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Fungal Systematics: Is a New Age to Some Fungal Taxonomists, the Changes Were Seismic11
Nature Reviews Microbiology | AOP, published online 3 January 2013; doi:10.1038/nrmicro2942 PERSPECTIVES Nomenclature for Algae, Fungi, and Plants ESSAY (ICN). To many scientists, these may seem like overdue, common-sense measures, but Fungal systematics: is a new age to some fungal taxonomists, the changes were seismic11. of enlightenment at hand? In the long run, a unitary nomenclature system for pleomorphic fungi, along with the other changes, will promote effective David S. Hibbett and John W. Taylor communication. In the short term, however, Abstract | Fungal taxonomists pursue a seemingly impossible quest: to discover the abandonment of dual nomenclature will require mycologists to work together and give names to all of the world’s mushrooms, moulds and yeasts. Taxonomists to resolve the correct names for large num‑ have a reputation for being traditionalists, but as we outline here, the community bers of fungi, including many economically has recently embraced the modernization of its nomenclatural rules by discarding important pathogens and industrial organ‑ the requirement for Latin descriptions, endorsing electronic publication and isms. Here, we consider the opportunities ending the dual system of nomenclature, which used different names for the sexual and challenges posed by the repeal of dual nomenclature and the parallels and con‑ and asexual phases of pleomorphic species. The next, and more difficult, step will trasts between nomenclatural practices for be to develop community standards for sequence-based classification. fungi and prokaryotes. We also explore the options for fungal taxonomy based on Taxonomists create the language of bio‑ efforts to classify taxa that are discovered environmental sequences and ask whether diversity, enabling communication about through metagenomics5. -
High Diversity of Fungi Recovered from the Roots of Mature Tanoak (Lithocarpus Densiflorus) in Northern California
1380 High diversity of fungi recovered from the roots of mature tanoak (Lithocarpus densiflorus)in northern California S.E. Bergemann and M. Garbelotto Abstract: We collected mature tanoak (Lithocarpus densiflorus (Hook. & Arn.) Rehder) roots from five stands to charac- terize the relative abundance and taxonomic richness of root-associated fungi. Fungi were identified using polymerase chain reaction (PCR), cloning, and sequencing of internal transcribed spacer (ITS) and 28S rDNA. A total of 382 cloned PCR inserts were successfully sequenced and then classified into 119 taxa. Of these taxa, 82 were basidiomycetes, 33 were ascomycetes, and 4 were zygomycetes. Thirty-one of the ascomycete sequences were identified as Cenococcum geo- philum Fr. with overall richness of 22 ITS types. Other ascomycetes that form mycorrhizal associations were identified in- cluding Wilcoxina and Tuber as well as endophytes such as Lachnum, Cadophora, Phialophora, and Phialocephela. The most abundant mycorrhizal groups were Russulaceae (Lactarius, Macowanites, Russula) and species in the Thelephorales (Bankera, Boletopsis, Hydnellum, Tomentella). Our study demonstrates that tanoak supports a high diversity of ectomycor- rhizal fungi with comparable species richness to that observed in Quercus root communities. Key words: Cenoccocum geophilum, community, dark septate endophytes, ectomycorrhiza, species richness. Re´sume´ : Les auteurs ont pre´leve´ des racines de Lithocarpus densiflorus (Hook. & Arn.) Rehder) dans cinq peuplements, afin de caracte´riser l’abondance relative et la richesse taxonomique des champignons associe´sa` ses racines. On a identifie´ les champignons a` l’aide du PCR, par clonage et se´quenc¸age de l’ITS et du 28S rADN. On a se´quence´ avec succe`s 382 segments clone´s par PCR avant de les classifier en 119 taxons. -
Porpomyces Submucidus (Hydnodontaceae, Basidiomycota), a New Species from Tropical China Based on Morphological and Molecular Evidence
