Industrial Microbiology

Description

Focusing on current and future uses of microbes as production organisms, this practice-oriented textbook complements traditional texts on microbiology and biotechnology.
The editors have brought together leading researchers and professionals from the entire field of industrial microbiology and together they adopt a modern approach to a well-known subject. Following a brief introduction to the technology of microbial processes, the twelve most important application areas for microbial technology are described, from crude bulk chemicals to such highly refined biomolecules as enzymes and antibodies, to the use of microbes in the leaching of minerals and for the treatment of municipal and industrial waste. In line with their application-oriented topic, the authors focus on the “translation” of basic research into industrial processes and cite numerous successful examples. The result is a first-hand account of the state of the industry and the future potential for microbes in industrial processes.
Interested students of biotechnology, bioengineering, microbiology and related disciplines will find this a highly useful and much consulted companion, while instructors can use the case studies and examples to add value to their teaching.

Table of Contents

1. Preface xvii
2. Historical Overview and Future Perspective 1
   Bernhard Eikmanns, Marcella Eikmanns, and Christopher J. Paddon
3. Use of Fermentation Procedures Before the Discovery of Microorganisms (Neolithic Era = New Stone Age Until 1850) 1
4. Investigation of Microorganisms and Beginning of Industrial Microbiology (1850 Until 1940) 7
5. Development of New Products and Procedures: Antibiotics and Other Biomolecules (From 1940) 11
6. Genetic Engineering is Introduced into Industrial Microbiology (From Roughly 1980) 15
7. Future Perspectives: Synthetic Microbiology 18
8. References 20
9. Further Reading 21
10. 2 Bioprocess Engineering 23
    Michael R. Ladisch, Eduardo Ximenes, Nathan Mosier, Abigail S. Engelberth, Kevin Solomon, and Robert Binkley
11. Introduction 23
12. Role of Bioreactors 25
13. Basic Bioreactor Configurations 26
14. Types of Growth Media 27
15. Nonstructured Models 28
16. Nonstructured Growth Models 28
17. Unstructured Models 29
18. Biotechnical Processes 30
19. Modeling Fermentations 32
20. Metabolic Pathways 39
21. Manipulation of Metabolic Pathways 40
22. Future of Pathway Design 42
23. Oxygen Transport 43
24. Aerobic versus Anaerobic Conditions 43
25. kLa – Volumetric Mass Transfer Coefficient 44
26. Heat Generating Aerobic Processes 46
27. Product Recovery 49
28. Basics 49
29. In Situ Product Recovery (ISPR) 49
30. Modeling and Simulation of Reactor Behavior 51
31. Basic Approaches and Software 51
32. Numerical Simulation of Bioreactor Function 51
33. Contamination of Bioreactors 52
34. Scale-up 53
35. References 54
36. Further Reading 57
37. Food 59
    Gülhan Ünlü and Barbara Nielsen
38. Fermented Foods 59
39. Food Preservation 59
40. Flavor and Texture 60
41. Health Benefits 60
42. Economic Impact 62
43. Microorganisms and Metabolism 62
44. Fermentation Processes 64
45. Starter Cultures 65
46. Yeast Fermentations – Industrial Application of Saccharomyces Species 65
47. Grain Fermentation for Ethanol Production – Beer 66
48. Grain Fermentation for CO2 Production – Bread 69
49. Yeast Preparation 69
50. Fruit Fermentation –Wines and Ciders 71
51. Vinegar – Incomplete Ethanol Oxidation by Acetic Acid Bacteria Such as Gluconobacter oxydans 75
52. Substrates: Wine, Cider, and Malt 75
53. Distilled (White) Vinegar 77
54. Balsamic and Other Specialty Vinegars 77
