Microbial Sensing in Fermentation
Description
Microbial Sensing in Fermentation presents the fundamental molecular mechanisms involved in the process of fermentation and explores the applied art of microbiology and fermentation technology. The text contains descriptions regarding the extraordinary sensing ability of microorganisms towards small physicochemical changes in their surroundings. The contributors -- noted experts in the field -- cover a wide range of topics such as microbial metabolism and production (fungi, bacteria, yeast etc); refined and non-refined carbon sources; bioprocessing; microbial synthesis, responses and performance; and biochemical, molecular and extra/intracellular controlling.
This resource contains a compilation of literature on biochemical and cellular level mechanisms for microbial controlled production and includes the most significant recent advances in industrial fermentation.
The text offers a balanced approach between theory and practical application, and helps readers gain a clear understanding of microbial physiological adaptation during fermentation and its cumulative effect on productivity. This important book:
* Presents the fundamental molecular mechanisms involved in microbial sensing in relation to fermentation technology
* Includes information on the significant recent advances in industrial fermentation
* Contains contributions from a panel of highly-respected experts in their respective fields
* Offers a resource that will be essential reading for scientists, professionals and researchers from academia and industry with an interest in the biochemistry and microbiology of fermentation technology
Written for researchers, graduate and undergraduate students from diverse backgrounds, such as biochemistry and applied microbiology, Microbial Sensing in Fermentation offers a review of the fundamental molecular mechanisms involved in the process of fermentation.
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About the Editors
Satinder Kaur Brar: Institut national de la recherche scientifique, Centre ??? Eau Terre Environnement, Québec, Canada
Ratul Kumar Das: TERI-Deakin Nanobiotechnology Centre, Biotechnology and Management of Bioresources Division, The Energy and Resources Institute, Haryana, India
Saurabh Jyoti Sarma: Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
Content
List of Contributors xi
1 Biochemical Aspects of Microbial Product Synthesis: a Relook 1
G. Gallastegui, A. Larrañaga, Antonio Avalos Ramirez, and Thi Than Ha Pham
1.1 Introduction 1
1.2 History of Industrial Production of Microbial Products 2
1.2.1 Advances of Biochemical Engineering and Their Effects on Global Market of Microbial Products 3
1.2.2 Importance of Microbial Sensing in Product Formation 6
1.3 Conclusion 7
Acknowledgments 8
References 8
2 Cellular Events of Microbial Production: Important Findings So Far 11
Devangana Bhuyan and Ratul Kumar Das
2.1 Introduction 11
2.2 Microbial Metabolism and Evolution of Metabolic Pathways 12
2.3 Microbial Fermentation 12
2.4 The Microbial Cellular Events 15
2.5 Cell Signalling in Microorganisms 19
2.6 Microbial Performance Under Stress Conditions 21
Acknowledgment 24
References 24
3 Microbial Metabolism in a Refined Carbon Source: Generalities 27
Vinayak Laxman Pachapur, Preetika Rajeev Kuknur, Satinder Kaur Brar, and Rosa Galvez-Cloutier
3.1 Introduction 27
3.2 Microbial Metabolism in Presence of Pure and Crude Substrate 29
3.3 Microbial Metabolism in Presence of Pure and Mixed Cultures 31
3.4 Microbial Metabolism in the Presence of Co-Substrate 33
3.5 Microbial Metabolism in the Presence of Input Parameters 35
3.6 Microbial Metabolism in the Presence of Varying Fermentation Conditions 37
3.7 Pros and Cons of Refined Substrate for Metabolic Metabolisms 38
3.8 Conclusions
39 Acknowledgment 40
References 40
4 Non-refined Carbon Sources and Microbial Performance 43
Guneet Kaur
4.1 Introduction 43
4.2 Non-refined Carbon Sources: a Brief Account 43
