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A Higher-Level Phylogenetic Classification of the Fungi
mycological research 111 (2007) 509–547 available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/mycres A higher-level phylogenetic classification of the Fungi David S. HIBBETTa,*, Manfred BINDERa, Joseph F. BISCHOFFb, Meredith BLACKWELLc, Paul F. CANNONd, Ove E. ERIKSSONe, Sabine HUHNDORFf, Timothy JAMESg, Paul M. KIRKd, Robert LU¨ CKINGf, H. THORSTEN LUMBSCHf, Franc¸ois LUTZONIg, P. Brandon MATHENYa, David J. MCLAUGHLINh, Martha J. POWELLi, Scott REDHEAD j, Conrad L. SCHOCHk, Joseph W. SPATAFORAk, Joost A. STALPERSl, Rytas VILGALYSg, M. Catherine AIMEm, Andre´ APTROOTn, Robert BAUERo, Dominik BEGEROWp, Gerald L. BENNYq, Lisa A. CASTLEBURYm, Pedro W. CROUSl, Yu-Cheng DAIr, Walter GAMSl, David M. GEISERs, Gareth W. GRIFFITHt,Ce´cile GUEIDANg, David L. HAWKSWORTHu, Geir HESTMARKv, Kentaro HOSAKAw, Richard A. HUMBERx, Kevin D. HYDEy, Joseph E. IRONSIDEt, Urmas KO˜ LJALGz, Cletus P. KURTZMANaa, Karl-Henrik LARSSONab, Robert LICHTWARDTac, Joyce LONGCOREad, Jolanta MIA˛ DLIKOWSKAg, Andrew MILLERae, Jean-Marc MONCALVOaf, Sharon MOZLEY-STANDRIDGEag, Franz OBERWINKLERo, Erast PARMASTOah, Vale´rie REEBg, Jack D. ROGERSai, Claude ROUXaj, Leif RYVARDENak, Jose´ Paulo SAMPAIOal, Arthur SCHU¨ ßLERam, Junta SUGIYAMAan, R. Greg THORNao, Leif TIBELLap, Wendy A. UNTEREINERaq, Christopher WALKERar, Zheng WANGa, Alex WEIRas, Michael WEISSo, Merlin M. WHITEat, Katarina WINKAe, Yi-Jian YAOau, Ning ZHANGav aBiology Department, Clark University, Worcester, MA 01610, USA bNational Library of Medicine, National Center for Biotechnology Information, -
Abbreviations
Abbreviations AfDD Acriflavine direct detection AODC Acridine orange direct count ARA Arachidonic acid BPE Bleach plant effluent Bya Billion years ago CFU Colony forming unit DGGE Denaturing gradient gel electrophoresis DHA Docosahexaenoic acid DOC Dissolved organic carbon DOM Dissolved organic matter DSE Dark septate endophyte EN Ectoplasmic net EPA Eicosapentaenoic acid FITC Fluorescein isothiocyanate GPP Gross primary production ITS Internal transcribed spacer LDE Lignin-degrading enzyme LSU Large subunit MAA Mycosporine-like amino acid MBSF Metres below surface Mpa Megapascal MPN Most probable number MSW Molasses spent wash MUFA Monounsaturated fatty acid Mya Million years ago NPP Net primary production OMZ Oxygen minimum zone OUT Operational taxonomic unit PAH Polyaromatic hydrocarbon PCR Polymerase chain reaction © Springer International Publishing AG 2017 345 S. Raghukumar, Fungi in Coastal and Oceanic Marine Ecosystems, DOI 10.1007/978-3-319-54304-8 346 Abbreviations POC Particulate organic carbon POM Particulate organic matter PP Primary production Ppt Parts per thousand PUFA Polyunsaturated fatty acid QPX Quahog parasite unknown SAR Stramenopile Alveolate Rhizaria SFA Saturated fatty acid SSU Small subunit TEPS Transparent Extracellular Polysaccharides References Abdel-Waheb MA, El-Sharouny HM (2002) Ecology of subtropical mangrove fungi with empha- sis on Kandelia candel mycota. In: Kevin D (ed) Fungi in marine environments. Fungal Diversity Press, Hong Kong, pp 247–265 Abe F, Miura T, Nagahama T (2001) Isolation of highly copper-tolerant yeast, Cryptococcus sp., from the Japan Trench and the induction of superoxide dismutase activity by Cu2+. Biotechnol Lett 23:2027–2034 Abe F, Minegishi H, Miura T, Nagahama T, Usami R, Horikoshi K (2006) Characterization of cold- and high-pressure-active polygalacturonases from a deep-sea yeast, Cryptococcus liquefaciens strain N6. -
A Taxonomic Revision and Phylogenetic Reconstruction of the Jahnulales (Dothideomycetes), and the New Family Manglicolaceae
Fungal Diversity (2011) 51:163–188 DOI 10.1007/s13225-011-0138-5 A taxonomic revision and phylogenetic reconstruction of the Jahnulales (Dothideomycetes), and the new family Manglicolaceae Satinee Suetrong & Nattawut Boonyuen & Ka-Lai Pang & Jureerat Ueapattanakit & Anupong Klaysuban & Veera Sri-indrasutdhi & Somsak Sivichai & E. B. Gareth Jones Received: 30 August 2011 /Accepted: 30 September 2011 /Published online: 11 November 2011 # Kevin D. Hyde 2011 Abstract Genera assigned to the Jahnulales are mor- are rejected (Speiropsis irregularis, Xylomyces aquaticus, X. phologically diverse, especially in ascospores equipped elegans) while the phylogenetic placement of 6 Xylomyces,7 with or without appendages, sheaths or apical caps. They Speiropsis,1Brachiosphaera