ADVANCES IN APPLIED MICROBIOLOGY
CONTENTS SECTION I: GRAPE AND WINE MICROORGANISMS CHAPTER 1: YEASTS 1 1 INTRODUCTION 1 2 REPRODUCTION SEXUAL REPRODUCTION ASEXUAL REPRODUCTION 1 3 TAXONOMY CANDIDA DEKKERA HANSENIASPORA ISSATCHENKIA METSCHNIKOWIA PICHIA SACCHAROMYCES SACCHAROMYCODES SCHIZOSACCHAROMYCES 1 3 10 ZYGOSACCHAROMYCES 1 4 NUTRITIONAL REQUIREMENTS NITROGEN GROWTH AND SURVIVAL FACTORS 1 5 METABOLISM GLUCOSE SULFUR ODOR/FLAVOR COMPOUNDS GLYCOSIDASES MANNOPROTEINS CHAPTER 2: LACTIC ACID BACTERIA 2 1 INTRODUCTION 2 2 TAXONOMY LACTOBACILLUS OENOCOCCUS PEDIOCOCCUS 2 3 NUTRITIONAL REQUIREMENTS 2 4 METABOLISM ARGININE MALATE MANNITOL AND ERYTHRITOL DIACETYL AND OTHER ODOR/FLAVOR COMPOUNDS CHAPTER 3: ACETIC ACID BACTERIA 3 1 INTRODUCTION 3 2 TAXONOMY 3 3 NUTRITIONAL REQUIREMENTS 3 4 METABOLISM CARBOHYDRATES ETHANOL CHAPTER 4: MOLDS AND OTHER MICROORGANISMS 4 1 INTRODUCTION 4 2 ECOLOGY HABITATS 4 3 TAXONOMY ASPERGILLUS (BLACK MOLD) BOTRYTIS (GRAY MOLD) PENICILLIUM (BLUE-GREEN MOLD) 4 4 NUTRITIONAL REQUIREMENTS 4 5 METABOLISM MYCOTOXINS 4 6 OTHER MICROORGANISMS BACILLUS CLOSTRIDIUM STREPTOMYCES SECTION II: VINI? CATION AND WINERY PROCESSING CHAPTER 5: MANAGING MICROBIAL GROWTH 5 1 INTRODUCTION 5 2 PRESERVATIVES AND STERILANTS SULFUR DIOXIDE DIMETHYL DICARBONATE LYSOZYME SORBIC ACID OTHER PRESERVATIVES AND STERILANTS 5 3 FILTRATION PERPENDICULAR-FLOW FILTRATION (“NOMINAL” OR “DEPTH”) PERPENDICULAR-FLOW FILTRATION (“ABSOLUTE” OR “STERILE”) CROSS-FLOW/TANGENTIAL FILTRATION CHAPTER 6: MICROBIAL ECOLOGY DURING VINI? CATION 6 1 INTRODUCTION 6 2 NON-SACCHAROMYCES AND SACCHAROMYCES YEASTS GRAPES AND MUSTS ALCOHOLIC FERMENTATION POST-FERMENTATION 6 3 DEKKERA/BRETTANOMYCES ALCOHOLIC AND POST-FERMENTATION 6 4 LACTIC ACID BACTERIA ALCOHOLIC AND MALOLACTIC FERMENTATIONS 6 5 ACETIC ACID BACTERIA 6 6 MICROBIAL INTERACTIONS SACCHAROMYCES AND OENOCOCCUS SACCHAROMYCES AND LACTOBACILLUS OENOCOCCUS, PEDIOCOCCUS, AND LACTOBACILLUS OTHER INTERACTIONS CHAPTER 7: HARVEST AND PRE-FERMENTATION PROCESSING INTRODUCTION 7 2 HARVEST AND TRANSPORT 7 3 FRUIT QUALITY ASSESSMENT SOLUBLE SOLIDS PH AND TITRATABLE ACIDITY MICROBIAL SPOILAGE 7 4 MUST PROCESSING ENZYMES SUSPENDED SOLIDS PRE-FERMENTATION MACERATION (COLD-SOAK) THERMOVINI? CATION INERT GASSING 