Supplementary Materials Cryptogams Signify Key Transition Of

Total Page:16

File Type:pdf, Size:1020Kb

Supplementary Materials Cryptogams Signify Key Transition Of Supplementary materials Cryptogams signify key transition of bacteria and fungi in Arctic sand dune succession Heli Juottonen1*, Minna Männistö2, Marja Tiirola1 & Minna-Maarit Kytöviita1 1Department of Biological and Environmental Science, University of Jyväskylä, Finland 2 Natural Resources Institute Finland (Luke), Rovaniemi, Finland Table S1 Table S2 Figure S1 Figure S2 Figure S3 Figure S4 Figure S5 Table S1. Vegetation, soil chemistry, environmental parameters and microbial characteristics of successional stages in sand dune deflation basins. Data are mean values ± SD of six deflation basins (vegetation, soil temperature) or four deflation basins (chemistry, microbial data) and three replicates per deflation basin. successional stage sand grass moss lichen heath forest vegetation - Deschampsia Polytrichum Stereocaulon Empetrum E. nigrum, flexuosa piliferum sp., nigrum Vaccinium vitis- Racomitrium idaea, ericoides, P. Pleurozium piliferum, schreberi, D. Cladonia sp. flexuosa, Linnea borealis sand cover (%) 100 ± 0 95 ± 3 92 ± 8 52 ± 36 39 ± 48 0 ± 0 organic matter (%) 0.4 ± 0.2 0.3 ± 0.1 0.5 ± 0.2 0.9 ± 0.3 1.8 ± 1.0 4.5 ± 1.7 pH 5.6 ± 0.2 5.8 ± 0.2 5.3 ± 0.2 5.2 ± 0.1 5.2 ± 0.2 4.7 ± 0.1 snow cover (cm)a 95±6 86±6 80±4 85±3 46±5 84±5 moisture (%) 0.16±0.02 0.17±0.04 0.17±0.02 0.25±0.05 0.36±0.11 0.51±0.14 N (%) 0.021 ± 0.022 ± 0.001 0.025 ± 0.003 0.036 ± 0.005 0.047 ± 0.088 ± 0.024 0.002 0.014 P (mg/kg) 2.4 ± 0.6 1.9 ± 0.7 3.1 ± 1.3 4.3 ± 1.2 6.7 ± 2.8 14.1 ± 3.2 Al (mg/kg) 118 ± 42 64 ± 28 91 ± 32 128 ± 42 94 ± 19 70 ± 27 Ca (mg/kg) 42 ± 64 84 ± 57 40 ± 33 50 ± 59 132 ± 90 269 ± 104 Mg (mg/kg) 9 ± 15 19 ± 16 8 ± 6 9 ± 9 27 ± 20 103 ± 30 Fe (mg/kg) 6.1 ± 1.6 6.7 ± 1.0 6.9 ± 1.5 9.8 ± 3.0 6.1 ± 1.8 24.9 ± 15.1 S (mg/kg) 2.4 ± 0.5 1.8 ± 0.6 2.8 ± 0.7 4.0 ± 0.8 4.8 ± 1.5 8.8 ± 3.3 microbial biomass 1.69±0.8 2.18±1.5 9.16±5.9 17.9±5.2 43.7±25.7 98.7±33.9 (nmol/g soil dw)b fungal:bacterial 0.04±0.02 0.04±0.04 0.24±0.13 0.18±0.07 0.48±0.14 0.29±0.10 biomassb minimum soil -3.8 ± 0.6 -3.9 ± 0.6 -3.5 ± 0.3 -2.8 ± 0.5 -6.2 ± 1.5 -2.2 ± 1.1 temperature (°C)c maximum soil 15.3 ± 1.1 15.3 ± 0.3 15.3 ± 0.2 15.0 ± 0.8 14.6 ± 0.2 10.7 ± 0.8 temperature (°C)d bacterial diversity 5.0 ± 0.3 5.3 ± 0.3 5.4 ± 0.1 5.5 ± 0.2 5.8 ± 0.1 5.3 ± 0.2 (Shannon) e fungal diversity 3.6 ± 0.7 2.8 ± 0.8 2.7 ± 0.6 2.4 ± 0.2 2.8 ± 0.8 2.9 ± 0.5 (Shannon)f a maximum snow depth (cm) measured in late March-early April, mean values ± SE in years 2016, 2017, 2018 b based on phospholipid fatty acid (PLFA) analysis c average temperature in January-February d average temperature in July e based on bacterial 16S rRNA gene sequencing f based on fungal ITS2 region sequencing Table S2. Bacterial