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N.Z.J.Ecol: Causes and consequences of changes to New Zealand’s fungal biota

N.Z.J.Ecol: Causes and consequences of changes to New Zealand’s fungal biota | fungi bacteria publications | Scoop.it

This paper briefly reviews advances in knowledge of the non-lichenised fungi of New Zealand over the past 25 years. Since 1980, the number of species recorded from New Zealand has doubled, and molecular techniques have revolutionised studies on fungal phylogeny and our understanding of fungal distribution, biology and origins. The origins of New Zealand’s fungi are diverse; a few appear to be ancient, whereas many have arrived in geologically more recent times following trans-oceanic dispersal. Some of these more recent arrivals have evolved subsequently to form local endemic species, while others may be part of larger populations maintained through regular, trans-oceanic gene flow. Although questions remain about which fungi truly are indigenous and which are exotic, about one-third of the fungi recorded from New Zealand are likely to have been introduced since human settlement. While most exotic species are confined to human-modified habitats, there are some exceptions. These include species with potential to have significant impacts at the landscape scale. Examples from saprobic, pathogenic, endophytic and ectomycorrhizal fungi are used to discuss the factors driving the distribution and dispersal of New Zealand’s fungi at both global and local scales, the impact that historical changes to New Zealand’s vascular plant and animal biota have had on indigenous fungi, and the broader ecological impact of some of the exotic fungal species that have become naturalised in native habitats. The kinds of fungi present in New Zealand, and the factors driving the distribution and behaviour of those fungi, are constantly changing. These changes have occurred over a wide scale, in both time and space, which means New Zealand’s indigenous fungi evolved in response to ecological pressures very different from those found in New Zealand today.

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Cryptic diversity in the sequestrate genus Stephanospora (Stephanosporaceae: Agaricales) in Australasia

Cryptic diversity in the sequestrate genus Stephanospora (Stephanosporaceae: Agaricales) in Australasia | fungi bacteria publications | Scoop.it

Prior to this treatment a single name, Stephanospora flava, was applied to all collections of the sequestrate genus Stephanospora in Australasia. We used morphological characters with molecular support to differentiate, describe and illustrate nine novel species and one new combination, and refine the circumscription of S. flava. Stephanospora flava is herein restricted to bispored collections from Tasmania, and the quadrisporic Stephanospora tetraspora is raised to species level. Six species (four new) are endemic to Australia, S. flava s.s, S. tetraspora comb. nov., Stephanospora sheoak, Stephanospora cribbae, Stephanospora hystrispora, and Stephanospora occidentiaustralis. Three speciesStephanospora poropingao, Stephanospora pounamu, and Stephanospora kanuka are endemic to New Zealand; and one species, Stephanospora aorangi occurs in both Australia and New Zealand. Two other new species, Stephanospora novae-caledoniae and Stephanospora papua, are endemic to New Caledonia, or Papua New Guinea, respectively.

Analyses of three nuclear gene regions (ITS, ef-1, and LSU) are consistent with current classifications of the family Stephanosporaceae, as a mix of three resupinate polypore genera and two sequestrate genera.Athelidium aurantiacum is included as an outlier, with a strongly supported core of Cristinia (Clade I),Lindtneria (Clade II), Stephanospora, Mayamontana, and Lindtneria trachyspora (Clade III), and a novel lineage of environmental and sporocarp sequences from a broad geographic range (Clade IV). Taxonomic and nomenclatural issues raised by the presence of both type species of Stephanospora (S. caroticolor) and Lindtneria (L. trachyspora) in the same clade are discussed.

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Plant associated fungi from Nauru, South Pacific. Plant Pathology & Quarantine Journals - Volume 4 Issue 1

Eighteen fungal taxa were collected in Nauru in 1980. They comprised four rust fungi, one smut fungus, several species that cause leaf spots and some saprobes. This is the first report of any plant associated fungi from Nauru.

