Phosphorus Retention and Transformation in Floodplain Forests of the Southeastern United States
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Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites
ORIGINAL RESEARCH published: 18 October 2017 doi: 10.3389/fmicb.2017.01997 Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites Grant T. Kirker 1*, Amy B. Bishell 1, Michelle A. Jusino 2, Jonathan M. Palmer 2, William J. Hickey 3 and Daniel L. Lindner 2 1 FPL, United States Department of Agriculture-Forest Service (USDA-FS), Durability and Wood Protection, Madison, WI, United States, 2 NRS, United States Department of Agriculture-Forest Service (USDA-FS), Center for Forest Mycology Research, Madison, WI, United States, 3 Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. The purpose of this study is to characterize soil fungal species and to determine if long term exposure to various wood preservatives impacts soil fungal community composition. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array. Data show that soil fungal community composition differs significantly Edited by: Florence Abram, between the two sites and that long-term exposure to different preservative chemistries National University of Ireland Galway, is correlated with different species composition of soil fungi. However, chemical analyses Ireland using ICP-OES found levels of select residual preservative actives (copper, chromium and Reviewed by: Seung Gu Shin, arsenic) to be similar to naturally occurring levels in unexposed areas. -
Multigene Phylogeny and Secondary ITS Structure
Persoonia 35, 2015: 21–38 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158515X687434 Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure M. Réblová1, K. Réblová2, V. Štěpánek3 Key words Abstract Thirteen morphologically similar strains of barbatosphaeria- and tectonidula-like fungi were studied based on the comparison of cultural and morphological features of sexual and asexual morphs and phylogenetic analyses phylogenetics of five nuclear loci, i.e. internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal Ramichloridium DNA, β-tubulin, and second largest subunit of RNA polymerase II. Phylogenetic results were supported by in-depth sequence analysis comparative analyses of common core secondary structure of ITS1 and ITS2 in all strains and the identification spacer regions of non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript. Barbatosphaeria is Sporothrix defined as a well-supported monophyletic clade comprising several lineages and is placed in the Sordariomycetes Tectonidula incertae sedis. The genus is expanded to encompass nine species with both septate and non-septate ascospores in clavate, stipitate asci with a non-amyloid apical annulus and non-stromatic ascomata with a long decumbent neck and carbonised wall often covered by pubescence. The asexual morphs are dematiaceous hyphomycetes with holoblastic conidiogenesis belonging to Ramichloridium and Sporothrix types. The morphologically similar Tectonidula, represented by the type species T. hippocrepida, grouped with members of Barbatosphaeria and is transferred to that genus. Four new species are introduced and three new combinations in Barbatosphaeria are proposed. A dichotomous key to species accepted in the genus is provided. -
Mycoportal: Taxonomic Thesaurus
Mycoportal: Taxonomic Thesaurus Scott Thomas Bates, PhD Purdue University North Central Campus Eukaryota, Opisthokonta, Fungi chitinous cell wall absorptive nutrition apical growth-hyphae Eukaryota, Opisthokonta, Fungi Macrobe chitinous cell wall absorptive nutrition apical growth-hyphae Eukaryota, Opisthokonta, Fungi Macrobe Microbe chitinous cell wall absorptive nutrition apical growth-hyphae Primary decomposers in terrestrial systems Essential symbiotic partners of plants and animals Penicillium chrysogenum Saccharomyces cerevisiae Geomyces destructans Magnaporthe oryzae Pseudogymnoascus destructans “In 2013, an analysis of the phylogenetic relationship indicated that this fungus was more closely related to the genus Pseudogymnoascus than to the genus Geomyces changing its latin binomial to Pseudogymnoascus destructans.” Magnaporthe oryzae Pseudogymnoascus destructans Magnaporthe oryzae Pseudogymnoascus destructans Magnaporthe oryzae “The