A Future Place for Saccharomyces Mixtures and Hybrids in Wine Making
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Molecular Evolution in Yeast: Role of Chromosomal Inversions and Translocations in Speciation, Adaptation and Gene Expression
Molecular evolution in yeast: Role of chromosomal inversions and translocations in speciation, adaptation and gene expression A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy (PhD) in the Faculty of Life Sciences 2011 Samina Naseeb Table of Contents List of tables 7 List of figures 9 Abstract 12 Declaration 13 Copyright statement 14 Acknowledgements 15 Dedication 16 Rational for submitting the thesis in alternative format 17 Chapter 1- Introduction 18 1.1 Saccharomyces cerevisiae as a model organism 19 1.1.1 DNA transformation and recombination in yeast 19 1.1.2 Life cycle 20 1.1.3 Genome of Saccharomyces cerevisiae 23 1.2 The taxonomy of yeast 25 1.3 Yeast genome evolution 28 1.4 Transposable elements (TE) and chromosomal rearrangements 30 1.5 Role of chromosomal inversions and translocations in gene order 34 evolution, speciation and fitness 1.6 Co-expressed gene clusters 35 1.6.1 Structure of the DAL cluster 36 1.6.2 Function of DAL cluster in allantoin degradation 37 1.7 Aim of the project 40 1.8 References 41 Chapter 2- Impact of chromosomal inversions in co-expressed gene clusters 49 2.1 Foreword 50 2 2.2 Abstract 50 2.3 Background 51 2.4 Results 55 2.4.1 Transcription factor analysis of DAL cluster structure 55 2.4.2 Fitness assays of the wild type strains 59 2.4.3 Construction of the strains with different gene 62 inversions 2.4.4 Plasmid extraction and digestion 62 2.4.5 Amplification of cassettes 63 2.4.6 Construction of the DAL2 inverted strain 64 2.4.6.1 Insertion of the lox P containing cassettes 64 2.4.6.2 Verification of cassette insertion 65 2.4.6.3 Cre transformation and induction 67 2.4.7 Construction of the strain with S. -
WINE YEAST: the CHALLENGE of LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013
WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art. 32 del Texto Refundido de la Ley de Propiedad Intelectual (RDL 1/1996). Para otros usos se requiere la autorización previa y expresa de la persona autora. En cualquier caso, en la utilización de sus contenidos se deberá indicar de forma clara el nombre y apellidos de la persona autora y el título de la tesis doctoral. -
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. -
Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations
Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations Sofia Dashko1, 2, Ping Liu3, Helena Volk2, Lorena Butinar2, Jure Piškur1, 2, Justin C. Fay3* 1Biology, Lund University, Sweden, 2Wine Research Center, University of Nova Gorica, Slovenia, 3Genetics, Washington University, USA Submitted to Journal: Frontiers in Microbiology Specialty Section: Food Microbiology ISSN: 1664-302X Article type: Original Research Article Received on: 10 Dec 2015 Accepted on: 09 Feb 2016 Provisional PDF published on: 09 Feb 2016 Frontiers website link: www.frontiersin.org ProvisionalCitation: Dashko S, Liu P, Volk H, Butinar L, Piškur J and Fay JC(2016) Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations. Front. Microbiol. 7:215. doi:10.3389/fmicb.2016.00215 Copyright statement: © 2016 Dashko, Liu, Volk, Butinar, Piškur and Fay. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution and reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. This Provisional PDF corresponds to the article as it appeared upon acceptance, after peer-review. Fully formatted PDF and full text (HTML) versions will be made available soon. Frontiers in Microbiology | www.frontiersin.org Provisional Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations Sofia Dashko1,2, Ping Liu3, Helena Volk1, Lorena Butinar1, Jure Piškur1,2 and Justin C. -
Interspecific Hybrids Reveal Increased Fermentation
fermentation Article Saccharomyces arboricola and Its Hybrids’ Propensity for Sake Production: Interspecific Hybrids Reveal Increased Fermentation Abilities and a Mosaic Metabolic Profile Matthew J. Winans 1,2,* , Yuki Yamamoto 1, Yuki Fujimaru 1, Yuki Kusaba 1, Jennifer E. G. Gallagher 2 and Hiroshi Kitagaki 1 1 Graduate School of Advanced Health Sciences, Saga University, 1, Honjo, Saga city, Saga 840-8502, Japan; [email protected] (Y.Y.); [email protected] (Y.F.); [email protected] (Y.K.); [email protected] (H.K.) 2 Biology Department, West Virginia University, 53 Campus Drive, Morgantown, WV 26506-6057, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-(304)-483-1786; Fax: +1-(304)-293-6363 Received: 4 December 2019; Accepted: 17 