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/283034971 Porpomyces submucidus (Hydnodontaceae, Basidiomycota), a new species from tropical China based on morphological and molecular evidence Article in Phytotaxa · October 2015 DOI: 10.11646/phytotaxa.230.1.5 CITATIONS READS 2 186 2 authors, including: Fang Wu Beijing Forestry University 73 PUBLICATIONS 838 CITATIONS SEE PROFILE All content following this page was uploaded by Fang Wu on 30 May 2018. The user has requested enhancement of the downloaded file. Phytotaxa 230 (1): 061–068 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ PHYTOTAXA Copyright © 2015 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.230.1.5 Porpomyces submucidus (Hydnodontaceae, Basidiomycota), a new species from tropical China based on morphological and molecular evidence FANG WU*, YUAN YUAN & CHANG-LIN ZHAO 1Institute of Microbiology, PO Box 61, Beijing Forestry University, Beijing 100083, China * Corresponding authors’ e-mails: [email protected] (FW) Abstract A new species is described from tropical China as Porpomyces submucidus on the basis of both morphological characters and molecular evidence. Phylogenetic analyse based on the ITS sequence, LSU sequence and the ITS+LSU sequence show that the new species belongs to Porpomyces and forms a distict clade as a sister group of Porpomyces mucidus. The fungus is characterized by thin, white to cream, resupinate basidiome with cottony to rhizomorphic margin, small pores (7–9 per mm), a monomitic hyphal structure with clamped generative hyphae, usually ampullated at most septa, and small, hyaline, thin-walled, ellipsoid basidiospores measuring 2.2–2.8 × 1.2–1.8 μm. -
The Resurgence of Mucormycosis in the Covid-19 Era – a Review
ISSN: 2687-8410 DOI: 10.33552/ACCS.2021.03.000551 Archives of Clinical Case Studies Mini Review Copyright © All rights are reserved by Kratika Mishra The Resurgence of Mucormycosis in the Covid-19 Era – A Review Amit Bhardwaj1, Kratika Mishra2*, Shivani Bhardwaj3, Anuj Bhardwaj4 1Department of Orthodontics and Dentofacial Orthopaedics, Modern Dental College and Research Centre, Indore, India 2Department of Orthodontics and Dentofacial Orthopaedics, Index Institute of Dental Sciences, Indore, Madhya Pradesh, India 3Department of Prosthodontics, College of Dental Sciences, Rau, Madhya Pradesh, India 4Department of Conservative Dentistry and Endodontics, College of Dental Sciences, India *Corresponding author: Received Date: June 7, 2021 Kratika Mishra, Department of Orthodontics and Published Date: June 25, 2021 Dentofacial Orthopaedics, Index Institute of Dental Sciences, Indore, Madhya Pradesh, India. Abstract Mucormycosis (MCM) is a life-threatening infection that carries high mortality rates with devastating disease symptoms and diverse clinical manifestations. This article briefly explains clinical manifestations and risk factors and focuses on putative virulence traits associated with mucormycosis, mainly in the group of diabetic ketoacidotic patients, immunocompromised patients. The diagnosis requires the combination of various clinical data and the isolation in culture of the fungus from clinical samples. Treatment of mucormycosis requires a rapid diagnosis, correction of predisposing factors, surgical resection, debridement and -
Major Clades of Agaricales: a Multilocus Phylogenetic Overview
Mycologia, 98(6), 2006, pp. 982–995. # 2006 by The Mycological Society of America, Lawrence, KS 66044-8897 Major clades of Agaricales: a multilocus phylogenetic overview P. Brandon Matheny1 Duur K. Aanen Judd M. Curtis Laboratory of Genetics, Arboretumlaan 4, 6703 BD, Biology Department, Clark University, 950 Main Street, Wageningen, The Netherlands Worcester, Massachusetts, 01610 Matthew DeNitis Vale´rie Hofstetter 127 Harrington Way, Worcester, Massachusetts 01604 Department of Biology, Box 90338, Duke University, Durham, North Carolina 27708 Graciela M. Daniele Instituto Multidisciplinario de Biologı´a Vegetal, M. Catherine Aime CONICET-Universidad Nacional de Co´rdoba, Casilla USDA-ARS, Systematic Botany and Mycology de Correo 495, 5000 Co´rdoba, Argentina Laboratory, Room 304, Building 011A, 10300 Baltimore Avenue, Beltsville, Maryland 20705-2350 Dennis E. Desjardin Department of Biology, San Francisco State University, Jean-Marc Moncalvo San Francisco, California 94132 Centre for Biodiversity and Conservation Biology, Royal Ontario Museum and Department of Botany, University Bradley R. Kropp of Toronto, Toronto, Ontario, M5S 2C6 Canada Department of Biology, Utah State University, Logan, Utah 84322 Zai-Wei Ge Zhu-Liang Yang Lorelei L. Norvell Kunming Institute of Botany, Chinese Academy of Pacific Northwest Mycology Service, 6720 NW Skyline Sciences, Kunming 650204, P.R. China Boulevard, Portland, Oregon 97229-1309 Jason C. Slot Andrew Parker Biology Department, Clark University, 950 Main Street, 127 Raven Way, Metaline Falls, Washington 99153- Worcester, Massachusetts, 01609 9720 Joseph F. Ammirati Else C. Vellinga University of Washington, Biology Department, Box Department of Plant and Microbial Biology, 111 355325, Seattle, Washington 98195 Koshland Hall, University of California, Berkeley, California 94720-3102 Timothy J. -
