Microbial Fermentations in Nature and as Designed Processes E-Book
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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
MICROBIAL FERMENTATIONS IN NATURE AND AS DESIGNED PROCESSES Fermentation is one of the most important metabolic tools that biology has developed and microorganisms in many ways seem to have become the true masters of fermentative metabolism. Each of the fermentative microbial functions evolved to fit an energetic opportunity, and each function has ecological value. This book provides its readers with: * Understanding regarding the commonalities and distinctions between aerobic and anaerobic fermentations as performed by microorganisms. * A summary of knowledge regarding the ways in which animals and plants depend upon symbiotic interactions with their fermenting microbial partners including the deconstruction of complex polysaccharides. Information is also included about how those natural technologies constitute adaptation into designed processes for anaerobic degradation of lignocellulosic materials. * The important role of rhizosphere microbes that facilitate availability of inorganic and organic phosphates for plants. These phosphates get stored in the plant's seeds. After ruminant animals ingest the seeds, enzymes produced by gastrointestinal microbial fermentation allow the animals to utilize their dietary phosphates. * History of how microbial fermentation has been harnessed from prehistoric times to the present for processing and preserving food products for humans and fodder for our domesticated animals. * Insight into the ways that microbial fermentations are used as an engineering tool for producing chemicals, including enzymes and pharmaceuticals, which improve the health of ourselves and our domesticated animals. * Perspectives on possible future research directions for the field of applied microbial fermentation that will help to advance agriculture and industry.
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Table of Contents
COVER
TITLE PAGE
COPYRIGHT PAGE
DEDICATION
LIST OF FIGURES
LIST OF CONTRIBUTORS
PREFACE
SECTION I: AN INTRODUCTION TO MICROBIAL FERMENTATION
CHAPTER 1: MICROBIAL FERMENTATION
1.1 INTRODUCTION TO FERMENTATION PROCESSES
1.2 EXAMPLES OF MICROBIAL FERMENTATIONS IN NATURE
1.3 DESIGNING FERMENTATION PROCESSES
1.4 THE DISPOSAL OF WASTE PRODUCTS FROM FERMENTATIONS
1.5 FERMENTATIONS THAT PRODUCE AND PRESERVE FOOD FOR HUMANS
1.6 SILAGE FERMENTATIONS THAT PRODUCE AND PRESERVE FOOD FOR LIVESTOCK
1.7 TOBACCO FERMENTATIONS
1.8 COMPOST FERMENTATIONS AND THE ANAEROBIC DIGESTION OF FOOD WASTES FOR GENERATING BIOGAS
1.9 FERMENTATIONS THAT PRODUCE CHEMICALS, ENZYMES, AND PHARMACEUTICALS
1.10 SUMMARY
REFERENCES
CHAPTER 2:
RHODOTORULA TORULOIDES
AS A BIOFACTORY OF CAROTENOIDS, LIPIDS, AND ENZYMES
2.1 INTRODUCTION
2.2
RHODOTORULA TORULOIDES
2.3 MECHANISM OF LIPID BIOSYNTHESIS
2.4 FACTORS AFFECTING INTRACELLULAR LIPID BIOSYNTHESIS
2.5 CAROTENOID BIOSYNTHESIS BY
RHODOTORULA TORULOIDES
2.6 MECHANISM OF CAROTENOID BIOSYNTHESIS
2.7 STRATEGIES TO INCREASE CAROTENOID SYNTHESIS
2.8 BIOSYNTHESIS OF PHENYLALANINE AMMONIA‐LYASE BY
R. TORULOIDES
2.9 CONCLUSIONS AND FUTURE TRENDS
REFERENCES
SECTION II: THE ROLE OF MICROBIAL FERMENTATION IN DIGESTION PROCESSES
CHAPTER 3: GUT MICROBIAL ECOLOGY
3.1 INTRODUCTION
3.2 VARIATION ALONG THE GUT
3.3 PHYLOGENY, GUT MORPHOLOGY, AND FEEDING STRATEGY SHAPE MICROBIAL COMMUNITIES
3.4 A PREDICTIVE ECOLOGICAL FRAMEWORK FOR THE GUT
3.5 APPLICATIONS TO HOST MANAGEMENT
3.6 CONCLUSION
REFERENCES
CHAPTER 4: FERMENTATION IN THE RUMEN
4.1 INTRODUCTION
4.2 NUTRITIONAL PHYSIOLOGY OF RUMINANTS
4.3 THE RUMEN MICROBIAL COMMUNITY
4.4 BIOCHEMISTRY OF RUMEN FERMENTATION
4.5 MANIPULATION OF RUMEN FERMENTATION
4.6 CONCLUSIONS
REFERENCES
CHAPTER 5: MICROBIAL DEGRADATION OF LIGNOCELLULOSE IN NATURAL AND ENGINEERED SYSTEMS – FROM THE SMALLEST TO THE BIGGEST BIOREACTOR
5.1 INTRODUCTION TO LIGNOCELLULOSE AND ITS DEGRADATION IN VARIOUS SYSTEMS
5.2 ENZYMATIC MECHANISMS OF LIGNOCELLULOSE DEGRADATION AND CARBOHYDRATE‐ACTIVE ENZYMES
5.3 ANAEROBIC DIGESTION OF PLANT BIOMASS
5.4 OVERVIEW OF THE MOST EFFICIENT LIGNOCELLULOSE‐DEGRADING SYSTEMS DEVELOPED BY NATURE
5.5 FROM COMPARISON TO BIOPROSPECTING: WHAT CAN WE LEARN FROM THE TERMITE GUT SYSTEM TO IMPROVE INDUSTRIAL LIGNOCELLULOSE BIOPROCESSING
5.6 BEYOND THE STANDARD LIGNOCELLULOSE DEGRADATION: NEW APPLICATIONS AND FUTURE CHALLENGES
5.7 CONCLUSIONS
ACKNOWLEDGMENTS
REFERENCES
SECTION III: USING MICROBIAL FERMENTATION TO PRODUCE BEER AND WINE
CHAPTER 6: ARCHEOLOGICAL EVIDENCE FOR FERMENTED ALCOHOLIC BEVERAGES IN RITUAL FEASTS OF NEOLITHIC CHINA
6.1 INTRODUCTION
6.2 METHODS: IDENTIFYING BREWING METHODS IN NEOLITHIC CHINA
6.3 BREWING BEER AND NEOLITHIC REVOLUTION IN THE EARLY NEOLITHIC (ca. 9000 TO 7000 cal. BP)
6.4 DEVELOPMENT OF DIVERSE BREWING METHODS IN THE MIDDLE NEOLITHIC (ca. 7000 TO 4600 cal. BP)
6.5 INDIVIDUALIZED DRINKING TRADITION AND DEVELOPMENT OF SOCIAL COMPLEXITY IN THE LATE NEOLITHIC (4600 TO 3800 BP)
6.6 DISCUSSION AND CONCLUSIONS
ACKNOWLEDGEMENTS
REFERENCES
CHAPTER 7: BREWS OF THE PAST: BIOARCHAEOLOGY OF MICROBIAL FERMENTATION
7.1 INTRODUCTION
7.2 HISTORIC ALE AND BEER
7.3 GOLDEN AGES OF BREWING
7.4 EARLY BEERS. EGYPTIAN AND MESOPOTAMIAN
7.5 GRUIT ALES
7.6 MONASTIC BREWING AND EARLY‐HOPPED ALES
7.7 VICTORIAN AND EDWARDIAN HIGH‐HOPPED BEERS
7.8 CONCLUSIONS
REFERENCES
CHAPTER 8: AN ACCIDENTAL ART FORM: SPONTANEOUS FERMENTATION OF BEER
8.1 INTRODUCTION
8.2 FERMENTATION AND ITS SPONTANEITY
8.3 MUCH A BREW ABOUT NOTHING
8.4 CURTAIN CALL
REFERENCES
