Molecular Wine Microbiology

Chapter 1. Yeast. Saccharomyces I. Yeast for primary alcoholic fermentation.

1.1. Yeasts of interest for wine making

1.1.1. Yeast microbiota from grapes, cellars and must

1.1.2. Morphology and cellular organization of yeasts

1.1.3. Genetic features of wine yeasts

1.2.. Growth features of Saccharomyces during fermentation

1.2.1 Must composition

1.2.2. Physical parameters of the fermentation

1.2.3. Yeast growth and fermentation kinetics

1.2.4. Biochemistry of the fermentation

1.3. Gene expression along the fermentation process

1.3.1. Glycolytic genes

1.3.2. Osmotic stress responsive genes

1.3.3. Genes induced during stationary phase

1.3.4. Gene expression in wine yeasts under particular stress conditions

1.4. Yeast activities during fermentation that deserve improvement

1.4.1. Improvement of the fermentation power

1.4.2. Improvement of ethanol resistance

1.4.3. Improvement of sensorial and nutritional properties of the wine
Bibliography

Chapter 2. Yeast. Saccharomyces II. Second fermentation yeasts.

2.1. Sparkling wine making process. Technology and normative

2.1.1. Sparkling wines and their classification

2.1.2. Sparkling wines made by the traditional method

2.2. Making cava

2.2.1. Must fermentation

2.2.2. "Prisse de mouse"

2.2.3. Second fermentation

2.3. Microbiological aspects of second fermentation

2.4. Ageing

2.4.1. Biochemical changes in the wine during wine ageing

2.4.2. Morphological changes of yeast cells during ageing

2.4.3. Genetics of autolysis. Autophagy

2.5. Effect of ageing on the quality of sparkling wines made by the traditional method

2.6. Methods to accelerate yeast autolysis, and their implication in the elaboration process

2.6.1. Temperature increase and addition of autolysates

2.6.2. Yeast genetic improvement
Bibliography

Chapter 3. Yeasts. Saccharomyces III. Yeast for wines with biological ageing.

3.1. Introduction

3.1.1. Making of wines with biological ageing

3.1.2. Fermentation and ageing yeasts from wines with biological ageing

3.2. Features of yeasts from wines with biological ageing

3.2.1. Physiological features

3.2.2. Genetic features

3.3. Effect of environmental factors on the features of yeasts from wines with biological ageing

3.3.1. Effect on the mitochondria

3.3.2. Effect on nuclear chromosome

3.3.3. Effect on the yeast membrane and cell membrane

3.4. Evolution of cellular genome and yeast populations from wines with biological ageing

3.5. Genetic improvement of wine yeasts.

3.5.1. Improvement of the features of fermentation yeasts

3.5.2. Improvement of the features of ageing yeasts

3.6. Conclusions
Bibliography

Chapter 4. Yeast. Non-Saccharomyces

4.1. Introduction

4.2. Isolation, identification and counting of non-Saccharomyces yeasts

4.2.1. Isolation and counting

4.2.2. Identification

4.3. Role of non-Saccharomyces yeasts in wine fermentation

4.3.1. Effect on the process

4.3.2. Effect on the aroma

4.4. Design of mixed starter cultures

4.5. Wine spoilage due to non-Saccharomyces yeasts

4.5.1. Refermentation

4.5.2. Excess of esther formation

4.5.3. Increase in volatile acid content

4.5.4. Production of volatile phenols and tetrahydropyridine derivatives

4.5.5. Formation of microbial biofilms

4.5.6. Deacidification

4.6. Final considerations
Bibliography

Chapter 5. Identification and molecular characterization of wine yeasts.

5.1. Yeast biodiversity during fermentation

5.2. Molecular methods for the identification and characterization of wine yeasts

5.2.1. Identification methods

5.2.2. Methods for the differentiation of strains within the S. cerevisiae species

5.3.1. Hybridization techniques

5.3.2. Pulse filed gel electrophoresis of chromosomes

5.3.3. Restriction analysis of the mitochondrial DNA

5.3.4. PCR based methods

5.3.5. Amplified fragment length polymorphism (AFLP)

5.4. Applications

5.4.1. Study of population dynamics during natural fermentations. Wine ecology.

5.4.2. Study of population dynamics during inoculated fermentations. Implantation monitoring

5.4.3. Characterization of commercial yeast strains

5.4.4. Screening of new species and hybrids involved in wine fermentations

5.4.5. Detection of wine spoilage yeasts
Bibliography

Chapter 6. Genomics and proteomics of wine yeasts.

6.1. Introduction

6.2. Genomic features of wine yeasts

6.3. Comparative genomics and the origin of the S. cerevisiae genome

6.4. DNA chips. The yeast S. cerevisiae as a model for technology development

6.4.1. Metabolic studies

6.4.2. Effect of drugs and other compounds

6.4.3. Application of DNA chips to the study of industrial yeast strains

6.4.4. Genomics studies

6.5. Proteomics of wine yeasts

6.6. Other global studies

6.7. Future prospects
Bibliography

Chapter 7. Improvement of wine yeasts by genetic engineering techniques

7.1. Wine, biotechnology and genetics

7.1.1. Wine and classical genetics

7.1.2. Wine and genetic engineering

7.2. Genetic transformation systems for wine yeasts

7.2.1. Transformation procedures

7.2.2. Selection markers

7.3. Regulation of gene expression: promoters with biotechnological interest

7.4. Transgenic wine yeasts

7.4.1. Improvement of the industrial winemaking process

7.4.2. Improvement of the physico-chemical features of wine

7.4.3. Sensorial and nutritional improvement

7.5. Regulations about genetic engineering in wine

7.5.1. Regulatory framework

7.5.2. Labeling

7.5.3. Situation in other countries

7.6. Future
Bibliography

Chapter 8. Lactic acid bacteria.