Resolving the Mortierellaceae Phylogeny Through Synthesis of Multi-Gene Phylogenetics and Phylogenomics
Lawrence Berkeley National Laboratory Recent Work Title Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Permalink https://escholarship.org/uc/item/25k8j699 Journal Fungal diversity, 104(1) ISSN 1560-2745 Authors Vandepol, Natalie Liber, Julian Desirò, Alessandro et al. Publication Date 2020-09-16 DOI 10.1007/s13225-020-00455-5 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Fungal Diversity https://doi.org/10.1007/s13225-020-00455-5 Resolving the Mortierellaceae phylogeny through synthesis of multi‑gene phylogenetics and phylogenomics Natalie Vandepol1 · Julian Liber2 · Alessandro Desirò3 · Hyunsoo Na4 · Megan Kennedy4 · Kerrie Barry4 · Igor V. Grigoriev4 · Andrew N. Miller5 · Kerry O’Donnell6 · Jason E. Stajich7 · Gregory Bonito1,3 Received: 17 February 2020 / Accepted: 25 July 2020 © MUSHROOM RESEARCH FOUNDATION 2020 Abstract Early eforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conficting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarifed, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierel- laceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequenc- ing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-efective means of generating a high-confdence phylogeny. -
Phylogenetic Relationships of Rhizoctonia Fungi Within the Cantharellales
fungal biology 120 (2016) 603e619 journal homepage: www.elsevier.com/locate/funbio Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales Dolores GONZALEZa,*, Marianela RODRIGUEZ-CARRESb, Teun BOEKHOUTc, Joost STALPERSc, Eiko E. KURAMAEd, Andreia K. NAKATANIe, Rytas VILGALYSf, Marc A. CUBETAb aInstituto de Ecologıa, A.C., Red de Biodiversidad y Sistematica, Carretera Antigua a Coatepec No. 351, El Haya, 91070 Xalapa, Veracruz, Mexico bDepartment of Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Campus Box 7251, Raleigh, NC 27695, USA cCBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands dDepartment of Microbial Ecology, Netherlands Institute of Ecology (NIOO/KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands eUNESP, Faculdade de Ci^encias Agronomicas,^ CP 237, 18603-970 Botucatu, SP, Brazil fDepartment of Biology, Duke University, Durham, NC 27708, USA article info abstract Article history: Phylogenetic relationships of Rhizoctonia fungi within the order Cantharellales were studied Received 2 January 2015 using sequence data from portions of the ribosomal DNA cluster regions ITS-LSU, rpb2, tef1, Received in revised form and atp6 for 50 taxa, and public sequence data from the rpb2 locus for 165 taxa. Data sets 1 January 2016 were analysed individually and combined using Maximum Parsimony, Maximum Likeli- Accepted 19 January 2016 hood, and Bayesian Phylogenetic Inference methods. All analyses supported the mono- Available online 29 January 2016 phyly of the family Ceratobasidiaceae, which comprises the genera Ceratobasidium and Corresponding Editor: Thanatephorus. Multi-locus analysis revealed 10 well-supported monophyletic groups that Joseph W. Spatafora were consistent with previous separation into anastomosis groups based on hyphal fusion criteria. -
Phylogenetic Classification of Trametes
