DOCSLIB.ORG

Comparative Genomics of Biotechnologically Important Yeasts

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Comparative Genomics of Biotechnologically Important Yeasts Comparative genomics of biotechnologically important yeasts Robert Rileya, Sajeet Haridasa, Kenneth H. Wolfeb, Mariana R. Lopesc,d, Chris Todd Hittingerc,e, Markus Gökerf, Asaf A. Salamova, Jennifer H. Wisecaverg, Tanya M. Longh,i, Christopher H. Calveyj, Andrea L. Aertsa, Kerrie W. Barrya, Cindy Choia, Alicia Cluma, Aisling Y. Coughlanb, Shweta Deshpandea, Alexander P. Douglassb, Sara J. Hansonb, Hans-Peter Klenkf,k, Kurt M. LaButtia, Alla Lapidusa,1, Erika A. Lindquista, Anna M. Lipzena, Jan P. Meier-Kolthofff, Robin A. Ohma,2, Robert P. Otillara, Jasmyn L. Pangilinana, Yi Penga, Antonis Rokasg, Carlos A. Rosad, Carmen Scheunerf, Andriy A. Sibirnyl,m, Jason C. Slotn, J. Benjamin Stielowf,o, Hui Suna, Cletus P. Kurtzmanp, Meredith Blackwellq,r, Igor V. Grigorieva,3, and Thomas W. Jeffriesh,3 aDepartment of Energy Joint Genome Institute, Walnut Creek, CA 94598; bUniversity College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland; cLaboratory of Genetics, Genetics/Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706; dDepartamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil; eDepartment of Energy Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI 53726; fDeutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany; gDepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37235; hDepartment of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706; iUS Department of Agriculture Forest Products Laboratory, Madison, WI 53726; jXylome Corporation, Madison, WI 53719; kSchool of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; lDepartment of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv 79005, Ukraine; mDepartment of Biotechnology and Microbiology, University of Rzeszow, Rzeszow 35-601, Poland; nDepartment of Plant Pathology, Ohio State University, Columbus, OH 43210; oCentraalbureau voor Schimmelcultures Fungal Biodiversity Centre, Royal Netherlands Academy of Arts and Sciences, 3508 AD, Utrecht, The Netherlands; pAgricultural Research Service, National Center for Agricultural Utilization Research, US Department of Agriculture, Peoria, IL 61604; qDepartment of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803; and rDepartment of Biological Sciences, University of South Carolina, Columbia, SC 29208 Edited by Chris R. Somerville, University of California, Berkeley, CA, and approved July 11, 2016 (received for review March 10, 2016) Ascomycete yeasts are metabolically diverse, with great potential for resistant to viruses. Their unicellular form is easy to cultivate, MICROBIOLOGY biotechnology. Here, we report the comparative genome analysis of scale up, and harvest. The objective of this study was, therefore, 29 taxonomically and biotechnologically important yeasts, including to put yeasts with diverse biotechnological applications in a 16 newly sequenced. We identify a genetic code change, CUG-Ala, in phylogenomic context and relate their physiologies to genomic Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such Significance as L-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode The highly diverse Ascomycete yeasts have enormous bio- many pathways of interest. Genomics can predict some biochemical technological potential. Collectively, these yeasts convert a broad traits precisely, but the genomic basis of others, such as xylose uti- range of substrates into useful compounds, such as ethanol, lization, remains unresolved. Our data also provide insight into early lipids, and vitamins, and can grow in extremes of temperature, evolution of ascomycetes. We document the loss of H3K9me2/3 het- salinity, and pH. We compared 29 yeast genomes with the goal erochromatin, the origin of ascomycete mating-type switching, and of correlating genetics