CHAPTER 9: JAPANESE TRADITIONAL FERMENTATION USES SOLID‐STATE FUNGAL CULTIVATION TO PRODUCE SAKE
9.1 INTRODUCTION TO TRADITIONAL JAPANESE FERMENTATIONS PERFORMED USING
ASPERGILLUS ORYZAE
9.2 PREPARATION OF RICE KOJI BY CONTROLLED FUNGAL GROWTH
9.3 FERMENTATION OF THE RICE AS A MASH TO PRODUCE ETHANOL
9.4 SUMMARY
REFERENCES
SECTION IV: USING MICROBIAL FERMENTATION TO PRODUCE FOOD AND FODDER
CHAPTER 10: SAFETY DEMONSTRATION OF FOOD AND FEED CULTURES
10.1 INTRODUCTION
10.2 FERMENTED FOOD PRODUCTS AND INTERNATIONAL TRADE
10.3 FOOD FERMENTATION. FOOD AND FEED CULTURES
10.4 HISTORY OF (SAFE) USE
10.5 SAFETY CONSIDERATIONS
10.6 OPPORTUNISTIC INFECTIONS BY LACTIC ACID BACTERIA
10.7 ANTIBIOTIC RESISTANCE
10.8 FOOD FERMENTATION AS END USE OF MICROBIAL FOOD CULTURES: HISTORY OF SAFE USE
10.9 BENEFIT – RISK ASSESSMENT OF FOOD AND FEED CULTURES
10.10 UNDERLYING FACTORS AND SPECIFIC HEALTH CONDITIONS OF CONCERN VS. OPPORTUNISTIC INFECTIONS
10.11 OPPORTUNISTIC INFECTIONS AND MICROBIAL FOOD CULTURES: GUIDELINES TO HEATH CARE PRACTITIONERS
10.12 FOOD FERMENTATION AS END USE OF FOOD AND FEED CULTURES
10.13 CONCLUSION
REFERENCES
CHAPTER 11: STARTER CULTURES AND THEIR ROLE IN FERMENTED FOODS
11.1 INTRODUCTION
11.2 FERMENTATION
11.3 FERMENTED FOODS
11.4 STARTERS
11.5 THE ROLE OF STARTERS IN FOOD SAFETY
11.6 THE ROLE OF STARTERS IN FOOD SENSORY PROPERTIES
11.7 STARTERS PROMOTE INNOVATION IN FERMENTED FOODS
11.8 THE HEALTH BENEFITS OF FERMENTED FOODS
11.9 CONCLUSIONS
ACKNOWLEDGMENTS
REFERENCES
CHAPTER 12: AFRICAN FERMENTED FOODS AND BEVERAGES. POTENTIAL IMPACT ON HEALTH
12.1 INTRODUCTION
12.2 SOME STAPLE FERMENTABLE FOODS IN AFRICA
12.3 THE DIVERSITY OF GUT MICROBIOTA
12.4 TRADITIONAL FERMENTATION STRATEGIES
12.5 FERMENTED NON‐ALCOHOLIC STARCHY FOODS
12.6 COMMON AFRICAN FERMENTED ALCOHOLIC BEVERAGES
12.7 SOME AFRICAN FERMENTED ANIMAL PRODUCTS
12.8 POPULAR AFRICAN TRADITIONAL FERMENTED FOODS AND BEVERAGES
12.9 EXAMPLES OF UNDESIRABLE EFFECTS OF FERMENTED PRODUCTS
12.10 CONCLUSIONS
FURTHER READING
CHAPTER 13: FERMENTED FOODS OF SOUTH ASIA
13.1 INTRODUCTION
13.2 ORIGIN, HISTORY, AND ROLE OF FERMENTATION
13.3 FERMENTATION OF FOODS
13.4 SOUTH ASIAN COUNTRIES AND INDIGENOUS FERMENTED FOODS – INDIA
13.5 INDIGENOUS FERMENTED FOODS OF SRI LANKA
13.6 INDIGENOUS FERMENTED FOODS OF BHUTAN
13.7 FERMENTATION – AN ECONOMIC APPROACH
13.8 FOOD SAFETY AND FOOD PRESERVATION
13.9 FOOD SAFETY RISKS IN TRADITIONAL FOODS
13.10 SUMMARY AND FUTURE PROSPECTS
13.11 CONCLUSION
REFERENCES
CHAPTER 14: THE ENSILING FERMENTATION OF FORAGE CROPS
14.1 INTRODUCTION
14.2 THE ENSILING FERMENTATION
14.3 THE FOUR PHASES OF ENSILING
14.4 STEPS OF ON‐FARM ENSILING
14.5 ENVIRONMENTAL ASPECTS OF ENSILING
14.6 UNCONVENTIONAL ENSILING
14.7 DEVELOPMENT OF SILAGE RESEARCH TOOLS
14.8 CONCLUSIONS
ACKNOWLEDGMENT
REFERENCES
SECTION V: A CLOSING PERSPECTIVE OF MICROBIAL FERMENTATION
CHAPTER 15: THE INTERSECTION OF MICROBIAL FERMENTATION AND EVOLUTIONARY ECOLOGY: WE PROVIDE THE HABITAT, YOU PROVIDE THE FERMENTATION
15.1 INTRODUCTION TO THE COMPETITIVE ECOLOGY OF MICROBIAL FERMENTATION
15.2 EXAMPLES OF SYMBIOTIC NICHE COOPERATIONS BETWEEN MICROBES AND THEIR ANIMAL HOSTS THAT DEPEND UPON MICROBIAL FERMENTATION
15.3 EXAMPLES OF USING SYMBIOTIC NICHE COMPETITIONS THAT RELY UPON MICROBIAL FERMENTATION TO PRODUCE FOOD FOR HUMANS AND LIVESTOCK
15.4 EXAMPLES OF USING MICROBIAL FERMENTATION TO PRODUCE INDUSTRIAL CHEMICALS
15.5 SUMMARY
REFERENCES
INDEX
END USER LICENSE AGREEMENT
List of Tables
Chapter 1
TABLE 1.1 Examples of bacteria that are present in food fermentations.
TABLE 1.2 Examples of fungi that are present in food fermentations.
TABLE 1.3 Examples of bacteria that are present in silage fermentations.
TABLE 1.4 Examples of fungi and oomycetes that are present in silage fermen...
TABLE 1.5 Examples of bacteria that are present in tobacco fermentations.
TABLE 1.6 Examples of fungi that are present in tobacco fermentations.
TABLE 1.7 Examples of bacteria that are present in compost fermentations.
TABLE 1.8 Examples of fungi that are present in compost fermentations.
TABLE 1.9 Examples of Archaea used in the fermentation production of chemic...
TABLE 1.10 Examples of bacteria used in the fermentation production of chem...
TABLE 1.11 Examples of fungi used in the fermentation production of chemica...
TABLE 1.12 A master list of viral families that affect prokaryotes.
TABLE 1.13 A master list of viral families and unassigned (floating) genera...
TABLE 1.14 Examples of how purified products from microbial fermentations a...
Chapter 2
TABLE 2.1 Lipid synthesis and growth of various Rhodotorula toruloides stra...
TABLE 2.2 Carotenoid biosynthesis by different Rhodotorula toruloides strai...
Chapter 3
TABLE 3.1 Predicted responses to major drivers of gut microbial diversity....
Chapter 5
TABLE 5.1 Main industrial processes relying on the microbial degradation of...
TABLE 5.2 Composition of the most common lignocellulosic biomasses of indus...
TABLE 5.3 Characteristics of the most efficient insect gut lignocellulose d...
Chapter 6
TABLE 6.1 Neolithic sites revealed alcohol remains in China.
Chapter 7
TABLE 7.1 Major components of gruit and their characteristics.
TABLE 7.2 Metagenomic profile of bacteria in three bottles retrieved from t...
Chapter 8
TABLE 8.1 Microbial cast list: in order of major appearance.
a
Chapter 10
TABLE 10.1 Microbiological cut‐off values (mg/l).
Chapter 11
TABLE 11.1 Classification of fermented foods based on their main fermentati...
TABLE 11.2 Categories of fermented foods (FF): examples and recent literatu...
TABLE 11.3 Main microbial groups of starter cultures.
