Publications by authors named "Urmas Kõljalg"

51 Publications

Temperature and pH define the realized niche space of arbuscular mycorrhizal fungi.

New Phytol 2021 Jan 28. Epub 2021 Jan 28.

Institute of Ecology and Earth Sciences, University of Tartu, 51005, Estonia, Tartu.

The arbuscular mycorrhizal (AM) fungi are a globally-distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected >300 soil samples from natural ecosystems worldwide and modelled the realized niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local- to regional-scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identifying the realized niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.
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http://dx.doi.org/10.1111/nph.17240DOI Listing
January 2021

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

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

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

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

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe.

Front Microbiol 2020 4;11:1953. Epub 2020 Sep 4.

Natural History Museum and Botanical Garden, University of Tartu, Tartu, Estonia.

Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularly , , and , and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.
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http://dx.doi.org/10.3389/fmicb.2020.01953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7510051PMC
September 2020

Reassessment of the generic limits for and (Thelephorales, Basidiomycota).

MycoKeys 2019 10;54:31-47. Epub 2019 Jun 10.

Gothenburg Global Biodiversity Centre, P.O. Box 461, SE 405 30 Göteborg, Sweden University of Oslo Oslo Norway.

DNA sequences from the nuclear LSU and ITS regions were used for phylogenetic analyses of Thelephorales with a focus on the stipitate hydnoid genera and . Analyses showed that and are distinct genera but that the current division, based on basidioma texture, makes paraphyletic with respect to . In order to make genera monophyletic several species are moved from to and the following new combinations are made: , , , , , , , , , , , and . Basidiospore size seems to separate the genera in most cases. species have basidiospore lengths in the range 4.45-6.95 µm while the corresponding range for is 7.4-9 µm. deviates from this pattern with an average spore length around 6 µm. Neotropical species represent a separate evolutionary lineage.
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http://dx.doi.org/10.3897/mycokeys.54.35386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6579789PMC
June 2019

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

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

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

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

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.

Nucleic Acids Res 2019 01;47(D1):D259-D264

Natural History Museum and Botanical Garden, University of Tartu, 46 Vanemuise Street, 51003 Tartu, Estonia.

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
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http://dx.doi.org/10.1093/nar/gky1022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324048PMC
January 2019

Considerations and consequences of allowing DNA sequence data as types of fungal taxa.

