Similarity and Differences Among Soil Fungal Assemblages in Managed Forests and Formerly Managed Forest Reserves
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Development and Evaluation of Rrna Targeted in Situ Probes and Phylogenetic Relationships of Freshwater Fungi
Development and evaluation of rRNA targeted in situ probes and phylogenetic relationships of freshwater fungi vorgelegt von Diplom-Biologin Christiane Baschien aus Berlin Von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktorin der Naturwissenschaften - Dr. rer. nat. - genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr. sc. techn. Lutz-Günter Fleischer Berichter: Prof. Dr. rer. nat. Ulrich Szewzyk Berichter: Prof. Dr. rer. nat. Felix Bärlocher Berichter: Dr. habil. Werner Manz Tag der wissenschaftlichen Aussprache: 19.05.2003 Berlin 2003 D83 Table of contents INTRODUCTION ..................................................................................................................................... 1 MATERIAL AND METHODS .................................................................................................................. 8 1. Used organisms ............................................................................................................................. 8 2. Media, culture conditions, maintenance of cultures and harvest procedure.................................. 9 2.1. Culture media........................................................................................................................... 9 2.2. Culture conditions .................................................................................................................. 10 2.3. Maintenance of cultures.........................................................................................................10 -
Resolving the Mortierellaceae Phylogeny Through Synthesis of Multi-Gene Phylogenetics and Phylogenomics
Lawrence Berkeley National Laboratory Recent Work Title Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Permalink https://escholarship.org/uc/item/25k8j699 Journal Fungal diversity, 104(1) ISSN 1560-2745 Authors Vandepol, Natalie Liber, Julian Desirò, Alessandro et al. Publication Date 2020-09-16 DOI 10.1007/s13225-020-00455-5 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Fungal Diversity https://doi.org/10.1007/s13225-020-00455-5 Resolving the Mortierellaceae phylogeny through synthesis of multi‑gene phylogenetics and phylogenomics Natalie Vandepol1 · Julian Liber2 · Alessandro Desirò3 · Hyunsoo Na4 · Megan Kennedy4 · Kerrie Barry4 · Igor V. Grigoriev4 · Andrew N. Miller5 · Kerry O’Donnell6 · Jason E. Stajich7 · Gregory Bonito1,3 Received: 17 February 2020 / Accepted: 25 July 2020 © MUSHROOM RESEARCH FOUNDATION 2020 Abstract Early eforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conficting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarifed, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierel- laceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequenc- ing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-efective means of generating a high-confdence phylogeny. -
Reviewing the World's Edible Mushroom Species: a New
Received: 5 September 2020 Revised: 4 December 2020 Accepted: 21 December 2020 DOI: 10.1111/1541-4337.12708 COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY Reviewing the world’s edible mushroom species: A new evidence-based classification system Huili Li1,2,3 Yang Tian4 Nelson Menolli Jr5,6 Lei Ye1,2,3 Samantha C. Karunarathna1,2,3 Jesus Perez-Moreno7 Mohammad Mahmudur Rahman8 Md Harunur Rashid8 Pheng Phengsintham9 Leela Rizal10 Taiga Kasuya11 Young Woon Lim12 Arun Kumar Dutta13 Abdul Nasir Khalid14 Le Thanh Huyen15 Marilen Parungao Balolong16 Gautam Baruah17 Sumedha Madawala18 Naritsada Thongklang19,20 Kevin D. Hyde19,20,21 Paul M. Kirk22 Jianchu Xu1,2,3 Jun Sheng23 Eric Boa24 Peter E. Mortimer1,3 1 CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China 2 East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming, Yunnan, China 3 Centre for Mountain Futures, Kunming Institute of Botany, Kunming, Yunnan, China 4 College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China 5 Núcleo de Pesquisa em Micologia, Instituto de Botânica, São Paulo, Brazil 6 Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), São Paulo, Brazil 7 Colegio de Postgraduados, Campus Montecillo, Texcoco, México 8 Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, -