and 1 Manglicola require are predominantly freshwater fungi occurring on woody molecular data to confirm their placement in the order. substrata, with Manglicola guatemalensis, Xylomyces Sequences are derived from ex-holotype isolates and new chlamydosporus and X. rhizophorae the only species collections made in Thailand. Most taxa are included in the known from marine habitats. The order Jahnulales with family Aliquandostipitaceae and a new family Manglicola- 4 teleomorphic genera: Jahnula (15 species), Aliquandos- ceae is erected for the marine ascomycete Manglicola tipite (5), Megalohypha (1), Manglicola (2) and the guatemalensis with its large ascomata (1,100–1,750×290– anamorphic genera Brachiosphaera (2), Speiropsis (9), 640 μm), wide ostioles and ascospores that are fusiform, Xylomyces (8), amounting to a total of 42 species, is unequally one-septate with the apical cell larger than the reviewed and nomenclatural changes are proposed. Twenty turbinate basal cell and bear apical gelatinous appendages. species are treated at the molecular level, with 94 sequences, The genus Jahnula is polyphyletic grouping in three clades 13 of which are newly generated for this review. -
Molecular Phylogeny of Speiropsis Pedatospora
Mycosphere 7 (5): 679–686 (2016) ISSN 2077 7019 www.mycosphere.org Article Mycosphere Copyright © 2016 Online Edition Doi 10.5943/mycosphere/7/5/12 Molecular phylogeny of Speiropsis pedatospora Pratibha J1, Bhat DJ2 and Prabhugaonkar A3 1Department of Botany, Goa University, Goa 403 206, India. Email: [email protected] 2128/1-J, Azad Co-op Housing Society, Curca, Goa Velha 403 108, India. Email:[email protected] 3Botanical Survey of India, Eastern Regional Centre, Shillong 79300, India. Pratibha J, Bhat DJ, Prabhugaonkar A 2016 – Molecular phylogeny of Speiropsis pedatospora. Mycosphere 7 (5), 679–686, Doi 10.5943/mycosphere/7/5/12 Abstract Speiropsis pedatospora, an aero-aquatic fungus, was isolated from submerged plant litter in freshwater streams from India. Based on analysis of combined ITS and LSU sequence data, the species was positioned in the family Weisneriomycetaceae, as a sister group to Tubeufiales in the Dothideomycetes, instead of its current placement in the order Jahnulales. Speiropsis pedatospora, is the type species of the genus Speiropsis, is morphologically characterised by macronematous, mononematous, erect, branched conidiophores, polyblastic, denticulate, discrete conidiogeneous cells and long catenate conidia linearly joined by narrow, small isthmi. All asexual morph members of Weisneriomycetaceae with isthmospores are morphologically similar to the genus Speiropsis. Key words – aquatic fungi – Dothideomycetes – fungal diversity – phylogeny of asexual fungi – Western Ghats Introduction A natural classification of asexual morph taxa in families, orders and classes of Ascomycota and Basidiomycota, are presently being undertaken, by analysing molecular sequence data along with morphology, in order to provide a natural classification. Asexual morph are also being linked to their sexual genera by molecular data and major revisions of the ascomycota are taking place (Hyde et al. -
The Genera of Fungi Œ G6: <I>Arthrographis
VOLUME 6 DECEMBER 2020 Fungal Systematics and Evolution PAGES 1–24 doi.org/10.3114/fuse.2020.06.01 The Genera of Fungi – G6: Arthrographis, Kramasamuha, Melnikomyces, Thysanorea, and Verruconis M. Hernández-Restrepo1*, A. Giraldo1,2, R. van Doorn1, M.J. Wingfield3, J.Z. Groenewald1, R.W. Barreto4, A.A. Colmán4, P.S.C. Mansur4, P.W. Crous1,2,3 1Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands 2Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa 3Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa 4Departamento de Fitopatologia, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil *Corresponding author: [email protected] Key words: Abstract: The Genera of Fungi series, of which this is the sixth contribution, links type species of fungal genera to their DNA barcodes morphology and DNA sequence data. Five genera of microfungi are treated in this study, with new species introduced fungal systematics in Arthrographis, Melnikomyces, and Verruconis. The genus Thysanorea is emended and two new species and nine ITS combinations are proposed.Kramasamuha sibika, the type species of the genus, is provided with DNA sequence data LSU for first time and shown to be a member ofHelminthosphaeriaceae (Sordariomycetes). Aureoconidiella is introduced new taxa as a new genus representing a new lineage in the Dothideomycetes. Corresponding editor: U. Braun Editor-in-Chief EffectivelyProf. dr P.W. Crous, published Westerdijk Fungal online: Biodiversity 5 February Institute, P.O. -