to useful traits. In one rare species, we panascomycete synteny at the MAT locus. These data and analyses discovered a genetic code that translates CUG codons to alanine will facilitate the engineering of efficient biosynthetic and degrada- rather than canonical leucine. Genome comparison enabled cor- tive pathways and gateways for genomic manipulation. relation of genes to useful metabolic properties and showed the synteny of the mating-type locus to be conserved over a billion genomics | bioenergy | biotechnological yeasts | genetic code | years of evolution. Our study provides a roadmap for future microbiology biotechnological exploitations. Author contributions: A.L., C.P.K., M.B., I.V.G., and T.W.J. designed research; T.M.L., C.H.C., easts are fungi that reproduce asexually by budding or fission C.C., A.Y.C., S.D., S.J.H., H.-P.K., Y.P., A.A. Sibirny, J.B.S., C.P.K., and T.W.J. performed Yand sexually without multicellular fruiting bodies (1, 2). research; C.H.C. contributed new reagents/analytic tools; R.R., S.H., K.H.W., M.R.L., C.T.H., Their unicellular, largely free-living lifestyle has evolved several M.G., A.A. Salamov, J.H.W., A.L.A., K.W.B., A.C., A.P.D., K.M.L., A.L., E.A.L., A.M.L., J.P.M.-K., times (3). Despite morphological similarities, yeasts constitute over R.A.O., R.P.O., J.L.P., A.R., C.A.R., C.S., J.C.S., H.S., C.P.K., I.V.G., and T.W.J. analyzed data; R.R., S.H., K.H.W., C.T.H., M.G., C.P.K., M.B., I.V.G., and T.W.J. wrote the paper; and K.W.B., C.P.K., 1,500 known species that inhabit many specialized environmental M.B., I.V.G., and T.W.J. coordinated the project. niches and associations, including virtually all varieties of fruits and Conflict of interest statement: C.H.C. and T.W.J. are employees of Xylome Corporation, flowers, plant surfaces and exudates, insects and other inverte- which is developing nonconventional yeasts for biotechnological applications. brates, birds, mammals, and highly diverse soils (4). Biochemical This article is a PNAS Direct Submission. — and genomic studies of the model yeast Saccharomyces cerevisiae Data deposition: The sequences reported in this paper have been deposited in the GenBank essential for making bread, beer, and wine—have established much database (accession nos. LWKO00000000, LYME00000000, LXTC00000000, LYBQ00000000, of our understanding of eukaryotic biology. However, in many ways, LYBR00000000, LWUO00000000, LSKT00000000, LTAD00000000, LXPE00000000, S. cerevisiae is an oddity among the yeasts, and many important AECK00000000, LSGR00000000, LXPB00000000, LZCH00000000, AEHA00000000, AEUO00000000,andLWUN00000000). biotechnological applications and highly divergent physiologi- 1Present address: Center for Algorithmic Biotechnology, St. Petersburg State University, cal capabilities of lesser-known yeast species have not been fully St. Petersburg 199004, Russia. exploited (5). Various species can grow on methanol or n-alkanes 2Present address: Microbiology, Department of Biology, Utrecht University, 3508, Utrecht, as sole carbon and energy sources, overproduce vitamins and The Netherlands. lipids, thrive under acidic conditions, and ferment unconventional 3To whom correspondence may be addressed. Email: [email protected] or twjeffri@ carbon sources. Many features of yeasts make them ideal platforms wisc.edu. for biotechnological processes. Their thick cell walls help them This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. survive osmotic shock, and in contrast to bacteria, they are 1073/pnas.1603941113/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1603941113 PNAS Early Edition | 1of6 Downloaded by guest on October 1, 2021 features, so that their useful properties may be developed through which may lower rates of leucylation (10), an Ser identity element genetic techniques. Backgrounds on 16 yeasts are given in in the variable loop, and a G discriminator base. Most CUG-Ser SI