and fungal generalist OTUs based on indicator species analysis. number of kingdom OTUs taxonomic classification bacteria 1 Proteobacteria, Alphaproteobacteria, Rhizobiales, unclassified 4 Proteobacteria, Alphaproteobacteria, Rhizobiales, Xanthobacteraceae 3 Proteobacteria, Alphaproteobacteria, Rhodospirillales, Acetobacteraceae 1 Proteobacteria, Betaproteobacteria, Burkholderiales, unclassified 1 Proteobacteria, Betaproteobacteria, Burkholderiales, Comamonadaceae 1 Proteobacteria, Gammaproteobacteria, Xanthomonadales, Incertae Sedis 1 Actinobacteria, Thermoleophilia, Solirubrobacterales, unclassified 2 Acidobacteria, Acidobacteriales, Acidobacteriaceae 1 Acidobacteria, Subgroup 2 fungi 1 Ascomycota, Leotiomycetes, Leotiales, Leotiaceae (Pezoloma ericae) 1 Ascomycota, Leotiomycetes, Helotiales, Hyaloscyphaceae 1 Ascomycota, Leotiomycetes, Helotiales, unclassified 1 Ascomycota, Dothideomycetes, Venturiales, Venturiaceae 1 Ascomycota, Lecanoromycetes, unclassified 1 Ascomycota, Pezizomycetes, Pezizales, Sarcosomataceae (Pseudoplectania nigrella) 1 Ascomycota, unclassified Figure S1 Deflation basin in an Arctic inland sand dune area and the six successional stages defined in this study. Figure S2 Non-metric multidimensional scaling (NMDS) plot of phospholipid fatty acid (PLFA) data of sand dune successional stages (stress= 0.11). Shapes of the symbols refer to four different deflation basins. Figure S3 Phylum level (class level for Proteobacteria) community composition of bacteria based on 16S rRNA gene sequencing of six sand dune successional stages. B1-B4 indicate four deflation basins, and three columns within a deflation basin are replicate soil samples. ‘Other’ includes Armatimonadetes, Verrucomicrobia, Planctomycetes, Saccharibacteria, unclassified Proteobacteria, Gracilibacteria, TM6, Firmicutes, Nitrospirae, Elusimicrobia, Parcubacteria, WCHB1-60, and Hydrogenedentes. Figure S4 Class-level community composition of fungi based on ITS2 region sequencing of six sand dune successional stages. B1-B4 indicate four deflation basins, and three columns within a deflation basin are replicate soil samples. ‘Other’ includes Microbotryomycetes, Mucoromycotina (Incertae sedis), Taphrinomycetes, Pucciniomycetes, Ustilaginomycotina (Incertae sedis), Chytridiomycetes, Exobasidiomycetes, Ascomycota Incertae sedis, Glomeromycetes, Cystobasidiomycetes, Saccharomycetes, Orbiliomycetes, Wallemiomycetes, and Ustilaginomycetes. Inc. sedis, Incertae sedis. Figure S5 Unclassified (A) bacterial phylum level groups (75% 16S rRNA gene sequence similarity) and (B) fungal class level groups (75% ITS2 sequence similarity) as percentage of total sequence reads per sand dune successional stage (four deflation basins and three replicate samples combined per stage). Groups with relative abundance of >0.15% of total reads are included..