4.3 Microbial Assimilation of Non-Refined Carbon Sources 45
4.4 Microbial Sensing to Non-Refined Carbon Sources 48
4.4.1 Microbial Metabolism and Regulatory Circuits 48
4.4.2 CCR Regulation of Carbon Uptake and Metabolism 51
4.5 Guiding Product Outcomes via Rewiring of Cellular Regulatory Circuit 53
4.5.1 Cellular Engineering in E. Coli for Bioprocessing of Non-Refined Carbon Sources 54
4.5.2 Rewiring S. cerevisiae for Accumulation and Conversion of Non-refined Carbon Sources 55
4.6 Conclusions 56
References 57
5 Cellular versus Biochemical Control over Microbial Products 61
Carlos S. Osorio-González, Krishnamoorthy Hegde, and Satinder Kaur Brar
5.1 Introduction 61
5.2 3 Hydroxy-propionic Acid 62
5.3 Fumaric Acid 64
5.4 Itaconic Acid 65
5.5 Glucaric Acid 67
5.6 Butanol 68
5.7 Malic Acid 69
5.8 Gluconic Acid 71
5.9 Aminovalaric Acid 71
5.10 Glutamic Acid 73
5.11 Cadaverine (1,5-diaminopentane) 74
5.12 Conclusion 76
Acknowledgment 76
References 76
6 Pre-Treatment of Alternative Carbon Source: How Does it Make Sense to Microorganism at Cellular Level? 89
Joseph Sebastian, Pratik Kumar, Krishnamoorthy Hegde, Satinder Kaur Brar, Mausam Verma, and Ratul Kumar Das
6.1 Introduction 89
6.2 Pre- Treated Carbon Source and Microbial Assimilation: Cellular and Biochemical Aspects 91
6.2.1 Alcohols 94
6.2.1.1 Bioethanol 94
6.2.1.2 Butanol and Acetone 96
6.2.2 Hydrogen 98
6.2.3 Methane/biogas 101
6.2.4 Organic Acids 103
6.3 Challenges of Inhibitory Hydrolysis Products and Strategic Solution 106
6.3.1 Inhibitory Products: Pretreatment Metabolites or By-products 106
6.3.1.1 Aliphatic Compounds 106
6.3.1.2 Aromatic Compounds 107
6.3.1.3 Furan Aldehydes 108
6.3.2 Strategies to Control Inhibitory Effects 109
6.3.2.1 Biological Detoxification Strategy for the Inhibitors 110
6.3.2.2 Understanding the Mechanism of Microorganism Adaptation for The Detoxification of Inhibitory Compounds 110
6.3.2.2.1 Homeostasis 110
6.3.2.2.2 Enzymatic Detoxification 111
6.3.2.3 Physical and Chemical Detoxification Strategy for Inhibitors 112
6.3.3 Correlation (Synergistic Effects) of Inhibitory Compounds and their Detoxification 118
6.4 Conclusion 126
Acknowledgments 127
References 127
7 Microbial Metabolic Pathways in the Production of Valued-added Products 137
Gilberto V. de Melo Pereira, Ana M. Finco, Luiz A. J. Letti, Susan Grace Karp, Maria G. B. Pagnoncelli, Juliana de Oliveira, Vanete Thomaz Soccol, Satinder Kaur Brar, and Carlos Ricardo Soccol
7.1 Introduction 137
7.2 Microbial Molecular Structure 138
7.3 Biomass Production 140
7.3.1 Single Cell Oil 140
7.3.2 Single Cell Protein 142
7.4 Enzymes 148
7.5 Biofuels 150
7.6 Alkaloids, Terpenoids, Polyketides and Flavonoids 153
7.7 Organic Acids 155
7.8 Rare Sugars 156
7.9 Conclusions 157
References 158
8 Communication for a Collective Response to Environmental Stress: Bacterial and Fungal Perspectives 169
Azadeh Kermanshahi Pour
8.1 Introduction 169
8.2 Quorum Sensing in Bacteria and the Related Phenotypes 172
8.3 Fermentation and Quorum Sensing in Bacteria 177
8.4 Quorum Sensing in Fungi and the Related Phenotypes 183
8.5 Fermentation and Quorum Sensing in Fungi 186
8.6 Quorum Sensing in Bacteria and Fungi: Similarities and Differences 188
Acknowledgment 189
References 189
9 Biochemical and Cellular Events in Controlling Microbial Performance: A Comparative Account 201
Shadab Ahmed, Shreyas Niphadkar, Somnath Nandi, Satya Eswari, Vishal Pandey, Aishwarya Shankapal, and Aishvarya Agrawal
9.1 Biochemical vs. Molecular Cues for Microbial Performances 201
9.1.1 Nutritional Parameters Optimization 201
9.1.2 Process Condition Optimization 202
9.1.3 Process Improvement by Using Batch and Fed-Batch via Process and Modeling 203
9.1.4 Metabolic Engineering for Improving Microbial Performance 203
9.1.4.1 Metabolic Flux Balance Analysis 203
9.1.4.1.1 Constraint Based Flux Balance Analysis 203
9.1.4.1.2 Defining Biological Objective to Optimize a Phenotype 204
9.1.4.1.3 Applications of Flux Analysis 204
9.1.5 Strain Improvement for Microbial Performance 205