Authors:
Juan Carlos Zamora Måns Svensson Roland Kirschner Ibai Olariaga Svengunnar Ryman Luis Alberto Parra József Geml Anna Rosling Slavomír Adamčík Teuvo Ahti M Catherine Aime A Martyn Ainsworth László Albert Edgardo Albertó Alberto Altés García Dmitry Ageev Reinhard Agerer Begoña Aguirre-Hudson Joe Ammirati Harry Andersson Claudio Angelini Vladimír Antonín Takayuki Aoki André Aptroot Didier Argaud Blanca Imelda Arguello Sosa Arne Aronsen Ulf Arup Bita Asgari Boris Assyov Violeta Atienza Ditte Bandini João Luís Baptista-Ferreira Hans-Otto Baral Tim Baroni Robert Weingart Barreto Henry Beker Ann Bell Jean-Michel Bellanger Francesco Bellù Martin Bemmann Mika Bendiksby Egil Bendiksen Katriina Bendiksen Lajos Benedek Anna Bérešová-Guttová Franz Berger Reinhard Berndt Annarosa Bernicchia Alona Yu Biketova Enrico Bizio Curtis Bjork Teun Boekhout David Boertmann Tanja Böhning Florent Boittin Carlos G Boluda Menno W Boomsluiter Jan Borovička Tor Erik Brandrud Uwe Braun Irwin Brodo Tatiana Bulyonkova Harold H Burdsall Bart Buyck Ana Rosa Burgaz Vicent Calatayud Philippe Callac Emanuele Campo Massimo Candusso Brigitte Capoen Joaquim Carbó Matteo Carbone Rafael F Castañeda-Ruiz Michael A Castellano Jie Chen Philippe Clerc Giovanni Consiglio Gilles Corriol Régis Courtecuisse Ana Crespo Cathy Cripps Pedro W Crous Gladstone Alves da Silva Meiriele da Silva Marjo Dam Nico Dam Frank Dämmrich Kanad Das Linda Davies Eske De Crop Andre De Kesel Ruben De Lange Bárbara De Madrignac Bonzi Thomas Edison E Dela Cruz Lynn Delgat Vincent Demoulin Dennis E Desjardin Paul Diederich Bálint Dima Maria Martha Dios Pradeep Kumar Divakar Clovis Douanla-Meli Brian Douglas Elisandro Ricardo Drechsler-Santos Paul S Dyer Ursula Eberhardt Damien Ertz Fernando Esteve-Raventós Javier Angel Etayo Salazar Vera Evenson Guillaume Eyssartier Edit Farkas Alain Favre Anna G Fedosova Mario Filippa Péter Finy Adam Flakus Simón Fos Jacques Fournier André Fraiture Paolo Franchi Ana Esperanza Franco Molano Gernot Friebes Andreas Frisch Alan Fryday Giuliana Furci Ricardo Galán Márquez Matteo Garbelotto Joaquina María García-Martín Mónica A García Otálora Dania García Sánchez Alain Gardiennet Sigisfredo Garnica Isaac Garrido Benavent Genevieve Gates Alice da Cruz Lima Gerlach Masoomeh Ghobad-Nejhad Tatiana B Gibertoni Tine Grebenc Irmgard Greilhuber Bella Grishkan Johannes Z Groenewald Martin Grube Gérald Gruhn Cécile Gueidan Gro Gulden Luis Fp Gusmão Josef Hafellner Michel Hairaud Marek Halama Nils Hallenberg Roy E Halling Karen Hansen Christoffer Bugge Harder Jacob Heilmann-Clausen Stip Helleman Alain Henriot Margarita Hernandez-Restrepo Raphaël Herve Caroline Hobart Mascha Hoffmeister Klaus Høiland Jan Holec Håkon Holien Karen Hughes Vit Hubka Seppo Huhtinen Boris Ivančević Marian Jagers Walter Jaklitsch AnnaElise Jansen Ruvishika S Jayawardena Thomas Stjernegaard Jeppesen Mikael Jeppson Peter Johnston Per Magnus Jørgensen Ingvar Kärnefelt Liudmila B Kalinina Gintaras Kantvilas Mitko Karadelev Taiga Kasuya Ivona Kautmanová Richard W Kerrigan Martin Kirchmair Anna Kiyashko Dániel G Knapp Henning Knudsen Kerry Knudsen Tommy Knutsson Miroslav Kolařík Urmas Kõljalg Alica Košuthová Attila Koszka Heikki Kotiranta Vera Kotkova Ondřej Koukol Jiří Kout Gábor M Kovács Martin Kříž Åsa Kruys Viktor Kučera Linas Kudzma Francisco Kuhar Martin Kukwa T K Arun Kumar Vladimír Kunca Ivana Kušan Thomas W Kuyper Carlos Lado Thomas Læssøe Patrice Lainé Ewald Langer Ellen Larsson Karl-Henrik Larsson Gary Laursen Christian Lechat Serena Lee James C Lendemer Laura Levin Uwe Lindemann Håkan Lindström Xingzhong Liu Regulo Carlos Llarena Hernandez Esteve Llop Csaba Locsmándi Deborah Jean Lodge Michael Loizides László Lőkös Jennifer Luangsa-Ard Matthias Lüderitz Thorsten Lumbsch Matthias Lutz Dan Mahoney Ekaterina Malysheva Vera Malysheva Patinjareveettil Manimohan Yasmina Marin-Felix Guilhermina Marques Rubén Martínez-Gil Guy Marson Gerardo Mata P Brandon Matheny Geir Harald Mathiassen Neven Matočec Helmut Mayrhofer Mehdi Mehrabi Ireneia Melo Armin Mešić Andrew S Methven Otto Miettinen Ana M Millanes Romero Andrew N Miller James K Mitchell Roland Moberg Pierre-Arthur Moreau Gabriel Moreno Olga Morozova Asunción Morte Lucia Muggia Guillermo Muñoz González Leena Myllys István Nagy László G Nagy Maria Alice Neves Tuomo Niemelä Pier Luigi Nimis Nicolas Niveiro Machiel E Noordeloos Anders Nordin Sara Raouia Noumeur Yuri Novozhilov Jorinde Nuytinck Esteri Ohenoja Patricia Oliveira Fiuza Alan Orange Alexander Ordynets Beatriz Ortiz-Santana Leticia Pacheco Ferenc Pál-Fám Melissa Palacio Zdeněk Palice Viktor Papp Kadri Pärtel Julia Pawlowska Aurelia Paz Ursula Peintner Shaun Pennycook Olinto Liparini Pereira Pablo Pérez Daniëls Miquel À Pérez-De-Gregorio Capella Carlos Manuel Pérez Del Amo Sergio Pérez Gorjón Sergio Pérez-Ortega Israel Pérez-Vargas Brian A Perry Jens H Petersen Ronald H Petersen Donald H Pfister Chayanard Phukhamsakda Marcin Piątek Meike Piepenbring Raquel Pino-Bodas Juan Pablo 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Svantesson Sigvard Svensson Tatyana Yu Svetasheva Krzysztof Świerkosz Heidi Tamm Hatira Taskin Adrien Taudière Jan-Olof Tedebrand Raúl Tena Lahoz Marina Temina Arne Thell Marco Thines Göran Thor Holger Thüs Leif Tibell Sanja Tibell Einar Timdal Zdenko Tkalčec Tor Tønsberg Gérard Trichies Dagmar Triebel Andrei Tsurykau Rodham E Tulloss Veera Tuovinen Miguel Ulloa Sosa Carlos Urcelay François Valade Ricardo Valenzuela Garza Pieter van den Boom Nicolas Van Vooren Aida M Vasco-Palacios Jukka Vauras Juan Manuel Velasco Santos Else Vellinga Annemieke Verbeken Per Vetlesen Alfredo Vizzini Hermann Voglmayr Sergey Volobuev Wolfgang von Brackel Elena Voronina Grit Walther Roy Watling Evi Weber Mats Wedin Øyvind Weholt Martin Westberg Eugene Yurchenko Petr Zehnálek Huang Zhang Mikhail P Zhurbenko Stefan Ekman