Recommended publications
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Differential Colonization by Ecto-, Arbuscular and Ericoid Mycorrhizal Fungi in Forested Wetland Plants. by Amanda Marie Griffin
    Differential colonization by ecto-, arbuscular and ericoid mycorrhizal fungi in forested wetland plants. By Amanda Marie Griffin A Thesis Submitted to Saint Mary’s University, Halifax, Nova Scotia in Partial Fulfillment of the Requirements for the Degree of Master of Science in Applied Science. August, 2019, Halifax, Nova Scotia © Amanda Marie Griffin, 2019 _____________________________ Approved: Gavin Kernaghan Supervisor _____________________ Approved: Dr. Jeremy Lundholm Supervisory Committee Member _____________________ Approved: Dr. Kevin Keys Supervisory Committee Member ______________________ Approved: Dr. Pedro Antunes External Examiner Date: August 26th, 2019 Differential colonization by ecto-, arbuscular and ericoid mycorrhizal fungi in forested wetland plants. by Amanda Marie Griffin Abstract The roots of most land plants are colonized by mycorrhizal fungi under normal soil conditions, yet the influence of soil moisture on different types of mycorrhizal symbioses is poorly understood. In wet soils, colonization of woody plants by ectomycorrhizal (ECM) fungi tends to be poor, and colonization of herbaceous plants by arbuscular mycorrhizal (AM) is highly variable. However, little information is available on the influence of soil moisture on the colonization of ericaceous roots by ericoid mycorrhizal (ErM) fungi. Colonization was assessed microscopically in the ECM plant Pinus strobus, two AM plants (Cornus canadensis and Lysimachia borealis) and two ErM plants (Kalmia angustifolia and Gaultheria hispidula) along two upland to wetland gradients in Southwestern Nova Scotia. For the ErM plants, fungal ITS sequencing was used to assess community structure. The data indicate that ErM colonization increases with soil moisture in forested wetlands and is associated with distinctive fungal communities. August 26th, 2019 2 For Heidi, my constant companion.
    [Show full text]
  • Mycorrhizal Fungi: Unlocking Their Ecology and Role in the Establishment and Growth Performance of Different Conifer Species in Nutrient-Poor Coastal Forests
    MYCORRHIZAL FUNGI: UNLOCKING THEIR ECOLOGY AND ROLE IN THE ESTABLISHMENT AND GROWTH PERFORMANCE OF DIFFERENT CONIFER SPECIES IN NUTRIENT-POOR COASTAL FORESTS by Shannon Heather Ann Guichon A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in The Faculty of Graduate and Postdoctoral Studies (Forestry) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) December 2015 © Shannon Heather Ann Guichon, 2015 Abstract This thesis explored the fungal communities of arbuscular mycorrhizal-dominated Cedar- Hemlock (CH) and ectomycorrhizal-dominated Hemlock-Amabilis fir (HA) forests on northern Vancouver Island, British Columbia, Canada and examined the role of mycorrhizal inoculum potential for conifer seedling productivity. Objectives of this research project were to: (1) examine the mycorrhizal fungal communities and infer the inoculum potential of CH and HA forests, (2) determine whether understory plants in CH and HA forest clearcuts share compatible mycorrhizal fungi with either western redcedar (Thuja plicata) or western hemlock (Tsuga heterophylla), (3) test whether differences in mycorrhizal inoculum potential between forest types influence attributes of seedling performance during reforestation and (4) test effectiveness of providing appropriate mycorrhizal inoculum at the time of planting on conifer seedling performance. Molecular and phylogenetic techniques were utilized to compare mycorrhizal fungal diversity between forest types and to identify mycorrhizal fungal associates of the plant species occurring in clearcuts. In a field trial utilizing seedling bioassays, the role of mycorrhization of western redcedar and western hemlock on seedling growth was evaluated; reciprocal forest floor transfers from uncut forests were incorporated into the project design as inoculation treatments. Though diversity was similar, ectomycorrhizal and saprophytic fungal community composition significantly differed between CH and HA forests; arbuscular mycorrhizae were widespread in CH forests, but rare in HA forests.