Appendix. clade species contained all three serylation features in their predicted tRNACAGs, indicating translation of CUG to Ser (SI Appendix, Results Fig. S7A). However, in the most basal taxa of this clade, not all of Organism Phylogeny. Genomes were sequenced and assembled as the features are present: M. bicuspidata lackstheSeridentityele- described in Materials and Methods (SI Appendix, Table S1). ment, and Babjeviella inositovora lacks the discriminator base. This Ser Using the predicted proteomes (SI Appendix, Fig. S1 and Table finding may reflect stepwise accumulation of tRNACAG features S2) of these plus an additional 13 ascomycete yeasts and 9 fungal in the evolution of alternative CUG translation. Species branching outgroups, we generated three phylogenomic data matrices: deeper in the tree do not show any of the three features. “full” (7,297 genes with four or more sequences), “MARE” To investigate CUG translation beyond CUG-Ser, we analyzed (1,559 genes from the full set filtered for informative quality), multiple alignments of 700 orthologous groups of proteins (SI and “core” (418 genes present in all organisms). The MARE-filtered Appendix). For each yeast, we identified its CUG-encoded positions supermatrix tree (6, 7) is shown (Fig. 1). The full supermatrix and
Load more

Recommended publications
  • The Role and Use of Non-Saccharomyces Yeasts in Wine Production
    The Role and Use of Non-Saccharomyces Yeasts in Wine Production N.P. Jolly1*, O.P.H. Augustyn1 and I.S. Pretorius2** (1) ARC Infruitec-Nietvoorbij***, Private Bag X5026, 7599 Stellenbosch, South Africa. (2) Institute for Wine Biotechnology, Department of Viticulture & Oenology, Stellenbosch University, Private Bag X1, 7602 Matieland (Stellenbosch), South Africa. Submitted for publication: September 2005 Accepted for publication: April 2006 Key words: Non-Saccharomyces, yeasts, vineyards, cellars, fermentation, wine. The contribution by the numerous grape-must-associated non-Saccharomyces yeasts to wine fermentation has been debated extensively. These yeasts, naturally present in all wine fermentations, are metabolically active and their metabolites can impact on wine quality. Although often seen as a source of microbial spoilage, there is substantial contrary evidence pointing to a positive contribution by these yeasts. The role of non-Saccharomyces yeasts in wine fermentation is therefore receiving increasing attention by wine microbiologists in Old and New World wine producing countries. Species that have been investigated for wine production thus far include those from the Candida, Kloeckera, Hanseniaspora, Zygosaccharomyces, Schizosaccharomyces, Torulaspora, Brettanomyces, Saccharomycodes, Pichia and Williopsis genera. In this review the use and role of non-Saccharomyces yeast in wine production is presented and research trends are discussed. INTRODUCTION roles of the numerous non-Saccharomyces yeasts normally asso- ciated with grape must and wine. These yeasts, naturally present Wine is the product of a complex biological and biochemical in all wine fermentations to a greater or lesser extent, are meta- interaction between grapes (grape juice) and different microor- bolically active and their metabolites can impact on wine quality.
    [Show full text]
  • Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)
    | YEASTBOOK GENOME ORGANIZATION AND INTEGRITY Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina) Bernard A. Dujon*,†,1 and Edward J. Louis‡,§ *Department Genomes and Genetics, Institut Pasteur, Centre National de la Recherche Scientifique UMR3525, 75724-CEDEX15 Paris, France, †University Pierre and Marie Curie UFR927, 75005 Paris, France, ‡Centre for Genetic Architecture of Complex Traits, and xDepartment of Genetics, University of Leicester, LE1 7RH, United Kingdom ORCID ID: 0000-0003-1157-3608 (E.J.L.) ABSTRACT Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs.
