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Coastal Marine Habitats Harbor Novel Early-Diverging Fungal Diversity
Fungal Ecology 25 (2017) 1e13 Contents lists available at ScienceDirect Fungal Ecology journal homepage: www.elsevier.com/locate/funeco Coastal marine habitats harbor novel early-diverging fungal diversity * Kathryn T. Picard Department of Biology, Duke University, Durham, NC, 27708, USA article info abstract Article history: Despite nearly a century of study, the diversity of marine fungi remains poorly understood. Historical Received 12 September 2016 surveys utilizing microscopy or culture-dependent methods suggest that marine fungi are relatively Received in revised form species-poor, predominantly Dikarya, and localized to coastal habitats. However, the use of high- 20 October 2016 throughput sequencing technologies to characterize microbial communities has challenged traditional Accepted 27 October 2016 concepts of fungal diversity by revealing novel phylotypes from both terrestrial and aquatic habitats. Available online 23 November 2016 Here, I used ion semiconductor sequencing (Ion Torrent) of the ribosomal large subunit (LSU/28S) to Corresponding Editor: Felix Barlocher€ explore fungal diversity from water and sediment samples collected from four habitats in coastal North Carolina. The dominant taxa observed were Ascomycota and Chytridiomycota, though all fungal phyla Keywords: were represented. Diversity was highest in sand flats and wetland sediments, though benthic sediments Marine fungi harbored the highest proportion of novel sequences. Most sequences assigned to early-diverging fungal Ion torrent groups could not be assigned -
S41467-021-25308-W.Pdf
ARTICLE https://doi.org/10.1038/s41467-021-25308-w OPEN Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota ✉ ✉ Luis Javier Galindo 1 , Purificación López-García 1, Guifré Torruella1, Sergey Karpov2,3 & David Moreira 1 Compared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living fla- gellated stages (zoospores) remain poorly known and their phylogenetic position is often 1234567890():,; unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and San- chytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchy- trids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages. 1 Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France. 2 Zoological Institute, Russian Academy of Sciences, St. ✉ Petersburg, Russia. 3 St. -
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, -
Identification of Culture-Negative Fungi in Blood and Respiratory Samples
IDENTIFICATION OF CULTURE-NEGATIVE FUNGI IN BLOOD AND RESPIRATORY SAMPLES Farida P. Sidiq A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2014 Committee: Scott O. Rogers, Advisor W. Robert Midden Graduate Faculty Representative George Bullerjahn Raymond Larsen Vipaporn Phuntumart © 2014 Farida P. Sidiq All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Fungi were identified as early as the 1800’s as potential human pathogens, and have since been shown as being capable of causing disease in both immunocompetent and immunocompromised people. Clinical diagnosis of fungal infections has largely relied upon traditional microbiological culture techniques and examination of positive cultures and histopathological specimens utilizing microscopy. The first has been shown to be highly insensitive and prone to result in frequent false negatives. This is complicated by atypical phenotypes and organisms that are morphologically indistinguishable in tissues. Delays in diagnosis of fungal infections and inaccurate identification of infectious organisms contribute to increased morbidity and mortality in immunocompromised patients who exhibit increased vulnerability to opportunistic infection by normally nonpathogenic fungi. In this study we have retrospectively examined one-hundred culture negative whole blood samples and one-hundred culture negative respiratory samples obtained from the clinical microbiology lab at the University of Michigan Hospital in Ann Arbor, MI. Samples were obtained from randomized, heterogeneous patient populations collected between 2005 and 2006. Specimens were tested utilizing cetyltrimethylammonium bromide (CTAB) DNA extraction and polymerase chain reaction amplification of internal transcribed spacer (ITS) regions of ribosomal DNA utilizing panfungal ITS primers. -
Chytridiomycetes, Chytridiomycota)
VOLUME 5 JUNE 2020 Fungal Systematics and Evolution PAGES 17–38 doi.org/10.3114/fuse.2020.05.02 Taxonomic revision of the genus Zygorhizidium: Zygorhizidiales and Zygophlyctidales ord. nov. (Chytridiomycetes, Chytridiomycota) K. Seto1,2,3*, S. Van den Wyngaert4, Y. Degawa1, M. Kagami2,3 1Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294, Sugadaira-Kogen, Ueda, Nagano 386-2204, Japan 2Department of Environmental Science, Faculty of Science, Toho University, 2-2-1, Miyama, Funabashi, Chiba 274-8510, Japan 3Graduate School of Environment and Information Sciences, Yokohama National University, 79-7, Tokiwadai, Hodogaya, Yokohama, Kanagawa 240- 8502, Japan 4Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, D-16775 Stechlin, Germany *Corresponding author: [email protected] Key words: Abstract: During the last decade, the classification system of chytrids has dramatically changed based on zoospore Chytridiomycota ultrastructure and molecular phylogeny. In contrast to well-studied saprotrophic chytrids, most parasitic chytrids parasite have thus far been only morphologically described by light microscopy, hence they hold great potential for filling taxonomy some of the existing gaps in the current classification of chytrids. The genus Zygorhizidium is characterized by an zoospore ultrastructure operculate zoosporangium and a resting spore formed as a result of sexual reproduction in which a male thallus Zygophlyctis and female thallus fuse via a conjugation tube. All described species of Zygorhizidium are parasites of algae and Zygorhizidium their taxonomic positions remain to be resolved. Here, we examined morphology, zoospore ultrastructure, host specificity, and molecular phylogeny of seven cultures of Zygorhizidium spp. Based on thallus morphology and host specificity, one culture was identified as Z. -
Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases LÁSZLÓ G
Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases LÁSZLÓ G. NAGY,1 RENÁTA TÓTH,2 ENIKŐ KISS,1 JASON SLOT,3 ATTILA GÁCSER,2 and GÁBOR M. KOVÁCS4,5 1Synthetic and Systems Biology Unit, Institute of Biochemistry, HAS, Szeged, Hungary; 2Department of Microbiology, University of Szeged, Szeged, Hungary; 3Department of Plant Pathology, Ohio State University, Columbus, OH 43210; 4Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary; 5Plant Protection Institute, Center for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary ABSTRACT The fungal lineage is one of the three large provides an overview of some of the most important eukaryotic lineages that dominate terrestrial ecosystems. fungal traits, how they evolve, and what major genes They share a common ancestor with animals in the eukaryotic and gene families contribute to their development. The supergroup Opisthokonta and have a deeper common ancestry traits highlighted here represent just a sample of the with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among characteristics that have evolved in fungi, including po- all living organisms. This article provides an overview of some of larized multicellular growth, fruiting body development, the most important fungal traits, how they evolve, and what dimorphism, secondary metabolism, wood decay, and major genes and gene families contribute to their development. mycorrhizae. However, a great deal of other important The traits highlighted here represent just a sample of the traits also underlie the evolution of the taxonomically characteristics that have evolved in fungi, including polarized and phenotypically hyperdiverse fungal kingdom, which multicellular growth, fruiting body development, dimorphism, could fill up a volume on its own. -
Calabon MS, Hyde KD, Jones EBG, Chandrasiri S, Dong W, Fryar SC, Yang J, Luo ZL, Lu YZ, Bao DF, Boonmee S
Asian Journal of Mycology 3(1): 419–445 (2020) ISSN 2651-1339 www.asianjournalofmycology.org Article Doi 10.5943/ajom/3/1/14 www.freshwaterfungi.org, an online platform for the taxonomic classification of freshwater fungi Calabon MS1,2,3, Hyde KD1,2,3, Jones EBG3,5,6, Chandrasiri S1,2,3, Dong W1,3,4, Fryar SC7, Yang J1,2,3, Luo ZL8, Lu YZ9, Bao DF1,4 and Boonmee S1,2* 1Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand 2School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand 3Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand 4Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand 5Department of Botany and Microbiology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Kingdom of Saudi Arabia 633B St Edwards Road, Southsea, Hants., PO53DH, UK 7College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia 8College of Agriculture and Biological Sciences, Dali University, Dali 671003, People’s Republic of China 9School of Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, 550003, Guizhou, People’s Republic of China Calabon MS, Hyde KD, Jones EBG, Chandrasiri S, Dong W, Fryar SC, Yang J, Luo ZL, Lu YZ, Bao DF, Boonmee S. 2020 – www.freshwaterfungi.org, an online platform for the taxonomic classification of freshwater fungi. Asian Journal of Mycology 3(1), 419–445, Doi 10.5943/ajom/3/1/14 Abstract The number of extant freshwater fungi is rapidly increasing, and the published information of taxonomic data are scattered among different online journal archives. -
A Worldwide List of Endophytic Fungi with Notes on Ecology and Diversity
Mycosphere 10(1): 798–1079 (2019) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/10/1/19 A worldwide list of endophytic fungi with notes on ecology and diversity Rashmi M, Kushveer JS and Sarma VV* Fungal Biotechnology Lab, Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, Puducherry, India Rashmi M, Kushveer JS, Sarma VV 2019 – A worldwide list of endophytic fungi with notes on ecology and diversity. Mycosphere 10(1), 798–1079, Doi 10.5943/mycosphere/10/1/19 Abstract Endophytic fungi are symptomless internal inhabits of plant tissues. They are implicated in the production of antibiotic and other compounds of therapeutic importance. Ecologically they provide several benefits to plants, including protection from plant pathogens. There have been numerous studies on the biodiversity and ecology of endophytic fungi. Some taxa dominate and occur frequently when compared to others due to adaptations or capabilities to produce different primary and secondary metabolites. It is therefore of interest to examine different fungal species and major taxonomic groups to which these fungi belong for bioactive compound production. In the present paper a list of endophytes based on the available literature is reported. More than 800 genera have been reported worldwide. Dominant genera are Alternaria, Aspergillus, Colletotrichum, Fusarium, Penicillium, and Phoma. Most endophyte studies have been on angiosperms followed by gymnosperms. Among the different substrates, leaf endophytes have been studied and analyzed in more detail when compared to other parts. Most investigations are from Asian countries such as China, India, European countries such as Germany, Spain and the UK in addition to major contributions from Brazil and the USA. -