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Free pdf: http://plantpathologyquarantine.org/PDFs/PPQ_4_1_3.pdf

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Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales) - Springer

Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales) - Springer | fungi bacteria publications | Scoop.it
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Molecular phylogenies using 1–4 gene regions and information on ecology, morphology and pigment chemistry were used in a partial revision of the agaric family Hygrophoraceae. The phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are: Acantholichen, Ampulloclitocybe, Arrhenia, Cantharellula, Cantharocybe, Chromosera, Chrysomphalina, Cora, Corella, Cuphophyllus, Cyphellostereum, Dictyonema, Eonema, Gliophorus, Haasiella, Humidicutis, Hygroaster, Hygrocybe, Hygrophorus, Lichenomphalia, Neohygrocybe, Porpolomopsis and Pseudoarmillariella. A new genus that is sister to Chromosera is described as Gloioxanthomyces. Revisions were made at the ranks of subfamily, tribe, genus, subgenus, section and subsection. We present three new subfamilies, eight tribes (five new), eight subgenera (one new, one new combination and one stat. nov.), 26 sections (five new and three new combinations and two stat. nov.) and 14 subsections (two new, two stat. nov.). Species of Chromosera, Gliophorus, Humidicutis, and Neohygrocybe are often treated within the genus Hygrocybe; we therefore provide valid names in both classification systems. We used a minimalist approach in transferring genera and creating new names and combinations. Consequently, we retain in the Hygrophoraceae the basal cuphophylloid grade comprising the genera Cuphophyllus, Ampulloclitocybe and Cantharocybe, despiteweak phylogenetic support. We include Aeruginospora and Semiomphalina in Hygrophoraceae based on morphology though molecular data are lacking. The lower hygrophoroid clade is basal to Hygrophoraceae s.s., comprising the genera Aphroditeola, Macrotyphula, Phyllotopsis, Pleurocybella, Sarcomyxa, Tricholomopsis and Typhula.

Keywords: Hygrophoraceae, Fungi, Revisionary systematics, Nomenclatural revision, Phylogenetics, Pigment chemistry, Lamellar trama construction, Hymenial morphology, Ecology

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The Colletotrichum gloeosporioides species complex

The Colletotrichum gloeosporioides species complex | fungi bacteria publications | Scoop.it

The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum (for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for species level identification, which is important because many of these fungi are of biosecurity significance. In addition to the accepted species, notes are provided for names where a possible close relationship with C. gloeosporioides sensu lato has been suggested in the recent literature, along with all subspecific taxa and formae speciales within C. gloeosporioides and its putative teleomorph Glomerella cingulata.


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NZJB: Hypocreopsis amplectens sp. nov., a rare fungus from New Zealand and Australia

NZJB: Hypocreopsis amplectens sp. nov., a rare fungus from New Zealand and Australia | fungi bacteria publications | Scoop.it

Hypocreopsis amplectens is distinguished from other Hypocreopsis species by its 3–4‐spored asci and multiseptate, rough‐walled ascospores. As the asci mature it is common for one spore to abort or for adjacent spores to fuse. This fungus has been referred to as Hypocreopsis sp. and Hypocreopsis sp. ‘Nyora’ in the Australian literature. In Victoria, Australia, H. amplectens has been classified as “vulnerable” under the Victorian Flora and Fauna Guarantee Act 1988, and the Nyora Flora and Fauna Reserve was created partly because of its occurrence there. Despite intensive surveys it is still known from only three sites in Australia. In New Zealand it is known from a single collection made more than 20 years ago in Nothofagus forest at a site visited regularly by mycologists. Its status as a rare fungus makes it eligible for inclusion on national threat status lists in Australia and New Zealand.

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Diversity: Response of Mycorrhizal Diversity to Current Climatic Changes

Diversity: Response of Mycorrhizal Diversity to Current Climatic Changes | fungi bacteria publications | Scoop.it

Form and function of mycorrhizas as well as tracing the presence of the mycorrhizal fungi through the geological time scale are herein first addressed. Then mycorrhizas and plant fitness, succession, mycorrhizas and ecosystem function, and mycorrhizal resiliency are introduced. From this, four hypotheses are drawn: (1) mycorrhizal diversity evolved in response to changes in Global Climate Change (GCC) environmental drivers, (2) mycorrhizal diversity will be modified by present changes in GCC environmental drivers, (3) mycorrhizal changes in response to ecological drivers of GCC will in turn modify plant, community, and ecosystem responses to the same, and (4) Mycorrhizas will continue to evolve in response to present and future changes in GCC factors. The drivers of climate change examined here are: CO2 enrichment, temperature rise, altered precipitation, increased N-deposition, habitat fragmentation, and biotic invasion increase. 