7 5 PROCESSING MICROBIALLY DETERIORATED FRUIT ENZYMATIC BROWNING FERMENTATION DIF? CULTIES CLARI? CATION CONCERNS MANAGEMENT STRATEGIES 7 6 JUICE STORAGE (MUTÉ) CHAPTER 8: FERMENTATION AND POST-FERMENTATION PROCESSING 8 1 INTRODUCTION 8 2 MUST SUPPLEMENTATION 8 3 ALCOHOLIC FERMENTATION HISTORICAL PERSPECTIVE OF STARTER CULTURES PREPARATION OF STARTER CULTURES STRAIN SELECTION TEMPERATURE IMMOBILIZED YEAST 8 4 “NATURAL” FERMENTATIONS 8 5 FERMENTATION PROBLEMS SLUGGISH/STUCK FERMENTATIONS HYDROGEN SUL? DE 8 6 MALOLACTIC FERMENTATION TIMING OF INOCULATION USE OF SCHIZOSACCHAROMYCES 8 7 POST-FERMENTATION PROCESSING AGING AND STORAGE ADJUSTMENT OF VOLATILE ACIDITY 8 8 BOTTLING CHAPTER 9: WINERY CLEANING AND SANITIZING 9 1 INTRODUCTION 9 2 SAFETY ISSUES 9 3 WATER QUALITY 9 4 PRELIMINARY CLEANING 9 5 DETERGENTS, CLEANERS, AND SURFACTANTS ALKALI ACIDS SURFACTANTS 9 6 RINSES 9 7 SANITIZERS IODINE QUATERNARY AMMONIUM COMPOUNDS ACIDULATED SULFUR DIOXIDE PEROXIDES CHLORINE AND CHLORINATED FORMULATIONS HOT WATER AND STEAM OZONE 9 8 SANITATION MONITORING 9 9 SCHEDULES AND DOCUMENTATION CHAPTER 10: QUALITY POINTS PROGRAM 10 1 INTRODUCTION 10 2 DEVELOPING QP PROGRAMS 10 3 PROCESSING AND FLOWCHART 10 4 QUALITY FACTOR ANALYSIS 10 4 1 EXAMPLES OF QUALITY FACTORS 10 4 2 PREVENTIVE MEASURES 10 4 3 CRITICAL QUALITY POINTS 10 5 CRITICAL LIMITS 10 6 MONITORING PROCEDURES 10 7 CORRECTIVE ACTIONS 10 8 RECORD-KEEPING AND DOCUMENTATION 10 9 VERIFICATION CHAPTER 11: WINE SPOILAGE 11 1 INTRODUCTION 11 2 SPOILAGE MICROORGANISMS 11 2 1 ACETOBACTER 11 2 2 DEKKERA/BRETTANOMYCES 11 2 3 FILM YEASTS 11 2 4 SACCHAROMYCODES 11 2 5 ZYGOSACCHAROMYCES 11 3 WINE FAULTS 11 3 1 VOLATILE ACIDITY 11 3 2 ETHYL CARBAMATE 11 3 3 MOUSINESS 11 3 4 POST-MLF BACTERIAL GROWTH 11 3 5 GERANIUM ODOR/TONE 11 3 6 BIOGENIC AMINES 11 3 7 ACROLEIN 11 3 8 MANNITOL 11 3 9 ROPINESS 11 3 10 TARTARIC ACID UTILIZATION SECTION III: LABORATORY PROCEDURES AND PROTOCOLS CHAPTER 12: BASIC MICROSCOPY 12 1 INTRODUCTION 12 2 MICROSCOPES 12 2 1 MAGNI? CATION 12 2 2 RESOLUTION 12 2 3 CONTRAST 12 2 4 FLUORESCENCE MICROSCOPY 12 3 USING MICROSCOPES 12 3 1 COMPONENTS 12 3 2 GENERAL USE 12 3 3 CALIBRATION 12 4 PREPARING SMEARS 12 4 1 FROM LIQUID MEDIA 12 4 2 FROM SOLID MEDIA 12 5 PREPARING WET