9.1.5.1 Mutagenesis for Strain Improvement 205
9.1.5.1.1 Physical Mutagenesis 205
9.1.5.1.2 Chemical Mutagenesis 206
9.1.5.1.3 Biological Mutagenesis 206
9.2 Sequential Evidences of Biochemical and Molecular Controlling Over Microbial Performances 206
9.3 Biochemically Influenced Molecular Events and Vice Versa 208
9.4 Facts at the Interface of Biochemical and Molecular Controlling: Products vs Applied Parameters 208
9.4.1 Sulfur-Delivery into Biosynthetic Pathway 208
9.4.2 Synthetic Biochemistry Platform for Production of Glucose 212
9.4.3 Biochemical and Molecular Aspects of Metabolic Engineering Approaches 212
9.4.3.1 Engineering Regulatory Network 212
9.4.3.2 Heterologous Expression of Entire Gene Cluster 213
9.4.3.3 Rerouting Metabolic Pathway 213
9.4.3.4 Integration of Metabolic Engineering and Process Engineering 213
9.5 Conclusions 214
References 214
10 Qualitative vs. Quantitative Control Over Microbial Products 223
Rachna Goswami, Vijay Kumar Mishra, and Radhika Pilli
10.1 Introduction 223
10.2 Qualitative vs. Quantitative Control Over Microbial Products/Fungal Products 224
10.2.1 Qualitative Control and Fungal Product 225
10.2.1.1 Diffusion Techniques 226
10.2.1.2 Thin Layer Chromatography (TLC) 229
10.2.1.3 Chromatography-bioautography for Screening of Antimicrobial Activity 231
10.2.1.4 High-performance Liquid Chromatography (HPLC) 232
10.2.2 Quantitative Control of Fungal Products 232
10.2.3 Speeding Up Fungal Product 234
10.3 Fungal Morphology and Product Spectrum: a Representative Theme 237
10.4 Effectiveness of Qualitative Domain for Different Microorganisms 241
10.5 Emphasizing the Need: Qualitative and Quantitative Importance 245
10.6 Conclusions 246
References 247
11 Microbes and Their Products as Sensors in Industrially Important Fermentations 253
Ritu Raval and Keyur Raval
11.1 Introduction 253
11.2 Sensors 254
11.3 Transducers in Conjunction With Microbe Sensors 254
11.3.1 Dissolved Oxygen (DO) Electrode 254
11.3.2 Electron Transfer Measuring Systems 255
11.4 Metabolite Measuring Systems 256
11.5 Other Measuring Systems 257
11.5.1 Bioluminescence Biosensor 257
11.6 Applications of Microbe Sensors in Some Commercially Important Products 258
11.6.1 Red Wine 260
11.6.2 Fermentation of Cereal Products 260
11.6.3 Mevalonate Production 261
11.6.4 Bioaerosols 261
11.6.5 Aptamers 262
11.7 Conclusions 263
References 263
12 Practical Aspects and Case Studies of Industrial Scale Fermentation 267
Sara Magdouli, Thana Saffar, Tayssir Guedri, Rouissi Tarek, Satinder Kaur Brar, and Jean François Blais
12.1 Introduction 267
12.2 Scale Up Challenges 269
12.2.1 Agitation 269
12.2.2 Mass Transfer of Oxygen (Mass Transfer, Morphology, and Rheology) 270
12.2.3 "Shear Damage" 271
12.2.4 Measurements for Control 273
12.2.5 Other Aspects 273
12.3 Microbial Tolerance 274
12.4 Phage Invasion 274
12.5 Process Failures 277
12.6 Potent Inhibitors (e.g. Substrate Inhibition) 278
12.7 Case Studies: Biofuels (Biodiesel, Ethanol) Enzymes (Novozymes), Antibiotics, Platform Chemicals 281
12.7.1 Biofuels (Biodiesel, Ethanol) 281
12.7.2 Enzymes (Novozymes) 283
12.7.3 Antibiotics 286
12.7.4 Platform Chemicals 288
12.8 Conclusions 289
Acknowledgments 290
References 290
13 Future Market and Policy Initiatives of New High Value Products 299
Ha Thi Thanh Pham, Maria Puig-Gamero, Luz Sanchez-Silva, Paula Sánchez, José Luis Valverde, Michele Heitz, and Antonio Avalos Ramirez
13.1 Introduction 299
13.2 Market Analysis, Market Trends and Statistics 299
13.2.1 Biofuels 299
13.2.2 Bio-surfactants 302
13.2.3 Enzymes 305
13.3 Public Mobilization Initiatives and Government Policies 306
13.3.1 Public Mobilization Initiatives 306
13.3.2 Government Policies 307
13.3.3 Regional Policy Development for Growing Bio-based Production 307
13.4 Regulations and Conformity - Case of Biofuels 307
13.5 Global Marketing and Competitiveness in Biofuel Sector 309
References 309
Index 311
1
Biochemical Aspects of Microbial Product Synthesis: a Relook
G. Gallastegui1, A. Larrañaga2, Antonio Avalos Ramirez3, and Thi Than Ha Pham3,4
