 2014 Jan 27;31(1):61-70. Epub 2013 Sep 27.

Institute for Glycomics, Griffith University, Gold Coast Campus, Griffith, QLD, 4222, Australia.

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.
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http://dx.doi.org/10.1007/s10719-013-9502-xDOI Listing
January 2014

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

Mycologia 2013 May-Jun;105(3):547-63. Epub 2013 Feb 8.

School of Botany, University of Melbourne, Victoria, 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.
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http://dx.doi.org/10.3852/12-266DOI Listing
July 2013

Comparative study of hemagglutination and lectin activity in Australian medicinal mushrooms (higher Basidiomycetes).

Int J Med Mushrooms 2011 ;13(6):493-504

Institute for Glycomics, Gold Coast campus, Griffith University, Queensland 4222, Australia.

Fifteen Australian mushroom species (higher Basidiomycetes) were assessed for hemagglutination and lectin activity. Hemagglutination activity was evaluated using both neuraminidase treated and untreated rabbit and human A, B, and O erythrocytes. Lectin activity was determined by the ability of various mono- and oligosaccharides to inhibit hemagglutination activity. Of the mushrooms evaluated, seven contained lectin activity. However, five (Agaricus bitorquis, Chlorophyllum brunneum, Coprinus comatus, Cortinarius sp. TWM 1710, and Omphalotus nidiformis) expressed lectin activity in only one of two collections tested. The two remaining lectin active mushroom species (Phlebopus marginatus and Psathyrella asperospora) possessed lectin activity with the same sugar specificity in both collections. Although lectins were identified with diverse specificity, lactose-specific lectin activity was most frequently identified, being present in Agaricus bitorquis, Copronus comatus, Omphalotus nidiformis, and Phlebopus marginatus. In contrast, Psathyrella asperospora, Cortinarius sp. TWM 1710, and Chlorophyllum brunneum were found to possess lectin activity specific for N-acetyl-D-glucosamine, galactose, and N-acetyl-neurammic acid, respectively. Significantly, the galactose-specific lectin activity identified in Cortinarius sp. TWM 1710 and the lactose-specific lectin activity in Phlebopus marginatus have not been previously reported.
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http://dx.doi.org/10.1615/intjmedmushr.v13.i6.10DOI Listing
March 2012

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

Mycologia 2011 May-Jun;103(3):458-65. Epub 2011 Jan 24.

School of Pharmacy, Griffith University, Gold Coast campus, Queensland 4222, Australia.

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.
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http://dx.doi.org/10.3852/10-121DOI Listing
September 2011

Antibacterial metabolites from Australian macrofungi from the genus Cortinarius.

Phytochemistry 2010 Jun 12;71(8-9):948-55. Epub 2010 Apr 12.

School of Pharmacy, Griffith University, Gold Coast Campus, QLD, Australia.

In this study, ethyl acetate and aqueous fractions from 117 collections of Australian macrofungi belonging to the mushroom genus Cortinarius were screened for antimicrobial activity against Staphylococcus aureus and Pseudomonas aeruginosa. Overall, the lipophilic fractions were more active than the aqueous fractions. The ethyl acetate fractions of most or all collections of 13 species, namely Cortinarius ardesiacus, C. archeri, C. austrosaginus, C. austrovenetus, C. austroviolaceus, C. coelopus, C. [Dermocybe canaria](2), C. clelandii, C. [D. kula], C. memoria-annae, C. persplendidus, C. sinapicolor, C. vinosipes and forty seven collections of un-described Cortinarius species exhibited IC(50) values of 0.09 mg/mL against S. aureus. In contrast, most or all collections of only four species, namely C. abnormis, C. austroalbidus, C. [D. kula], C. persplendidus, and eleven un-described Cortinarius collections exhibited similar effects against P. aeruginosa (IC(50)
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http://dx.doi.org/10.1016/j.phytochem.2010.03.016DOI Listing
June 2010

Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages.

