Extremophiles: Sustainable Resources and Biotechnological Implications

ExtremophilesExtremophiles

Contributors xv

Introduction xix

1 MOLECULAR EVOLUTION OF EXTREMOPHILES 1
Debamitra Chakravorty, Ashwinee Kumar Shreshtha, V. R. Sarath Babu, and Sanjukta Patra

1.1 Introduction 1

1.2 Molecular Evolution of Thermophiles 2

1.2.1 Habitat 2

1.2.2 Cellular Organization 3

1.2.3 Genome 3

1.2.4 Proteome 3

1.3 Molecular Evolution of Psychrophiles 4

1.3.1 Habitat 4

1.3.2 Cellular Organization 4

1.3.3 Genome 5

1.3.4 Proteome 5

1.4 Molecular Evolution of Halophiles 6

1.4.1 Habitat 6

1.4.2 Cellular Organization 6

1.4.3 Genome 6

1.4.4 Proteome 6

1.5 Molecular Evolution of Alkaliphiles 7

1.5.1 Habitat 7

1.5.2 Cellular Organization 7

1.5.3 Genome 7

1.5.4 Proteome 8

1.6 Molecular Evolution of Acidophiles 8

1.6.1 Habitat 8

1.6.2 Cellular Organization 8

1.6.3 Genome 9

1.6.4 Proteome 10

1.7 Molecular Evolution of Barophiles 10

1.7.1 Habitat 10

1.7.2 Cellular Organization 10

1.7.3 Genome 11

1.7.4 Proteome 11

1.8 Engineering Extremophiles 12

1.8.1 Microbiology 12

1.8.2 Molecular Biology 13

1.8.3 Bioinformatics 16

1.9 Case Studies 17

1.9.1 Biofuel Production 17

1.9.2 Bioremediation 18

1.9.3 Pesticide Biodegradation 18

1.9.4 Escherichia coli: A Candidate Extremophile 19

1.9.5 Oil-Spill-Cleaning Bacteria 19

1.9.6 Potential Applications and Benefits 19

1.10 Implications of Engineered Extremophiles on Ecology, Environment, and Health 20

1.11 Conclusions and Recommendations 20

References 21

2 ATTAINING EXTREMOPHILES AND EXTREMOLYTES: METHODOLOGIES AND LIMITATIONS 29
Debamitra Chakravorty and Sanjukta Patra

2.1 Introduction 29

2.2 Extremophiles: Types and Diversity 30

2.2.1 Thermophiles 30

2.2.2 Psychrophiles 37

2.2.3 Halophiles 41

2.2.4 Alkaliphiles 46

2.2.5 Acidophiles 49

2.2.6 Barophiles 52

2.3 Extremolytes 54

2.3.1 Production and Purification of Extremolytes 56

2.3.2 Detection, Identification, and Quantification of Extremolytes 63

2.3.3 Limitations 63

2.4 Conclusions 64

References 64

3 STRATEGIES FOR THE ISOLATION AND CULTIVATION OF HALOPHILIC MICROORGANISMS 75
Aharon Oren

3.1 Introduction 75

3.2 Thalassohaline and Athalassohaline Hypersaline Environments 76

3.3 Case Studies 79

3.3.1 Isolation of Aerobic Chemoheterotrophic Archaea from Solar Salterns 79

3.3.2 Magnesium-Requiring and Magnesium-Tolerant Archaea from the Dead Sea 81

3.3.3 Isolation of Acidophilic Halophilic Archaea 82

3.3.4 Isolation of Unusual Anaerobic Halophiles from Deep-Sea Brines 82

3.3.5 Isolation of Polyextremophilic Anaerobic Halophiles 83

3.3.6 Isolation of Halophilic Microorganisms Associated with Plants and Animals 84

3.3.7 Isolation of Halophilic Archaea from Low-Salt Environments 84

3.4 The Upper Salinity Limits of Different Types of Energy Generation 85

3.5 Final Comments 88

References 89

4 HALOPHILIC PROPERTIES AND THEIR MANIPULATION AND APPLICATION 95
Tsutomu Arakawa, Hiroko Tokunaga, Matsujiro Ishibashi, and Masao Tokunaga