Chapter 12
TABLE 12.1 The most at‐risk of food insecurity among the 54 African countri...
Chapter 13
TABLE 13.1 History of fermented foods.
TABLE 13.2 Indigenous fermented foods of Gujarat and Rajasthan.
TABLE 13.3 Indigenous fermented foods of Uttarakhand, Uttar Pradesh, Haryan...
TABLE 13.4 Indigenous fermented foods of Himachal Pradesh.
TABLE 13.5 Indigenous fermented foods of Madhya Pradesh and Goa.
Chapter 14
TABLE 14.1 Typical fermentation end‐products of various silage.
TABLE 14.2 The effect of maturity stage on yields and wheat plants composit...
TABLE 14.3 Results of microbiome analysis of 90–100 days laboratory silages...
List of Illustrations
Chapter 2
FIGURE 2.1 Metabolic pathways of
Rhodosporidium toruloides
. The metabolites ...
FIGURE 2.2
Rhodotorula toruloides
carotenoid biosynthetic pathway.
Chapter 3
FIGURE 3.1 (a) Grime's ecological model describes three primary strategies i...
Chapter 4
FIGURE 4.1 Overall scheme of rumen digestion of polysaccharides (inside of s...
FIGURE 4.2 Metabolism of pyruvate to acetate and butyrate. Main routes of ca...
FIGURE 4.3 Propionate formation via randomizing (succinate) and non‐randomiz...
FIGURE 4.4 Main pathways of metabolic hydrogen transactions in rumen ferment...
FIGURE 4.5 Simplified scheme of rumen, small intestine, and liver nitrogen m...
Chapter 5
FIGURE 5.1 Schematic overview of the anaerobic digestion of plant biomass an...
FIGURE 5.2 Simplified structure of the main lignocellulosic polysaccharides ...
FIGURE 5.3 Characterization of the termite gut system and proposed exploitat...
FIGURE 5.4 Comparison of microbial communities and their polysaccharide degr...
FIGURE 5.5 Glucoside hydrolases in microbial genomes from the anaerobic dige...
FIGURE 5.6 Comparison of the main glycoside hydrolase (GH) families targetin...
FIGURE 5.7 Anaerobic fungi in full‐scale anaerobic digestion systems (a) and...
Chapter 6
FIGURE 6.1 Examples of ancient fungal elements found on Neolithic pottery ve...
FIGURE 6.2 Globular jars unearthed from major sites in early Neolithic China...
FIGURE 6.3 Regional archeological cultural development and alcohol‐related p...
FIGURE 6.4 Examples of serving and drinking vessels during the late Neolithi...
Chapter 7
FIGURE 7.1 Embossed and screw top Victorian beer bottles.
FIGURE 7.2 Profiles of major features of brewing through periods of developm...
FIGURE 7.3 Example ingredients of gruit. (a) Bob myrtle/sweet gale; (b) Juni...
FIGURE 7.4 (a) Bottle #2 from the Wallachia shipwreck in preparation for ana...
Chapter 8
FIGURE 8.1 Allagash Brewing Company coolship room. Windows are propped open ...
FIGURE 8.2 Allagash Brewing Company aging barrels. “CS” refers to “Coolship....
Chapter 9
FIGURE 9.1 An electron microscopy image of an
A. oryzae
conidiophore and a p...
FIGURE 9.2 Haze komi and invasive growth of
A. oryzae
(green) into steamed r...
FIGURE 9.3 A tank to create the fermentation mash and fresh sale.
Chapter 11
FIGURE 11.1 Major mycotoxins and fungal species that produce them.
Chapter 12
FIGURE 12.1 Cassava roots and leaves.
FIGURE 12.2 Moringa leaves and trees.
FIGURE 12.3
Uapaka kirkiana
or wild loquat (
mushuku/muzhanje
);
Ziziphus maur
...
FIGURE 12.4 A diet high in fermented food or beverage decreases inflammatory...
FIGURE 12.5 Mitochondrial yeast metabolism, maltose being the best sugar sou...
FIGURE 12.6
Brassica tournefortii
on the left. Coffee beans in the middle. K...
FIGURE 12.7 Typical Sudanese
kissra
making and a full meal with several ferm...
FIGURE 12.8 Ripe bananas being prepared for fermentation in Burundi.
FIGURE 12.9 Preparation of wild water mellon wine.
FIGURE 12.10 Cashew apple fruit on the left with the unique external seed an...
FIGURE 12.11 Traditional preparation of amarula drink (“ocanhu”) in Mozambiq...
FIGURE 12.12 Images of masau (
Ziziphus mauritiana
), tambarind (
Tamarindus in
...
FIGURE 12.13 Milk and butter
smen
.
FIGURE 12.14 The multipurpose dawadawa tree, known as the African locust bea...
FIGURE 12.15 Commercially cassava beer is produced in Mozambique, brand name...
FIGURE 12.16 Palm wine created from the sap of various species of palm trees...
FIGURE 12.17 Aspartame, a well‐known artificial sweetener of sodas, candy, c...
Chapter 13
FIGURE 13.1 Types of food fermentation.
FIGURE 13.2 Fermented foods of Tamil Nadu.
FIGURE 13.3 Fermented foods of Kerala.
FIGURE 13.4 Fermented foods of North East–Indo‐Nepal Himalayan region.
FIGURE 13.5 Fermented foods of Sri Lanka.
Chapter 14
FIGURE 14.1 Some forage crops for ensiling.
FIGURE 14.2 The major steps of silage making.
FIGURE 14.3 Assessing corn grain maturity by milk line. The Milk Line (the b...
FIGURE 14.4 The effect of applying
L. plantarum
at ensiling on rate of pH de...
FIGURE 14.5 Ideal (left) vs. poor sealing (right).
FIGURE 14.6 Silage silo types.
FIGURE 14.7 Anaerobic mini‐silos (Weck™, Wehr‐Offlingen, Germany). The sprin...
Guide
Cover Page
Title Page
Copyright Page
Dedication
LIST OF FIGURES
LIST OF CONTRIBUTORS
PREFACE
Table of Contents
Begin Reading
Index
WILEY END USER LICENSE AGREEMENT
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MICROBIAL FERMENTATIONS IN NATURE AND AS DESIGNED PROCESSES
Edited by
CHRISTON J. HURST
Cincinnati, OH, USA
Universidad del Valle, Santiago de Cali, Valle, Colombia
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DEDICATION
Daniel Yee‐Chak Fung was born in Hong Kong on May 15, 1942 and loving support from his family enabled Daniel to emerge from the Pacific War with a tremendous sense of optimism about life. Daniel eventually began his university training with a scholarship at the International Christian University in Tokyo, Japan, where he received a Bachelor of Arts Degree during 1965. He next earned a Master of Science degree in Public Health at the University of North Carolina, Chapel Hill during 1967. Soon afterward, during 1969 he was awarded a Doctor of Philosophy degree from Iowa State University. Daniel then found a place that truly felt like home when he became a professor of food science at Kansas State University in Manhattan, Kansas. He also found humor in explaining to his relatives that yes, he was at a university in Manhattan, but it was in the middle of the Kansas prairie and not in New York City. Daniel’s professional interest was to understand and explain the microbiology of food science. He earned tremendous international recognition for his efforts on the rapid detection of microbial contamination in food. Although, perhaps Daniel had the most fun when teaching a course on authentic Chinese cooking in what he described as small‐town USA.
I had the extremely good fortune to meet Daniel around 1990 during the annual meetings of the American Society for Microbiology. From then onward, I hoped to see him each time that I attended a microbiology conference. Daniel was one of the most enthusiastic people who ever could be imagined. His positive attitude constantly was encouraging to everyone around him. His smile and kindness seemed to brighten any room.
Eventually, many years ago I came to guess that something was wrong with Daniel’s health when he did not return a telephone call. I then spoke with the chairman of his department and learned that Daniel was in a group home for Alzheimer’s patients. I sent to Daniel a greeting card and included a photograph of myself with my name on the back of the photograph. I guessed that Daniel might recognize my face as being familiar even if remembering my name and the circumstances of our acquaintance might be challenging. Unfortunately, my good friend Daniel passed away on December 1, 2019.