1 Department of Chemical and Environmental Engineering, Faculty of Engineering Vitoria-Gasteiz, University of the Basque Country (UPV/EHU), Spain
2 Department of Mining-Metallurgy Engineering and Materials Science & POLYMAT, Faculty of Engineering of Bilbao, University of the Basque Country (UPV/EHU), Spain
3 Centre National en Électrochimie et en Technologies Environnementales, Shawinigan, Québec, Canada
4 Université de Sherbrooke, Sherbrooke, Québec, Canada
1.1 Introduction
Microbes are living unicellular or multicellular organisms (bacteria, archaea, most protozoa, and some fungi and algae) that must be greatly magnified to be seen. Despite their tiny size, they play an indispensable role for humanity and the health of ecosystems. For instance, until the discovery of an artificial nitrogen fixation process by the German chemists Fritz Haber and Carl Bosch in the first half of the 20th century, some soil microbes on the roots of peas, beans, and a few other plants were the solely responsible for the nitrogen release necessary for plants growth (Hager, 2008). This invention allowed to feed billions more people than the earth could support otherwise.
Besides, humanity has exploited some of the vast microbial diversity like miniature chemical factories for thousands of years in the production of fermented foods and drinks, such as wine, beer, yogurt, cheese and bread. In fact, the use of yeast as the biocatalyst in foodstuffs making is thought to have begun around the Neolithic period (ca. 10 000-4000 BCE), when early humans transitioned from hunter-gatherers to living in permanent farming communities (Rasmussen, 2015). Vinegar, the first bio-based chemical (not intended as a beverage) produced at a commercial scale was known, used and traded internationally before the time of the Roman Empire (Licht, 2014).
The staggering transformation undergone by biotechnology from serendipity and black-box concepts to rational science and increasing understanding of biological systems has led to not only a direct influence of microbes on human lives, but the emergence of new industries that take advantage of these organisms in large-scale processes devoted to the manufacture of high value-added compounds, energy production and environmental protection. Nevertheless, scientists and engineers are still discovering the broad array of complex signalling that microorganisms have developed to ensure their survival in a wide range of environmental conditions, and making their utmost effort to direct them towards our own ends (Manzoni et al., 2016). In this chapter, a brief summary regarding the historical production of microbial products, their niche in the current global market and the importance of microbial sensing (and other new disciplines) to convert biological systems in industrially relevant actors is presented.
1.2 History of Industrial Production of Microbial Products
In the 1800s, Louis Pasteur (and later Eduard Buchner) proved that fermentation was the result of microbial activity and, consequently, the different types of fermentations were associated with different types of microorganisms. In more recent times (1928), Alexander Fleming understood that the Penicillium mould produces an antibacterial bio-chemical (antibiotics discovery), which was extracted, isolated and named penicillin. Subsequent periods of conflicts (e.g., World Wars I and II) intensified the needs of the population and, at the same time, the creativity and inventiveness of scientists and engineers, who developed large-scale fermentation techniques to make industrial quantities of drugs, such as penicillin, and biofuels, such as biobutanol and glycerol, giving rise to industrial biotechnology. In 1952, Austrian chemists at Biochemie (now Sandoz) developed the first acid-stable form of penicillin (Penicillin V) suitable for oral-administration and achieved an extraordinary success in the treatment of infections during World War II (Williams, 2013).
