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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