IMA Fungus 2018 Jun 24;9(1):167-175. Epub 2018 May 24.

Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11 International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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http://dx.doi.org/10.5598/imafungus.2018.09.01.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048565PMC
June 2018

Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK).

MycoKeys 2018 8(28):65-82. Epub 2018 Jan 8.

University of Tartu, Tartu, Estonia.

Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were , , , and , all of them of significant importance in both culture-based and culture-independent surveys of the built environment.
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http://dx.doi.org/10.3897/mycokeys.28.20887DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5804120PMC
January 2018

Taxonomy based on science is necessary for global conservation.

Authors:
Scott A Thomson Richard L Pyle Shane T Ahyong Miguel Alonso-Zarazaga Joe Ammirati Juan Francisco Araya John S Ascher Tracy Lynn Audisio Valter M Azevedo-Santos Nicolas Bailly William J Baker Michael Balke Maxwell V L Barclay Russell L Barrett Ricardo C Benine James R M Bickerstaff Patrice Bouchard Roger Bour Thierry Bourgoin Christopher B Boyko Abraham S H Breure Denis J Brothers James W Byng David Campbell Luis M P Ceríaco István Cernák Pierfilippo Cerretti Chih-Han Chang Soowon Cho Joshua M Copus Mark J Costello Andras Cseh Csaba Csuzdi Alastair Culham Guillermo D'Elía Cédric d'Udekem d'Acoz Mikhail E Daneliya René Dekker Edward C Dickinson Timothy A Dickinson Peter Paul van Dijk Klaas-Douwe B Dijkstra Bálint Dima Dmitry A Dmitriev Leni Duistermaat John P Dumbacher Wolf L Eiserhardt Torbjørn Ekrem Neal L Evenhuis Arnaud Faille José L Fernández-Triana Emile Fiesler Mark Fishbein Barry G Fordham André V L Freitas Natália R Friol Uwe Fritz Tobias Frøslev Vicki A Funk Stephen D Gaimari Guilherme S T Garbino André R S Garraffoni József Geml Anthony C Gill Alan Gray Felipe G Grazziotin Penelope Greenslade Eliécer E Gutiérrez Mark S Harvey Cornelis J Hazevoet Kai He Xiaolan He Stephan Helfer Kristofer M Helgen Anneke H van Heteren Francisco Hita Garcia Norbert Holstein Margit K Horváth Peter H Hovenkamp Wei Song Hwang Jaakko Hyvönen Melissa B Islam John B Iverson Michael A Ivie Zeehan Jaafar Morgan D Jackson J Pablo Jayat Norman F Johnson Hinrich Kaiser Bente B Klitgård Dániel G Knapp Jun-Ichi Kojima Urmas Kõljalg Jenő Kontschán Frank-Thorsten Krell Irmgard Krisai-Greilhuber Sven Kullander Leonardo Latella John E Lattke Valeria Lencioni Gwilym P Lewis Marcos G Lhano Nathan K Lujan Jolanda A Luksenburg Jean Mariaux Jader Marinho-Filho Christopher J Marshall Jason F Mate Molly M McDonough Ellinor Michel Vitor F O Miranda Mircea-Dan Mitroiu Jesús Molinari Scott Monks Abigail J Moore Ricardo Moratelli Dávid Murányi Takafumi Nakano Svetlana Nikolaeva John Noyes Michael Ohl Nora H Oleas Thomas Orrell Barna Páll-Gergely Thomas Pape Viktor Papp Lynne R Parenti David Patterson Igor Ya Pavlinov Ronald H Pine Péter Poczai Jefferson Prado Divakaran Prathapan Richard K Rabeler John E Randall Frank E Rheindt Anders G J Rhodin Sara M Rodríguez D Christopher Rogers Fabio de O Roque Kevin C Rowe Luis A Ruedas Jorge Salazar-Bravo Rodrigo B Salvador George Sangster Carlos E Sarmiento Dmitry S Schigel Stefan Schmidt Frederick W Schueler Hendrik Segers Neil Snow Pedro G B Souza-Dias Riaan Stals Soili Stenroos R Douglas Stone Charles F Sturm Pavel Štys Pablo Teta Daniel C Thomas Robert M Timm Brian J Tindall Jonathan A Todd Dagmar Triebel Antonio G Valdecasas Alfredo Vizzini Maria S Vorontsova Jurriaan M de Vos Philipp Wagner Les Watling Alan Weakley Francisco Welter-Schultes Daniel Whitmore Nicholas Wilding Kipling Will Jason Williams Karen Wilson Judith E Winston Wolfgang Wüster Douglas Yanega David K Yeates Hussam Zaher Guanyang Zhang Zhi-Qiang Zhang Hong-Zhang Zhou