Knowing Daniel was a great honor. The memory of his presence remains with me as a source of inspiration and I do very proudly dedicate my efforts on this book to him.
Daniel Yee‐Chak Fung 1942–2019
LIST OF FIGURES
2.1
Metabolic pathways of
Rhodosporidium toruloides
. The metabolites connected by arrows (a single arrow represents a step) and involved enzymes (named in the center of the arrow) are represented. Abbreviations are shown for the commonly used names of metabolites and enzymes. The endoplasmic reticulum, mitochondria, lipid body, and peroxisome are also present as cellular compartments. The enzymes with names in green coincide with genes that have been previously defined. FA is an abbreviation for fatty acid; FAME is an abbreviation for fatty acid methyl ester; FFA is an abbreviation for free fatty acid; FAEE is an abbreviation for fatty acid ethyl ester; TAG is an abbreviation for triacylglycerol, and VLFA is an abbreviation for very long chain fatty acid.
2.2
Rhodotorula toruloides
carotenoid biosynthetic pathway.
3.1
(a) Grime’s ecological model describes three primary strategies in plants (ruderal, competitive, and stress‐tolerant) in response to the environment. Grime originally defined “competitive species” as competing for resources and/or overlapping niche space. (b) Here, I adapt that framework to predict which types of microbial taxa are favored in species with different gut lengths and associated transit time; feeding strategies, specifically with regard to dietary fiber; and oxygen levels present in the gut. In my microbial model, “opportunistic species” include potential pathogens, and “competitive species” include microbial taxa that compete amongst themselves and with the host for easily digestible nutrients (e.g. sugar, starch, proteins, and lipids).
4.1
Overall scheme of rumen digestion of polysaccharides (inside of sky blue squircle), fermentation of hexoses and pentoses to pyruvate via glycolysis (inside of red squircle), pyruvate metabolism to volatile fatty acids (inside of purple squircle), pentose cycle and phosphoketolase cleavage (inside of green squircle), and hydrogenotrophic methanogenesis (inside of orange squircle).
4.2
Metabolism of pyruvate to acetate and butyrate. Main routes of carbon compounds are marked with sky blue arrows. Alternative pathway involving butyryl‐CoA: acetate CoA transferase is shown in gray arrows. Link with propionate randomizing pathway involving succinyl‐CoA: acetate CoA transferase is shown in purple. Generation of ATP by substrate‐level phosphorylation is shown with light green arrows. Reactions of cofactor reduction are shown in red arrows. Abbreviations: ADP, adenosine diphosphate; ATP, adenosine triphosphate; CO
2
, carbon dioxide; Fe
ox
, oxidized ferredoxin; Fe
red
2−
, reduced ferredoxin; H+, proton; HS‐CoA, coenzyme A; NAD+, oxidized nicotinamide adenine dinucleotide; NADH, reduced nicotinamide adenine dinucleotide; P
i
, phosphate group.
4.3
Propionate formation via randomizing (succinate) and non‐randomizing (acrylate) pathways. Main routes of carbon compounds are marked with sky blue arrows. Reactions involving transfer of coenzyme A are shown with gray arrows. Generation of ATP by substrate level and electron transport‐linked phosphorylation is shown with light green arrows. Reactions of cofactor re‐oxidation are shown in red arrows. Abbreviations: ADP, adenosine diphosphate; ATP, adenosine triphosphate; B
7
, biotin; B
12
, cobalamin; CO
2
, carbon dioxide; H
+
, proton; HS‐CoA, coenzyme A; NAD
+
, oxidized nicotinamide adenine dinucleotide; NADH, reduced nicotinamide adenine dinucleotide; P
i
, phosphate group.
4.4
Main pathways of metabolic hydrogen transactions in rumen fermentation. Reduction of NAD
+
to NADH in glycolysis and of ferredoxin in pyruvate oxidative decarboxylation is depicted in sky blue arrows. Formate formation in pyruvate oxidative decarboxylation and dissociation into carbon dioxide (CO
2
) and dihydrogen (H
2
) previously to its incorporation into methane (CH
4
) and other electron sinks is shown in gray arrows. Under low dihydrogen concentration NADH is re‐oxidized by [FeFe] A3 type hydrogenases in confurcation with reduced ferredoxin (Fd
red
2−
; yellow arrows). Under relatively high dihydrogen concentration NADH donates electrons in intracellular reactions and reduced ferredoxin is re‐oxidized to its oxidized species (Fd
ox
) by fermentative, dihydrogen‐evolving [FeFe] A1 type hydrogenases (purple arrows). Hydrogenotrophic methanogenesis incorporates dihydrogen and carbon dioxide (sky blue arrows). Incorporation of metabolic hydrogen into methyl‐reducing and fermentative methylotrophic methanogenesis is depicted in light green arrows.
4.5
Simplified scheme of rumen, small intestine, and liver nitrogen metabolism. Endogenous protein is not depicted for simplicity. Liver synthesized urea is recycled to the rumen through the rumen wall and in saliva (not depicted for simplicity). Abbreviations: AA, amino acids; N, nitrogen; NH
4
+
, ammonium.
5.1
Schematic overview of the anaerobic digestion of plant biomass and its position within the lignocellulose biorefinery concept.
5.2
Simplified structure of the main lignocellulosic polysaccharides and their enzymatic degradation mechanisms (a). Lignin degradation pathway is omitted here. Classification of main enzymes involved in lignocellulosic polysaccharides degradation (b). EC, enzyme commission number; CAZyme, carbohydrate‐active enzyme; GH, glycoside hydrolase; CE, carbohydrate esterase.
5.3
Characterization of the termite gut system and proposed exploitation of its potential toward improved lignocellulose utilization in engineered systems. Figure inspired by the work from Godon et al. (2013) and further modified. The highly compartmented gut model is characteristic of soil feeding termites, e.g.
Labiotermes
sp. The gut compartments involved in the degradation of the main lignocellulose fractions were identified after Marynowska et al. (2022). PFR, plug flow reactor; CSTR, continuously stirred tank reactor.
5.4
Comparison of microbial communities and their polysaccharide degrading potential in the anaerobic digestion (AD) reactors and the termite gut (Termite) system. Multidimensional scaling (MDS) of the calculated Jaccard similarity coefficient comparing the genomic content of the carbohydrate active enzymes (CAZymes) encoded in microbial genomes from the two systems (a). This subfigure was compiled based on microbial genomes generated in previous studies (Campanaro et al. 2020; Hervé et al. 2020). Main bacterial phyla present in the different types of AD reactors (i.e. alimented with different feedstocks), and higher termites feeding on distinct substrates (b). This subfigure was compiled based on (Calusinska et al. 2018b; Marynowska et al. 2020). WWTP, wastewater treatment plant, OFMSW, organic fraction of municipal solid waste.
5.5
Glucoside hydrolases in microbial genomes from the anaerobic digestion reactors (AD) and the termite gut system (Termite). (a) Shared diversity of glucoside hydrolase (GH) families in bacterial genomes from AD and the termite gut systems. (b) Average GH family diversity per microbial genome (only genomes with >70% completeness and <10% contamination were used), displayed for the main bacterial phyla. All pair‐wise comparisons are statistically significant (t.test, p < 0.005). (c) Linear discriminant analysis (LDA) of GH gene families differentially enriched in microbial genomes (community‐wise) in the two systems. This figure was compiled based on microbial genomes generated in previously published studies (Campanaro et al. 2020; Hervé et al. 2020).
5.6
Comparison of the main glycoside hydrolase (GH) families targeting the different lignocellulose fractions and other non‐lignocellulosic polysaccharides and their phylogenetic distribution among major bacterial phyla, for the anaerobic digestion reactors (a) and the termite gut system (b). This figure was compiled based on microbial genomes generated in previously published studies (Campanaro et al. 2020; Hervé et al. 2020).