Mycorrhiza 2010 Apr 16;20(4):217-63. Epub 2009 Sep 16.

Institute of Ecology and Earth Sciences and Natural History Museum of Tartu University, 40 Lai Street, 51005, Tartu, Estonia.

The ectomycorrhizal (EcM) symbiosis involves a large number of plant and fungal taxa worldwide. During studies on EcM diversity, numerous misidentifications, and contradictory reports on EcM status have been published. This review aims to: (1) critically assess the current knowledge of the fungi involved in the EcM by integrating data from axenic synthesis trials, anatomical, molecular, and isotope studies; (2) group these taxa into monophyletic lineages based on molecular sequence data and published phylogenies; (3) investigate the trophic status of sister taxa to EcM lineages; (4) highlight other potentially EcM taxa that lack both information on EcM status and DNA sequence data; (5) recover the main distribution patterns of the EcM fungal lineages in the world. Based on critically examining original reports, EcM lifestyle is proven in 162 fungal genera that are supplemented by two genera based on isotopic evidence and 52 genera based on phylogenetic data. Additionally, 33 genera are highlighted as potentially EcM based on habitat, although their EcM records and DNA sequence data are lacking. Molecular phylogenetic and identification studies suggest that EcM symbiosis has arisen independently and persisted at least 66 times in fungi, in the Basidiomycota, Ascomycota, and Zygomycota. The orders Pezizales, Agaricales, Helotiales, Boletales, and Cantharellales include the largest number of EcM fungal lineages. Regular updates of the EcM lineages and genera therein can be found at the UNITE homepage http://unite.ut.ee/EcM_lineages . The vast majority of EcM fungi evolved from humus and wood saprotrophic ancestors without any obvious reversals. Herbarium records from 11 major biogeographic regions revealed three main patterns in distribution of EcM lineages: (1) Austral; (2) Panglobal; (3) Holarctic (with or without some reports from the Austral or tropical realms). The holarctic regions host the largest number of EcM lineages; none are restricted to a tropical distribution with Dipterocarpaceae and Caesalpiniaceae hosts. We caution that EcM-dominated habitats and hosts in South America, Southeast Asia, Africa, and Australia remain undersampled relative to the north temperate regions. In conclusion, EcM fungi are phylogenetically highly diverse, and molecular surveys particularly in tropical and south temperate habitats are likely to supplement to the present figures. Due to great risk of contamination, future reports on EcM status of previously unstudied taxa should integrate molecular identification tools with axenic synthesis experiments, detailed morphological descriptions, and/or stable isotope investigations. We believe that the introduced lineage concept facilitates design of biogeographical studies and improves our understanding about phylogenetic structure of EcM fungal communities.
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http://dx.doi.org/10.1007/s00572-009-0274-xDOI Listing
April 2010

Taxonomic and functional characterisation of fungi from the Sebacina vermifera complex from common and rare orchids in the genus Caladenia.

Mycorrhiza 2010 Aug 7;20(6):375-90. Epub 2010 Jan 7.

Department of Resource Management and Geography, University of Melbourne, Burnley Campus, Richmond, VIC 3121, Australia.

The terrestrial orchid genus Caladenia contains many species which are threatened with extinction. They have highly specific associations with Sebacina vermifera and closely related fungi, and conservation of these terrestrial orchids, in part, relies on symbiotic propagation to produce plants for reintroduction and ex situ conservation collections. However, little is known of the diversity of mycorrhizal fungi associating with natural populations. Here, restriction fragment polymorphism analysis, internal transcribed spacer and nuclear large subunit sequencing and symbiotic seed germination were used to investigate the taxonomic and functional diversity of fungal isolates from single populations of six endangered Caladenia species and one common species across the same biogeographic range. Fifty-nine fungal isolates were collected for investigation including ten isolates from the six endangered species Caladenia audasii, Caladenia amoena, Caladenia sp. aff. fragrantissima (Central Victoria), Caladenia sp. aff. patersonii, Caladenia rosella and Caladenia orientalis and 49 isolates from six populations of the common species Caladenia tentaculata. While the common species associated with three distinct S. vermifera-like taxa, the six endangered species were restricted to one of these fungal taxa. No direct relationship between the taxonomic identity of the fungi and their ability to stimulate seed germination was observed; however, the majority of the fungi isolated from the Caladenia species were capable of germinating seed in vitro, indicating their mycorrhizal status and potential for symbiotic propagation in conservation programmes.
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http://dx.doi.org/10.1007/s00572-009-0290-xDOI Listing
August 2010