Temporal Changes in the Ectomycorrhizal Community in Two Soil Horizons of a Temperate Oak Forest Pierre-Emmanuel Courty, Alain Franc, J-Claude Pierrat, Jean Garbaye
Temporal changes in the ectomycorrhizal community in two soil horizons of a temperate oak forest Pierre-Emmanuel Courty, Alain Franc, J-Claude Pierrat, Jean Garbaye To cite this version: Pierre-Emmanuel Courty, Alain Franc, J-Claude Pierrat, Jean Garbaye. Temporal changes in the ectomycorrhizal community in two soil horizons of a temperate oak forest. Applied and Environmental Microbiology, American Society for Microbiology, 2008, 74 (18), pp.5792-5801. 10.1128/AEM.01592- 08. hal-01195010 HAL Id: hal-01195010 https://hal.archives-ouvertes.fr/hal-01195010 Submitted on 31 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2008, p. 5792–5801 Vol. 74, No. 18 0099-2240/08/$08.00ϩ0 doi:10.1128/AEM.01592-08 Copyright © 2008, American Society for Microbiology. All Rights Reserved. Temporal Changes in the Ectomycorrhizal Community in Two Soil Horizons of a Temperate Oak Forestᰔ† Pierre-Emmanuel Courty,1* Alain Franc,2 Jean-Claude Pierrat,3 and Jean Garbaye1 UMR 1136 INRA-Nancy Universite´, Interactions Arbres/Micro-organisms, INRA-Nancy, 54280 Champenoux, France1; INRA Pierroton, UMR Biodiversite´, Ge`nes et Communaute´s, 33612 Cestas, France2; and UMR 1092 INRA-ENGREF Etudes des Ressources Foreˆt/Bois, ENGREF Nancy, 54000 Nancy, France3 Received 11 July 2008/Accepted 11 July 2008 The species structure of an ectomycorrhizal (ECM) community was assessed monthly for 15 months in the two horizons (A1 and A2) of an oak temperate forest in northeastern France. -
Preliminary Classification of Leotiomycetes
Mycosphere 10(1): 310–489 (2019) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/10/1/7 Preliminary classification of Leotiomycetes Ekanayaka AH1,2, Hyde KD1,2, Gentekaki E2,3, McKenzie EHC4, Zhao Q1,*, Bulgakov TS5, Camporesi E6,7 1Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China 2Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand 3School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand 4Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand 5Russian Research Institute of Floriculture and Subtropical Crops, 2/28 Yana Fabritsiusa Street, Sochi 354002, Krasnodar region, Russia 6A.M.B. Gruppo Micologico Forlivese “Antonio Cicognani”, Via Roma 18, Forlì, Italy. 7A.M.B. Circolo Micologico “Giovanni Carini”, C.P. 314 Brescia, Italy. Ekanayaka AH, Hyde KD, Gentekaki E, McKenzie EHC, Zhao Q, Bulgakov TS, Camporesi E 2019 – Preliminary classification of Leotiomycetes. Mycosphere 10(1), 310–489, Doi 10.5943/mycosphere/10/1/7 Abstract Leotiomycetes is regarded as the inoperculate class of discomycetes within the phylum Ascomycota. Taxa are mainly characterized by asci with a simple pore blueing in Melzer’s reagent, although some taxa have lost this character. The monophyly of this class has been verified in several recent molecular studies. However, circumscription of the orders, families and generic level delimitation are still unsettled. This paper provides a modified backbone tree for the class Leotiomycetes based on phylogenetic analysis of combined ITS, LSU, SSU, TEF, and RPB2 loci. In the phylogenetic analysis, Leotiomycetes separates into 19 clades, which can be recognized as orders and order-level clades. -
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. -
S41467-021-25308-W.Pdf
ARTICLE https://doi.org/10.1038/s41467-021-25308-w OPEN Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota ✉ ✉ Luis Javier Galindo 1 , Purificación López-García 1, Guifré Torruella1, Sergey Karpov2,3 & David Moreira 1 Compared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living fla- gellated stages (zoospores) remain poorly known and their phylogenetic position is often 1234567890():,; unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and San- chytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchy- trids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages. 1 Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France. 2 Zoological Institute, Russian Academy of Sciences, St. ✉ Petersburg, Russia. 3 St. -