January 2020; Published: 20 January 2020 Abstract: The use of interspecific hybrids during the industrial fermentation process has been well established, positioning the frontier of advancement in brewing to capitalize on the potential of Saccharomyces hybridization. Interspecific yeast hybrids used in modern monoculture inoculations benefit from a wide range of volatile metabolites that broaden the organoleptic complexity. This is the first report of sake brewing by Saccharomyces arboricola and its hybrids. S. arboricola x S. cerevisiae direct-mating generated cryotolerant interspecific hybrids which increased yields of ethanol and ethyl hexanoate compared to parental strains, important flavor attributes of fine Japanese ginjo sake rice wine. Hierarchical clustering heatmapping with principal component analysis for metabolic profiling was used in finding low levels of endogenous amino/organic acids clustered S. arboricola apart from the S. -
Fungal Diversity During Fermentation Correlates with Thiol Concentrations in Wine
Fungal diversity during fermentation correlates with thiol concentrations in wine Sarah J. Knight1*, Steffen Klaere2, Peter Morrison-Whittle1 and Matthew R. Goddard1,3 1School of Biological Sciences, 2Department of Statistics, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand; 3The School of Life Sciences, The University of Lincoln, Lincoln, LN6 7DL, United Kingdom Authorship declaration: We declare that all authors have contributed significantly and that all authors agree with the manuscript. *Corresponding author: Sarah Knight School of Biological Sciences University of Auckland Private Bag 92019 Auckland Mail Centre Auckland 1142 New Zealand Ph: +64 9 923 1238 Email: [email protected] Acknowledgements: We thank Amisfield, Ata Rangi, Churton, Coal Pit, Constellation, Delegats, Domain Road, Frey Vineyard, Huia, Misha’s Vineyard, Mt Difficulty, Mt Riley, Neudorf, Palliser, Pernod Ricard, Rippon, Seifried, Seresin, Te Kairanga, Te Whare Ra, Tohu, Trinity Hill, Villa Maria and Vita Brevis for access to their land and providing samples. This work was funded by a University of Auckland doctoral scholarship to S Knight and grants to MG from the New Zealand Ministry of Business, Innovation and Employment, New Zealand Winegrowers and Plant and Food Research. Disclosure statement: The authors declare no conflicts of interest Short running title (50 characters): Fungal diversity correlates with wine thiol levels Abstract Background and Aims: Agricultural products deriving from the same genotypic clone often have different physical and sensorial properties that influences their overall quality and value. Microbes may play key roles throughout the production of many crops, affecting plant and fruit health and modifying plant materials to produce socially and economically important commodities. -
Hybrids Saccharomyces Cerevisiae X Saccharomyces Bayanus Var
HYBRIDS SACCHAROMYCES CEREVISIAE X SACCHAROMYCES BAYANUS VAR. UVARUM HAVING A HIGH LIBERATING ABILITY OF SOME SULFUR VARIETAL AROMAS OF VITIS VINIFERA SAUVIGNON BLANC WINES DES HYBRIDES SACCHAROMYCES CEREVISIAE X SACCHAROMYCES BAYANUS VAR. UVARUM PRÉSENTANT UNE FORTE APTITUDE À RÉVÈLER DES COMPOSÉS SOUFRÉS CARACTÉRISTIQUES DE L’ARÔME VARIÉTAL DES VINS BLANCS DE SAUVIGNON Isabelle MASNEUF1, Marie-Laure MURAT2, G.I. NAUMOV3, T. TOMINAGA2 and D. DUBOURDIEU2 1 : ENITA de Bordeaux, 1 cours du Général de Gaulle, BP 201, 33175 Gradignan cedex, France 2 : Faculté d'Œnologie, Université Victor Segalen Bordeaux 2, 351 cours de la Libération, 33400 Talence, France. 3 : State Institute for Genetics and Selection of Industrial Microorganisms, I-Dorozhnyi 1, Moscow 113545, Russia Summary : We measured ability of some indigenousSaccharomyces bayanus var. uvarum wine yeasts to release volatile thiols from their S-cysteine conjugate precursors, odorous compounds responsible for the characteristic aroma of Sauvignon blanc wines. We also made interspecific hybrids between Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum strains and verified their hybrid origin with karyotypes and MET2 PCR-RFLP analysis. As compared to the parents, some hybrids could release high amounts of volatile thiols from the S-cysteine conjugate precursor without producing excessive amounts of β-phenylethyl alcohol and its acetate. One hybrid was retained for industrial production under a dry form and successfully compared with Saccharomyces cerevisiae strains in experimental tests in different cellars. Résumé : L’aptitude de certaines souches de l’espèce Saccharomyces bayanus var. uvarum à libérer, au cours de la fermentation alcoolique, les thiols volatils de leurs précurseurs cystéinylés est étudiée dans ce travail. -