    [Show full text]
  • Bulgariella Pulla, a Leotiomycete of Uncertain Placement, with an Uncommon Type of Ascus Opening
    Mycologia ISSN: 0027-5514 (Print) 1557-2536 (Online) Journal homepage: http://www.tandfonline.com/loi/umyc20 Bulgariella pulla, a Leotiomycete of uncertain placement, with an uncommon type of ascus opening Teresa Iturriaga, Katherine F. LoBuglio & Donald H. Pfister To cite this article: Teresa Iturriaga, Katherine F. LoBuglio & Donald H. Pfister (2017) Bulgariella pulla, a Leotiomycete of uncertain placement, with an uncommon type of ascus opening, Mycologia, 109:6, 900-911, DOI: 10.1080/00275514.2017.1418590 To link to this article: https://doi.org/10.1080/00275514.2017.1418590 Accepted author version posted online: 09 Mar 2018. Published online: 14 Mar 2018. Submit your article to this journal Article views: 79 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=umyc20 MYCOLOGIA 2017, VOL. 109, NO. 6, 900–911 https://doi.org/10.1080/00275514.2017.1418590 Bulgariella pulla, a Leotiomycete of uncertain placement, with an uncommon type of ascus opening Teresa Iturriaga a,b, Katherine F. LoBuglioa, and Donald H. Pfister a aFarlow Herbarium, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138; bDepartamento Biología de Organismos, Universidad Simón Bolívar, Caracas, Venezuela ABSTRACT ARTICLE HISTORY Bulgariella pulla (Leotiomycetes) is redescribed with the addition of characters of the ascus, spores, Received 8 December 2016 and habitat that were previously unconsidered. The ascus dehiscence mechanism in Bulgariella is Accepted 14 December 2017 unusual among Leotiomycetes. In this genus, asci lack a pore and open by splitting to form valves. KEYWORDS α α Phylogenetic analyses of partial sequences of translation elongation factor 1- (TEF1- ), the second Ascus dehiscence; Helotiales; largest subunit of RNA polymerase II (RPB2), and the 18S and 28S nuc rRNA genes determined that Pezizomycotina; phylogeny; Bulgariella belongs within Leotiomycetes but without conclusive assignment to an order or family.
    [Show full text]
  • A New Species from Spain and Its Phylogenetic Position Within the Genus Hymenoscyphus
    ZOBODAT - www.zobodat.at Zoologisch-Botanische Datenbank/Zoological-Botanical Database Digitale Literatur/Digital Literature Zeitschrift/Journal: Sydowia Jahr/Year: 2006 Band/Volume: 58 Autor(en)/Author(s): Baral Hans-Otto, Galan R., Lopez J., Arenal F., Villarreal M. Osvaldo, Rubio V., Collado J., Platas G., Pelaez Artikel/Article: Hymenoscyphus crataegi (Helotiales), a new species from Spain and its phylogenetic position within the genus Hymenoscyphus. 145- 162 ©Verlag Ferdinand Berger & Söhne Ges.m.b.H., Horn, Austria, download unter www.biologiezentrum.at Hymenoscyphus crateeg7(Helotiales), a new species from Spain and its phylogenetic position within the genus Hymenoscyphus* H.-O. Baral1, R. Galan2, J. Lopez3, F. Arenal4, M. Villarreal4, V. Rubio4, J. Collado5, G. Platas5 & F. Peläez5 1 Blaihofstrasse 42, Tübingen, D-72074, Germany; e-mail: [email protected] 2 Department of Plant Biology, University of Alcalä, Alcalä de Henares, E-28871, Spain 3 Mycetus Biotech, S.L., Poligono Campollano, 4, Albacete, E-02007, Spain 4 Dpto. Protecciön Vegetal, Centro Ciencias Medioambientales (CCMA-CSIC), Serrano, 115, Madrid, E-28006, Spain 5 Centro de Investigaciön Bäsica. Merck, Sharp & Dohme de Espana, S.A., Josefa Valcärcel, 38, Madrid, E-28027, Spain H.-O. Baral, R. Galan, J. Lopez, F. Arenal, M. Villarreal, V. Rubio, J. Collado, G. Platas & F. Peläez (2006). Hymenoscyphus crataegi (Helotiales), a new species from Spain and its phylogenetic position within the genus Hymenoscyphus. Sydowia 58(2): 145-162. Hymenoscyphus crataegi is described as new to science. The species was found growing on Crataegus monogyna leaves collected in Spain. It is characterized by homopolar, non-scutuloid ascospores, being acute at both ends, with a high lipid content of large guttules, in combination with asci arising from simple septa.