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Studies in Mycology: Two new pathogenic ascomycetes in Guignardia and Rosenscheldiella on New Zealand's pygmy mistletoes (Korthalsella: Viscaceae)

Studies in Mycology: Two new pathogenic ascomycetes in Guignardia and Rosenscheldiella on New Zealand's pygmy mistletoes (Korthalsella: Viscaceae) | fungi bacteria publications | Scoop.it

Two new pathogens, Guignardia korthalsellae and Rosenscheldiella korthalsellae, are described from New Zealand's pygmy mistletoes (Korthalsella, Viscaceae). Both form ascomata on living phylloclades with minimal disruption of the tissue. Fungal hyphae within the phylloclade are primarily intercellular. Guignardia korthalsellae disrupts a limited number of epidermal cells immediately around the erumpent ascoma, while the ascomata of Rosenscheldiella korthalsellae develop externally on small patches of stromatic tissue that form above stomatal cavities. Rosenscheldiella is applied in a purely morphological sense. LSU sequences show that R. korthalsellae as well as another New Zealand species, Rosenscheldiella brachyglottidis, are members of the Mycosphaerellaceae sensu stricto. Genetically, Rosenscheldiella, in the sense we are using it, is polyphyletic; LSU and ITS sequences place the two New Zealand species in different clades within the Mycosphaerellaceae. Rosenscheldiella is retained for these fungi until generic relationships within the family are resolved. Whether or not the type species of Rosenscheldiella, R. styracis, is also a member of the Mycosphaerellaceae is not known, but it has a similar morphology and relationship to its host as the two New Zealand species.

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Mycological Research: Diversity and distribution of fungal foliar endophytes in New Zealand Podocarpaceae

Mycological Research: Diversity and distribution of fungal foliar endophytes in New Zealand Podocarpaceae | fungi bacteria publications | Scoop.it

The diversity and distribution of fungal endophytes in the leaves of four podocarps (Dacrydium cupressinum, Prumnopitys ferruginea, Dacrycarpus dacrydioides, and Podocarpus totara, all Podocarpaceae) and an angiosperm (Kunzea ericoides, Myrtaceae) occurring in close stands were studied. The effects of host species, locality, and season on endophyte assemblages were investigated. Host species was the major factor shaping endophyte assemblages. The spatial separation of sites and seasonal differences played significant but lesser roles. The mycobiota of each host species included both generalist and largely host-specialised fungi. The host-specialists were often observed at low frequencies on some of the other hosts. There was no clear evidence for family-level specialisation across the Podocarpaceae. Of the 17 species found at similar frequencies on several of the podocarp species, 15 were found also on Kunzea. Many of the endophytes isolated appear to represent species of fungi not previously recognised from New Zealand.

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A new species of rust fungus on the New Zealand endemic plant, Myosotidium, from the isolated Chatham Islands

Pucciniastrum myosotidii sp. nov. is described from plants of the Chatham Island forget-me-not (Myosotidium  hortensium), a host plant that has a conservation status of “nationally endangered”. The rust has been found only on  cultivated plants and not on wild plants. Although no teliospores were found, LSU and SSU sequence analysis showed  that the new rust is closely related to some species of Pucciniastrum and Thekopsora forming a weakly supported  clade together with P. boehmeriae, P. epilobii, P.  ircaeae, P. goeppertianum, P. guttatum, P. pustulatum, T. minima and Melampsorella symphyti. If this rust is endemic to Chatham Islands, then it must be accepted as a species of  conservation value since the host plant is under threat from grazing animals and habitat loss.

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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi | fungi bacteria publications | Scoop.it

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.

Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353

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PNAS: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

PNAS: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi | fungi bacteria publications | Scoop.it

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.


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Mycologia: Molecular phylogeny reveals a core clade of Rhytismatales

Mycologia: Molecular phylogeny reveals a core clade of Rhytismatales | fungi bacteria publications | Scoop.it

Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and in particular the genus taxonomy in the order has been criticized for being unnatural. We used nuclear LSU and mitochondrial SSU sequences in Bayesian phylogenetic analyses to define a core clade of Rhytismatales sensu stricto. Some of the genera traditionally placed within the Rhytismatales, Ascodichaena, Marthamyces, Mellitiosporium, Potebniamyces, Propolis and Pseudophacidium, are shown to be phylogenetically distinct, all related to various other taxa at present placed in the polyphyletic Helotiales. Within the core clade only Cudonia, Spathularia and Terriera are supported as monophyletic. The large genera Coccomyces, Hypoderma and Lophodermium all are polyphyletic as are a few smaller genera. The traditionally used characters of ascoma and spore shape are shown to be unreliable for the delimitation of monophyletic genera but in some cases can be useful when combined with other characters. In this study we provide 72 new nrLSU and 64 new mtSSU sequences. Together with publicly available sequences data for 103 specimens representing 91 species of Rhytismatales are now available. Despite this taxon sampling intensity is still too low to propose an alternative generic taxonomy.