Surrogates for macrofungi and mosses in reservation planning.

Conserv Biol 2010 Jun 24;24(3):730-6. Epub 2009 Nov 24.

School of Geography and Environmental Studies, University of Tasmania, Hobart, Tasmania, Australia.

Our knowledge of cryptogam taxonomy and species distributions is currently too poor to directly plan for their conservation. We used inventory data from four distinct vegetation types, near Hobart Tasmania, to address the proposition that vegetation type, vascular plant taxon composition, and environmental variables can act as surrogates for mosses and macrofungi in reservation planning. The four vegetation types proved distinct in their taxon composition for all macrofungi, mosses, and vascular plants. We tested the strength of the relationships between the composition of cryptogam taxonomic groups and vascular plant composition and between the environmental variables and canopy cover. Taxon composition of woody vascular plants and vascular plants was the best predictor of the taxon composition of mosses and macrofungi. Combinations of environmental variables and canopy cover were also strong predictors of the taxon composition of mosses and macrofungi. We used an optimization routine for vascular plant taxa and woody plant species and determined the representation of cryptogam taxa in these selections. We identified sites with approximately 10% and 30% of the greatest proportions of vascular plants and woody vascular plants and calculated representation of mosses and macrofungi at these sites. We compared the results of these site selections with random site selections and random selections stratified by vegetation type. Random selection of sites by vegetation type generally captured more cryptogams than site selection by vascular plants at the 10% level. Vascular plant and woody plant taxon composition, vegetation type, and environmental and structural characteristics, all showed promise as surrogates for capturing common cryptogams in reserve systems.
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http://dx.doi.org/10.1111/j.1523-1739.2009.01378.xDOI Listing
June 2010

Establishment of ectomycorrhizal fungal community on isolated Nothofagus cunninghamii seedlings regenerating on dead wood in Australian wet temperate forests: does fruit-body type matter?

Mycorrhiza 2009 Aug 18;19(6):403-416. Epub 2009 Apr 18.

Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Street, 51005, Tartu, Estonia.

Decaying wood provides an important habitat for animals and forms a seed bed for many shade-intolerant, small-seeded plants, particularly Nothofagus. Using morphotyping and rDNA sequence analysis, we compared the ectomycorrhizal fungal community of isolated N. cunninghamii seedlings regenerating in decayed wood against that of mature tree roots in the forest floor soil. The /cortinarius, /russula-lactarius, and /laccaria were the most species-rich and abundant lineages in forest floor soil in Australian sites at Yarra, Victoria and Warra, Tasmania. On root tips of seedlings in dead wood, a subset of the forest floor taxa were prevalent among them species of /laccaria, /tomentella-thelephora, and /descolea, but other forest floor dominants were rare. Statistical analyses suggested that the fungal community differs between forest floor soil and dead wood at the level of both species and phylogenetic lineage. The fungal species colonizing isolated seedlings on decayed wood in austral forests were taxonomically dissimilar to the species dominating in similar habitats in Europe. We conclude that formation of a resupinate fruit body type on the underside of decayed wood is not necessarily related to preferential root colonization in decayed wood. Rather, biogeographic factors as well as differential dispersal and competitive abilities of fungal taxa are likely to play a key role in structuring the ectomycorrhizal fungal community on isolated seedlings in decaying wood.
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http://dx.doi.org/10.1007/s00572-009-0244-3DOI Listing
August 2009