8.1. Introduction. General features

8.2. Identification of lactic acid bacteria

8.2.1. Classical methods

8.2.2. Molecular methods

8.3. Population dynamics during wine making

8.4. Metabolism.

8.4.1. Metabolism of carbohydrates

8.4.2. Metabolism of organic acids

8.4.3. Metabolism of phenolic compounds

8.4.4. Catabolism of aldehydes

8.4.5. Hydrolysis of glycosides

8.4.6. Synthesis and hydrolysis of esthers

8.4.7. Hydrolysis of lipids

8.4.8. Degradation of peptides and proteins

8.4.9. Catabolism of amino acids

8.5. Malolactic fermentation

8.5.1. Use of malolactic starter cultures

8.5.2.Contribution of MLF to the sensorial properties of wine

8.6. Other relevant aspects

8.6.1. Production of biogenic amines

8.6.2. Formation of ethyl carbamate precursors

8.6.3. Stress resistance

8.6.4. Presence of bacteriphages

8.6.5. Bacteriocine production

8.7. Interactions between lactic acid bacteria and other microorganisms

8.8. Wine spoilage by lactic acid bacteria

8.8.1. Lactic acid spoilage

8.8.2. Glycerol degradation and acrolein production

8.8.3. Extracellular polysaccharides

8.8.4. Off-flavors
Bibliography

Chapter 9. Acetic acid bacteria.

9.1. Introduction

9.2. General features

9.3. Nutrition and metabolism

9.3.1. Metabolism of carbohydrates

9.3.2. Metabolism of ethanol and other alcohols

9.3.3. Metabolism of organic acids

9.3.4. Metabolism of nitrogen

9.4. Taxonomy

9.4.1. Isolation

9.4.2. Identification

9.4.3. Molecular techniques for rapid identification of acetic acid bacteria

9.4.4. Molecular techniques for strain characterization of acetic acid bacteria

9.5. Development of acetic acid bacteria in wine enological processes

9.5.1. Association of acetic acid bacteria with grapes

9.5.2. Population dynamics of acetic acid bacteria during alcoholic fermentation

9.6. Critical factors for acetic acid bacteria development. Control methods

9.7. Wine spoilage by acetic acid bacteria

9.8. Interactions with other wine microorganisms

9.9. Final suggestions to avoid undesirable effects of acetic acid bacteria in wine
Bibliography

Chapter 10. Filamentous fungi

10.1. Introduction

10.2. Main phytopathogenic fungi in grapevine

10.2.1. Oidium

10.2.2. Midiu

10.2.3. Black rot

10.2.4. Excoriosis

10.2.5. Eutipiosis

10.3. Botrytuis cinerea as a model case study of grapevine phytopathogenic fungi

10.3.1. Infection of cultures

10.3.2. Chemical penetration mechanism

10.3.3. Research strategies for the phytopathogenic fungus B. cinerea
Bibliography

Chapter 11. Production of starter cultures for winemaking

11.1. Introduction

11.2. Yeasts

11.2.1. Historic notes

11.2.2. Isolation and selection

11.2.3. Production of biomass

11.2.4. Drying

11.2.5. Usage

11.3. Lactic acid bacteria

11.3.1. Selection and identification of strains

11.3.2. Biomass production

11.3.3. Freeze-drying packing and storage

11.3.4. Usage
Bibliography

Chapter 12. Conservation of wine related microbial strains

12.1. Introduction

12.2. Conservation methods for microbial strains

12.2.1. Methods for long-term storage

12.2.2. Alternative methods

12.2.3. Other conservation methods

12.2.4. Recovery

12.3. Conservation of yeast of enological interest

12.3.1. Long-term conservation

12.3.2. Short-term conservation

12.4. Conservation of wine bacteria

12.4.1. Long-term conservation methods

12.4.2. Short-term conservation

12.5. Conservation of wine filamentous fungi

12.5.1. Conservation methods for filamentous fungi
Bibliography

Chapter 13. HACPC in wine making. Ochratoxin A.

13.1. Introduction

13.2. Generalities on HACPC

13.2.1. Principles of HACPC

13.2.2. Previous programs required

13.3. Application of HACPC to winemaking

13.3.1. Background

13.3.2. Application of HACPC to ochratoxin A during winemaking
Bibliography

Chapter 14. Applied enological microbiology

14.1. Introduction

14.2. Microbiological control of grapes

14.3. Inoculation procedures

14.3.1. Direct inoculation

14.3.2. Preparation of ?pie de cuba? and calculation of inoculation percentages

14.4. Molecular methods for the monitoring of the microorganisms employed

14.5. Quality control of commercial yeasts and their implantation

14.6. Control of lactic acid bacteria implantation

14.7. Stuck fermentations, quick solutions

14.7.1. Procedures in case of stuck fermentations

14.8. Control of spoilage microorganisms

14.8.1. Cautions against yeast spoilage

14.8.2. Cautions against lactic acid bacteria spoilage

14.8.3. Cautions against acetic acid bacteria spoilage

14.9. Microbiology of the production of specific wines (Sherry wines, cava)

14.9.1. ?Fino? wines

14.9.2. ?Cava? wines

14.10. Microbiological quality control of the final product

14.11. New challenges for the scientific community: Genetically modified organisms.
Bibliography