Jahnula Species from North and Central America, Including Three New Species
Mycologia, 98(2), 2006, pp. 319–332. # 2006 by The Mycological Society of America, Lawrence, KS 66044-8897 Jahnula species from North and Central America, including three new species H.A. Raja1 MATERIALS AND METHODS C.A. Shearer Submerged woody debris was collected from lotic and lentic Department of Plant Biology, University of Illinois, freshwater habitats along latitudinal gradients in North Room 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, Illinois 61801 America, with sites in Alaska and Florida representing latitudinal extremes within North America. Tropical sam- ples also were collected in Costa Rica. Samples were placed in zippered plastic bags containing paper towels, returned Abstract: Three new species of loculoascomycetes to the laboratory, and incubated in plastic storage boxes collected from freshwater habitats in North America with moistened paper towels at ambient temperatures (ca. are described as new species of Jahnula ( Jahnulales, 24 C) under 12/12 h (light/dark) conditions. Water Dothideomycetes). All three share these morpholog- temperature, pH and latitude and longitude were measured ical features: hyaline to blackish translucent, mem- and recorded in the field and are presented in the branous ascomata with subtending, wide, septate specimen examined sections. brown, spreading hyphae; peridia composed of large Samples were examined with a dissecting microscope angular cells; hamathecium of septate pseudopara- immediately after collection and periodically over the sub- physes; 8-spored, clavate to cylindrical asci; and 1- sequent 12 mo. Crush mounts of ascomata were made in % septate, broadly fusiform, brown, multiguttulate distilled water that was replaced with glycerin (100 )orlactic acid (85%) containing azure A. India ink or aqueous nigrosin ascospores. -
Microbiological Insights Into Ecology and Taphonomy of Prehistoric Wetlands
Microbiological insights into ecology and taphonomy of prehistoric wetlands. By © 2018 Ashley A Klymiuk M.Sc. Systematics & Evolution, University of Alberta, 2011 B.Sc. Paleontology, University of Alberta, 2009 Submitted to the graduate degree program in Ecology & Evolutionary Biology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Chair: Benjamin Sikes Mark Holder Ari Jumpponen Leonard Krishtalka Jennifer Roberts Date Defended: 04 December 2018 ii The dissertation committee for Ashley A Klymiuk certifies that this is the approved version of the following dissertation: Microbiological insights into ecology and taphonomy of prehistoric wetlands. Chair: Benjamin Sikes Date Approved: 7 December 2018 iii Abstract In the course of this dissertation, I present investigations of the microbial constituents of fossil plants preserved at an anatomical level of detail, and detail the results of an ecological survey of root-endogenous fungi within the cosmopolitan emergent macrophyte, Typha. These studies together elucidate processes in the taphonomy of fossil plants. Biostratinomy is addressed through descriptions of saprotrophic communities within the Eocene Princeton Chert mire assemblage, and within a Carboniferous fern which previous studies had suggested contained fossilized actinobacteria. Re-investigation of the ‘actinobacteria’ suggests instead that the structures are disordered ferrous dolomites, raising implications for the contribution of sulfate- reducing bacteria to the early-diagenesis mineralization of plants preserved in carbonaceous concretions. The fossilized remains of saprotrophic and putatively endophytic fungi within roots of in-situ plants from the Princeton Chert also provide insight into early diagenesis. Some of the fungi described herein are preserved in several co-occurring developmental phases, providing evidence that early phases of silicification in this assemblage were rapid. -
Molecular Taxonomy, Origins and Evolution of Freshwater Ascomycetes