    [Show full text]
  • 42 Genome Scale Model Reconstruction of the Methylotrophic
    GENOME SCALE MODEL RECONSTRUCTION OF THE METHYLOTROPHIC YEAST OGATAEA POLYMORPHA Simone Schmitz, RWTH Aachen University, Germany [email protected] Ulf W. Liebal, RWTH Aachen University, Germany Aarthi Ravikrishnan, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences; Institute of Technology Madras, India Constantin V.L. Schedel, RWTH Aachen University, Germany Lars M. Blank, RWTH Aachen University, Germany Birgitta E. Ebert, RWTH Aachen University, Germany Key words: Ogataea (Hansenula) polymorpha, metabolic model, phenotype microarray experiments, methylotrophic yeast Ogataea polymorpha is a thermotolerant, methylotrophic yeast with significant industrial applications. It is a promising host to generate platform chemicals from methanol, derived e.g. from carbon capture and utilization streams. Full development of the organism into a production strain requires additional strain design, supported by metabolic modeling on the basis of a genome-scale metabolic model. However, to date, no genome-scale metabolic model is available for O. polymorpha. To overcome this limitation, we used a published reconstruction of the closely related yeast Pichia pastoris as reference and corrected reactions based on KEGG annotations. Additionally, we conducted phenotype microarray experiments to test O. polymorpha’s metabolic capabilities to grown on or respire 192 different carbon sources. Over three-quarter of the substrate usage was correctly reproduced by the model. However, O. polymorpha failed to metabolize eight substrates and gained 38 new substrates compared to the P. pastoris reference model. To enable the usage of these compounds, metabolic pathways were inferred from literature and database searches and potential enzymes and genes assigned by conducting BLAST searches. To facilitate strain engineering and identify beneficial mutants, gene-protein-reaction relationships need to be included in the model.
    [Show full text]
  • Phylogenetic Circumscription of Saccharomyces, Kluyveromyces
    FEMS Yeast Research 4 (2003) 233^245 www.fems-microbiology.org Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora Cletus P. Kurtzman à Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University Street, Peoria, IL 61604, USA Received 22 April 2003; received in revised form 23 June 2003; accepted 25 June 2003 First published online Abstract Genera currently assigned to the Saccharomycetaceae have been defined from phenotype, but this classification does not fully correspond with species groupings determined from phylogenetic analysis of gene sequences. The multigene sequence analysis of Kurtzman and Robnett [FEMS Yeast Res. 3 (2003) 417^432] resolved the family Saccharomycetaceae into 11 well-supported clades. In the present study, the taxonomy of the Saccharomyctaceae is evaluated from the perspective of the multigene sequence analysis, which has resulted in reassignment of some species among currently accepted genera, and the proposal of the following five new genera: Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. ß 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. Keywords: Saccharomyces; Kluyveromyces; New ascosporic yeast genera; Molecular systematics; Multigene phylogeny 1. Introduction support the maintenance of three distinct genera. Yarrow [8^10] revived the concept of three genera and separated The name Saccharomyces was proposed for bread and Torulaspora and Zygosaccharomyces from Saccharomyces, beer yeasts by Meyen in 1838 [1], but it was Reess in 1870 although species assignments were often di⁄cult.
    [Show full text]
  • Oxylipin Distribution in Eremothecium
    1 Oxylipin distribution in Eremothecium by Ntsoaki Joyce Leeuw Submitted in accordance with the requirements for the degree Magister Scientiae in the Department of Microbial, Biochemical and Food Biotechnology Faculty of Natural and Agricultural Sciences University of the Free State Bloemfontein South Africa Supervisor: Prof J.L.F. Kock Co- supervisors: Dr C.H. Pohl Prof P.W.J. Van Wyk November 2006 2 This dissertation is dedicated to the following people: My mother (Nkotseng Leeuw) My brother (Kabelo Leeuw) My cousins (Bafokeng, Lebohang, Mami, Thabang and Rorisang) Mr. Eugean Malebo 3 ACKNOWLEDGEMENTS I wish to thank and acknowledge the following: ) God, to You be the glory for the things You have done in my life. ) My family (especially my