4.1 Introduction 95

4.2 Industrial Applications of Halophilic Organisms and Their Proteins 96

4.3 Extreme and Moderate Halophiles and Their Proteins 98

4.4 Generation of Low-Salt Stable Extreme-Halophilic Proteins 99

4.5 Interconversion of Halophilic and Nonhalophilic Proteins 105

4.5.1 Dimer–Tetramer Conversion of HaNDK and PaNDK 106

4.5.2 Generation of Halophilic PaNDK 108

4.6 Soluble Expression of Recombinant Proteins 110

4.7 Natively Unfolded Proteins 113

4.8 Organic Solvent Tolerance 113

References 114

5 FEATURES AND APPLICATIONS OF HALOPHILIC ARCHAEA 123
Ximena C. Abrevaya

5.1 Introduction 123

5.2 General Features 124

5.2.1 Morphology 124

5.2.2 Metabolism 125

5.2.3 Osmoadaptation 126

5.2.4 Natural Habitats 126

5.2.5 Pigments 128

5.2.6 Genetics 130

5.3 Applications of Halophilic Archaea 130

5.3.1 Production of Enzymes 131

5.3.2 Production of Biopolymers 135

5.3.3 Uses in Fermented Foods 137

5.3.4 Uses in Bioremediation and Xenobiotic Degradation 138

5.3.5 Uses in Solar Salt Production 139

5.3.6 Carotenoid Derivative Production and Biotechnological Uses 140

5.3.7 Other Applications 141

5.3.8 Applications in Astrobiology-Related Research 142

5.4 Concluding Remarks 143

Acknowledgment 144

References 144

6 BIOTECHNOLOGICAL APPLICATIONS OF COLD-ADAPTED BACTERIA 159
Laura Garcia-Descalzo, Alberto Alcazar, Fernando Baquero, and Cristina Cid