PLoS Biol 2018 03 14;16(3):e2005075. Epub 2018 Mar 14.

International Commission on Zoological Nomenclature, Singapore.

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http://dx.doi.org/10.1371/journal.pbio.2005075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851535PMC
March 2018

Polyozellus multiplex (Thelephorales) is a species complex containing four new species.

Mycologia 2017 1;109(6):975-992. Epub 2018 Mar 1.

b Institute of Ecology and Earth Sciences, University of Tartu , 14A Ravila Street, 50411 Tartu , Estonia.

Geographic, morphological, and internal transcribed spacer (ITS)-based molecular review of collections identified as Polyozellus multiplex revealed that it is a complex of five phylogenetic species. Average spore size-either less or more than 7 × 6 µm-splits the complex into a small-spored group of two (P. multiplex and P. atrolazulinus) and a large-spored group of three (P. mariae, P. marymargaretae, and P. purpureoniger). Basidiocarps of the small-spored species are somewhat smaller than the large-spored ones, are various shades of blue, dark all the way to black, with brownish tomentum only in early growth, have dark context, and have pilei that tend to flare out at the edge. The large-spored species produce somewhat larger sporocarps, have light or lighter context than the pileipelis, and usually retain some brown on the mature pileipellis, the edge of which tends to curl like a cabbage leaf. All will darken or blacken with age. The species of the P. multiplex complex are distributed in the northern coniferous region, with the exception of Europe. One species (P. atrolazulinus) is known from three regions, eastern Asia, western North America, and northeastern North America. Two species are known from two regions: P. purpureoniger in eastern Asia and northwestern North America and P. multiplex in eastern Asia and eastern North America. Two species have been documented in one region only: P. mariae in northeastern North America and P. marymargaretae in western North America. A combination of location, macromorphology, and spore size will usually differentiate the species of the complex.
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http://dx.doi.org/10.1080/00275514.2017.1416246DOI Listing
November 2018

Aphyllophoroid fungi in insular woodlands of eastern Ukraine.

Biodivers Data J 2017 22(5):e22426. Epub 2017 Dec 22.

Department of Ecology, University of Kassel, Kassel, Germany.

Background: Fungi play crucial roles in ecosystems and are among the species-richest organism groups on Earth. However, knowledge on their occurrence lags behind the data for animals and plants. Recent analyses of fungal occurrence data from Western, Central and Northern Europe provided important insights into response of fungi to global warming. The consequences of the global changes for biodiversity on a larger geographical scale are not yet understood. Landscapes of Eastern Europe and particularly of eastern Ukraine, with their specific geological history, vegetation and climate, can add substantially new information about fungal diversity in Europe.