International Botanical Congress in Melbourne in July 2011 made a change in the International Code of Nomenclature for algae, fungi, and plants and adopted the principle "one fungus, one name.” Pseudogymnoascus destructans Magnaporthe oryzae Pseudogymnoascus destructans Pyricularia oryzae Pseudogymnoascus destructans Magnaporthe oryzae Pseudogymnoascus destructans (Blehert & Gargas) Minnis & D.L. Lindner Magnaporthe oryzae B.C. Couch Pseudogymnoascus destructans (Blehert & Gargas) Minnis & D.L. Lindner Fungi, Ascomycota, Ascomycetes, Myxotrichaceae, Pseudogymnoascus Magnaporthe oryzae B.C. Couch Fungi, Ascomycota, Pezizomycotina, Sordariomycetes, Sordariomycetidae, Magnaporthaceae, Magnaporthe Symbiota Taxonomic Thesaurus Pyricularia oryzae How can we keep taxonomic information up-to-date in the portal? Application Programming Interface (API) MiCC Team New Taxa/Updates Other workers Mycobank DB Page Views Mycoportal DB Mycobank API Monitoring for changes regular expression: /.*aceae THANKS!. -
Savoryellales (Hypocreomycetidae, Sordariomycetes): a Novel Lineage
Mycologia, 103(6), 2011, pp. 1351–1371. DOI: 10.3852/11-102 # 2011 by The Mycological Society of America, Lawrence, KS 66044-8897 Savoryellales (Hypocreomycetidae, Sordariomycetes): a novel lineage of aquatic ascomycetes inferred from multiple-gene phylogenies of the genera Ascotaiwania, Ascothailandia, and Savoryella Nattawut Boonyuen1 Canalisporium) formed a new lineage that has Mycology Laboratory (BMYC), Bioresources Technology invaded both marine and freshwater habitats, indi- Unit (BTU), National Center for Genetic Engineering cating that these genera share a common ancestor and Biotechnology (BIOTEC), 113 Thailand Science and are closely related. Because they show no clear Park, Phaholyothin Road, Khlong 1, Khlong Luang, Pathumthani 12120, Thailand, and Department of relationship with any named order we erect a new Plant Pathology, Faculty of Agriculture, Kasetsart order Savoryellales in the subclass Hypocreomyceti- University, 50 Phaholyothin Road, Chatuchak, dae, Sordariomycetes. The genera Savoryella and Bangkok 10900, Thailand Ascothailandia are monophyletic, while the position Charuwan Chuaseeharonnachai of Ascotaiwania is unresolved. All three genera are Satinee Suetrong phylogenetically related and form a distinct clade Veera Sri-indrasutdhi similar to the unclassified group of marine ascomy- Somsak Sivichai cetes comprising the genera Swampomyces, Torpedos- E.B. Gareth Jones pora and Juncigera (TBM clade: Torpedospora/Bertia/ Mycology Laboratory (BMYC), Bioresources Technology Melanospora) in the Hypocreomycetidae incertae -
Discovered and Re- Evaluation of Pleurophragmium
Fungal Diversity Teleomorph of Rhodoveronaea (Sordariomycetidae) discovered and re- evaluation of Pleurophragmium 1* Martina Réblová 1Department of Plant Taxonomy, Institute of Botany, Academy of Sciences, CZ-252 43 Průhonice, Czech Republic Réblová, M. (2009). Teleomorph of Rhodoveronaea (Sordariomycetidae) discovered and re-evolution of Pleurophragmium. Fungal Diversity 36: 129-139. An undescribed teleomorph was discovered for Rhodoveronaea (Sordariomycetidae), a previously known anamorph genus with the single species R. varioseptata characterized by pigmented, septate conidia and holoblastic-denticulate conidiogenesis. The teleomorph is a lignicolous perithecial ascomycete with nonstromatic, dark perithecia, consisting of a globose immersed venter and stout conical emerging neck; cylindrical long-stipitate asci, nonamyloid apical annulus and fusiform, septate, hyaline ascospores. The fertile conidiophores of R. varioseptata were associated with the perithecia on the natural substratum and they were also obtained in vitro. Because no teleomorph was designated in the protologue of Rhodoveronaea, the new Article 59.7 of the International Code of Botanical Nomenclature is applied in this case and Rhodoveronaea is expanded to holomorphic application by teleomorphic epitypification of the type species R. varioseptata. The name R. varioseptata is fully adopted for the discovered teleomorph. On the basis of detailed morphology, cultivation studies and phylogenetic analyses of ncLSU rDNA sequences, Rhodoveronaea is segregated from the morphologically similar genera Lentomitella and Ceratosphaeria; its relationship with Ceratosphaeria fragilis and C. rhenana is discussed. The relationship of Rhodoveronaea with the morphologically similar Dactylaria parvispora is investigated using morphological features and molecular sequence data. Phylogenetic findings based on ncLSU rDNA sequence data indicate that Dactylaria is polyphyletic. The genus Pleurophragmium is excluded from the synonymy of Dactylaria and is re-evaluated for P. -