SYSTEMATICS of DIVISION ASCOMYCOTA 1 Group
References: Kirk PM, Cannon PF, Minter DW, Stalpers JA. 2008. Dictionary of the Fungi (10th ed.). Wallingford, UK: CABI. Webster, J., & Weber, R. (2007). Introduction to fungi. Cambridge, UK: Cambridge University Press. Url1.: https://en.wikipedia.org/wiki/Ascomycota SYSTEMATICS OF DIVISION ASCOMYCOTA 1 Group: Plectomycetes Plectomycetes is an artificial group of Ascomycota and it originally contained all Ascomycete fungi which produce their asci within a cleistothecium. Plectomycetes can be defined by the following set of characters; Cleistothecium or gymnothecium is usually present, ascogenous hyphae are usually not conspicuous, asci are scattered throughout the cleistothecium, asci are mostly globose and thin-walled, and the ascospores are released passively after disintegration of the ascus wall, not by active discharge, ascospores are small, unicellular and usually spherical or ovoid, conidia are commonly produced from phialides or as arthroconidia. Class: Eurotiomycetes Most members of the class produce an enclosed structure cleistothecium within which they produce their spores. It contains 10 order, 27 families 280 genus and about 3400 species. Order: Onygenales Onygenales members are able to digest keratin and because of this have become dominant organisms in environments where keratin is available. The most members have colorless cleistothecia and ascospores. The spherical to egg-shaped asci are always uniformly packed in the centrum and may be dispersed among hyphal elements. The ascospores are always single-celled (example: Chrysosporium, Microsporum and Trichophyton). Order: Eurotiales Most members of the order have phialidic asexual stages belonging to the genera Aspergillus and Penicillium or, less commonly, to Paecilomyces or even simpler types. Rarely there is no anamorph at all. -
Brewing Efficacy of Non-Conventional Saccharomyces Non-Cerevisiae Yeasts Authors: James Bruner 1,2 (Orcid: 0000-0003-3691-0711)
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 19 July 2021 doi:10.20944/preprints202107.0423.v1 Brewing Efficacy of Non-Conventional Saccharomyces Non-Cerevisiae Yeasts Authors: James Bruner 1,2 (ORCiD: 0000-0003-3691-0711), Andrew Marcus 1, Glen Fox 1* (ORCiD: 0000-0001-7502-0637) Addresses: 1. Food Science and Technology Department, University of California, 1 Shields Ave, Davis, CA, USA 95616 2. Creature Comforts Brewing Company, 271 W. Hancock Ave, Athens, GA, USA 30601 *Corresponding authors: [email protected] © 2021 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 19 July 2021 doi:10.20944/preprints202107.0423.v1 Abstract Consumer demands for new sensory experiences have driven the research of unconventional yeasts in beer. While much research exists on the use of various common Saccharomyces cerevisiae strains as well as non-Saccharomyces yeasts, there exists a gap in knowledge regarding other non-cerevisiae Saccharomyces species in the fermentation of beer, outside that of S. pastorianus. Here, five distinct species of Saccharomyces from the UC Davis Phaff Yeast Culture Collection, as well as one interspecies hybrid from Fermentis, were chosen to ferment 40 L pilot scale beers. S. kudriavzevii, S. mikatae, S. paradoxus, S. bayanus, and S. uvarum yeasts were fermented in duplicate, with one fermenter in each pair receiving 10 g/L dry- hop during fermentation. Analytical measurements were made each day of fermentation and compared to controls of SafAle US-05 and SafLager W 34/70 for commercial brewing parameters of interest. Finished beers were also analyzed for aroma, taste, and mouthfeel to determine the flavor of each yeast as it pertains to brewing potential. -
Evaluation of Saccharomyces Pastorianus Impact to Sauvignon Blanc Chemical & Sensory Profile Compared to Different Strains of S
BIO Web of Conferences 12, 02025 (2019) https://doi.org/10.1051/bioconf/20191202025 41st World Congress of Vine and Wine Evaluation of Saccharomyces pastorianus impact to Sauvignon blanc chemical & sensory profile compared to different strains of S. cerevisiae/bayanus V. Troianou1, C. Toumpeki1, E. Dorignac2, C. Kogkou3, S. Kallithraka3, and Y. Kotseridis3 1 Innovino, Applied Research for Wine, Pallini, Athens 2 Societ´ e´ Industrielle Lesaffre, Division Fermentis, France 3 Laboratory of Enology, Department of Food Science & Human Nutrition, Agricultural University, Athens Abstract. Enhancing flavors and/or improving fermentation parameters through the use of different species of yeast strains is nowadays a