5.7
Anaerobic fungi in full‐scale anaerobic digestion systems (a) and their lignocellulolytic potential (b and c). OFMSW, organic fraction of the municipal solid waste; WWTP, wastewater treatment plant; PL, polysaccharide lyase; GT, glycosyl transferase; GH, glycoside hydrolase; CE, carbohydrate esterase; CBM, carbohydrate‐binding module; AA, auxiliary enzyme. This figure was compiled based on own, unpublished data (a), and relying on the analysis of Neocallimastigomycota genomes available in public databases (b and c).
6.1
Examples of ancient fungal elements found on Neolithic pottery vessels in China. 1, 2:
Monascus
cleistothecia; 3, 4:
Aspergillus
vesicles; 5: cf.
28 pt
hyphae; 6:
Rhizopus
sporangium, showing structure of collarette and columella; 7:
Mucor
sporangium connecting to hypha; 8:
Rhizopus
or
Mucor
sporangia; 9: yeast cells in budding position; 10: a cluster of yeast cells.
6.2
Globular jars unearthed from major sites in early Neolithic China, ca. 9000 to 7000 cal. BP. 1: Dadiwan; 2: Guantaoyuan; 3: Baijia‐Lingkou; 4: Peiligang; 5: Jiahu; 6: Pengtoushan; 7: Kuahuqiao; 8: Shangshan; 9: Qiaotou; 10: Xiaohuangshan; 11: Cishan; 12: Houli.
6.3
Regional archeological cultural development and alcohol‐related pottery vessels in the Yellow River valley, the middle Neolithic period. (a) Distribution of the Beixin‐Dawenkou and Yangshao cultures. (b) Alcohol‐related pottery vessels in the Yangshao culture; 1: stove‐cauldron; 2: funnel; 3: amphora; 4, 5:
dakougang
vats (from Xipo). (c). Alcohol‐related pottery vessels in the Beixin‐Dawenkou cultures; 1: globular jar; 2:
gui
pitcher; 3, 4: goblets; 5–8:
dakougang
vats (from Yuchisi).
6.4
Examples of serving and drinking vessels during the late Neolithic Longshan culture. (a) Distribution of the Longshan culture in the Yellow River region. (b) Examples of alcohol‐related vessels from the Shandong Longshan culture; 1: cup; 2, 3: goblets; 4: pitcher. (c). Examples of alcohol‐related vessels from Shimao; 5: cups; 6, 7: pitchers.
7.1
Embossed and screw top Victorian beer bottles.
7.2
Profiles of major features of brewing through periods of development. Wheat – proportion used as a major ingredient: barley — proportion used as a major ingredient; fruit & herbs — prevalence in recipes, particularly as gruit; ABV — general level of alcohol achieved: shelf life — likely drinkable period (days to months); yeast management — awareness of value of yeast repatching; dispense — sophistication of draught and packaged product.
7.3
Example ingredients of gruit. (a) Bob myrtle/sweet gale; (b) Juniper berries; (c) Yarrow.
7.4
(a) Bottle #2 from the Wallachia shipwreck in preparation for analysis. (b) Yeast colonies isolated from Wallachia shipwreck bottle.
8.1
Allagash Brewing Company coolship room. Windows are propped open at all times and the wooden ceiling is important for harboring organisms. The fans help circulate airflow. The beer sits overnight and is then drained back into the main brewing building to be placed into barrels.
8.2
Allagash Brewing Company aging barrels. “CS” refers to “Coolship.” Apple refers to the fresh pomades added while lavender refers to the lavender‐smoked malt used. Beer was poured into barrels to begin aging on March 27th, 2019, November 20th, 2020, or January 4th, 2022.
9.1
An electron microscopy image of an
A. oryzae
conidiophore and a photo of rice
koji
.
9.2
Haze komi and invasive growth of
A. oryzae
(green) into steamed rice (red).
9.3
A tank to create the fermentation mash and fresh sale.
11.1
Major mycotoxins and fungal species that produce them.
12.1
Cassava roots and leaves.
12.2
Moringa leaves and trees.
12.3
Uapaka kirkiana
or wild loquat (
mushuku/muzhanje
);
Ziziphus mauritiana
in an open informal market.
12.4
A diet high in fermented food or beverage decreases inflammatory proteins, reduces molecular signs of inflammation, and improves immune response. Therefore, improving digestive health with a high‐quality fermented diet may improve immunity against infections and diseases.
12.5
Mitochondrial yeast metabolism, maltose being the best sugar source. Secondary metabolites and metabolism intermediates are shown in ethanol formation.
12.6
Brassica tournefortii
on the left. Coffee beans in the middle. Kombucha on the right.
12.7
Typical Sudanese
kissra
making and a full meal with several fermented foods.
12.8
Ripe bananas being prepared for fermentation in Burundi.
12.9
Preparation of wild water mellon wine.
12.10
Cashew apple fruit on the left with the unique external seed and women preparing cashew fruit wine in Guiné‐Bissau.
12.11
Traditional preparation of amarula drink (“ocanhu”) in Mozambique.
12.12
Images of masau (
Ziziphus mauritiana
), tambarind (
Tamarindus indica
), millet (
Cenchrus americanus
), bulrush (
Scirpoides holoschoenus
), monkey orange msala (
Strychnos spinosa
), and baobab (
Adansonia digitata
) fruit.
12.13
Milk and butter
smen
.
12.14
The multipurpose dawadawa tree, known as the African locust bean tree (
Parkia biglobosa
and
Parkia filicoidea
).
12.15
Commercially cassava beer is produced in Mozambique, brand name
Impala
.
Chibuku
sorghum beer is made in several countries.
Burukutu
preparation in Nigeria.
12.16
Palm wine created from the sap of various species of palm trees; hibiscus wine.
12.17
Aspartame, a well‐known artificial sweetener of sodas, candy, chewing gum, and energy drinks, is a synthetic chemical composed of the amino acids phenylalanine and aspartic acid, with a methyl ester. The methanol produced by the metabolism of aspartame is absorbed and quickly converted into formaldehyde and then completely oxidized to formic acid. The acceptable daily intake (ADI) for aspartame is 40 mg/kg of body weight. Ethanol, drinking alcohol, is mainly produced from maize fermentation. Ethylene glycol, used as antifreeze, if ingested is rapidly absorbed from the gastrointestinal tract and slowly absorbed through the skin or lungs.
13.1
Types of food fermentation.
13.2
Fermented foods of Tamil Nadu.
13.3
Fermented foods of Kerala.
13.4
Fermented foods of North East–Indo‐Nepal Himalayan region.
13.5
Fermented foods of Sri Lanka.
14.1
Some forage crops for ensiling.
14.2
The major steps of silage making.
14.3
Assessing corn grain maturity by milk line. The Milk Line (the border between the deep yellow and the milky parts) proceeds from the external perimeter toward the center of the cobs as the plant matures (A and B, respectively).
14.4
The effect of applying
L. plantarum
at ensiling on rate of pH decrease in wheat silage.
14.5
Ideal (left) vs. poor sealing (right).
14.6
Silage silo types.
14.7
Anaerobic mini‐silos (Weck™, Wehr‐Offlingen, Germany). The springs which secure the lids enable gas release from inside only but not air penetration.