Fungal Diversity Molecular taxonomy, origins and evolution of freshwater ascomycetes Dhanasekaran Vijaykrishna*#, Rajesh Jeewon and Kevin D. Hyde* Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, University of Hong Kong, Pokfulam Road, Hong Kong SAR, PR China Vijaykrishna, D., Jeewon, R. and Hyde, K.D. (2006). Molecular taxonomy, origins and evolution of freshwater ascomycetes. Fungal Diversity 23: 351-390. Fungi are the most diverse and ecologically important group of eukaryotes with the majority occurring in terrestrial habitats. Even though fewer numbers have been isolated from freshwater habitats, fungi growing on submerged substrates exhibit great diversity, belonging to widely differing lineages. Fungal biodiversity surveys in the tropics have resulted in a marked increase in the numbers of fungi known from aquatic habitats. Furthermore, dominant fungi from aquatic habitats have been isolated only from this milieu. This paper reviews research that has been carried out on tropical lignicolous freshwater ascomycetes over the past decade. It illustrates their diversity and discusses their role in freshwater habitats. This review also questions, why certain ascomycetes are better adapted to freshwater habitats. Their ability to degrade waterlogged wood and superior dispersal/ attachment strategies give freshwater ascomycetes a competitive advantage in freshwater environments over their terrestrial counterparts. Theories regarding the origin of freshwater ascomycetes have largely been based on ecological findings. In this study, phylogenetic analysis is used to establish their evolutionary origins. Phylogenetic analysis of the small subunit ribosomal DNA (18S rDNA) sequences coupled with bayesian relaxed-clock methods are used to date the origin of freshwater fungi and also test their relationships with their terrestrial counterparts. -
Phylogenetic Placement of Bahusandhika, Cancellidium and Pseudoepicoccum (Asexual Ascomycota)
Phytotaxa 176 (1): 068–080 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ Article PHYTOTAXA Copyright © 2014 Magnolia Press ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.176.1.9 Phylogenetic placement of Bahusandhika, Cancellidium and Pseudoepicoccum (asexual Ascomycota) PRATIBHA, J.1, PRABHUGAONKAR, A.1,2, HYDE, K.D.3,4 & BHAT, D.J.1 1 Department of Botany, Goa University, Goa 403206, India 2 Nurture Earth R&D Pvt Ltd, MIT Campus, Aurangabad-431028, India; email: [email protected] 3 Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand 4 School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand Abstract Most hyphomycetous conidial fungi cannot be presently placed in a natural classification. They need recollecting and sequencing so that phylogenetic analysis can resolve their taxonomic affinities. The type species of the asexual genera, Bahusandhika, Cancellidium and Pseudoepicoccum were recollected, isolated in culture, and the ITS and LSU gene regions sequenced. The sequence data were analysed with reference data obtained through GenBank. The DNA sequence analyses shows that Bahusandhika indica has a close relationship with Berkleasmium in the order Pleosporales and Pseudoepicoccum cocos with Piedraia in Capnodiales; both are members of Dothideomycetes. Cancellidium applanatum forms a distinct lineage in the Sordariomycetes. Key words: anamorphic fungi, ITS, LSU, phylogeny Introduction Asexually reproducing ascomycetous fungi are ubiquitous in nature and worldwide in distribution, occurring from the tropics to the polar regions and from mountain tops to the deep oceans. These fungi colonize, multiply and survive in diverse habitats, such as water, soil, air, litter, dung, foam, live plants and animals, as saprobes, pathogens and mutualists. -
Molecular Taxonomy of Bambusicolous Fungi: Tetraplosphaeriaceae, a New Pleosporalean Family with Tetraploa-Like Anamorphs
available online at www.studiesinmycology.org StudieS in Mycology 64: 175–209. 2009. doi:10.3114/sim.2009.64.10 Molecular taxonomy of bambusicolous fungi: Tetraplosphaeriaceae, a new pleosporalean family with Tetraploa-like anamorphs K. Tanaka1*, K. Hirayama1, H. Yonezawa1, S. Hatakeyama1, Y. Harada1, T. Sano1, T. Shirouzu2 and T. Hosoya3 1Faculty of Agriculture & Life Sciences, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan; 2Fungus/Mushroom Resource and Research Center, Tottori University, Minami 4-101, Koyama, Tottori, Tottori 680-8553 Japan; 3National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan *Correspondence: Kazuaki Tanaka, [email protected] Abstract: A new pleosporalean family Tetraplosphaeriaceae is established to accommodate five new genera; 1) Tetraplosphaeria with small ascomata and anamorphs belonging to Tetraploa s. str., 2) Triplosphaeria