Yeasts: From Nature to Bioprocesses

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Contents
Preface
List of Contributors
Origin and Evolution of Yeasts
Thato Yoliswa Motlhalamme1, Nerve Zhou2, Amparo Gamero3, Ngwekazi Nwabisa Mehlomakulu4, Neil Jolly5, Carolina Albertyn-Pohl6 and Mathabatha Evodia Setati1,*
INTRODUCTION
MOLECULAR DRIVERS OF EVOLUTION
EVOLUTION OF CARBON METABOLISM IN YEASTS: PREFERENCE FOR GLUCOSE AND FRUCTOSE
PREFERENCE FOR GLUCOSE AND EVOLUTION OF ETHANOL PRODUCTION
MOLECULAR EVENTS OF ETHANOL PRODUCTION AMONG GLUCOPHILES
ECOLOGICAL BASIS SUPPORTING GLUCOPHILY AND EVOLUTION OF ETHANOL PRODUCTION
EVOLUTION OF FRUCTOPHILY, A NON-ETHANOL PRODUCING SUGAR UTILISATION STRATEGY AMONG SOME YEASTS
Molecular Mechanisms of Fructophily
YEAST DOMESTICATION
Utilization of Carbon Substrates in Domesticated Yeast
ADAPTATION TO NITROGEN UPTAKE
Modifications in Thiamine Metabolism
ADAPTATION TO ABIOTIC STRESSORS
FLAVOUR PRODUCTION SPECIALISATIONS
ELIMINATING SEXUAL REPRODUCTION
EVOLUTION OF PATHOGENIC YEASTS
CONCLUDING REMARKS
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Ecology: Yeasts on their Natural Environment
Sergio Álvarez-Pérez1,*
INTRODUCTION
YEAST HABITATS
Yeasts in Soil
Yeasts in Aquatic Habitats
Freshwater Habitats
Marine and Oceanic Habitats
Other Aquatic Habitats
Yeasts in the Atmosphere
Yeasts in Polar and other Terrestrial Cold Habitats
Yeasts in Anthropogenic Habitats
INTERACTION WITH OTHER ORGANISMS
Yeasts in the Insect Microbiome
Yeasts in the Phylloplane
Yeasts is Decaying Cactus Tissues
Yeasts in the Floral Microbiome
Yeasts in the Human Microbiome
Yeasts in Industrial Processes
FUTURE CHALLENGES IN YEAST ECOLOGY
CONCLUDING REMARKS
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Yeast Taxonomy
J. Alfredo Hernández-García1, 2, Esaú De-la-Vega-Camarillo2, Lourdes Villa-Tanaca2 and César Hernández-Rodríguez2,*
INTRODUCTION
Phenotypic Taxonomy of Yeast
MOLECULAR TAXONOMY OF YEAST
GENOMIC AND PHYLOGENOMIC APPROACHES
MAIN TAXONOMIC GROUPS WITH POTENTIAL FOR BIOTECHNOLOGICAL APPLICATION
CONCLUSION
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENT
REFERENCES
Saccharomyces: The 5 Ws and One H
Thiago Olitta Basso1, Thalita Peixoto Basso2, Sérgio Luiz Alves Júnior3, Boris U. Stambuk4,* and Luiz Carlos Basso5,*
INTRODUCTION
SACCHAROMYCES HABITATS: WHERE?
HYSTORY AND DOMESTICATION OF SACCHAROMYCES: WHEN AND WHO?
SACCHAROMYCES HYBRIDS: WHY AND HOW?
SACCHAROMYCES IN SUGARCANE-BASED BIOETHANOL PRODUCTION: WHAT AND HOW?