mom) – for always being there for me when I’m in need. ) Prof. J.L.F Kock for his patience, constructive criticisms and guidance during the course of this study. ) Dr. C.H. Pohl for her encouragement and assistance in the writing up of this dissertation. ) Mr. P.J. Botes for assistance with the GC-MS. ) Prof. P.W.J. Van Wyk and Miss B. Janecke for assistance with the CLSM and SEM. ) My fellow colleagues (especially Chantel and Desmond) for their assistance, support and encouragement. ) Mr. Eugean Malebo for always being there when I needed you. 4 CONTENTS Page Title page I Acknowledgements II Contents III CHAPTER 1 Introduction 1.1 Motivation 2 1.2 Definition and classification of yeasts 3 1.3 Classification of Eremothecium and related genera 5 1.4 Pathogenicity 12 1.5 Oxylipins 13 1.5.1 Definition
    [Show full text]
  • Candida Albicans from Wikipedia, the Free Encyclopedia
    Candida albicans From Wikipedia, the free encyclopedia Candida albicans is a type of yeast that is a common member of the human gut flora. It does not proliferate outside the human body.[4] It is Candida albicans detected in the gastrointestinal tract and mouth in 40-60% of healthy adults.[5][6] It is usually a commensal organism, but can become pathogenic in immunocompromised individuals under a variety of conditions.[6][7] It is one of the few species of the Candida genus that causes the human infection candidiasis, which results from an overgrowth of the fungus.[6][7] Candidiasis is for example often observed in HIV-infected patients.[8] C. albicans is the most common fungal species isolated from biofilms either formed on (permanent) implanted medical devices or on human Candida albicans visualised using [9][10] tissue. C. albicans, together with C. tropicalis, C. parapsilosis scanning electron microscopy. Note the and C. glabrata, is responsible for 50–90% of all cases of candidiasis in abundant hypal mass. humans.[7][11][12] A mortality rate of 40% has been reported for patients with systemic candidiasis due to C. albicans.[13] Estimates Scientific classification range from 2800 to 11200 deaths caused annually in the USA due to C. Kingdom: Fungi albicans causes candidiasis.[14] Division: Ascomycota C. albicans is commonly used as a model organism for biology. It is generally referred to as a dimorphic fungus since it grows both as yeast Class: Saccharomycetes and filamentous cells. However it has several different morphological Order: Saccharomycetales phenotypes. C. albicans was for a long time considered an obligate diploid organism without a haploid stage.
    [Show full text]
  • Pathogenicity Classification of Fungi Status December 2014 (CGM/141218-03)
    Classification of Organisms: Pathogenicity classification of fungi Status December 2014 (CGM/141218-03) COGEM advice CGM/141218-03 Pathogenicity classification of fungi COGEM advice CGM/141218-03 Dutch Regulations Genetically Modified Organisms In the Decree on Genetically Modified Organisms (GMO Decree) and its accompanying more detailed Regulations (GMO Regulations) genetically modified micro-organisms are grouped in four pathogenicity classes, ranging from the lowest pathogenicity Class 1 to the highest Class 4.1 The pathogenicity classifications are used to determine the containment level for working in laboratories with GMOs. A micro-organism of Class 1 should at least comply with one of the following conditions: a) the micro-organism does not belong to a species of which representatives are known to be pathogenic for humans, animals or plants, b) the micro-organism has a long history of safe use under conditions without specific containment measures, c) the micro-organism belongs to a species that includes representatives of class 2, 3 or 4, but the particular strain does not contain genetic material that is responsible for the virulence, d) the micro-organism has been shown to be non-virulent through adequate tests. A micro-organism is grouped in Class 2 when it can cause a disease in humans or animals whereby it is unlikely to spread within the population while an effective prophylaxis, treatment or control strategy exists, as well as an organism that can cause a disease in plants. A micro-organism is grouped in Class 3 when it can cause a serious disease in humans or animals whereby it is likely to spread within the population while an effective prophylaxis, treatment or control strategy exists.
    [Show full text]
  • Brettanomyces Spoilage: Friend Or Foe?