55. Bacterial and Mixed Fermentations – Industrial Application of Lactic Acid Bacteria, with or without Yeast or Molds 78
56. Milk – Cultured Milks – Buttermilk, Yogurt, Kefir, and Cheese 78
57. Bacteriophage Contamination – Death of a Culture 81
58. Meats – Sausages, Fish Sauces, and Pastes 82
59. Vegetables – Sauerkrauts and Pickles, Olives 83
60. Grains and Legumes – Soy Sauce, Miso, Natto, and Tempeh 86
61. Cocoa and Coffee 87
62. Fungi as Food 88
63. Mushrooms 88
64. Single-Cell Protein – Fusarium venenatum 90
65. Conclusions and Outlook 91
66. References 92
67. Further Reading 92
68. Technical Alcohols and Ketones 95
    Peter Dürre
69. Introduction 95
70. Ethanol Synthesis by Saccharomyces cerevisiae and Clostridium autoethanogenum 97
71. Application 97
72. Metabolic Pathways and Regulation 97
73. Production Strains 98
74. Production Processes 98
75. Ethanol – Fuel of the Future? 100
76. Alternative Substrates for Ethanol Fermentation by Cellulolytic Bacteria and Clostridium autoethanogenum 100
77. Propanediol Synthesis by Escherichia coli 101
78. Application 101
79. Metabolic Pathways and Regulation 102
80. Production Strains 102
81. Production Processes 104
82. Butanol and Isobutanol Synthesis by Clostridia and Yeast 105
83. History of Acetone–Butanol–Ethanol (ABE) Fermentation by Clostridium acetobutylicum and C. beijerinckii 105
84. Application 106
85. Metabolic Pathways and Regulation 107
86. Production Strains 110
87. Production Processes 110
88. Product Toxicity 113
89. Acetone Synthesis by Solventogenic Clostridia 113
90. Application 113
91. Metabolic Pathways and Regulation 113
92. Production Strains 114
93. Production Processes 114
94. Outlook 115
95. Further Reading 115
96. Organic Acids 117
    Michael Sauer and Diethard Mattanovich
97. Introduction 117
98. Citric Acid 119
99. Economic Impact and Applications 120
100. Biochemistry of Citric Acid Accumulation 120
101. Industrial Production by the Filamentous Fungus Aspergillus niger 122
102. Yarrowia lipolytica: A Yeast as an Alternative Production Platform 123
103. Lactic Acid 124
104. Economic Impact and Applications 124
105. Anaerobic Bacterial Metabolism Generating Lactic Acid 125
106. Lactic Acid Production by Bacteria 125
107. Lactic Acid Production by Yeasts 126
108. Gluconic Acid 127
109. Economic Impact and Applications 127
110. Extracellular Biotransformation of Glucose to Gluconic Acid by Aspergillus niger 128
111. Production of Gluconic Acid by Bacteria 129
112. Succinic Acid 129
113. Economic Impact and Applications 130
114. Pilot Plants for Anaerobic or Aerobic Microbes 130
115. Itaconic Acid 132
116. Economic Impact and Applications 132
117. Decarboxylation as a Driver in Itaconic Acid Accumulation 132
118. Production Process by Aspergillus terreus 132
119. Metabolic Engineering for Itaconic Acid Production 132
120. Downstream Options for Organic Acids 134
121. Perspectives 135
122. Targeting Acrylic Acid – Microbes Can Replace Chemical Process Engineering 136
123. Lignocellulose-Based Biorefineries 136
124. Further Reading 137
125. Amino Acids 139
     Lothar Eggeling
126. Introduction 139
127. Importance and Areas of Application 139
128. Amino Acids in the Feed Industry 140
129. Economic Significance 141
130. Production of Amino Acids 142
131. Conventional Development of Production Strains 142
132. Advanced Development of Production Strains 144
133. Glutamate Synthesis by Corynebacterium glutamicum 145
134. Synthesis Pathway and Regulation 145
135. Production Process 148
136. Lysine 148
137. Synthesis Pathway and Regulation 148
138. Production Strains 150
139. Production Process 152