    [Show full text]
  • Notizbuchartige Auswahlliste Zur Bestimmungsliteratur Für Europäische Pilzgattungen Der Discomyceten Und Hypogäischen Ascomyc
    Pilzgattungen Europas - Liste 8: Notizbuchartige Auswahlliste zur Bestimmungsliteratur für Discomyceten und hypogäische Ascomyceten Bernhard Oertel INRES Universität Bonn Auf dem Hügel 6 D-53121 Bonn E-mail: [email protected] 24.06.2011 Beachte: Ascomycota mit Discomyceten-Phylogenie, aber ohne Fruchtkörperbildung, wurden von mir in die Pyrenomyceten-Datei gestellt. Erstaunlich ist die Vielzahl der Ordnungen, auf die die nicht- lichenisierten Discomyceten verteilt sind. Als Überblick soll die folgende Auflistung dieser Ordnungen dienen, wobei die Zuordnung der Arten u. Gattungen dabei noch sehr im Fluss ist, so dass mit ständigen Änderungen bei der Systematik zu rechnen ist. Es darf davon ausgegangen werden, dass die Lichenisierung bestimmter Arten in vielen Fällen unabhängig voneinander verlorengegangen ist, so dass viele Ordnungen mit üblicherweise lichenisierten Vertretern auch einige wenige sekundär entstandene, nicht-licheniserte Arten enthalten. Eine Aufzählung der zahlreichen Familien innerhalb dieser Ordnungen würde sogar den Rahmen dieser Arbeit sprengen, dafür muss auf Kirk et al. (2008) u. auf die neuste Version des Outline of Ascomycota verwiesen werden (www.fieldmuseum.org/myconet/outline.asp). Die Ordnungen der europäischen nicht-lichenisierten Discomyceten und hypogäischen Ascomyceten Wegen eines fehlenden modernen Buches zur deutschen Discomycetenflora soll hier eine Übersicht über die Ordnungen der Discomyceten mit nicht-lichenisierten Vertretern vorangestellt werden (ca. 18 europäische Ordnungen mit nicht- lichenisierten Discomyceten): Agyriales (zu Lecanorales?) Lebensweise: Zum Teil lichenisiert Arthoniales (= Opegraphales) Lebensweise: Zum Teil lichenisiert Caliciales (zu Lecanorales?) Lebensweise: Zum Teil lichenisiert Erysiphales (diese aus praktischen Gründen in der Pyrenomyceten- Datei abgehandelt) Graphidales [seit allerneuster Zeit wieder von den Ostropales getrennt gehalten; s. Wedin et al. (2005), MR 109, 159-172; Lumbsch et al.
    [Show full text]
  • Discovery of New Mycoviral Genomes Within Publicly Available Fungal Transcriptomic Datasets
    bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Discovery of new mycoviral genomes within publicly available fungal transcriptomic datasets 1 1 1,2 1 Kerrigan B. Gilbert ,​ Emily E. Holcomb ,​ Robyn L. Allscheid ,​ James C. Carrington *​ ​ ​ ​ ​ 1 ​ Donald Danforth Plant Science Center, Saint Louis, Missouri, USA 2 ​ Current address: National Corn Growers Association, Chesterfield, Missouri, USA * Address correspondence to James C. Carrington E-mail: [email protected] Short title: Virus discovery from RNA-seq data ​ bioRxiv preprint doi: https://doi.org/10.1101/510404; this version posted January 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. ​ ​ Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina.
    [Show full text]
  • Lichenicolous Species of Hainesia Belong to Phacidiales (Leotiomycetes) and Are Included in an Extended Concept of Epithamnolia
    Mycologia ISSN: 0027-5514 (Print) 1557-2536 (Online) Journal homepage: http://www.tandfonline.com/loi/umyc20 Lichenicolous species of Hainesia belong to Phacidiales (Leotiomycetes) and are included in an extended concept of Epithamnolia Ave Suija, Pieter van den Boom, Erich Zimmermann, Mikhail P. Zhurbenko & Paul Diederich To cite this article: Ave Suija, Pieter van den Boom, Erich Zimmermann, Mikhail P. Zhurbenko & Paul Diederich (2017): Lichenicolous species of Hainesia belong to Phacidiales (Leotiomycetes) and are included in an extended concept of Epithamnolia, Mycologia, DOI: 10.1080/00275514.2017.1413891 To link to this article: https://doi.org/10.1080/00275514.2017.1413891 View supplementary material Accepted author version posted online: 13 Dec 2017. Published online: 08 Mar 2018. Submit your article to this journal Article views: 72 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=umyc20 MYCOLOGIA https://doi.org/10.1080/00275514.2017.1413891 Lichenicolous species of Hainesia belong to Phacidiales (Leotiomycetes) and are included in an extended concept of Epithamnolia Ave Suija a, Pieter van den Boomb, Erich Zimmermannc, Mikhail P. Zhurbenko d, and Paul Diederiche aInstitute of Ecology and Earth Sciences, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia; bArafura 16, NL-5691 JA Son, The Netherlands; cScheunenberg 46, CH-3251 Wengi, Switzerland; dKomarov Botanical Institute, Professor Popov 2, St. Petersburg, 197376, Russia; eMusée national d’histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg ABSTRACT ARTICLE HISTORY The lichenicolous taxa currently included in the genus Hainesia were studied based on the nuclear Received 4 April 2017 rDNA (18S, 28S, and internal transcribed spacer [ITS]) genes.