    Microbial Faults Trevor Phister, PhD Assistant Professor Overview • Wine microbiology • Microbial faults – Brettanomyces – Lactic acid bacteria – Cork Taint • Controlling microbial faults – Sanitation – Quality programs Saccharomyces cerevisiae Saccharomyces cerevisiae (Piskur et al 2006) Does Not Always Work The Wine Fermentation OD ETOH Yeasts Bacteria • Metschnikowia sp. • acetic acid bacteria • Pichia sp. • lactic acid bacteria • Candida sp. • Kluveromyces sp. Molds • Hanseniaspora sp. Sugar • Botrytis & others • Saccharomyces Time Three common microbial contaminants • Brettanomyces • Lactobacilli • Cork taint Brettanomyces Brettanomyces bruxellensis 45000 0.8 Slow40000 growing soft drink and wine spoilage yeast 0.7 35000 0.6 30000 0.5 25000 Produces 4-ethylphenol or “wet dog”taint cfu 0.4 4EP CFU/ml 20000 0.3 45000 0.8 15000 4-Ethylphenol (mg/ml) 40000 0.7 35000 0.6 30000 0.5 0.2 25000 cfu 0.4 10000 4EP CFU/ml 20000 0.3 15000 4-Ethylphenol (mg/ml) 0.2 10000 4-ethylphenol produced in absence of platable population 0.1 0.1 5000 5000 0 0 1 20 34 45 64 81 99 115 137 158 184 202 217 230 244 265 307 351 391 434 473 712 Days 0 0 1 20 34 45 64 81 99 115 137 158 184 202 217 230 244 265 307 351 391 434 473 712 Days Am J. Enol Vitic 54:294-300 Brettanomyces bruxellensis Isolated by Dr. Clausen in 1904 Provides missing element of traditional beers The brewing industry just started using yeast Friend or Foe? For Now Brett On Your Table 4 - Ethylguaiacol (4-EG): ~175 ppb 4 - Ethylphenol (4-EP): 600 - 800 ppb Diacetyl: 2-4 ppm Geraniol: 0.5 – 1
    [Show full text]
  • Biology of Fungi, Lecture 2: the Diversity of Fungi and Fungus-Like Organisms
    Biology of Fungi, Lecture 2: The Diversity of Fungi and Fungus-Like Organisms Terms You Should Understand u ‘Fungus’ (pl., fungi) is a taxonomic term and does not refer to morphology u ‘Mold’ is a morphological term referring to a filamentous (multicellular) condition u ‘Mildew’ is a term that refers to a particular type of mold u ‘Yeast’ is a morphological term referring to a unicellular condition Special Lecture Notes on Fungal Taxonomy u Fungal taxonomy is constantly in flux u Not one taxonomic scheme will be agreed upon by all mycologists u Classical fungal taxonomy was based primarily upon morphological features u Contemporary fungal taxonomy is based upon phylogenetic relationships Fungi in a Broad Sense u Mycologists have traditionally studied a diverse number of organisms, many not true fungi, but fungal-like in their appearance, physiology, or life style u At one point, these fungal-like microbes included the Actinomycetes, due to their filamentous growth patterns, but today are known as Gram-positive bacteria u The types of organisms mycologists have traditionally studied are now divided based upon phylogenetic relationships u These relationships are: Q Kingdom Fungi - true fungi Q Kingdom Straminipila - “water molds” Q Kingdom Mycetozoa - “slime molds” u Kingdom Fungi (Mycota) Q Phylum: Chytridiomycota Q Phylum: Zygomycota Q Phylum: Glomeromycota Q Phylum: Ascomycota Q Phylum: Basidiomycota Q Form-Phylum: Deuteromycota (Fungi Imperfecti) Page 1 of 16 Biology of Fungi Lecture 2: Diversity of Fungi u Kingdom Straminiplia (Chromista)
    [Show full text]
  • 2014 ASBC Annual Meeting
    2014 ASBC Annual Meeting 76th ASBC Annual Meeting June 4–6, 2014 57 Analyzing the sugar and flavor profile of Brettanomyes wild yeast Palmer House, a Hilton Hotel Chicago, IL during primary versus secondary fermentation (Tiffany Andres, White Labs, Inc.) Abstract Brewing with Brettanomyces yeast has been rising in popularity as such yeast can create different flavors and aromas to increase the unique character of a particular beer. Recent research on Brettanomyces strains available in the brewing industry focused on strain-specific fermentations and have attempted to identify the major compounds produced during fermentation. This study attempts to investigate the differences in flavor compounds after experimenting in primary and secondary fermentation with various Brettanomyces strains. The concept of primary versus secondary fermentation relates to different sugars being available for Brettanomyces to metabolize since Saccharomyces yeast will readily consume most of the fermentable sugars. By analyzing the performance of various Brettanomyces strains during primary versus secondary fermentation, it will be essential to measure the carbohydrate sugar profile before and after fermentation, as well as look at attenuation. The focus of this research will be to explore the flavor compounds produced when Brettanomyces has fermentable sugars available in contrast to which flavor compounds are produced from dextrins after secondary fermentation. The Brettanomyces strains that will be able to metabolize different sugars resulting in differences on a sensory level will be evaluated. Introduction Results Brettanomyces create different flavors and aromas that can contribute to the unique character of the finished beer. The type and quantity of sugars present will affect the fermentation flavors.