MOUNTS 12 6 PREPARING MOLD SLIDE CULTURES CHAPTER 13: MEDIA PREPARATION AND CULTURE TECHNIQUES 13 1 INTRODUCTION 13 2 PHYSICAL/CHEMICAL REQUIREMENTS FOR CULTIVATION 13 2 1 CARBON AND NITROGEN 13 2 2 OXYGEN 13 2 3 HYDROGEN ION CONCENTRATION (PH) 13 2 4 MOISTURE AND WATER ACTIVITY 13 2 5 INCUBATION TEMPERATURE AND CONDITIONS 13 2 6 SELECTIVE AGENTS 13 3 STERILIZATION OF LABORATORY MEDIA AND SUPPLIES 13 3 1 BOILING WATER 13 3 2 STEAM STERILIZATION 13 3 3 DRY HEAT 13 3 4 STERILE FILTRATION 13 3 5 CHEMICAL STERILIZATION 13 4 STORAGE OF PREPARED MEDIA 13 5 MEDIA FOR YEASTS AND MOLDS 13 5 1 WORT MEDIUM 13 5 2 GRAPE JUICE MEDIUM 13 5 3 WL MEDIUM 13 5 4 BRETTANOMYCES MEDIUM A 13 5 5 BRETTANOMYCES MEDIUM B 13 5 6 BRETTANOMYCES MEDIUM C 13 5 7 BRETTANOMYCES MEDIUM D 13 5 8 LYSINE MEDIUM 13 5 9 ZYGOSACCHAROMYCES MEDIUM 13 6 MEDIA FOR LACTIC ACID BACTERIA 13 6 1 APPLE JUICE ROGOSA MEDIUM 13 6 2 TOMATO JUICE–GLUCOSE–FRUCTOSE–MALATE MEDIUM 13 6 3 HETEROFERMENTATION-ARGININE BROTH 13 7 MEDIA FOR ACETIC ACID BACTERIA GLUCOSE–YEAST EXTRACT–CARBONATE MEDIUM 13 7 2 MANNITOL–YEAST EXTRACT–PEPTONE MEDIUM 13 7 3 YEAST EXTRACT–PEPTONE–ETHANOL MEDIUM 13 8 ASEPTIC TRANSFER TECHNIQUES 13 8 1 TRANSFERS FROM SOLID TO SOLID MEDIA 13 8 2 TRANSFERS FROM SOLID TO LIQUID MEDIA 13 8 3 TRANSFERS FROM LIQUID TO SOLID MEDIA 13 9 ISOLATION OF MICROORGANISMS 13 10 MAINTENANCE AND STORAGE OF CULTURES 13 10 1 PREPARATION OF AGAR SLANTS AND STABS 13 10 2 GLYCEROL SUSPENSIONS 13 10 3 FREEZE-DRYING (YEASTS) 13 10 4 FREEZE-DRYING (LACTIC ACID BACTERIA) CHAPTER 14: ESTIMATION OF POPULATION DENSITY 14 1 INTRODUCTION 14 2 SAMPLING 14 3 SAMPLE DILUTION 14 4 DIRECT MICROSCOPIC COUNT 14 4 1 USING A MICROSCOPE COUNTING CHAMBER 14 4 2 METHYLENE BLUE 14 4 3 PONCEAU-S 14 4 4 WOLFORD’S STAIN 14 5 DIRECT PLATING 14 5 1 POUR PLATES 14 5 2 SPREAD PLATES 14 5 3 MEMBRANE FILTRATION 14 6 BIOLUMINESCENCE 14 7 NEPHELOMETRY AND OPTICAL DENSITY CHAPTER 15: IDENTI? CATION OF WINE MICROORGANISMS 15 1 INTRODUCTION 15 2 IDENTIFYING MICROORGANISMS 15 3 YEASTS AND MOLDS 15 3 1 ASSIMILATION OF CARBON AND NITROGEN 15 3 2 DEMONSTRATION OF ASCOSPORES 15 3 3 DEMONSTRATION OF MYCELIA/PSEUDOMYCELIA 15 3 4 FERMENTATION OF CARBOHYDRATES 15 4 BACTERIA 15 4 1 AMMONIA FROM ARGININE 15 4 2 CATALASE 