9B Taxonomy to Genus
Fungus and Lichen Genera in the NEMF Database Taxonomic hierarchy: phyllum > class (-etes) > order (-ales) > family (-ceae) > genus. Total number of genera in the database: 526 Anamorphic fungi (see p. 4), which are disseminated by propagules not formed from cells where meiosis has occurred, are presently not grouped by class, order, etc. Most propagules can be referred to as "conidia," but some are derived from unspecialized vegetative mycelium. A significant number are correlated with fungal states that produce spores derived from cells where meiosis has, or is assumed to have, occurred. These are, where known, members of the ascomycetes or basidiomycetes. However, in many cases, they are still undescribed, unrecognized or poorly known. (Explanation paraphrased from "Dictionary of the Fungi, 9th Edition.") Principal authority for this taxonomy is the Dictionary of the Fungi and its online database, www.indexfungorum.org. For lichens, see Lecanoromycetes on p. 3. Basidiomycota Aegerita Poria Macrolepiota Grandinia Poronidulus Melanophyllum Agaricomycetes Hyphoderma Postia Amanitaceae Cantharellales Meripilaceae Pycnoporellus Amanita Cantharellaceae Abortiporus Skeletocutis Bolbitiaceae Cantharellus Antrodia Trichaptum Agrocybe Craterellus Grifola Tyromyces Bolbitius Clavulinaceae Meripilus Sistotremataceae Conocybe Clavulina Physisporinus Trechispora Hebeloma Hydnaceae Meruliaceae Sparassidaceae Panaeolina Hydnum Climacodon Sparassis Clavariaceae Polyporales Gloeoporus Steccherinaceae Clavaria Albatrellaceae Hyphodermopsis Antrodiella -
The Phylogeny of Plant and Animal Pathogens in the Ascomycota
Physiological and Molecular Plant Pathology (2001) 59, 165±187 doi:10.1006/pmpp.2001.0355, available online at http://www.idealibrary.com on MINI-REVIEW The phylogeny of plant and animal pathogens in the Ascomycota MARY L. BERBEE* Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada (Accepted for publication August 2001) What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also concentrated, but in two ascomycete classes that contain few, if any, plant pathogens. Rather than appearing as a constant character of a class, the ability to cause disease in plants and animals was gained and lost repeatedly. The genes that code for some traits involved in pathogenicity or virulence have been cloned and characterized, and so the evolutionary relationships of a few of the genes for enzymes and toxins known to play roles in diseases were explored. In general, these genes are too narrowly distributed and too recent in origin to explain the broad patterns of origin of pathogens. Co-evolution could potentially be part of an explanation for phylogenetic patterns of pathogenesis. Robust phylogenies not only of the fungi, but also of host plants and animals are becoming available, allowing for critical analysis of the nature of co-evolutionary warfare. Host animals, particularly human hosts have had little obvious eect on fungal evolution and most cases of fungal disease in humans appear to represent an evolutionary dead end for the fungus. -
(Boletaceae, Basidiomycota) – a New Monotypic Sequestrate Genus and Species from Brazilian Atlantic Forest
A peer-reviewed open-access journal MycoKeys 62: 53–73 (2020) Longistriata flava a new sequestrate genus and species 53 doi: 10.3897/mycokeys.62.39699 RESEARCH ARTICLE MycoKeys http://mycokeys.pensoft.net Launched to accelerate biodiversity research Longistriata flava (Boletaceae, Basidiomycota) – a new monotypic sequestrate genus and species from Brazilian Atlantic Forest Marcelo A. Sulzbacher1, Takamichi Orihara2, Tine Grebenc3, Felipe Wartchow4, Matthew E. Smith5, María P. Martín6, Admir J. Giachini7, Iuri G. Baseia8 1 Departamento de Micologia, Programa de Pós-Graduação em Biologia de Fungos, Universidade Federal de Pernambuco, Av. Nelson Chaves s/n, CEP: 50760-420, Recife, PE, Brazil 2 Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Odawara-shi, Kanagawa 250-0031, Japan 3 Slovenian Forestry Institute, Večna pot 2, SI-1000 Ljubljana, Slovenia 4 Departamento de