    [Show full text]
  • Fungal Ecology 33 (2018) 1E12
    Fungal Ecology 33 (2018) 1e12 Contents lists available at ScienceDirect Fungal Ecology journal homepage: www.elsevier.com/locate/funeco Decaying Picea abies log bark hosts diverse fungal communities * Igor Kazartsev a, b, c, Ekaterina Shorohova a, b, d, , Ekaterina Kapitsa a, b, Helena Kushnevskaya a, e a Forest Research Institute of the Karelian Research Centre, Russian Academy of Science, Pushkinskaya Str. 11, Petrozavodsk, 185910, Russia b Saint-Petersburg State Forest Technical University, Institutsky Str. 5, St. Petersburg, 194021, Russia c All-Russian Institute of Plant Protection, Podbelskogo Shosse 3, St. Petersburg, 196608, Russia d Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790, Helsinki, Finland e Saint-Petersburg State University, University Embankment 7-9, St Petersburg, 199034, Russia article info abstract Article history: We examined taxonomic composition of fungal communities in Picea abies log bark using next gener- Received 20 June 2017 ation sequencing. Three successional stages along gradients of log attributes were identified. In the initial Received in revised form stage, the communities were composed by yeasts, plant pathogens and cosmopolitan saprotrophic fungi 19 October 2017 with broad substrate utilization. In the intermediate stage, bark was colonized mainly by saprotrophs Accepted 20 December 2017 common in decaying wood, symbionts of epixylic plants and nematode-trapping fungi. The final stage was characterized by the dominance of mycorrhizal fungi. Wood-decaying fungi occurred in all stages. Corresponding Editor: Jacob Heilmann- However, their sporadic appearance in bark samples suggests that they are not essential for bark Clausen decomposition. Our results provide an insight into the hidden diversity of wood-inhabiting communities e fungal communities, associated with decomposition of bark as a component of coarse woody debris.
    [Show full text]
  • The Phylogeny of Plant and Animal Pathogens in the Ascomycota
    Physiological and Molecular Plant Pathology (2001) 59, 165±187 doi:10.1006/pmpp.2001.0355, available online at http://www.idealibrary.com on MINI-REVIEW The phylogeny of plant and animal pathogens in the Ascomycota MARY L. BERBEE* Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada (Accepted for publication August 2001) What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also concentrated, but in two ascomycete classes that contain few, if any, plant pathogens. Rather than appearing as a constant character of a class, the ability to cause disease in plants and animals was gained and lost repeatedly. The genes that code for some traits involved in pathogenicity or virulence have been cloned and characterized, and so the evolutionary relationships of a few of the genes for enzymes and toxins known to play roles in diseases were explored. In general, these genes are too narrowly distributed and too recent in origin to explain the broad patterns of origin of pathogens. Co-evolution could potentially be part of an explanation for phylogenetic patterns of pathogenesis. Robust phylogenies not only of the fungi, but also of host plants and animals are becoming available, allowing for critical analysis of the nature of co-evolutionary warfare. Host animals, particularly human hosts have had little obvious eect on fungal evolution and most cases of fungal disease in humans appear to represent an evolutionary dead end for the fungus.
    [Show full text]