frequent challenge in winemaking research, especially for aromatic varieties such as Sauvignon Blanc. In this work, the aim was to focus on the impact of a species not already studied in wine: Saccharomyces pastorianus. Twenty-two fermentations were conducted on a Sauvignon Blanc must by addition of different strains and mixtures of them by using two different inoculation temperatures. The must was inoculated in cold condition with two similar mixtures of S. pastorianus 1 or 2 (70%) and S. bayanus (30%), with S. pastorianus 1 or 2 alone, with the correspondent S. bayanus alone and with two other S. cerevisiae 1 and 2 alone as well. For classic condition, the must was inoculated with only one mixture S. pastorianus 1 (70%) / S. bayanus (30%), and respectively with S. pastorianus 1, S. bayanus and S. cerevisiae 2 alone. Samples were taken all along the fermentations for both conditions in order to check chemical and microbial analyses as well as yeast implantations. -
Novel Non-Cerevisiae Saccharomyces Yeast Species Used in Beer and Alcoholic Beverage Fermentations
fermentation Review Novel Non-Cerevisiae Saccharomyces Yeast Species Used in Beer and Alcoholic Beverage Fermentations James Bruner * and Glen Fox * Food Science and Technology, University of California, Davis, CA 95616, USA * Correspondence: [email protected] (J.B.); [email protected] (G.F.) Received: 28 October 2020; Accepted: 22 November 2020; Published: 24 November 2020 Abstract: A great deal of research in the alcoholic beverage industry was done on non-Saccharomyces yeast strains in recent years. The increase in research interest could be attributed to the changing of consumer tastes and the search for new beer sensory experiences, as well as the rise in popularity of mixed-fermentation beers. The search for unique flavors and aromas, such as the higher alcohols and esters, polyfunctional thiols, lactones and furanones, and terpenoids that produce fruity and floral notes led to the use of non-cerevisiae Saccharomyces species in the fermentation process. Additionally, a desire to invoke new technologies and techniques for making alcoholic beverages also led to the use of new and novel yeast species. Among them, one of the most widely used non-cerevisiae strains is S. pastorianus, which was used in the production of lager beer for centuries. The goal of this review is to focus on some of the more distinct species, such as those species of Saccharomyces sensu stricto yeasts: S. kudriavzevii, S. paradoxus, S. mikatae, S. uvarum, and S. bayanus. In addition, this review discusses other Saccharomyces spp. that were used in alcoholic fermentation. Most importantly, the factors professional brewers might consider when selecting a strain of yeast for fermentation, are reviewed herein. -
Saccharomyces Cerevisiae in the Production of Fermented Beverages
beverages Review Saccharomyces cerevisiae in the Production of Fermented Beverages Graeme M Walker 1,* and Graham G Stewart 2 1 Abertay University, Dundee, Scotland DD1 1HG, UK 2 Heriot-Watt University, Edinburgh, Scotland EH14 4AS, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-1382-308658 Academic Editor: Edgar Chambers IV Received: 20 October 2016; Accepted: 11 November 2016; Published: 17 November 2016 Abstract: Alcoholic beverages are produced following the fermentation of sugars by yeasts, mainly (but not exclusively) strains of the species, Saccharomyces cerevisiae. The sugary starting materials may emanate from cereal starches (which require enzymatic pre-hydrolysis) in the case of beers and whiskies, sucrose-rich plants (molasses or sugar juice from sugarcane) in the case of rums, or from fruits (which do not require pre-hydrolysis) in the case of wines and brandies. In the presence of sugars, together with other essential nutrients such as amino acids, minerals and vitamins, S. cerevisiae will conduct fermentative metabolism to ethanol and carbon dioxide (as the primary fermentation metabolites) as the cells strive to make energy and regenerate the coenzyme NAD+ under anaerobic conditions. Yeasts will also produce numerous secondary metabolites which act as important beverage flavour congeners, including higher alcohols, esters, carbonyls and sulphur compounds. These are very important in dictating the final flavour and aroma characteristics of beverages such as beer and wine, but also in distilled beverages such as whisky, rum and brandy. Therefore, yeasts are of vital importance in providing the alcohol content and the sensory profiles of such beverages. This Introductory Chapter reviews, in general, the growth, physiology and metabolism of S.