New Information: We describe the dataset and provide a checklist of aphyllophoroid fungi (non-gilled macroscopic ) from eastern Ukraine sampled in 16 areas between 2007 and 2011. The dataset was managed on the PlutoF biodiversity workbench (http://dx.doi.org/10.15156/BIO/587471) and can also be accessed via Global Biodiversity Information Facility (GBIF, parts of datasets https://doi.org/10.15468/kuspj6 and https://doi.org/10.15468/h7qtfd). This dataset includes 3418 occurences, namely 2727 specimens and 691 observations of fructifications belonging to 349 species of fungi. With these data, the digitised CWU herbarium (V. N. Karazin Kharkiv National University, Ukraine) doubled in size A most detailed description of the substrate's properties and habitat for each record is provided. The specimen records are supplemented by 26 nuclear ribosomal DNA ITS sequences and six 28S sequences. Additionally, 287 photographs depicting diagnostic macro- and microscopic features of fungal fruitbodies as well as studied habitats are linked to the dataset. Most of the specimens have at least one mention in literature and relevant references are displayed as associated with specimen data. In total, 16 publication references are linked to the dataset. The dataset sheds new light on the fungal diversity of Eastern Europe. It is expected to complement other public sources of fungal occurrence information on continental and global levels in addressing macroecological and biogeographical questions.
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http://dx.doi.org/10.3897/BDJ.5.e22426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769729PMC
December 2017

Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands.

Mycorrhiza 2017 May 30;27(4):355-367. Epub 2016 Dec 30.

Institute of Ecology and Earth Sciences, University of Tartu, 14A Ravila, 50411, Tartu, Estonia.

Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.
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http://dx.doi.org/10.1007/s00572-016-0755-7DOI Listing
May 2017

Sequence-based classification and identification of Fungi.

Mycologia 2016 Nov/Dec;108(6):1049-1068

l Department of Plant Pathology and Environmental Microbiology, 121 Buckhout Laboratory, Penn State University, University Park, Pennsylvania 16802.

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.
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http://dx.doi.org/10.3852/16-130DOI Listing
January 2018

PESI - a taxonomic backbone for Europe.

Authors:
Yde de Jong Juliana Kouwenberg Louis Boumans Charles Hussey Roger Hyam Nicola Nicolson Paul Kirk Alan Paton Ellinor Michel Michael D Guiry Phillip S Boegh Henrik Ærenlund Pedersen Henrik Enghoff Eckhard von Raab-Straube Anton Güntsch Marc Geoffroy Andreas Müller Andreas Kohlbecker Walter Berendsohn Ward Appeltans Christos Arvanitidis Bart Vanhoorne Joram Declerck Leen Vandepitte Francisco Hernandez Róisín Nash Mark John Costello David Ouvrard Pascale Bezard-Falgas Thierry Bourgoin Florian Tobias Wetzel Falko Glöckler Günther Korb Caroline Ring Gregor Hagedorn Christoph Häuser Nihat Aktaç Ahmet Asan Adorian Ardelean Paulo Alexandre Vieira Borges Dhimiter Dhora Hasmik Khachatryan Michael Malicky Shaig Ibrahimov Alexander Tuzikov Aaike De Wever Snejana Moncheva Nikolai Spassov Karel Chobot Alexi Popov Igor Boršić Spyros Sfenthourakis Urmas Kõljalg Pertti Uotila Gargominy Olivier Jean-Claude Dauvin David Tarkhnishvili Giorgi Chaladze Michael Tuerkay Anastasios Legakis László Peregovits Gudmundur Gudmundsson Erling Ólafsson Liam Lysaght Bella Sarah Galil Francesco M Raimondo Gianniantonio Domina Fabio Stoch Alessandro Minelli Voldermars Spungis Eduardas Budrys Sergej Olenin Armand Turpel Tania Walisch Vladimir Krpach Marie Therese Gambin Laurentia Ungureanu Gordan Karaman Roy M J C Kleukers Elisabeth Stur Kaare Aagaard Nils Valland Toril Loennechen Moen Wieslaw Bogdanowicz Piotr Tykarski Jan Marcin Węsławski Monika Kędra Antonio M de Frias Martins António Domingos Abreu Ricardo Silva Sergei Medvedev Alexander Ryss Smiljka Šimić Karol Marhold Eduard Stloukal Davorin Tome Marian A Ramos Benito Valdés Francisco Pina Sven Kullander Anders Telenius Yves Gonseth Pascal Tschudin Oleksandra Sergeyeva Volodymyr Vladymyrov Volodymyr Bohdanovych Rizun Chris Raper Dan Lear Pavel Stoev Lyubomir Penev Ana Casino Rubio Thierry Backeljau Hannu Saarenmaa Sandrine Ulenberg

Biodivers Data J 2015 28(3):e5848. Epub 2015 Sep 28.

Naturalis Biodiversity Center, Leiden, Netherlands.