Biobutanol production is recognized as one of the oldest industrial-scale fermentation processes. It was generated by anaerobic ABE (acetone-butanol-ethanol) fermentation of sugar extract using solventogenic clostridia strains, with a typical butanol:acetone:ethanol mass fraction ratio around 6:3:1. Until the 1920s, acetone was the most sought-after bioproduct of commercial interest. An emerging automotive paint industry and the need of quick-drying lacquers, such as butyl acetate, changed the economic landscape and by 1927 butanol displaced acetone as the target product (Rangaswamy et al., 2012). From 1945 to 1960, about two thirds of the butanol production in North America was based on the conventional ABE fermentation. Nevertheless, butanol yield by anaerobic fermentation remained sub-optimal, and this biobased product was progressively replaced by low cost petrochemical production (Maiti et al., 2016).
When Watson and Crick (with the valuable help from Wilkins and Franklin) worked out the structure of DNA in 1953, they barely imagined that this latter discovery supposed a milestone in the development of modern industrial biotechnology. Thus, in the following decades traditional industrial biotechnology merged with molecular biology to yield more than 40 biopharmaceutical products, such as erythropoietin, human growth hormone and interferons (Demain, 2000). Since then, biotechnology has steadily developed and now plays a key role in several industrial sectors, such as industrial applications, food and beverages, nutritional and pharmaceuticals or plastics and fibers, providing both high value products and commodity products (Heux et al., 2015).
Although, as shown in the previous paragraphs, the use of microorganisms and enzymes for the production of essential items has a long history, the recent linguistic term "white biotechnology" has been assigned to the application of biotechnology for the processing and production of chemicals, materials and energy. It is based on microbial fermentation processes and it works with nature in order to maximize and optimize existing biochemical pathways that can be used in manufacturing. The development of cost effective fermentation processes has allowed industry to target previously abandoned fermentation products and new ones which used to be of small interest for the naphtha-relying chemical industry, such as succinic acid or lactic acid. In the latter case, and although the chemical synthesis of lactic acid from petrochemical feedstock is more familiar to chemists, approximately 90% of its production is accomplished by microbial fermentation (Wang et al., 2015). Nowadays, this platform molecule is used as a building block for the synthesis of chemicals such as acrylic acid and esters (by catalytic dehydration), propylene glycol (by hydrogenolysis) and lactic acid esters (by esterification) (Figure 1.1).
Figure 1.1 Production of lactic acid by microbial fermentation and its derivatives.
1.2.1 Advances of Biochemical Engineering and Their Effects on Global Market of Microbial Products
Economic viability of bio-derived products, especially in the case of biofuels, has been traditionally limited to a large extent by the selection of cheap carbon-rich raw materials as feedstock, applied production mode, downstream processing and the scarcity of naturally occurring microorganisms that are able to deliver the desired compounds at a high production-rate. Conventional bio-based products ultimately turned out so expensive to compete with petroleum-derived chemicals that they were hardly worth producing.
Despite these drawbacks, advances in biotechnology in recent years have enabled the reengineering of the bioprocesses incorporating several transformation or purification steps into only one, reducing time and operating costs. This has involved the increase of bioprocesses yield, boosting production of biobased materials. Currently, biotechnology advances (microbial, enzymatic and biology engineering) can be considered among the new technological revolutions, having huge impacts in industry, society and economy, as nanotechnology-materials, informatics and artificial intelligence.
Therefore, a resurgence in the production of fermentation chemicals including biofuels, chemical building blocks, such as organic acids, amino acids, alcohols (diols, thiols) and specialty chemicals, such as surfactants, thickeners, enzymes, antibiotics and fine chemicals (pigments, fragrances, etc.) is expected in the years to come. The global fermentation chemicals market was 51.83 ·106 tons in 2013 and is expected to reach 70.76 ·106 tons by 2020, growing at a Compound Annual Growth Rate (CAGR) of 4.5% from 2014 to 2020, with North America emerging as the leading regional market and accounting for 33.8% of total market volume (Grand View Research, 2014).
Among all the possible products and value streams obtained from biomass in the biorefineries, the chemical market (both commodity and fine chemicals) is expected to grow at a rate almost double to that of biofuels, since chemicals are on average priced 15 times higher than energy (Deloitte, 2014), which will entail that by 2025 at least a 45% share...