characterised by hemispherical ascomata with rim-like side walls and anamorphs similar to Tetraploa but with three conidial setose appendages, 3) Polyplosphaeria with large ascomata surrounded by brown hyphae and anamorphs producing globose conidia with several setose appendages, 4) Pseudotetraploa, an anamorphic genus, having obpyriform conidia with pseudosepta and four to eight setose appendages, and 5) Quadricrura, an anamorphic genus, having globose conidia with one or two long setose appendages at the apex and four to five short setose appendages at the base. Fifteen new taxa in these genera mostly collected from bamboo are described and illustrated. They are linked by their Tetraploa s. l. anamorphs. To infer phylogenetic placement in the Pleosporales, analyses based on a combined dataset of small- and large-subunit nuclear ribosomal DNA (SSU+LSU nrDNA) was carried out. -
The Molecular Phylogeny of Freshwater Dothideomycetes
available online at www.studiesinmycology.org StudieS in Mycology 64: 145–153. 2009. doi:10.3114/sim.2009.64.08 The molecular phylogeny of freshwater Dothideomycetes C.A. Shearer1*, H.A. Raja1, A.N. Miller2, P. Nelson3, K. Tanaka4, K. Hirayama4, L. Marvanová5, K.D. Hyde6 and Y. Zhang7 1Department of Plant Biology, University of Illinois, 505 S. Goodwin Ave., Urbana, IL 61801, U.S.A.; 2Illinois Natural History Survey, University of Illinois, 1816 South Oak St., Champaign, IL, 61820, U.S.A.; 3University of Minnesota, Ecology, Evolution, and Behavior, 100 Ecology Building, St. Paul, MN 55108, U.S.A.; 4Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan; 5Czech Collection of Mircroorganisms, Institute of Experimental Biology, Faculty of Science, Masaryk University, Tvrdého 14, Brno CZ-602 00, Czech Republic; 6School of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai 57100, Thailand; 7Division of Microbiology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P.R. China *Correspondence: C.A. Shearer, [email protected] Abstract: The freshwater Dothideomycetes species are an ecological rather than taxonomic group and comprise approximately 178 meiosporic and mitosporic species. Due to convergent or parallel morphological adaptations to aquatic habitats, it is difficult to determine phylogenetic relationships among freshwater taxa and among freshwater, marine and terrestrial taxa based solely on morphology. We conducted molecular sequence-based phylogenetic analyses using nuclear ribosomal sequences (SSU and/or LSU) for 84 isolates of described and undescribed freshwater Dothideomycetes and 85 additional taxa representative of the major orders and families of Dothideomycetes. -
Palm Leaf Fungi in Portugal: Ecological, Morphological and Phylogenetic Approaches
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Palm leaf fungi in Portugal: ecological, morphological and phylogenetic approaches Diogo Rafael Santos Pereira Mestrado em Microbiologia Aplicada Dissertação orientada por: Alan John Lander Phillips Rogério Paulo de Andrade Tenreiro 2019 This Dissertation was fully performed at Lab Bugworkers | M&B-BioISI, Biosystems & Integrative Sciences Institute, under the direct supervision of Principal Investigator Alan John Lander Phillips Professor Rogério Paulo de Andrade Tenreiro was the internal supervisor designated in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon To my grandpa, our little old man Acknowledgments This dissertation would not have been possible without the support and commitment of all the people (direct or indirectly) involved and to whom I sincerely thank. Firstly, I would like to express my deepest appreciation to my supervisor, Professor Alan Phillips, for all his dedication, motivation and enthusiasm throughout this long year. I am grateful for always push me to my limits, squeeze the best from my interest in Mycology and letting me explore a new world of concepts and ideas. Your expertise, attentiveness and endless patience pushed me to be a better investigator, and hopefully a better mycologist. You made my MSc dissertation year be beyond better than everything I would expect it to be. Most of all, I want to thank you for believing in me as someone who would be able to achieve certain goals, even when I doubt it, and for guiding me towards them. Thank you for always teaching me, above all, to make the right question with the care and accuracy that Mycology demands, which is probably the most important lesson I have acquired from this dissertation year.