Background: Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

New Information: This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
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http://dx.doi.org/10.3897/BDJ.3.e5848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609752PMC
October 2015

FUNGAL BIOGEOGRAPHY. Response to Comment on "Global diversity and geography of soil fungi".

Science 2015 Aug 27;349(6251):936. Epub 2015 Aug 27.

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

Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)-free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.
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http://dx.doi.org/10.1126/science.aaa5594DOI Listing
August 2015

Standardizing metadata and taxonomic identification in metabarcoding studies.

Gigascience 2015 31;4:34. Epub 2015 Jul 31.

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

High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.
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http://dx.doi.org/10.1186/s13742-015-0074-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521374PMC
July 2016

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.

Microbes Environ 2015 19;30(2):145-50. Epub 2015 Mar 19.

Department of Biological and Environmental Sciences, University of Gothenburg.

The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric-artificially joined-DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
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http://dx.doi.org/10.1264/jsme2.ME14121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462924PMC
March 2016

Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing.

New Phytol 2015 Mar 24;205(4):1608-18. Epub 2014 Dec 24.

Institute of Ecology and Earth Sciences, University of Tartu, 14A Ravila, 50411, Tartu, Estonia.

Orchid mycorrhizal (OrM) symbionts play a key role in the growth of orchids, but the temporal variation and habitat partitioning of these fungi in roots and soil remain unclear. Temporal changes in root and rhizosphere fungal communities of Cypripedium calceolus, Neottia ovata and Orchis militaris were studied in meadow and forest habitats over the vegetation period by using 454 pyrosequencing of the full internal transcribed spacer (ITS) region. The community of typical OrM symbionts differed by plant species and habitats. The root fungal community of N. ovata changed significantly in time, but this was not observed in C. calceolus and O. militaris. The rhizosphere community included a low proportion of OrM symbionts that exhibited a slight temporal turnover in meadow habitats but not in forests. Habitat differences in OrM and all fungal associates are largely attributable to the greater proportion of ectomycorrhizal fungi in forests. Temporal changes in OrM fungal communities in roots of certain species indicate selection of suitable fungal species by plants. It remains to be elucidated whether these shifts depend on functional differences inside roots, seasonality, climate or succession.
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http://dx.doi.org/10.1111/nph.13223DOI Listing
March 2015

Fungal biogeography. Global diversity and geography of soil fungi.

Science 2014 Nov;346(6213):1256688

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

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

Global biogeography of Alnus-associated Frankia actinobacteria.

New Phytol 2014 Dec 13;204(4):979-88. Epub 2014 Aug 13.

Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005, Tartu, Estonia; Natural History Museum of Tartu University, 46 Vanemuise Street, 51014, Tartu, Estonia.

Macroecological patterns of microbes have received relatively little attention until recently. This study aimed to disentangle the determinants of the global biogeographic community of Alnus-associated actinobacteria belonging to the Frankia alni complex. By determining a global sequence similarity threshold for the nitrogenase reductase (nifH) gene, we separated Frankia into operational taxonomic units (OTUs) and tested the relative effects of Alnus phylogeny, geographic relatedness, and climatic and edaphic variables on community composition at the global scale. Based on the optimal nifH gene sequence similarity threshold of 99.3%, we distinguished 43 Frankia OTUs from root systems of 22 Alnus species on four continents. Host phylogeny was the main determinant of Frankia OTU-based community composition, but there was no effect on the phylogenetic structure of Frankia. Biogeographic analyses revealed the strongest cross-continental links over the Beringian land bridge. Despite the facultative symbiotic nature of Frankia, phylogenetic relations among Alnus species play a prominent role in structuring root-associated Frankia communities and their biogeographic patterns. Our results suggest that Alnus species exert strong phylogenetically determined selection pressure on compatible Actinobacteria.
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http://dx.doi.org/10.1111/nph.12962DOI Listing
December 2014

Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses.

Mol Ecol 2014 Aug 23;23(16):4168-83. Epub 2014 Jul 23.