LIST OF CONTRIBUTORS
Lourdes Georgina Michelena Álvarez, ICIDCA‐Instituto Cubano de Investigaciones de los Derivados de la caña de azúcar. Ciudad de La Habana, Cuba
Roberto Arredondo Valdés, Faculty of Chemical Sciences of the Autonomous University of Coahuila, Coahuila, México
Victoria Bell, Faculty of Pharmacy, University of Coimbra; Pólo das Ciências da Saúde, Azinhaga de Santa Comba, Coimbra, Portugal
HD Bhimani, Division of Microbial & Environmental Biotechnology, Navsari Agricultural University, Gujarat, India
Simana Bora, Department of Physics, Silapathar College, Silapathar, Department of Botany, Bahona College, Assam, India
François Bourdichon, Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica Del Sacro Cuore, Piacenza, Italy
Magdalena Calusinska, Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
Nathaly Cancino‐Padilla, Centro Regional de Investigación Carillanca; Instituto de Investigaciones Agropecuarias INIA, Vilcún, La Araucanía, Chile
Sagarika Ekanayake, Department of Biochemistry, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
Dania Alonso Estrada, Faculty of Chemical Sciences of the Autonomous University of Coahuila, Coahuila, México
Evelyn Faife Pérez, ICIDCA‐Instituto Cubano de Investigaciones de los Derivados de la caña de azúcar. Ciudad de La Habana, Cuba
Tito H. Fernandes, CIISA ‐ Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisboa, Portugal. Former CEIL, Lúrio University, Nampula, Mozambique
Alessandra Fontana, Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica Del Sacro Cuore, Piacenza, Italy
Gomathy M, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Tamil Nadu, India
Xavier Goux, Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
José Guina, Instituto Superior de Estudos Universitários, Polytechnic University, Nampula, Mozambique
Christon J. Hurst, Cincinnati, OH, USA; Universidad del Valle, Santiago de Cali, Valle del Cauca, Colombia
Anna Iliná, Faculty of Chemical Sciences of the Autonomous University of Coahuila, Coahuila, México.
Priya John, Department of Plant Pathology, Navsari Agricultural University, Gujarat, India
Marta Laranjo, MED‐Mediterranean Institute for Agriculture, Environment and Development & CHANGE‐Global Change and Sustainability Institute, IIFA‐Institute for Advanced Studies and Research, Universidade de Évora, Évora, Portugal
Li Liu, Department of East Asian Languages and Cultures, Stanford University Stanford, CA, USA
Tong Liu, Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
Uma Maheswari, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Tamil Nadu, India
Manoj M, Department of Microbiology, Navsari Agricultural University, Gujarat, India
José Luis Martínez‐Hernández, Faculty of Chemical Sciences of the Autonomous University of Coahuila, Coahuila, México
Erin A. McKenney, Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
Lorenzo Morelli, Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica Del Sacro Cuore, Piacenza, Italy
Arianna Núñez Caraballo, Autonomous University of Coahuila, Coahuila, México
Nayra Ochoa Viñals, Faculty of Chemical Sciences of the Autonomous University of Coahuila, Coahuila, México
Ken Oda, National Research Institute of Brewing, Higashi‐hiroshima, Hiroshima, Japan
Vania Patrone, Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica Del Sacro Cuore, Piacenza, Italy
Rajakumar D, Department of Agronomy, Tamil Nadu Agricultural University, Tamil Nadu, India
Anu S. Rajan, Department of Agricultural Microbiology, Kerala Agricultural University, Kerala, India
Ramya P, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Tamil Nadu, India
Sabarinathan KG, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Tamil Nadu, India
Dilip Saikia, Department of Physics, Silapathar College, Silapathar, Department of Botany, Bahona College, Assam, India
Cassandra Suther, Department of Food Science, University of Massachusetts Amherst, Amherst, MA, USA
Norio Takeshita, Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
Dilip Tamang, Kakajan Govt. M.E. School, Assam, India
Theradimani M, Department of Plant Pathology, Tamil Nadu Agricultural University, Tamil Nadu, India
Keith Thomas, Brewlab Ltd., University of Sunderland, England
Emilio M. Ungerfeld, Centro Regional de Investigación Carillanca; Instituto de Investigaciones Agropecuarias INIA, Vilcún, La Araucanía, Chile
Nelson Vera‐Aguilera, Centro Regional de Investigación Carillanca; Instituto de Investigaciones Agropecuarias INIA, Vilcún, La Araucanía, Chile
Zwi G. Weinberg, Forage Preservation and By‐Products Research Unit, Agricultural Research Organization, The Volcani Institute, Rishon Le Zion, Israel (Retired)
Maria Westerholm, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
Tharanee Wijayaratne, Department of Biochemistry, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
PREFACE
Microbial Fermentations in Nature and as Designed Processes
Christon J. Hurst, Editor
Fermentation is one of the most important metabolic tools that biology has developed and microorganisms do in many ways seem to have become the true masters of fermentative metabolism. There are times when microbial fermentation processes seem to occupy nature’s center stage, although microbial fermentation processes often function less obviously by serving as part of biology’s stabilizing foundation and by providing the backstage support for more noticeable activities.
Animals and plants very importantly depend upon their own fermentative capabilities at times and in places where neither aerobic nor anaerobic respiration are energetically suitable. Those capabilites are overshadowed by the extensive and reliably successful symbiotic interactions which the same animals and plants have developed with their fermenting microbial partners.
Each of the fermentative microbial functions evolved to fit an energetic opportunity and each function has ecological value. It is important for us to acknowledge those values and understand the balance that exists between beneficial versus detrimental perspectives of microbial fermentation. For example, fermentative recycling processes which are so crucial in soil and aquatic sediments, and which also have a necessary role in the gastrointestinal tract of animals, can seem detrimental when they contribute to disease in animals and plants.
This book provides a summary of our understanding with regard to the commonalities and distinctions of aerobic versus anaerobic fermentations as performed by microorganisms. The authors explain how animals, including ruminants and termites, have evolved to use their symbiont fermentative microbes as tools for deconstruction of complex polysaccharides, and how we have adopted those natural technologies into our designed processes for anaerobic degradation of lignocellulosic materials. The important role of rhizosphere microbes that facilitate availability of inorganic and organic phosphates for plants also is explained. Those phosphates get stored in the plant’s seeds. And, after animals ingest the seeds, enzymes produced by symbiotic microbial fermentation allow the animals to utilize their dietary phosphates.
The authors provide understanding of the ways that fermentation has been harnessed from prehistoric times to the present for food processing and food preservation, and that technology valuably helps to sustain our species by allowing seasonal harvests to provision us throughout the year. The authors also explain how natural microbial activities have been similarly harnessed for creation of fermented fodder that sustains many of our domesticated agricultural animals.
During my efforts to understand the microbiology of food fermentations, I have asked myself several times if using microbial fermentation to produce and preserve food items may represent a collaborative genetic selection process. The microbes which are prevalent in spontaneous fermentations of food would have selected for a human population which could survive ingesting those microbes. Similarly, those microbes which are spontaneously present in the silage materials that we produce as fodder for our ruminant livestock would have exerted a selection process on our livestock. In cooperative response, we have learned to design food and silage fermentation processes in ways that would favor growth of the most easily survivable microbial populations. Those microbial populations have become our symbionts. That collaborative selection process has not been perfect as evidenced by the opportunistic pathogenicity associated with some of the microbes that exist in fermented food products and fermented fodder.
This book also offers insight into the ways that we have learned to use microbial fermentations as an engineering tool for producing chemicals, including enzymes and pharmaceuticals, which improve the health of ourselves and our domesticated animals. Additionally, the book offers some insight into possible future research directions for the field of applied microbial fermentation that will help to advance agriculture and industry.
I wish to thank Scott Robbins and Andrea Siefring‐Robbins who own Urban Stead Cheese, which is an artisanal cheese company in Cincinnati, Ohio, for very kindly having allowed me to watch their crew perform the almost magical process by which microbial fermentation produces cheddar cheese.
This book is the twenty‐second and final microbiology volume that I will have edited during a period of thirty four and a half years, beginning in February of 1989 when I started organizing the first volume. Those volumes have contained in total five hundred and thirty eight chapters of which I wrote fifty two. I have enjoyed the honor of representing the six hundred and eighty seven colleagues who joined me on this long interesting adventure as authors and coauthors, especially those who also joined me as coeditors, and I offer my thanks to each of them. Edited books are collaborative efforts similar to good fermentations, intended to share collective knowledge with an appreciative audience. Many of those authors and coauthors kindly have contributed to more than a single book project. In particular, I thank Professor Gideon Wolfaardt who graciously always agreed to participate each of the five times he was asked to write a chapter that would help us present the unfolding story of science. Gideon, collaborative projects have success because of the helpful and reliable efforts made by people such as you. A dream of mine would be to invite all of those colleagues to meet together in a large pub, I would buy a pint of nicely fermented beer for each, and then I would raise my glass to them and say “Together, we have accomplished something very good”. That could not happen, and many contributors to the earlier books have since passed away. Instead, I will think of them and say these lines from an old song,
“So fill to me the parting glass … Good night and joy be to you all”.