Ethanol in Brazil
The Fermentation Process
The Various Stresses in the Industrial Scenario
Ethanol Stress
Acidic Stress
Osmotic Stress
Biotic Stress
Quorum Sensing & Stress
Heavy Metal Stress
Selection of Yeast Strains for Industrial Fermentation
CONCLUDING REMARKS
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Candida
Atrayee Chattopadhyay1 and Mrinal K. Maiti1,*
INTRODUCTION
(I). CANDIDA: A POLYPHYLETIC GENUS
(II). CANDIDIASIS IN HUMAN AND ANIMALS
Cutaneous Candidiasis
Mucosal Candidiasis
Systemic Candidiasis
Epidemiology
Antifungal Drug Resistance
Immune Response
(III). CANDIDA IN NATURE
Pathogenesis
Sexuality
Biofilm
(IV). CANDIDA IN BIOPROCESSES
SCP Production
SCO Production
Sugar Alcohols
Xylitol
Erythritol
Citric Acid
Dicarboxylic Acids
Ethanol
Enzymes
Lipase
Invertase
Biosurfactants
Food Applications
Biocontrol
Biodegradation
CONCLUDING REMARKS
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Pichia: From Supporting Actors to the Leading Roles
Rosicler Colet1, Guilherme Hassemer1, Sérgio Luiz Alves Júnior2, Natalia Paroul1, Jamile Zeni1, Geciane Toniazzo Backes1, Eunice Valduga1 and Rogerio Luis Cansian1,*
INTRODUCTION
PICHIA: A DIVERSITY OF ENVIRONMENTS
THE USE OF PICHIA YEASTS IN BIOPROCESSES
Production of Vaccines and Biopharmaceutical Products
Protein and Enzymes
Pigments
Xylitol and Oligosaccharide Production
Ethanol
Alcoholic Beverages
Coffee Fermentation
Cocoa Fermentation
Olive Fermentation
Biodegradation of Dyes
Biocontrol
REASSIGNMENTS FROM AND TO PICHIA
CONCLUDING REMARKS
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENT
REFERENCES
Brettanomyces: Diversity and Potential Applications in Industrial Fermentation
Manoela Martins1, Maria Paula Jiménez Castro1, Marcus Bruno Soares Forte1 and Rosana Goldbeck1,*
INTRODUCTION
DIVERSITY OF BRETTANOMYCES HABITATS
BRETTANOMYCES YEASTS IN BIOPROCESSES
Spoilage and Off-Flavors
Methods to Eliminate or Reduce Brettanomyces Populations
Growth and Fermentation
Oxygen
Nitrogen
Carbon Source
Temperature
pH
Bioethanol Production
Production of Beer and Wine with Unique Aromas
CONCLUDING REMARKS
CONSENT FOR PUBLICATION
CONFLICT OF INTERESTS
ACKNOWLEDGEMENTS
REFERENCES
Spathaspora and Scheffersomyces: Promising Roles in Biorefineries
Thamarys Scapini1, Aline F. Camargo1, Jéssica Mulinari2, Camila E. Hollas3, Charline Bonatto1, Bruno Venturin3, Alan Rempel4, Sérgio L. Alves Jr.5 and Helen Treichel1,*
INTRODUCTION
SCHEFFERSOMYCES AND SPATHASPORA PHYLOGENY AND TAXONOMY
WHERE HAVE SPATHASPORA AND SCHEFFERSOMYCES YEASTS BEEN FOUND?
THE INDUSTRIAL POTENTIAL OF THE SPECIES OF SPATHASPORA AND SCHEFFERSOMYCES
WHOLE-GENOME SEQUENCED SPECIES OF SPATHASPORA AND SCHEFFERSOMYCES
CONCLUSION
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENT
REFERENCES
Engineered Saccharomyces or Prospected non-Saccharomyces: Is There Only One Good Choice for Biorefineries?
Sérgio L. Alves Jr1, Thamarys Scapini2, Andressa Warken2, Natalia Klanovicz2,3, Dielle P. Procópio4, Viviani Tadioto1, Boris U. Stambuk5, Thiago O. Basso4 and Helen Treichel2,*
INTRODUCTION
FEEDSTOCK STRUCTURE AND FERMENTATION CHALLENGES
Metabolism of Xylooligosaccharides by S. cerevisiae
CRISPRING BIOREFINERIES IN HOPES OF A (BIO)SAFE CIRCULAR ECONOMY
WHAT ABOUT EVOLUTIONARY ENGINEERING?