TAXON 60 (6) • December 2011: 1567–1583 Justo & Hibbett • Phylogenetic classification of Trametes SYSTEMATICS AND PHYLOGENY Phylogenetic classification of Trametes (Basidiomycota, Polyporales) based on a five-marker dataset Alfredo Justo & David S. Hibbett Clark University, Biology Department, 950 Main St., Worcester, Massachusetts 01610, U.S.A. Author for correspondence: Alfredo Justo, [email protected] Abstract: The phylogeny of Trametes and related genera was studied using molecular data from ribosomal markers (nLSU, ITS) and protein-coding genes (RPB1, RPB2, TEF1-alpha) and consequences for the taxonomy and nomenclature of this group were considered. Separate datasets with rDNA data only, single datasets for each of the protein-coding genes, and a combined five-marker dataset were analyzed. Molecular analyses recover a strongly supported trametoid clade that includes most of Trametes species (including the type T. suaveolens, the T. versicolor group, and mainly tropical species such as T. maxima and T. cubensis) together with species of Lenzites and Pycnoporus and Coriolopsis polyzona. Our data confirm the positions of Trametes cervina (= Trametopsis cervina) in the phlebioid clade and of Trametes trogii (= Coriolopsis trogii) outside the trametoid clade, closely related to Coriolopsis gallica. The genus Coriolopsis, as currently defined, is polyphyletic, with the type species as part of the trametoid clade and at least two additional lineages occurring in the core polyporoid clade. In view of these results the use of a single generic name (Trametes) for the trametoid clade is considered to be the best taxonomic and nomenclatural option as the morphological concept of Trametes would remain almost unchanged, few new nomenclatural combinations would be necessary, and the classification of additional species (i.e., not yet described and/or sampled for mo- lecular data) in Trametes based on morphological characters alone will still be possible. -
Fungal Community Structural and Functional Responses to Disturbances in a North Temperate Forest
Fungal Community Structural and Functional Responses to Disturbances in a North Temperate Forest By Buck Tanner Castillo A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Ecology and Evolutionary Biology) in The University of Michigan 2020 Doctoral Committee: Professor Timothy Y. James, Co-Chair Professor Knute J. Nadelhoffer, Co-Chair Associate Professor Vincent Denef Professor Donald R. Zak Buck T. Castillo [email protected] ORCID ID: 0000-0002-5426-3821 ©Buck T. Castillo 2020 Dedication To my mother: Melinda Kathryn Fry For always instilling in me a sense of wonder and curiosity. For all the adventures down dirt roads and imaginations of centuries past. For all your love, Thank you. ii Acknowledgements Many people have guided, encouraged and inspired me throughout this process. I am eternally grateful for this network of support. First, I must thank my advisors, Knute and Tim for all of the excellent advice, unfaltering confidence, and high expectations they continually provided and set for me. My committee members, Don Zak and Vincent Denef, have been fantastic sources of insight, inspiration, and encouragement. Thank you all so much for your time, knowledge, and most of all for always making me believe in myself. A special thanks to two incredible researchers that were always great mentors who became even better friends: Luke Nave and Jim Le Moine. Jim Le Moine has taught me so much about being a critical thinker and was always more than generous with his time, insight, and advice. Thank you, Jim, for midnight walks through bugcamp and full bowls of delicious popping corn. -
An Ectomycorrhizal Thelephoroid Fungus of Malaysian Dipterocarp Seedlings
Journal of Tropical Forest Science 22(4): 355–363 (2010) Lee SS et al. AN ECTOMYCORRHIZAL THELEPHOROID FUNGUS OF MALAYSIAN DIPTEROCARP SEEDLINGS Lee SS*, Thi BK & Patahayah M Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia Received April 2010 LEE SS, THI BK & PATAHAYAH M. 2010. An ectomycorrhizal thelephoroid fungus of Malaysian dipterocarp seedlings. The ectomycorrhizal Dipterocarpaceae are among the most well-known trees in the tropics and this is the most important family of timber trees in Malaysia and South-East Asia. Recent studies and molecular data reveal that members of the Thelephoraceae are common ectomycorrhizal fungi associated with the Dipterocarpaceae. The suspected thelephoroid fungus FP160 was isolated from ectomycorrhizal roots of a Shorea parvifolia (Dipterocarpaceae) seedling and kept in the Forest Research Institute Malaysia (FRIM) culture collection. In subsequent inoculation experiments it was able to form morphologically similar ectomycorrhizas with seedlings of two other dipterocarps, namely, Hopea odorata and S. leprosula, and the exotic fast-growing legume, Acacia mangium. A taxonomic identity of this fungus would benefit its possible