Christon J. Hurst in 2022
Christon J. Hurst
Cincinnati, Ohio
SECTION IAN INTRODUCTION TO MICROBIAL FERMENTATION
CHAPTER 1MICROBIAL FERMENTATION: UNDERSTANDING AND USING ONE OF NATURE'S TOOLS
CHRISTON J. HURST1,2
1Cincinnati, OH, USA
2Universidad del Valle, Santiago de Cali, Valle del Cauca, Colombia
CONTENTS
1.1 Introduction to Fermentation Processes
1.2 Examples of Microbial Fermentations in Nature
1.2.1 Fermentation Contributes to the Nutrient Recycling Capabilities Within Extreme Environments
1.2.2 Fermentative Microbes Support the Biological Availability of Phosphates in Soil
1.2.3 Fermentative Microbes Are Important for the Biological Availability of Dietary Phosphate
1.2.4 Natural Ethanol Production in Sap, Its Ingestion by Animals, and Human Intestinal Production of Ethanol
1.3 Designing Fermentation Processes
1.3.1 The Levels of Liquid and Oxygen Are Perhaps the Two Most Defining Characteristics of Fermentations
1.3.2 Microbial Ecology Largely Determines the Chemical Profile of Designed Fermentation Products
1.3.3 Spontaneous Fermentations and the Use of Back Slopping
1.3.4 The Importance of Using Defined Starter Cultures and Monitoring Fermentations for Product Quality Control
1.4 The Disposal of Waste Products from Fermentations
1.5 Fermentations That Produce and Preserve Food for Humans
1.5.1 Food Fermentation Is Largely About Lactic Acid and Ethanol
1.5.2 Fermentations That Preserve Fruits and Vegetables
1.5.3 Fermentations of Grains and Other Seeds Including Beans
1.5.4 Fermentations That Produce Alcoholic Beverages
1.5.5 Fermentations That Produce Vinegar
1.5.6 Fermentations That Create Dairy Products
1.5.7 Fermentations That Preserve Meat Products
1.5.8 The Microbial Safety of Fermented Food
1.6 Silage Fermentations That Produce and Preserve Food for Livestock
1.6.1 The Effect of Nitrate in Fertilizers
1.6.2 The Microbial Safety of Fermented Fodder
1.7 Tobacco Fermentations
1.8 Compost Fermentations and the Anaerobic Digestion of Food Wastes for Generating Biogas
1.9 Fermentations That Produce Chemicals, Enzymes, and Pharmaceuticals
1.9.1 Basic Reactor Designs
Submerged Fermentations
Solid State Fermentations
1.9.2 The Types of Microbes That Are Used for These Fermentations
1.9.3 The Types of Products and Their Applications
1.10 Summary
References
1.1 INTRODUCTION TO FERMENTATION PROCESSES
When we consider the ways in which living beings gain energy by degrading organic compounds, most of us first think of the aerobic respiration process which relies upon oxygen as its terminal electron acceptor and generates water molecules. Nearly all of the eukaryotic species that possess mitochondria, including many groups of microorganisms, use aerobic respiration with oxygen as their electron acceptor. Humans gain almost all of our energy by that process.
There are groups of microbes that survive and thrive under conditions where the presence of oxygen is limited. Those microbes often will degrade organic compounds by using anaerobic respiration processes which rely upon either nitrate, sulfate, or elemental sulfur as terminal electron acceptors (Lecomte et al. 2018). Microbes additionally may use metals and metalloids as electron acceptors, and that can occur under aerobic as well as anaerobic conditions (Hurst 2021).
Metabolic fermentation processes degrade organic compounds in ways that use either the same organic molecule, or a different organic molecule, as the terminal electron acceptor. Metabolic fermentation generates a wide range of products including organic acids and their conjugate bases, alcohols, aldehydes, ketones, carbon dioxide, and hydrogen. The amount of energy that can be gained by using metabolic fermentation to catabolize carbohydrates, lipids, and proteins is low in comparison with the amount of energy that could be gained if the organism were able to process those same compounds by either aerobic or anaerobic respiration. The energetic inefficiency of using fermentation to degrade organic materials is associated with the fact that potential energy remains in the molecular bonds of the organic products. Among the particularly well‐known examples of metabolic fermentation processes are those which rely upon pyruvic acid as final electron acceptor to produce lactic acid, and the use of acetaldehyde as final electron acceptor which produces ethanol.
Macroorganisms do at times use metabolic fermentation processes as a supplemental means for obtaining energy. Animals, including humans, rely upon fermentation to produce lactic acid within our muscle tissues when those tissues are stressed by a shortage of intracellular oxygen. Plants growing in soil use fermentation processes in their root tissues when the surrounding soil is saturated with water and the level of oxygen supplied from photosynthesis performed in aerial parts of the plants is insufficient to supply the metabolic needs of those root tissues. Rice plants very notably can produce acetaldehyde and ethanol as a short‐term emergency survival mechanism during darkness and oxygen deprivation, as might occur when the soil is completely flooded with turbid water (Boamfa et al. 2003).
Microorganisms living freely in the environment will use metabolic fermentation processes to satisfy their energy needs when the conditions of their surroundings are unfavorable for supporting either aerobic or anaerobic respiration. There additionally are symbiotic partnerships by which macroorganisms serve as physical hosts for many of the microbial fermenters and these are interdependencies that enable the macroorganisms to gain benefits from their fermenting microbial partners. Examples of such beneficial partnerships are the microbial fermentations that naturally occur in the gastrointestinal tracts of animals (Mississippi State University 2022) and humans (Oliphant and Allen‐Vercoe 2019). Coevolution has developed those gastrointestinal processes as a way of helping both the animals and microbes to optimally benefit from the ingested food. Our developments in food technology include using Propionibacterium and Anaerotignum propionicum (previously Clostridium propionicum) for the propionic acid fermentations of cheese, and we understand that the natural ecology of those microbes includes residence in the rumen and intestinal tract, as well as on the skin of mammals (Ciani et al. 2010). Plants also have many types of partnerships with fermenting microbes, with an example being the fact that bacteria in the rhizosphere use metabolic fermentation processes to generate organic acids which assist with the availability of phosphates, as will be described a bit later in this chapter.
Many of the natural microbial fermentation processes that are so important to putrefaction are proteolytic and they serve by liberating amino acids from proteins. Our designed microbial fermentation processes that create miso and soy sauce from soybeans, and those processes that produce meat products like ham and salami, are examples of similarly using proteolytic microbial fermentation to liberate amino acids. And yet, there are unfortunate times when gastrointestinal microbes that naturally represent those same nutrient recycling processes cause disease (Diether and Willing 2019) including associations with intestinal infections, peritoneal infections, and gangrene (Ciani et al. 2010). Fermentations which produce amino acids are termed amino acid fermentations.
We additionally have applied our skills at technological design processes to harness some of the other microbial metabolic fermentation mechanisms. The numerous applications of these processes prominently include the preservation of food that is intended for us to consume (Tables 1.1 and 1.2).
The microbial ecology of food preservation greatly depends upon fermentations which accomplish anaerobic conversions of sugars into acids and ethanol. As you already may have guessed, fermentations, and the microbes which perform those metabolic activities, often are named descriptively based on the desired product. Acetic acid, butyric acid, lactic acid, and propionic acid, respectively, represent products from acetic acid fermentations, butyric acid fermentations, lactic acid fermentations, and propionic acid fermentations. The fermentations which typically produce ethanol are termed either alcoholic or ethanolic fermentations. All of these acids and the ethanol are chemical weapons that fermenting microbes use in an effort to control the ecology of their environment and these chemical products are important to the microbial successions that occur during fermentation processes.