    [Show full text]
  • The Root-Symbiotic Rhizoscyphus Ericae Aggregate and Hyaloscypha (Leotiomycetes) Are Congeneric: Phylogenetic and Experimental Evidence
    available online at www.studiesinmycology.org STUDIES IN MYCOLOGY 92: 195–225 (2019). The root-symbiotic Rhizoscyphus ericae aggregate and Hyaloscypha (Leotiomycetes) are congeneric: Phylogenetic and experimental evidence J. Fehrer1*,3,M.Reblova1,3, V. Bambasova1, and M. Vohník1,2 1Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; 2Department of Plant Experimental Biology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic *Correspondence: J. Fehrer, [email protected] 3These authors contributed equally to the paper. Abstract: Data mining for a phylogenetic study including the prominent ericoid mycorrhizal fungus Rhizoscyphus ericae revealed nearly identical ITS sequences of the bryophilous Hyaloscypha hepaticicola suggesting they are conspecific. Additional genetic markers and a broader taxonomic sampling furthermore suggested that the sexual Hyaloscypha and the asexual Meliniomyces may be congeneric. In order to further elucidate these issues, type strains of all species traditionally treated as members of the Rhizoscyphus ericae aggregate (REA) and related taxa were subjected to phylogenetic analyses based on ITS, nrLSU, mtSSU, and rpb2 markers to produce comparable datasets while an in vitro re-synthesis experiment was conducted to examine the root-symbiotic potential of H. hepaticicola in the Ericaceae. Phylogenetic evidence demonstrates that sterile root-associated Meliniomyces, sexual Hyaloscypha and Rhizoscyphus, based on R. ericae, are indeed congeneric. To this monophylum also belongs the phialidic dematiaceous hyphomycetes Cadophora finlandica and Chloridium paucisporum. We provide a taxonomic revision of the REA; Meliniomyces and Rhizoscyphus are reduced to synonymy under Hyaloscypha. Pseudaegerita, typified by P. corticalis, an asexual morph of H. spiralis which is a core member of Hyaloscypha, is also transferred to the synonymy of the latter genus.
    [Show full text]
  • A Multigene Phylogeny Toward a New Phylogenetic Classification of Leotiomycetes Peter R
    Johnston et al. IMA Fungus (2019) 10:1 https://doi.org/10.1186/s43008-019-0002-x IMA Fungus RESEARCH Open Access A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes Peter R. Johnston1* , Luis Quijada2, Christopher A. Smith1, Hans-Otto Baral3, Tsuyoshi Hosoya4, Christiane Baschien5, Kadri Pärtel6, Wen-Ying Zhuang7, Danny Haelewaters2,8, Duckchul Park1, Steffen Carl5, Francesc López-Giráldez9, Zheng Wang10 and Jeffrey P. Townsend10 Abstract Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such character-poor samples increasingly relies on DNA sequencing. However, the current classification of Leotiomycetes is still largely based on morphologically defined taxa, especially at higher taxonomic levels. Consequently, the formal Leotiomycetes classification is frequently poorly congruent with the relationships suggested by DNA sequencing studies. Previous class-wide phylogenies of Leotiomycetes have been based on ribosomal DNA markers, with most of the published multi-gene studies being focussed on particular genera or families. In this paper we collate data available from specimens representing both sexual and asexual morphs from across the genetic breadth of the class, with a focus on generic type species, to present a phylogeny based on up to 15 concatenated genes across 279 specimens. Included in the dataset are genes that were extracted from 72 of the genomes available for the class, including 10 new genomes released with this study. To test the statistical support for the deepest branches in the phylogeny, an additional phylogeny based on 3156 genes from 51 selected genomes is also presented.
    [Show full text]