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

Compared with plants and animals, large-scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45-57 Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.
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http://dx.doi.org/10.1111/mec.12849DOI Listing
August 2014

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

Authors:
Conrad L Schoch Barbara Robbertse Vincent Robert Duong Vu Gianluigi Cardinali Laszlo Irinyi Wieland Meyer R Henrik Nilsson Karen Hughes Andrew N Miller Paul M Kirk Kessy Abarenkov M Catherine Aime Hiran A Ariyawansa Martin Bidartondo Teun Boekhout Bart Buyck Qing Cai Jie Chen Ana Crespo Pedro W Crous Ulrike Damm Z Wilhelm De Beer Bryn T M Dentinger Pradeep K Divakar Margarita Dueñas Nicolas Feau Katerina Fliegerova Miguel A García Zai-Wei Ge Gareth W Griffith Johannes Z Groenewald Marizeth Groenewald Martin Grube Marieka Gryzenhout Cécile Gueidan Liangdong Guo Sarah Hambleton Richard Hamelin Karen Hansen Valérie Hofstetter Seung-Beom Hong Jos Houbraken Kevin D Hyde Patrik Inderbitzin Peter R Johnston Samantha C Karunarathna Urmas Kõljalg Gábor M Kovács Ekaphan Kraichak Krisztina Krizsan Cletus P Kurtzman Karl-Henrik Larsson Steven Leavitt Peter M Letcher Kare Liimatainen Jian-Kui Liu D Jean Lodge Janet Jennifer Luangsa-ard H Thorsten Lumbsch Sajeewa S N Maharachchikumbura Dimuthu Manamgoda María P Martín Andrew M Minnis Jean-Marc Moncalvo Giuseppina Mulè Karen K Nakasone Tuula Niskanen Ibai Olariaga Tamás Papp Tamás Petkovits Raquel Pino-Bodas Martha J Powell Huzefa A Raja Dirk Redecker J M Sarmiento-Ramirez Keith A Seifert Bhushan Shrestha Soili Stenroos Benjamin Stielow Sung-Oui Suh Kazuaki Tanaka Leho Tedersoo M Teresa Telleria Dhanushka Udayanga Wendy A Untereiner Javier Diéguez Uribeondo Krishna V Subbarao Csaba Vágvölgyi Cobus Visagie Kerstin Voigt Donald M Walker Bevan S Weir Michael Weiß Nalin N Wijayawardene Michael J Wingfield J P Xu Zhu L Yang Ning Zhang Wen-Ying Zhuang Scott Federhen

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

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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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Towards a unified paradigm for sequence-based identification of fungi.

Mol Ecol 2013 Nov 24;22(21):5271-7. Epub 2013 Sep 24.

Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia; Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia.

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.
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http://dx.doi.org/10.1111/mec.12481DOI Listing
November 2013

Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide.

New Phytol 2013 Jul 28;199(1):288-99. Epub 2013 Mar 28.

Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.
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http://dx.doi.org/10.1111/nph.12243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712477PMC
July 2013

Biogeography of ectomycorrhizal fungi associated with alders (Alnus spp.) in relation to biotic and abiotic variables at the global scale.

New Phytol 2013 Jun 20;198(4):1239-49. Epub 2013 Feb 20.

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

· Much of the macroecological information about microorganisms is confounded by the lack of standardized methodology, paucity of metadata and sampling effect of a particular substrate or interacting host taxa. · This study aims to disentangle the relative effects of biological, geographical and edaphic variables on the distribution of Alnus-associated ectomycorrhizal (ECM) fungi at the global scale by using comparable sampling and analysis methods. · Ribosomal DNA sequence analysis revealed 146 taxa of ECM fungi from 22 Alnus species across 96 sites worldwide. Use of spatial and phylogenetic eigenvectors along with environmental variables in model selection indicated that phylogenetic relations among host plants and geographical links explained 43 and 10%, respectively,in ECM fungal community composition, whereas soil calcium concentration positively influenced taxonomic richness. · Intrageneric phylogenetic relations among host plants and regional processes largely account for the global biogeographic distribution of Alnus-associated ECM fungi. The biogeography of ECM fungi is consistent with ancient host migration patterns from Eurasia to North America and from southern Europe to northern Europe after the last glacial maximum, indicating codispersal of hosts and their mycobionts.
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http://dx.doi.org/10.1111/nph.12170DOI Listing
June 2013

Enzymatic activities and stable isotope patterns of ectomycorrhizal fungi in relation to phylogeny and exploration types in an afrotropical rain forest.

New Phytol 2012 Sep 3;195(4):832-43. Epub 2012 Jul 3.

Natural History Museum of Tartu University, 46 Vanemuise, 51005 Tartu, Estonia.