use in inoculation and planting programmes. This information is also important to expand our limited knowledge of Malaysian mycodiversity. In this paper the morphological characteristics of the ectomycorrhizas formed by FP160 with H. odorata and A. mangium are described and the fungus identified using molecular methods as a member of the family Thelephoraceae, most likely a Tomentella sp. It was not possible to identify the fungus more precisely due to the limited number of sequences available for tropical Thelephoraceae in the public databases. Keywords: Acacia mangium, Dipterocarpaceae, ectomycorrhizas, ITS, Thelephoraceae LEE SS, THI BK & PATAHAYAH M. -
Fruiting Body Form, Not Nutritional Mode, Is the Major Driver of Diversification in Mushroom-Forming Fungi
Fruiting body form, not nutritional mode, is the major driver of diversification in mushroom-forming fungi Marisol Sánchez-Garcíaa,b, Martin Rybergc, Faheema Kalsoom Khanc, Torda Vargad, László G. Nagyd, and David S. Hibbetta,1 aBiology Department, Clark University, Worcester, MA 01610; bUppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75005 Uppsala, Sweden; cDepartment of Organismal Biology, Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden; and dSynthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, 6726 Szeged, Hungary Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved October 16, 2020 (received for review December 22, 2019) With ∼36,000 described species, Agaricomycetes are among the and the evolution of enclosed spore-bearing structures. It has most successful groups of Fungi. Agaricomycetes display great di- been hypothesized that the loss of ballistospory is irreversible versity in fruiting body forms and nutritional modes. Most have because it involves a complex suite of anatomical features gen- pileate-stipitate fruiting bodies (with a cap and stalk), but the erating a “surface tension catapult” (8, 11). The effect of gas- group also contains crust-like resupinate fungi, polypores, coral teroid fruiting body forms on diversification rates has been fungi, and gasteroid forms (e.g., puffballs and stinkhorns). Some assessed in Sclerodermatineae, Boletales, Phallomycetidae, and Agaricomycetes enter into ectomycorrhizal symbioses with plants, Lycoperdaceae, where it was found that lineages with this type of while others are decayers (saprotrophs) or pathogens. We constructed morphology have diversified at higher rates than nongasteroid a megaphylogeny of 8,400 species and used it to test the following lineages (12). -
New Species and New Records of Clavariaceae (Agaricales) from Brazil
Phytotaxa 253 (1): 001–026 ISSN 1179-3155 (print edition) http://www.mapress.com/j/pt/ PHYTOTAXA Copyright © 2016 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.253.1.1 New species and new records of Clavariaceae (Agaricales) from Brazil ARIADNE N. M. FURTADO1*, PABLO P. DANIËLS2 & MARIA ALICE NEVES1 1Laboratório de Micologia−MICOLAB, PPG-FAP, Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, Brazil. 2Department of Botany, Ecology and Plant Physiology, Ed. Celestino Mutis, 3a pta. Campus Rabanales, University of Córdoba. 14071 Córdoba, Spain. *Corresponding author: Email: [email protected] Phone: +55 83 996110326 ABSTRACT Fourteen species in three genera of Clavariaceae from the Atlantic Forest of Brazil are described (six Clavaria, seven Cla- vulinopsis and one Ramariopsis). Clavaria diverticulata, Clavulinopsis dimorphica and Clavulinopsis imperata are new species, and Clavaria gibbsiae, Clavaria fumosa and Clavulinopsis helvola are reported for the first time for the country. Illustrations of the basidiomata and the microstructures are provided for all taxa, as well as SEM images of ornamented basidiospores which occur in Clavulinopsis helvola and Ramariopsis kunzei. A key to the Clavariaceae of Brazil is also included. Key words: clavarioid; morphology; taxonomy Introduction Clavariaceae Chevall. (Agaricales) comprises species with various types of basidiomata, including clavate, coralloid, resupinate, pendant-hydnoid and hygrophoroid forms (Hibbett & Thorn 2001, Birkebak et al. 2013). The family was first proposed to accommodate mostly saprophytic club and coral-like fungi that were previously placed in Clavaria Vaill. ex. L., including species that are now in other genera and families, such as Clavulina J.Schröt.