15 4 3 DEXTRAN FROM SUCROSE 15 4 4 FERMENTATION OF CARBOHYDRATES 15 4 5 GAS FROM GLUCOSE 15 4 6 GRAM STAIN 15 4 7 KETOGENESIS 15 4 8 LACTATE FROM GLUCOSE 15 4 9 MALATE UTILIZATION (MONITORING MLF) 15 4 10 MANNITOL FROM FRUCTOSE 15 4 11 OXIDATION OF ETHANOL 15 4 12 OXIDATION OF LACTATE CHAPTER 16: OTHER TECHNOLOGIES FOR IDENTI? CATION AND ENUMERATION 16 1 INTRODUCTION 16 2 PHENOTYPICAL IDENTIFICATION 16 2 1 BIOLOG SYSTEM 16 2 2 FATTY ACID METHYL ESTER ANALYSIS 16 2 3 PROTEIN CHARACTERIZATION 16 2 4 ELECTROPHORETIC CHARACTERIZATION OF ISOZYMES (ZYMOGRAMS) 16 3 IMMUNOCHEMICAL TECHNIQUES 16 3 1 ENZYME-LINKED IMMUNOSORBENT ASSAY 16 3 2 IMMUNOCHEMICAL FLUORESCENCE MICROSCOPY 16 4 PHYLOGENETIC ANALYSES 16 4 1 POLYMERASE CHAIN REACTION 16 4 2 GEL ELECTROPHORESIS 16 4 3 QUANTITATIVE POLYMERASE CHAIN REACTION 16 4 4 HYBRIDIZATION PROBES 16 4 5 FLUORESENCE IN SITU HYBRIDIZATION 16 4 6 RIBONUCLEIC ACID ANALYSIS 16 5 PROBE DETECTION SYSTEMS 16 5 1 TAQMAN® PROBES 16 5 2 MOLECULAR BEACONS 16 5 3 SCORPIONS® 16 5 4 PEPTIDE NUCLEIC ACID CHEMILUMINESCENT IN SITU HYBRIDIZATION PROBES 16 6 OTHER MOLECULAR METHODS 16 6 1 RESTRICTION FRAGMENT LENGTH POLYMORPHISMS 16 6 2 PULSED FIELD GEL ELECTROPHORESIS 16 6 3 ADDITIONAL METHODS 16 7 EXTRACHROMOSOMAL ELEMENTS (SATELLITES) CHAPTER 17: CHEMICAL AND PHYSICAL INSTABILITIES CRYSTALLINE INSTABILITIES TARTRATES 17 3 “CRYSTAL-LIKE” INSTABILITIES CORK DUST 17 3 2 DIATOMACEOUS EARTH FIBROUS INSTABILITIES 17 5 AMORPHOUS INSTABILITIES PROTEIN 17 5 2 PHENOLICS 17 5 3 GLUCANS, PECTINS, AND STARCH METAL CASSE CHAPTER 18: LABORATORY SETUP 18 1 INTRODUCTION 18 2 MICROSCOPE AND PH METER 18 3 AUTOCLAVE 18 4 CENTRIFUGE AND FILTERS 18 5 INCUBATORS 18 6 WATER BATHS 18 7 GLASS AND PLASTICWARE 18 8 MEDIA 18 9 PHOTOMETERS 18 10 LAMINAR FLOW HOODS 18 11 MISCELLANEOUS CHAPTER 19: LABORATORY SAFETY 19 1 INTRODUCTION 19 2 INJURY AND ILLNESS PREVENTION PROGRAM 19 2 1 TRAINING 19 2 2 INFORMATION 19 2 3 COMMUNICATION 19 2 4 EYEWASH STATIONS AND SAFETY SHOWERS 19 2 5 FIRE ALARMS AND PREVENTION 19 2 6 FIRST AID 19 2 7 PERSONAL PROTECTIVE EQUIPMENT 19 3 EXAMPLES OF SAFETY ISSUES 19 3 1 BIOHAZARD AND CHEMICAL WASTE 19 3 2 ELECTRICITY 19 3 3 HEAT AND STEAM 19 3 4 MACHINERY SAFEGUARDS 19 3 5 STORAGE 19 3 6 ULTRAVIOLET LIGHT