Comparative Genomics of Chytrid Fungi Reveal Insights Into the Obligate
www.nature.com/scientificreports OPEN Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and Received: 4 February 2019 Accepted: 31 May 2019 pathogenic lifestyle of Synchytrium Published: xx xx xxxx endobioticum Bart T. L. H. van de Vossenberg1,2, Sven Warris 1, Hai D. T. Nguyen3, Marga P. E. van Gent-Pelzer1, David L. Joly 4, Henri C. van de Geest1, Peter J. M. Bonants1, Donna S. Smith5, C. André Lévesque 3 & Theo A. J. van der Lee1 Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identifed S. endobioticum specifc candidate efectors that are associated with repeat-rich regions. These candidate efectors share a highly conserved motif, and show isolate specifc duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, refects characteristic biological diferences between the phyla, and shows commonalities in genomic features among pathogenic fungi. -
Toward a Fully Resolved Fungal Tree of Life
Annual Review of Microbiology Toward a Fully Resolved Fungal Tree of Life Timothy Y. James,1 Jason E. Stajich,2 Chris Todd Hittinger,3 and Antonis Rokas4 1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; email: [email protected] 2Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA; email: [email protected] 3Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science and Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, Wisconsin 53726, USA; email: [email protected] 4Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA; email: [email protected] Annu. Rev. Microbiol. 2020. 74:291–313 Keywords First published as a Review in Advance on deep phylogeny, phylogenomic inference, uncultured majority, July 13, 2020 classification, systematics The Annual Review of Microbiology is online at micro.annualreviews.org Abstract https://doi.org/10.1146/annurev-micro-022020- Access provided by Vanderbilt University on 06/28/21. For personal use only. In this review, we discuss the current status and future challenges for fully 051835 Annu. Rev. Microbiol. 2020.74:291-313. Downloaded from www.annualreviews.org elucidating the fungal tree of life. In the last 15 years, advances in genomic Copyright © 2020 by Annual Reviews. technologies have revolutionized fungal systematics, ushering the field into All rights reserved the phylogenomic era. This has made the unthinkable possible, namely ac- cess to the entire genetic record of all known extant taxa. -
High-Level Classification of the Fungi and a Tool for Evolutionary Ecological Analyses
Fungal Diversity (2018) 90:135–159 https://doi.org/10.1007/s13225-018-0401-0 (0123456789().,-volV)(0123456789().,-volV) High-level classification of the Fungi and a tool for evolutionary ecological analyses 1,2,3 4 1,2 3,5 Leho Tedersoo • Santiago Sa´nchez-Ramı´rez • Urmas Ko˜ ljalg • Mohammad Bahram • 6 6,7 8 5 1 Markus Do¨ ring • Dmitry Schigel • Tom May • Martin Ryberg • Kessy Abarenkov Received: 22 February 2018 / Accepted: 1 May 2018 / Published online: 16 May 2018 Ó The Author(s) 2018 Abstract High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomoph- thoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example -
GENERAL FEATURES of CHYTRIDIOMYCOTA Chytridiomycota, Also Known As Chytrids, Is a Division of Zoosporic Organisms in the Kingdom
References: Webster, J., & Weber, R. (2007). Introduction to fungi. Cambridge, UK: Cambridge University Press. GENERAL FEATURES OF CHYTRIDIOMYCOTA Chytridiomycota, also known as chytrids, is a division of zoosporic organisms in the kingdom Fungi. Members of the division occur mainly in aquatic or moist habitats where they live as parasites on plants, insects, or amphibians, while others are saprobes. Like other fungi, chytrids have chitin in their cell walls, but one group of chytrids has both cellulose and chitin in the cell wall. Most chytrids are unicellular; a few form multicellular organisms and hyphae, which have no septa between cells (coenocytic). They produce gametes and diploid zoospores that swim with the help of a single flagellum. Over 900 described chytrid species are currently exist. Sexual reproduction of most Chytridiomycota members is not known. Asexual reproduction occurs through the release of zoospores derived through mitosis. Sexual reproduction is common among members of the Monoblepharidomycetes. They practice a version of oogamy: the male is motile and the female is stationary. This is the first occurrence of oogamy in kingdom Fungi. HABITATS Zoospores require free water in which to swim many occur in aquatic habitats, also found in soil water. Many species are saprotrophic – grow on a variety of substrates, most are aerobic, some anaerobic. Some are parasitic on algae, other fungi, aquatic animals, some parasitic on higher plants (crops) SYSTEMATICS OF CHYTRIDIOMYCOTA Division: Chytridiomycota The division Chytridiomycota contains1 class and 5 orders, distinguished on basis of habitat, zoospore ultrastructure, other characterisitics. Class: Chytridiomycetes: It is the major class of the phylum Chytridiomycota, which includesa number of parasitic species.