A Molecular Re-Appraisal of Taxa in the Sordariomycetidae and a New Species of Rimaconus from New Zealand
available online at www.studiesinmycology.org StudieS in Mycology 68: 203–210. 2011. doi:10.3114/sim.2011.68.09 A molecular re-appraisal of taxa in the Sordariomycetidae and a new species of Rimaconus from New Zealand S.M. Huhndorf1* and A.N. Miller2 1Field Museum of Natural History, Botany Department, Chicago, Illinois 60605–2496, USA; 2University of Illinois, Illinois Natural History Survey, Champaign, Illinois 61820-6970, USA *Correspondence: Sabine M. Huhndorf, [email protected] Abstract: Several taxa that share similar ascomatal and ascospore characters occur in monotypic or small genera throughout the Sordariomycetidae with uncertain relationships based on their morphology. Taxa in the genera Duradens, Leptosporella, Linocarpon, and Rimaconus share similar morphologies of conical ascomata, carbonised peridia and elongate ascospores, while taxa in the genera Caudatispora, Erythromada and Lasiosphaeriella possess clusters of superficial, obovoid ascomata with variable ascospores. Phylogenetic analyses of 28S large-subunit nrDNA sequences were used to test the monophyly of these genera and provide estimates of their relationships within the Sordariomycetidae. Rimaconus coronatus is described as a new species from New Zealand; it clusters with the type species, R. jamaicensis. Leptosporella gregaria is illustrated and a description is provided for this previously published taxon that is the type species and only sequenced representative of the genus. Both of these genera occur in separate, well-supported clades among taxa that form unsupported groups near the Chaetosphaeriales and Helminthosphaeriaceae. Lasiosphaeriella and Linocarpon appear to be polyphyletic with species occurring in several clades throughout the subclass. Caudatispora and Erythromada represented by single specimens and two putative Duradens spp. -
Molecular Systematics of the Sordariales: the Order and the Family Lasiosphaeriaceae Redefined
Mycologia, 96(2), 2004, pp. 368±387. q 2004 by The Mycological Society of America, Lawrence, KS 66044-8897 Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae rede®ned Sabine M. Huhndorf1 other families outside the Sordariales and 22 addi- Botany Department, The Field Museum, 1400 S. Lake tional genera with differing morphologies subse- Shore Drive, Chicago, Illinois 60605-2496 quently are transferred out of the order. Two new Andrew N. Miller orders, Coniochaetales and Chaetosphaeriales, are recognized for the families Coniochaetaceae and Botany Department, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496 Chaetosphaeriaceae respectively. The Boliniaceae is University of Illinois at Chicago, Department of accepted in the Boliniales, and the Nitschkiaceae is Biological Sciences, Chicago, Illinois 60607-7060 accepted in the Coronophorales. Annulatascaceae and Cephalothecaceae are placed in Sordariomyce- Fernando A. FernaÂndez tidae inc. sed., and Batistiaceae is placed in the Euas- Botany Department, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496 comycetes inc. sed. Key words: Annulatascaceae, Batistiaceae, Bolini- aceae, Catabotrydaceae, Cephalothecaceae, Ceratos- Abstract: The Sordariales is a taxonomically diverse tomataceae, Chaetomiaceae, Coniochaetaceae, Hel- group that has contained from seven to 14 families minthosphaeriaceae, LSU nrDNA, Nitschkiaceae, in recent years. The largest family is the Lasiosphaer- Sordariaceae iaceae, which has contained between 33 and 53 gen- era, depending on the chosen classi®cation. To de- termine the af®nities and taxonomic placement of INTRODUCTION the Lasiosphaeriaceae and other families in the Sor- The Sordariales is one of the most taxonomically di- dariales, taxa representing every family in the Sor- verse groups within the Class Sordariomycetes (Phy- dariales and most of the genera in the Lasiosphaeri- lum Ascomycota, Subphylum Pezizomycotina, ®de aceae were targeted for phylogenetic analysis using Eriksson et al 2001). -