Ectomycorrhizal (ECM) fungi obtain both mineral and simple organic nutrients from soil and transport these to plant roots. Natural abundance of stable isotopes (¹⁵N and ¹³C) in fruit bodies and potential enzymatic activities of ECM root tips provide insights into mineral nutrition of these mutualistic partners. By combining rDNA sequence analysis with enzymatic and stable isotope assays of root tips, we hypothesized that phylogenetic affinities of ECM fungi are more important than ECM exploration type, soil horizon and host plant in explaining the differences in mineral nutrition of trees in an African lowland rainforest. Ectomycorrhizal fungal species belonging to extraradical mycelium-rich morphotypes generally displayed the strongest potential activities of degradation enzymes, except for laccase. The signature of ¹⁵N was determined by the ECM fungal lineage, but not by the exploration type. Potential enzymatic activities of root tips were unrelated to ¹⁵N signature of ECM root tip. The lack of correlation suggests that these methods address different aspects in plant nutrient uptake. Stable isotope analysis of root tips could provide an additional indirect assessment of fungal and plant nutrition that enables enhancement of taxonomic coverage and control for soil depth and internal nitrogen cycling in fungal tissues.
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http://dx.doi.org/10.1111/j.1469-8137.2012.04217.xDOI Listing
September 2012

The amsterdam declaration on fungal nomenclature.

IMA Fungus 2011 Jun 7;2(1):105-12. Epub 2011 Jun 7.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, E-28040 Madrid, Spain; and Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, UK;

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.
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http://dx.doi.org/10.5598/imafungus.2011.02.01.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317370PMC
June 2011

Ectomycorrhizal fungi of exotic pine plantations in relation to native host trees in Iran: evidence of host range expansion by local symbionts to distantly related host taxa.

Mycorrhiza 2013 Jan 17;23(1):11-9. Epub 2012 May 17.

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

Introduction of exotic plants change soil microbial communities which may have detrimental ecological consequences for ecosystems. In this study, we examined the community structure and species richness of ectomycorrhizal (EcM) fungi associated with exotic pine plantations in relation to adjacent native ectomycorrhizal trees in Iran to elucidate the symbiont exchange between distantly related hosts, i.e. Fagales (Fagaceae and Betulaceae) and Pinaceae. The combination of morphological and molecular identification approaches revealed that 84.6 % of species with more than one occurrence (at least once on pines) were shared with native trees and only 5.9 % were found exclusively on pine root tips. The community diversity of ectomycorrhizal fungi in the pine plantations adjacent to native EcM trees was comparable to their adjacent native trees, but the isolated plantations hosted relatively a species-poor community. Specific mycobionts of conifers were dominant in the isolated plantation while rarely found in the plantations adjacent to native EcM trees. These data demonstrate the importance of habitat isolation and dispersal limitation of EcM fungi in their potential of host range expansion. The great number of shared and possibly compatible symbiotic species between exotic Pinaceae and local Fagales (Fagaceae and Betulaceae) may reflect their evolutionary adaptations and/or ancestral compatibility with one another.
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http://dx.doi.org/10.1007/s00572-012-0445-zDOI Listing
January 2013

Towards global patterns in the diversity and community structure of ectomycorrhizal fungi.

Mol Ecol 2012 Sep 9;21(17):4160-70. Epub 2012 May 9.

Institute of Ecology and Earth Sciences, Tartu University, 14A Ravila, 50411 Tartu, Estonia.

Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next-generation sequencing techniques and relevant soil metadata.
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http://dx.doi.org/10.1111/j.1365-294X.2012.05602.xDOI Listing
September 2012

Regional and local patterns of ectomycorrhizal fungal diversity and community structure along an altitudinal gradient in the Hyrcanian forests of northern Iran.

New Phytol 2012 Jan 11;193(2):465-73. Epub 2011 Oct 11.

Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.

• Altitudinal gradients strongly affect the diversity of plants and animals, yet little is known about the altitudinal effects on the distribution of microorganisms, including ectomycorrhizal fungi. • By combining morphological and molecular identification methods, we addressed the relative effects of altitude, temperature, precipitation, host community and soil nutrient concentrations on species richness and community composition of ectomycorrhizal fungi in one of the last remaining temperate old-growth forests in Eurasia. • Molecular analyses revealed 367 species of ectomycorrhizal fungi along three altitudinal transects. Species richness declined monotonically with increasing altitude. Host species and altitude were the main drivers of the ectomycorrhizal fungal community composition at both the local and regional scales. The mean annual temperature and precipitation were strongly correlated with altitude and accounted for the observed patterns of richness and community. • The decline of ectomycorrhizal fungal richness with increasing altitude is consistent with the general altitudinal richness patterns of macroorganisms. Low environmental energy reduces the competitive ability of rare species and thus has a negative effect on the richness of ectomycorrhizal fungi. Because of multicollinearity with altitude, the direct effects of climatic variables and their seasonality warrant further investigation at the regional and continental scales.
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http://dx.doi.org/10.1111/j.1469-8137.2011.03927.xDOI Listing
January 2012