Basic Concept of Evolutionary Engineering
Operational Approaches Used in Adaptive Laboratory Evolution
Evolutionary Engineering with Ethanol Production Purpose
Evolutionary Engineering in Biorefineries Context
EXPERIENCES WITH NON-SACCHAROMYCES YEASTS
Xylanolytic Non-Saccharomyces Yeasts
CONCLUSION
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Yeasts in the Beverage Industry: Patagonia Gets Wild
Melisa Gonzalez Flores1, María C. Bruzone2, Andrea Origone1, Julieta A. Burini2, María E. Rodríguez1, Christian A. Lopes1 and Diego Libkind2,*
INTRODUCTION
Natural Environments for Yeast Bioprospection: The Case of Andean Patagonia
BEER INNOVATION AND YEAST BIOTECHNOLOGY
Search for Brewing Potential in Wild Yeasts
Saccharomyces eubayanus, the Mother of the Lager Brewing Yeast
Technological Features of S. eubayanus for Brewing
Expanding the Limits for Brewing
From Nature to Beer Industry
CIDER INNOVATION AND YEAST BIOTECHNOLOGY
Screening of S. uvarum Strains for Cider Production
i). Sulphite Tolerance
ii). Temperature
iii). Fructose Consumption
Selection of S. uvarum Cider Starter Cultures
i). Impact of the Fermentation Temperature on Starter Implantation and Aromatic Properties of Ciders
ii). Impact of the Apple Variety and the Addition of Sulphite on the Fermentative, Aromatic and Sensory Attributes of Ciders Conducted with Different S. uvarum Strains
Bioprospecting of Yeast for Cider: From Nature to Industry
WINE INNOVATION AND YEAST BIOTECHNOLOGY
Cryotolerant Yeasts for Patagonian White Wines
Screening of Non-Conventional Yeasts for White Wines Elaboration at Low Temperature
Yeast Response to Winemaking Stress Factors
Technological Features of S. uvarum and S. eubayanus for Winemaking
The Hybridization Strategy
From the Laboratory to The Winemaking Industry
CONCLUSION
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENT
REFERENCES
Yeasts and Breadmaking
Caiti Smukowski Heil1,†, Kate Howell2,† and Delphine Sicard3,*
INTRODUCTION
HISTORY OF BREADMAKING
EVOLUTION OF BAKERY YEASTS
Different Evolutionary Roads for Industrial and Sourdough Yeasts
Genetic and Phenotypic Signatures of Yeast Domestication for Breadmaking
Biodiversity, Ecology and Evolution of Sourdough Yeast Species
MICROBIAL INTERACTIONS DURING SOURDOUGH PRODUCTION
METABOLIC FUNCTIONS OF BAKERY YEASTS
STRESS TOLERANCE OF BAKERY YEASTS: OSMOTOLERANCE, FREEZING, AND DESICCATION TOLERANCE
CONCLUSION
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Biotechnological Applications of Oleaginous Yeasts
Yasmi Louhasakul1 and Benjamas Cheirsilp2,*
INTRODUCTION
CHARACTERISTICS OF OLEAGINOUS YEASTS
Lipid Synthesis by Oleaginous Yeasts
Lipid Composition of Oleaginous Yeasts
Low-cost Feedstocks and Wastes as Substrates for Oleaginous Yeasts
Biodiesel Production via Direct Transesterification from Yeast Lipids
CONCLUSION
LIST OF ABBREVIATIONS
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Improvement of Organic Agriculture with Growth-Promoting and Biocontrol Yeasts
Karen A. Achilles1, Aline F. Camargo2, Francisco Wilson Reichert Júnior1, Lindomar Lerin1, Thamarys Scapini2, Fábio S. Stefanski2, Caroline Dalastra2, Helen Treichel2 and Altemir J. Mossi1,*
INTRODUCTION
YEASTS IN THE NATURAL ENVIRONMENT
GROWTH-PROMOTING YEASTS APPLIED TO ORGANIC AGRICULTURE
Plant Growth Promoting
Biocontrol
CONCLUSION
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENT
REFERENCES
Yeasts: From the Laboratory to Bioprocesses
Barbara Dunn1,* and Boris U. Stambuk2
INTRODUCTION
CLASSICAL GENETIC APPROACHES TO IMPROVE INDUSTRIAL STRAINS
Direct Mating (Cell-to-cell; Spore-to-spore)
Rare Mating
Mating within Insect Guts
Induced Mating-Type Switching
Protoplast Fusion
Cytoduction
Utilizing Genomic Diversity to Select for Desired Phenotypic Traits and Identify Causal Genomic Elements
Mutagenesis
Mass-Mating and Mass Cell Fusion
Genome Shuffling
Bulk Segregant Analysis and QTL-Mapping to Identify Genes/Pathways Involved in Phenotypes
Adaptive (Directed) Evolution to Select for Enhanced Phenotypes
Whole-genome and High-throughput Sequencing
MODERN TECHNOLOGIES FOR STRAIN IMPROVEMENT
Genomic Engineering Through Homologous Recombination
CRISPR-Cas9
Synthetic Chromosomes, Synthetic Genomes and SCRaMbLE
GENETIC MODIFICATION OF NON-CONVENTIONAL YEASTS
FROM THE LABORATORY TO BIOPROCESSES
CONCLUSION
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Are Yeasts “Humanity’s Best Friends”?
Sérgio L. Alves Jr1,*, Helen Treichel2, Thiago O. Basso3 and Boris U. Stambuk4
INTRODUCTION
THE THINGS WE LOVE THE MOST
Alcoholic Beverages
Bread
Chocolate
Cheese
WHAT ELSE CAN YEASTS OFFER US?
Biopharmaceuticals
Single-cell Market
Probiotics and Prebiotics
Fuels
Products and Services for the Textile Industry
Nutrient Cycling and Decomposition
Insect Attraction and Pollination
Biological Control
Plant-growth Promoting Activities
CONCLUSION AND FURTHER CONSIDERATIONS
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Subject index
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