140. Threonine Synthesis by Escherichia coli 153
141. Synthesis Pathway and Regulation 153
142. Production Strains 154
143. Production Process 155
144. Phenylalanine 155
145. Synthesis Pathway and Regulation 155
146. Production Strains 156
147. Production Process 157
148. Outlook 158
149. Further Reading 159
150. Vitamins, Nucleotides, and Carotenoids 161
     Klaus-Peter Stahmann and Hans-Peter Hohmann
151. Application and Economic Impact 161
152. lAscorbic Acid (Vitamin C) 163
153. Biochemical Significance, Application, and Biosynthesis 163
154. Regioselective Oxidation with Bacteria in the Production Process 164
155. Riboflavin (Vitamin B2) 166
156. Significance as a Precursor for Coenzymes and as a Pigment 166
157. Biosynthesis by Fungi and Bacteria 167
158. Production by Ashbya gossypii 168
159. Production by Bacillus subtilis 171
160. Downstream Processing and Environmental Compatibility 173
161. Cobalamin (Vitamin B12) 174
162. Physiological Relevance 174
163. Biosynthesis 176
164. Production with Pseudomonas denitrificans 176
165. Purine Nucleotides 178
166. Impact as Flavor Enhancer 178
167. Development of Production Strains 178
168. Production of Inosine or Guanosine with Subsequent Phosphorylation 179
169. β-Carotene 180
170. Physiological Impact and Application 180
171. Production with Blakeslea trispora 181
172. Perspectives 181
173. Further Reading 183
174. Antibiotics and Pharmacologically Active Compounds 185
     Lei Fang, Guojian Zhang, and Blaine A. Pfeifer
175. Microbial Substances Active Against Infectious Disease Agents or Affecting Human Cells 185
176. Distribution and Impacts 185
177. Diversity of Antibiotics Produced by Bacteria and Fungi 189
178. β-Lactams 190
179. History, Effect, and Application 190
180. β-Lactam Biosynthesis 190
181. Penicillin Production by Penicillium chrysogenum 193
182. Cephalosporin Production by Acremonium chrysogenum 193
183. Lipopeptides 193
184. History, Effect, and Application 193
185. Lipopeptide Biosynthesis 194
186. Daptomycin Production by Streptomyces roseosporus 194
187. Cyclosporine Production by Tolypocladium inflatum 194
188. Macrolides 197
189. History, Effect, and Application 197
190. Macrolide Biosynthesis 197
191. Erythromycin Production by Saccharopolyspora erythraea 197
192. Tetracyclines 200
193. History, Effect, and Application 200
194. Tetracycline Biosynthesis 200
195. Tetracycline Production by Streptomyces rimosus 201
196. Aminoglycosides 201
197. History, Effect, and Application 201
198. Aminoglycoside Biosynthesis 201
199. Tobramycin Production by Streptomyces tenebrarius 203
200. Claviceps Alkaloids 203
201. History, Effect, and Application 203
202. Alkaloid Biosynthesis 203
203. Ergotamine Production by Claviceps purpurea 203
204. Perspectives 203
205. Antibiotic Resistance 203
206. New Research Model for Compound Identification 206
207. Future Opportunities 207
208. Further Reading 211
209. Pharmaceutical Proteins 213
     Heinrich Decker, Susanne Dilsen, and Jan Weber
210. History, Main Areas of Application, and Economic Importance 213
211. Industrial Expression Systems, Cultivation and Protein Isolation, and Legal Framework 215
212. Development of Production Strains 215
213. Isolation of Pharmaceutical Proteins 221
214. Regulatory Requirements for the Production of Pharmaceutical Proteins 222
215. Insulins 223
216. Application and Structures 223
217. Manufacturing Processes by Escherichia coli and Saccharomyces cerevisiae 225
218. Production of a Fusion Protein in E. coli 226
219. Production of a Precursor Protein, the So-Called Mini Proinsulin with the Host Strain S. cerevisiae 228