Freshwater Ascomycetes: Hyalorostratum Brunneisporum, a New Genus and Species in the Diaporthales (Sordariomycetidae, Sordariomycetes) from North America
Mycosphere Freshwater Ascomycetes: Hyalorostratum brunneisporum, a new genus and species in the Diaporthales (Sordariomycetidae, Sordariomycetes) from North America Raja HA1*, Miller AN2, and Shearer CA1 1Department of Plant Biology, University of Illinois at Urbana-Champaign, Room 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801 2Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL 61820. Raja HA, Miller AN, Shearer CA. 2010 – Freshwater Ascomycetes: Hyalorostratum brunneisporum, a new genus and species in the Diaporthales (Sordariomycetidae, Sordariomycetes) from North America. Mycosphere 1(4), 275–288. Hyalorostratum brunneisporum gen. et sp. nov. (ascomycetes) is described from freshwater habitats in Alaska and New Hampshire. The new genus is considered distinct based on morphological studies and phylogenetic analyses of combined nuclear ribosomal (18S and 28S) sequence data. Hyalorostratum brunneisporum is characterized by immersed to erumpent, pale to dark brown perithecia with a hyaline, long, emergent, periphysate neck covered with a tomentum of hyaline, irregularly shaped hyphae; numerous long, septate paraphyses; unitunicate, cylindrical asci with a large apical ring covered at the apex with gelatinous material; and brown, one-septate ascospores with or without a mucilaginous sheath. The new genus is placed basal within the order Diaporthales based on combined 18S and 28S sequence data. It is compared to other morphologically similar aquatic taxa and to taxa reported from freshwater -
An Overview of the Systematics of the Sordariomycetes Based on a Four-Gene Phylogeny
Mycologia, 98(6), 2006, pp. 1076–1087. # 2006 by The Mycological Society of America, Lawrence, KS 66044-8897 An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny Ning Zhang of 16 in the Sordariomycetes was investigated based Department of Plant Pathology, NYSAES, Cornell on four nuclear loci (nSSU and nLSU rDNA, TEF and University, Geneva, New York 14456 RPB2), using three species of the Leotiomycetes as Lisa A. Castlebury outgroups. Three subclasses (i.e. Hypocreomycetidae, Systematic Botany & Mycology Laboratory, USDA-ARS, Sordariomycetidae and Xylariomycetidae) currently Beltsville, Maryland 20705 recognized in the classification are well supported with the placement of the Lulworthiales in either Andrew N. Miller a basal group of the Sordariomycetes or a sister group Center for Biodiversity, Illinois Natural History Survey, of the Hypocreomycetidae. Except for the Micro- Champaign, Illinois 61820 ascales, our results recognize most of the orders as Sabine M. Huhndorf monophyletic groups. Melanospora species form Department of Botany, The Field Museum of Natural a clade outside of the Hypocreales and are recognized History, Chicago, Illinois 60605 as a distinct order in the Hypocreomycetidae. Conrad L. Schoch Glomerellaceae is excluded from the Phyllachorales Department of Botany and Plant Pathology, Oregon and placed in Hypocreomycetidae incertae sedis. In State University, Corvallis, Oregon 97331 the Sordariomycetidae, the Sordariales is a strongly supported clade and occurs within a well supported Keith A. Seifert clade containing the Boliniales and Chaetosphaer- Biodiversity (Mycology and Botany), Agriculture and iales. Aspects of morphology, ecology and evolution Agri-Food Canada, Ottawa, Ontario, K1A 0C6 Canada are discussed. Amy Y. -
Pacific Northwest Fungi