6.1 Introduction 159

6.2 Molecular Mechanisms of Adaptation to Cold Environments 162

6.3 Exopolysaccharides 163

6.4 Lipids 164

6.5 Proteins 164

6.5.1 Stable Proteins at Cold Temperatures 164

6.5.2 Cold-Adapted Enzymes 167

6.6 Biotechnological Applications of Cold-Adapted Enzymes 168

6.6.1 Detergents 168

6.6.2 Food Industry 168

6.6.3 Pharmaceutical Industry 168

6.6.4 Biofuels 169

6.6.5 Molecular Biology 169

6.7 Biodegradation and Bioremediation in Cold Environments 169

6.7.1 Biodegradation of Petroleum 169

6.7.2 Biodegradation of Phenolic Compounds 170

6.7.3 Bioremediation of Radionuclides, Halogenated Organics, and Nitramines 171

6.7.4 Treatment of Acid Mine Drainage 172

6.8 Conclusions 172

Acknowledgments 172

References 173

Webliography 174

7 ECOLOGY AND BIOTECHNOLOGY OF EXTREMOPHILIC MICROORGANISMS, PARTICULARLY ANAEROBIC HERMOPHILES 175
Francesco Canganella

7.1 Introduction 175

7.2 Thermophiles 176

7.2.1 Thermophilic Anaerobes and Clostridia 178

7.2.2 Ecology of Thermophiles 179

7.2.3 Ecology of Extreme Thermophilic Archaea 181

7.2.4 Ecology of Extreme Thermophilic Bacteria 182

7.2.5 Biotechnology of Thermophiles 182

7.3 Acidophiles 187

7.3.1 Acidophilic Ecosystems 191

7.4 Alkaliphiles 191

7.4.1 Alakalyphilic Ecosystems 192

7.4.2 Biotechnology of Acidophilic and Alkaliphilic Microorganisms 192

7.5 Halophiles 193

7.5.1 NaCl-Enriched Ecosystems 193

7.5.2 Biotechnology of Halophilic Microorganisms 194

7.6 Piezophiles 194

7.6.1 Ecology of Piezophiles 196

7.6.2 Biotechnology of Piezophiles 196

References 196

8 THE ROLE OF EXTREMOPHILIC MICROORGANISMS AND THEIR BIOPRODUCTS IN FOOD PROCESSING AND PRODUCTION 205
Jane A. Irwin

8.1 Introduction 205

8.2 Enzymes from Extremophiles in Food Processing 206

8.2.1 Enzymes from Thermophiles 208

8.2.2 Enzymes from Cold-Adapted Organisms 212

8.2.3 Molecules from Halophiles 215

8.3 Alkaliphiles, Acidophiles, and Piezophiles 217

8.4 Extremophiles in Food Spoilage and Contamination 218

8.4.1 Meat and Fish 218

8.4.2 Milk and Dairy Products 219

8.4.3 Canned and Dried Food 220

8.5 Extremophiles as Pathogens of Food Species 221

8.6 Conclusions 222

References 222

9 EXTREMOPHILES AND THEIR APPLICATION TO BIOFUEL RESEARCH 233
M.P. Taylor, R. Bauer, S. Mackay, M. Tuffin, and D.A. Cowan

9.1 Introduction 233

9.2 Extremophiles and Fuels 235

9.2.1 Thermophiles and Liquid Fuels: Butanol and Ethanol 235

9.2.2 Thermophiles and Gaseous Fuels: Methane and Hydrogen 239

9.2.3 Psychrophiles and Acidophile Whole-Cell Biocatalysts for Fuels 240

9.3 Exploiting Extremophilic Enzymes in Biomass Conversion to Biofuel 241

9.3.1 Lignocellulose: A Recalcitrant but Valuable Biomass Resource 241

9.3.2 Other Polymeric Biomass Resources 246

9.3.3 Enhancing Enzyme Efficiency 248

9.4 Conclusions and Future Prospects 249

References 249

10 SUSTAINABLE ROLE OF THERMOPHILES IN THE SECOND GENERATION OF ETHANOL PRODUCTION 267
Anuj K. Chandel, Ellen C. Giese, Om V. Singh, and Silvio Silv´erio da Silva