220. Somatropin 230
221. Application 230
222. Manufacturing Process 231
223. Interferons – Application and Manufacturing 232Human Granulocyte Colony-Stimulating Factor 234
224. Application 234
225. Manufacturing Process 235
226. Vaccines 235
227. Application 235
228. Manufacturing Procedure Using the Example of GardasilTM 236
229. Manufacturing Process Based on the Example of a Hepatitis B Vaccine 237
230. Antibody Fragments 238
231. Enzymes 239
232. Peptides 240
233. View – Future Economic Importance 240
234. Further Reading 242
235. Enzymes 243
     David B.Wilson, Maxim Kostylev, Karl-Heinz Maurer, Marina Schramm, Wolfgang Kronemeyer, and Klaus-Peter Stahmann
236. Fields of Application and Economic Impacts 243
237. Enzymes are Biocatalysts 243
238. Advantages and Limitations of Using Enzymatic Versus Chemical Methods 244
239. Brief History of Enzyme Used for the Industrial Production of Valuable Products 245
240. Diverse Ways That Enzymes are Used in Industry 246
241. Enzyme Discovery and Improvement 250
242. Screening for New Enzymes and Optimization of Enzymes by Protein Engineering 250
243. Classical Development of Production Strains 251
244. Genetic Engineering of Producer Strains 253
245. Production Process for Bacterial or Fungal Enzymes 255
246. Polysaccharide-Hydrolyzing Enzymes 255
247. Starch-Cleaving Enzymes Produced by Bacillus and Aspergillus Species 257
248. Cellulose-Cleaving Enzymes: A Domain of Trichoderma reesei 259
249. Production Strains 261
250. Enzymes Used as Cleaning Agents 263
251. Subtilisin-Like Protease 264
252. Bacillus sp. Production Strains and Production Process 265
253. Feed Supplements – Phytases 266
254. Fields of Applications of Phytase 267
255. Phytase in the Animals Intestine 267
256. Production of a Bacterial Phytase in Aspergillus niger 269
257. Enzymes for Chemical and Pharmaceutical Industry 271
258. Examples for Enzymatic Chemical Production 271
259. Production of (S)-Profens by Fungal Lipase 271
260. Enzymes as Highly Selective Tools for Research and Diagnostics 272
261. Microbial Enzymes for Analysis and Engineering of Nucleic Acids 272
262. Specific Enzymes for Quantitative Metabolite Assays 275
263. Perspectives 276
264. l-DOPA by Tyrosine Phenol Lyase 276
265. Activation of Alkanes 276
266. Enzyme Cascades 276
267. References 277
268. Further Reading 277
269. Microbial Polysaccharides 279
     Volker Sieber, Jochen Schmid, and Gerd Hublik
270. Introduction 279
271. Heteropolysaccharides 282
272. Xanthan: A Product of the Bacterium Xanthomonas campestris 282
273. Introduction 282
274. Regulatory Status 282
275. Structure 282
276. Biosynthesis 284
277. Industrial Production of Xanthan 286
278. Physicochemical Properties 287
279. Applications 289
280. Sphingans: Polysaccharides from Sphingomonas sp. 291
281. Hyaluronic Acid: A High-Value Polysaccharide for Cosmetic Applications 293
282. Alginate: Alternatives to Plant-Based Products by Pseudomonas and Azotobacter sp. 294
283. Succinoglycan: Acidic Polysaccharide from Rhizobium sp. 294
284. Homopolysaccharides 295
285. α-Glucans 296
286. Pullulan 296
287. Dextran 296
288. β-Glucans 297
289. Linear β-glucans like cellulose and curdlan 297
290. Branched β-Glucans Like Scleroglucan and Schizophyllan 297
291. Fructosylpolymers like Levan 298
292. Perspectives 298
293. Further Reading 299
294. Steroids 301
     Shuvendu Das and Sridhar Gopishetty
295. Fields of Applications and Economic Importance 301
296. Advantages of Biotransformations During Production of Steroids 303
297. Development of Production Strains and Production Processes 305
298. Applied Types of Biotransformation 307