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N.Z.J.Ecol: Causes and consequences of changes to New Zealand’s fungal biota

N.Z.J.Ecol: Causes and consequences of changes to New Zealand’s fungal biota | fungi bacteria publications | Scoop.it

This paper briefly reviews advances in knowledge of the non-lichenised fungi of New Zealand over the past 25 years. Since 1980, the number of species recorded from New Zealand has doubled, and molecular techniques have revolutionised studies on fungal phylogeny and our understanding of fungal distribution, biology and origins. The origins of New Zealand’s fungi are diverse; a few appear to be ancient, whereas many have arrived in geologically more recent times following trans-oceanic dispersal. Some of these more recent arrivals have evolved subsequently to form local endemic species, while others may be part of larger populations maintained through regular, trans-oceanic gene flow. Although questions remain about which fungi truly are indigenous and which are exotic, about one-third of the fungi recorded from New Zealand are likely to have been introduced since human settlement. While most exotic species are confined to human-modified habitats, there are some exceptions. These include species with potential to have significant impacts at the landscape scale. Examples from saprobic, pathogenic, endophytic and ectomycorrhizal fungi are used to discuss the factors driving the distribution and dispersal of New Zealand’s fungi at both global and local scales, the impact that historical changes to New Zealand’s vascular plant and animal biota have had on indigenous fungi, and the broader ecological impact of some of the exotic fungal species that have become naturalised in native habitats. The kinds of fungi present in New Zealand, and the factors driving the distribution and behaviour of those fungi, are constantly changing. These changes have occurred over a wide scale, in both time and space, which means New Zealand’s indigenous fungi evolved in response to ecological pressures very different from those found in New Zealand today.

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Mycologia: Toward a phylogenetic classification of the Leotiomycetes based on rDNA data

Mycologia: Toward a phylogenetic classification of the Leotiomycetes based on rDNA data | fungi bacteria publications | Scoop.it

Phylogenetic relationships of one of the largest nonlichen-forming ascomycetous groups, the Leotiomycetes, were inferred from genes encoding three rDNA regions (SSU+LSU+5.8S rDNA). A dataset was prepared with rDNA sequences data from 108 isolates, among which we sampled 85 taxa representing four orders and 16 families in the Leotiomycetes. Equally weighted parsimony and Bayesian analyses were performed. Bootstrap proportion and Bayesian posterior probability under the GTR+Γ+I model were estimated along the branches. Based on our results the Leotiomycetes is relatively well defined as a class and it includes the Cyttariales, Erysiphales, Helotiales, Rhytismatales and two families of uncertain position, Myxotrichaceae and Pseudeurotiaceae. The placements of the Thelebolales and Ascocorticiaceae are not examined and are accepted as tentative in the Leotiomycetes. Our results agree with previous studies to remove the Geoglossaceae, including Geoglossum, Trichoglossum and Sarcoleotia, from the Leotiomycetes. Positions of the Erysiphales and Rhytismatales in the Leotiomycetes are confirmed. The Helotiales and Myxotrichaceae are paraphyletic. Close relationships are supported strongly among the Hemiphacidiaceae, Rutstroemiaceae and Sclerotiniaceae, among Loramycetaceae, the northern hemisphere Vibrisseaceae, the Dark Septate Endophyte fungus Phialocephala fortinii and Mollisia cinerea, and between species of Bulgaria and Phadidiopycnis. Sequence data of rDNA regions are not adequate to resolve the relationships among major groups of the Leotiomycetes.

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Mycotaxon: Characterisation and neotypification of Gloeosporium kaki Hori as Colletotrichum horii nom. nov.

Mycotaxon: Characterisation and neotypification of Gloeosporium kaki Hori as Colletotrichum horii nom. nov. | fungi bacteria publications | Scoop.it

A neotype is designated for the persimmon anthracnose pathogen Gloeosporium kaki Hori and the fungus is transferred to Colletotrichum as Colletotrichum horii nom. nov. Molecular and morphological analyses place this species as a distinct group within the Colletotrichum gloeosporioides sensu lato species complex. The fungus is associated with dieback and canker of twigs and young branches of persimmon, as well as spots on unripe fruit. The disease occurs on persimmon in China, Japan, and Korea, and is reported for the first time from New Zealand.


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