North American Fungi Volume 8, Number 10, Pages 1-13 Published June 19, 2013 Vialaea insculpta revisited R.A. Shoemaker, S. Hambleton, M. Liu Biodiversity (Mycology and Botany) / Biodiversité (Mycologie et Botanique) Agriculture and Agri-Food Canada / Agriculture et Agroalimentaire Canada 960 Carling Avenue / 960, avenue Carling, Ottawa, Ontario K1A 0C6 Canada Shoemaker, R.A., S. Hambleton, and M. Liu. 2013. Vialaea insculpta revisited. North American Fungi 8(10): 1-13. doi: http://dx.doi: 10.2509/naf2013.008.010 Corresponding author: R.A. Shoemaker: [email protected]. Accepted for publication May 23, 2013 http://pnwfungi.org Copyright © Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada Abstract: Vialaea insculpta, occurring on Ilex aquifolium, is illustrated and redescribed from nature and pure culture to assess morphological features used in its classification and to report new molecular studies of the Vialaeaceae and its ordinal disposition. Tests of the germination of the distinctive ascospores in water containing parts of Ilex flowers after seven days resulted in the production of appressoria without mycelium. Phylogenetic analyses based on a fragment of ribosomal RNA gene small subunit suggest that the taxon belongs in Xylariales. Key words: Valsaceae and Vialaeaceae, (Diaporthales), Diatrypaceae (Diatrypales), Amphisphaeriaceae and Hyphonectriaceae (Xylariales), Ilex, endophyte. 2 Shoemaker et al. Vialaea inscupta. North American Fungi 8(10): 1-13 Introduction: Vialaea insculpta (Fr.) Sacc. is on oatmeal agar at 20°C exposed to daylight. a distinctive species occurring on branches of Isolation attempts from several other collections Ilex aquifolium L. Oudemans (1871, tab. -
AR TICLE Recommendations for Competing Sexual-Asexually Typified
IMA FUNGUS · 7(1): 131–153 (2016) doi:10.5598/imafungus.2016.07.01.08 Recommendations for competing sexual-asexually typified generic names in ARTICLE Sordariomycetes (except Diaporthales, Hypocreales, and Magnaporthales) Martina Réblová1, Andrew N. Miller2, Amy Y. Rossman3*, Keith A. Seifert4, Pedro W. Crous5, David L. Hawksworth6,7,8, Mohamed A. Abdel-Wahab9, Paul F. Cannon8, Dinushani A. Daranagama10, Z. Wilhelm De Beer11, Shi-Ke Huang10, Kevin D. Hyde10, Ruvvishika Jayawardena10, Walter Jaklitsch12,13, E. B. Gareth Jones14, Yu-Ming Ju15, Caroline Judith16, Sajeewa S. N. Maharachchikumbura17, Ka-Lai Pang18, Liliane E. Petrini19, Huzefa A. Raja20, Andrea I Romero21, Carol Shearer2, Indunil C. Senanayake10, Hermann Voglmayr13, Bevan S. Weir22, and Nalin N. Wijayawarden10 1Department of Taxonomy, Institute of Botany of the Academy of Sciences of the Czech Republic, Průhonice 252 43, Czech Republic 2Illinois Natural History Survey, University of Illinois, Champaign, Illinois 61820, USA 3Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA; *corresponding author e-mail: amydianer@ yahoo.com 4Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6 Canada 5CBS-KNAW Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands 6Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramón y Cajal s/n, Madrid 28040, Spain 7Department of Life Sciences, -
Phylogeny of Penicillium and the Segregation of Trichocomaceae Into Three Families
available online at www.studiesinmycology.org StudieS in Mycology 70: 1–51. 2011. doi:10.3114/sim.2011.70.01 Phylogeny of Penicillium and the segregation of Trichocomaceae into three families J. Houbraken1,2 and R.A. Samson1 1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; 2Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. *Correspondence: Jos Houbraken, [email protected] Abstract: Species of Trichocomaceae occur commonly and are important to both industry and medicine. They are associated with food spoilage and mycotoxin production and can occur in the indoor environment, causing health hazards by the formation of β-glucans, mycotoxins and surface proteins. Some species are opportunistic pathogens, while others are exploited in biotechnology for the production of enzymes, antibiotics and other products. Penicillium belongs phylogenetically to Trichocomaceae and more than 250 species are currently accepted in this genus. In this study, we investigated the relationship of Penicillium to other genera of Trichocomaceae and studied in detail the phylogeny of the genus itself. In order to study these relationships, partial RPB1, RPB2 (RNA polymerase II genes), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences were obtained. The Trichocomaceae are divided in three separate families: Aspergillaceae, Thermoascaceae and Trichocomaceae. The Aspergillaceae are characterised by the formation flask-shaped or cylindrical phialides, asci produced inside cleistothecia or surrounded by Hülle cells and mainly ascospores with a furrow or slit, while the Trichocomaceae are defined by the formation of lanceolate phialides, asci borne within a tuft or layer of loose hyphae and ascospores lacking a slit.