Anaerobic lactic acid fermentations are performed by lactic acid bacteria and also by some yeasts. These fermentation processes are described as either homolactic or heterolactic. Homolactic fermentation converts one molecule of glucose initially into two molecules of pyruvate, then converts those into two molecules of lactic acid. Heterolactic fermentation performs that same conversion of glucose into lactic acid, but then further converts one of the lactic acid molecules into amolecule of carbon dioxide plus a molecule of ethanol. The products of heterolactic fermentation thus are a combination of carbon dioxide, ethanol, and lactic acid. Generation of the three additional organic acids that have earned prominence in the creation and preservation of food, those being propionic, butyric, and acetic, all follow lactic acid production. Fermentation by propionic acid bacteria anaerobically converts lactic acid to acetic and propionic acids, carbon dioxide, and water. Fermentation by butyric acid bacteria anaerobically converts lactic acid to acetic and butyric acids, carbon dioxide, and hydrogen. Butyric acid production occurs when the pH of either food or silage fermentations is not sufficiently low to exclusively allow control by microbes that produce lactic acid fermentation.
TABLE 1.1Examples of bacteria that are present in food fermentations.
Genus
Species
Primary Material Being Fermented
Product
Geographical Origin
Acetobacter
aceti
Milk
Fermented beverage (Kefir)
North Caucasus
Acetobacter
aceti
Palm wine
Palm wine vinegar
Philippines
Acetobacter
aceti
Previously alcoholic fermented coconut water (liquid from coconuts plus sugar)
Coconut water vinegar
Philippines
Acetobacter
aceti
Previously alcoholic fermented fruit juices
Vinegar
Global
Acetobacter
aceti
Previously alcoholic fermented molasses (Molasses beer)
Molasses vinegar
Global
Acetobacter
cerevisiae
Previously alcoholic fermented fruit juices
Vinegar
Global
Acetobacter
fabarum
Cacao seeds
Cocoa beans
Ghana
Acetobacter
fabarum
Milk
Fermented beverage (Kefir)
North Caucasus
Acetobacter
lovaniensis
Milk
Fermented beverage (Kefir)
North Caucasus
Acetobacter
lovaniensis
Sugar
Fermented beverage (Tibicos, also called Water Kefir)
Global
Acetobacter
malorum
Previously alcoholic fermented fruit juices
Vinegar
Global
Acetobacter
oeni
Previously alcoholic fermented fruit juices
Vinegar
Global
Acetobacter
orientalis
Milk
Fermented beverage (Kefir)
North Caucasus
Acetobacter
orleanensis
Vanilla
pods
Vanilla
Mexico
Acetobacter
pasteurianus
Cacao seeds
Cocoa beans
Equatorial South America
Acetobacter
pasteurianus
Cassava
Beer (Cassava beer, Chicha)
Africa (Cassava beer), Brazil (Chicha)
Acetobacter
pasteurianus
Chañar fruit
Beer (Chicha)
Chile
Acetobacter
pasteurianus
Kañiwa
Beer (Chicha)
Andean South America
Acetobacter
pasteurianus
Maize
Beer (Chicha)
Andean South America and Costa Rica
Acetobacter
pasteurianus
Oca
Beer (Chicha)
Brazil
Acetobacter
pasteurianus
Palm fruit
Beer (Chicha, Palm beer)
Central and South America (Chicha), Fiji (Palm beer)
Acetobacter
pasteurianus
Peanut
Beer (Chicha)
Peru
Acetobacter
pasteurianus
Potato
Beer (Chicha, Potato beer)
Germany and Netherlands (Potato beer), Northern South America (Chicha)
Acetobacter
pasteurianus
Previously alcoholic fermented fruit juices
Vinegar
Global
Acetobacter
pasteurianus
Previously alcoholic fermented pineapple peel and sugar
Pineapple peel vinegar
Asia, Latin America
Acetobacter
pasteurianus
Quinoa
Beer (Cusqueña)
Peru
Acetobacter
pasteurianus
Rice
Beer (Chicha, Rice beer)
Japan (Rice beer), South America (Chicha)
Acetobacter
pomorum
Previously alcoholic fermented fruit juices
Vinegar
Global
Acetobacter
tropicalis
Vanilla
pods
Vanilla
Mexico
Acetobacterium
tundrae
Barley
Beer (Historical ale)
United Kingdom
Acidipropionibacterium
acidipropionici
Milk
Cheese (Swiss type)
Europe
Acidipropionibacterium
jensenii
Milk
Cheese (Swiss type)
Europe
Acidipropionibacterium
thoenii
Milk
Cheese (Swiss type)
Europe
Actinotignum
urinale
Barley
Beer (Historical ale)
United Kingdom
Aerococcus
viridans
Fish with rice
Fermented seasoning (Pla ra)
Thailand
Anaerotignum
propionicum
Milk
Cheese
Global
Bacillus
amyloliquefaciens
Barley
Beer (Historical ale)
United Kingdom
Bacillus
amyloliquefaciens
Lentils
Griddle cake (Dosa)
India
Bacillus
amyloliquefaciens
Rice
Steamed cake (Idli)
India and Sri Lanka
Bacillus
amyloliquefaciens
Soybean
Fermented soybean (Hawaijar, Peruyaan)
India
Bacillus
atrophaeus
Vanilla
pods
Vanilla
Mexico
Bacillus
cereus
Rice
Steamed cake (Idli)
India and Sri Lanka
Bacillus
cereus
Soybean
Fermented soybean (Hawaijar), Curry (Kinema)
India
Bacillus
licheniformis
Barley
Beer (Historical ale)
United Kingdom
Bacillus
licheniformis
Locust bean
Dry condiment (Eware, Irú)
Africa
Bacillus
licheniformis
Soybean
Fermented paste or curry (Bekang), Curry (Kinema)
India
Bacillus
pumilus
Locust bean
Dry condiment (Eware, Irú)
Africa
Bacillus
pumilus
Soybean
Fermented paste (Tungrymba), Paste or curry (Bekang)
India
Bacillus
pumilus
Vanilla
pods
Vanilla
Mexico
Bacillus
subtilis
Barley
Beer (Historical ale)
United Kingdom
Bacillus
subtilis
Cassava
Fermented cassava root subsequently granulated into a flour (Garri)
West Africa
Bacillus
subtilis
Locust bean
Dry condiment (Eware, Irú)
Africa
Bacillus
subtilis
Maize
Porridge (Ogi)
Nigeria
Bacillus
subtilis
Millet
Porridge (Ogi)
Nigeria
Bacillus
subtilis
Rice
Steamed cake (Idli)
India and Sri Lanka
Bacillus
subtilis
Sorghum
grain
Porridge (Ogi)
Nigeria
Bacillus
subtilis
Soybean
Coagulated soy milk (Tofu), Fermented bean served whole often as an alternative to meat (Hawaijar, Natto), Fermented paste (Miso, Tungrymbai)
China (Tofu), India (Hawaijar, Tungrymbai), Japan (Miso, Nattō)
Bacillus
subtilis
Tea leaves
Fermented tea leaves [To be brewed for beverage] (Qingzhuan brick tea)
China
Bacillus
subtilis
subsp.
subtilis
Vanilla
pods
Vanilla
Mexico
Bacillus
tequilensis
Rice
Steamed cake (Idli)
India and Sri Lanka
Bacillus
thuringiensis
Soybean
Curry (Kinema)
India
Bacillus
thuringiensis
Vanilla
pods
Vanilla
Mexico
Bifidobacterium
animalis subsp. lactis
Milk
Fermented beverage
Europe
Bifidobacterium
breve
Milk
Fermented beverage
Europe
Brachybacterium
alimentarium
Milk
Cheese (Gruyère type, including Beaufort)
France (Beaufort), Switzerland (Gruyère)
Brevibacillus
brevis
Soybean
Fermented paste or curry (Bekang)
India
Brevibacterium
jeotgali
Bivalve mollusks (intact)
Jeotgal
Korea
Brevibacterium
jeotgali
Cephalopods (intact)
Jeotgal
Korea
Brevibacterium
jeotgali
Crustaceans (intact)
Jeotgal
Korea
Brevibacterium
jeotgali
Fish (intact)
Jeotgal
Korea
Brevibacterium
jeotgali
Fish (internal organs)
Jeotgal
Korea
Brevibacterium
jeotgali