Sistemática e Ecologia/CCEN, Universidade Federal da Paraíba, CEP: 58051-970, João Pessoa, PB, Brazil 5 Department of Plant Pathology, University of Flori- da, Gainesville, Florida 32611, USA 6 Departamento de Micologia, Real Jardín Botánico, RJB-CSIC, Plaza Murillo 2, Madrid 28014, Spain 7 Universidade Federal de Santa Catarina, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Campus Trindade – Setor F, CEP 88040-900, Flo- rianópolis, SC, Brazil 8 Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, CEP: 59072-970, Natal, RN, Brazil Corresponding author: Tine Grebenc ([email protected]) Academic editor: A.Vizzini | Received 4 September 2019 | Accepted 8 November 2019 | Published 3 February 2020 Citation: Sulzbacher MA, Orihara T, Grebenc T, Wartchow F, Smith ME, Martín MP, Giachini AJ, Baseia IG (2020) Longistriata flava (Boletaceae, Basidiomycota) – a new monotypic sequestrate genus and species from Brazilian Atlantic Forest. -
Jauhenuija, Phleogena Faginea 2/2015 Vsk. 67
2/2015 Vsk. 67 ISSN 0357-1335 Jauhenuija, Phleogena faginea 34 SIENILEHTI 67(2) Sisällys Huhtinen, S. & Karhilahti, A.: Sieniviä eläimiä etsimässä – roosahiipusen, jauhenuijan ja ”valkohaulin” tarinat .................................................................. 35 Kosonen, T: Tuoretta kotelosienitutkimusta – valjukarvakoiden (Hyaloscyphaceae) systematiikan peruskorjaus käynnistyy .......................... 40 Härkönen, M.: Sieniä leirinuotiolla ........................................................................ 45 Härkönen, M.: Etnomykologisia mietteitä ............................................................ 48 Laakso, O.: Kystidejä ja artefakteja – Sienten mikroskopointityöpaja 7.−8.3.2015............................................................................................................... 49 Sienikirjoja Sienet ja metsien luontoarvot. Arvostelu Heikki Kotiranta ............................ 51 Paavo Eini: Mitä kirjailijat sienistä 6 ...................................................................... 53 Kysykää sienistä ........................................................................................................ 54 Suomen Sieniseuran toimintakertomus 2014 ........................................................ 55 Lukijoiden sienilöytöjä ............................................................................................. 57 Kansikuva: Toinen etsintäkuulutus jauhenuijasta, Phleogena faginea (kuva A. Karhilahti). − Asiasta enemmän S. Huhtisen ja A. Karhilahden artikkelissa s. 35 alkaen. Etukannen -
Notes on British Species of Byssonectria
Mycol. Res 100 (7). 881-882 (1996) Prmled in Greal Bnlam 881 Notes on British species of Byssonectria Y.-J. YA01,2 AND B. M. SPOONERl 1 Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK 2 School of Biomolecular Sciences, Liverpool John Moores UnIVerslly, Byrom Street, LIverpool L3 3Ar, UK Notes on the taxonomy of the species reported from Britain as Byssonectria and Inermisia are presented. Two species, B. fusispora and B. terrestris, are retained in the British list, although fresh collections are required to confirm the distinction between them. Byssoneetna tetraspora and Inermisia pi/ifera should be placed in Oetospora. Observations on the type of O. pi/ifera are provided to update the species description. Byssonectria P. Karst., originally referred to the Hypocreales cyanobacteria grow, and in having larger ascospores (24'0• Lindau, was shown by Korf (1971) to be an earlier name for 29'0 x 7'0-II'0 I-lm). The subiculum is, in fact, variable Inermisia Rifai (Rifai, 1968). The genus has been distinguished amongst British collections previously named as either B. from Octospora Hedw. on the basis of excipular structure, and fusispora or Peziza aggregata, ranging from very conspicuous to the non-bryophilous (Benkert, 1987) or nitrogen-rich (Pfister, scanty or even absent. Such variation is seen especially in 1993) habitat, although Khare & Tewari (1978) treated these those collections from plant debris; collections on soil rarely names as synonyms. exhibit development of a subiculum. This may imply that the Three accepted names in Byssonectria and Inermisia, B. development of subiculum is related to the substrate.