299. Synthesis of Steroids in Organic – Aqueous Biphasic System 310
300. Side-chain Degradation of Phytosterols by Mycobacterium to Gain Steroid Intermediates 311
301. Biotransformation of Cholesterol to Gain Key Steroid Intermediates 313
302. 11-Hydroxylation by Fungi During Synthesis of Corticosteroids 313
303. Δ1-Dehydrogenation by Arthrobacter for the Production of Prednisolone 316
304. 17-Keto Reduction by Saccharomyces in Testosterone Production 317
305. Double-Bond Isomerization of Steroids 318
306. Perspectives 319
307. References 320
308. Further Reading 321
309. Bioleaching 323
     Sören Bellenberg, Mario Vera Véliz, and Wolfgang Sand
310. Acidophilic Microorganisms Dissolve Metals from Sulfide Ores 323
311. Brief Overview on the Diversity of Acidophilic Mineral-Oxidizing Microorganisms 325
312. Natural and Man-Made Habitats of Mineral-oxidizing Microorganisms 325
313. Biological Catalysis of Metal Sulfide Oxidation 328
314. Importance of Biofilm Formation and Extracellular Polymeric Substances for Bioleaching by Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans 330
315. Bioleaching of Copper, Nickel, Zinc, and Cobalt 334
316. Economic Impact 334
317. Heap, Dump, or Stirred-tank Bioleaching of Copper, Nickel, Zinc, and Cobalt 337
318. Gold 342
319. Economic Impact 343
320. Unlocking Gold by Biooxidation of the Mineral Matrix 343
321. Uranium 346
322. Economic Impact 346
323. In Situ Biomining of Uranium 346
324. Perspectives 347
325. Urban Mining – Processing of Electronic Waste and Industrial Residues 347
326. Microbial Iron Reduction for Dissolution of Mineral Oxides 348
327. Biomining Goes Underground – In Situ Leaching as a Green Mining Technology? 348
328. References 351
329. Further Reading 351
330. Wastewater Treatment Processes 353
     Claudia Gallert and Josef Winter
331. Introduction 354
332. Historical Development of Sewage Treatment 354
333. Resources from Wastewater Treatment 357
334. Wastewater and Storm Water Drainage 358
335. Wastewater Characterization and Processes for Effective Wastewater Treatment 358
336. Suspended or Immobilized Bacteria as Biocatalysts for Effective Sewage Treatment 360
337. Biological Basics of Carbon, Nitrogen, and Phosphorus Removal from Sewage 362
338. Aerobic and Anaerobic Degradation of Carbon Compounds 362
339. Mass and Energy Balance 366
340. Fundamentals of Nitrification 368
341. Elimination of Nitrate by Denitrification 371
342. New Nitrogen Elimination Processes 371
343. Microbial Phosphate Elimination 372
344. Wastewater Treatment Processes 374
345. Typical Process Sequence in Municipal Sewage Treatment Plants 374
346. Activated Sludge Process 376
347. Trickling Filters 378
348. Technical Options for Denitrification 379
349. Biological Phosphate Elimination 381
350. Sewage Sludge Treatment 382
351. Aerobic and Anaerobic Sewage Sludge Treatment 382
352. Sanitation and Quality Assurance of Sewage Sludge 384
353. Advanced Wastewater Treatment 384
354. Elimination of Micropollutants 385
355. Wastewater Disinfection 385
356. uture Perspectives 386
357. References 386
358. Further Reading 388
359. Index 389

Authors Biography

David Wilson, PhD, was a Professor of Biochemistry, Molecular and Cell Biology at Cornell University in Ithaca (USA).

Hermann Sahm, PhD, is Emeritus Professor of Biotechnology at the University of Düsseldorf (Germany).

Peter Stahmann, PhD, is Professor for Technical Microbiology at Brandenburg University of Technology Cottbus-Senftenberg in Senftenberg (Germany).

Mattheos Koffas, PhD, is Professor of Biology at Rensselaer Polytechnic Institute in Troy (USA).