10.1 Introduction 267

10.2 Thermophilic Cellulases for Deconstruction of the Plant Cell Wall 269

10.2.1 Thermophilic Cellulase Production and Characteristics 270

10.2.2 Alterations in Thermophiles for High-Cellulase Titers 273

10.2.3 -Glucosidases from Thermophilic Microorganisms 274

10.3 Ethanol Production at Elevated Temperatures 274

10.3.1 Thermotolerant Microorganisms for Ethanol Production 276

10.3.2 Improvements in Thermophilic Ethanol Producers 277

10.3.3 Process Development and Thermophiles 279

10.4 Future Perspectives and Challenges 281

10.5 Conclusions 283

Acknowledgments 283

References 283

11 ECOFRIENDLY ASPECTS OF THE USE OF EXTREMOPHILIC ENZYMES IN TEXTILE SUBSTRATES 291
Bipin J. Agrawal and Sandhya Mishra

11.1 Introduction 291

11.2 Biopolymeric Fibers 292

11.3 Extremophilic Enzymes and Their Use in the Textile Industry 293

11.3.1 Amylases 294

11.3.2 Cellulases 295

11.3.3 Pectinases 295

11.3.4 Catalases 296

11.3.5 Proteases 296

11.3.6 Esterases 296

11.3.7 Laccases 297

11.4 Utilization of Extremophilic Enzymes in Textile Wet Processing 297

11.4.1 Fiber Preparation 297

11.4.2 Fabric Preparation 300

11.4.3 Enzymes in Biopreparation of Textiles 303

11.5 Finishing with Extremophilic Enzymes 306

11.5.1 Biopolishing of Cotton 306

11.5.2 Bio-Denim Washing 307

11.5.3 Biopolishing of Jute 309

11.5.4 Biopolishing of Wool 310

11.5.5 Biopolishing of Silk 310

11.5.6 Biopolishing of Lyocell 310

11.6 Role of Enzymes in Textile After-Care 311

11.7 Role of Enzymes in Effluent Treatment of Textiles 314

11.8 Conclusions 315

References 315

12 THE USE OF EXTREMOPHILIC MICROORGANISMS IN THE INDUSTRIAL RECOVERY OF METALS 319
Carlos A. Jerez

12.1 Introduction 319

12.2 Biomining Extremophiles and Their Industrial Applications 320

12.3 Molecular Studies in Acidophilic Biomining Microorganisms 322

12.4 Microbial Resistance to Acid and Metals 324

12.4.1 Acidophilic Bacteria 324

12.4.2 Acidophilic Archaeons 328

Acknowledgments 331

References 331

13 BACTERIAL POLYMERS PRODUCED BY EXTREMOPHILES: BIOSYNTHESIS, CHARACTERIZATION, AND APPLICATIONS OF EXOPOLYSACCHARIDES 335
Nicolaus Barbara, Anzelmo Gianluca, and Poli Annarita

13.1 Introduction 335

13.2 EPS Produced by Extremophilic Bacteria 336

13.3 Examples of Proposed EPS Biosynthesis from Extremophiles 345

13.4 Physicochemical Investigations for Potential Applications 349

Acknowledgment 351

References 351

14 BIOMEDICAL APPLICATIONS OF EXOPOLYSACCHARIDES PRODUCED BY MICROORGANISMS ISOLATED FROM EXTREME ENVIRONMENTS 357
Ignacio J. Molina, Carmen Ruiz-Ruiz, Emilia Quesada, and Victoria B´ejar

14.1 Introduction 357

14.2 Chemical Composition and Structure of EPSs 358

14.3 Physical Properties of EPSs 358

14.4 Biological Functions of EPSs 359

14.5 Exopolysaccharides Deriving from Extremophilic Organisms 359

14.6 Clinical Applications of EPSs 359

14.7 Exopolysaccharides of Halophilic Microorganisms 361

14.7.1 Halomonas stenophila B-100 361

14.8 Concluding Remarks 362

Acknowledgments 362

References 362

15 BIOSYNTHESIS OF EXTREMOLYTES: RADIATION RESISTANCE AND BIOTECHNOLOGICAL IMPLICATIONS 367
Erin Copeland, Nicholas Choy, Prashant Gabani, and Om V. Singh

15.1 Introduction 367

15.2 Biotechnological Implications of Extremolytes 369

15.2.1 Industrial Implications 369

15.2.2 Therapeutic Implications 370

15.3 Fermentative Production of Extremolytes 371

15.3.1 Microorganisms: An Asset in Extremolyte Fermentation 371

15.3.2 Evaluation of the Fermentation Process 375

15.4 Commercialization of Extremolytes and Extremozymes 380

15.5 Product Recovery 382

15.6 Conclusions 383

References 383

16 SMART THERAPEUTICS FROM EXTREMOPHILES: UNEXPLORED APPLICATIONS AND TECHNOLOGICAL CHALLENGES 389
Raj Kumar and Ajeet Singh

16.1 Introduction 389

16.2 Extremolytes as Protein Protectants 391

16.3 Extremolytes as Cell Protectants 391

16.3.1 Mycosporine-like Amino Acids 392

16.3.2 Bacterioruberin 393

16.3.3 Sphaerophorin and Pannarin 393

16.4 Novel Therapeutics in the Developmental Stage 393

16.5 Homeland Security and Military Medicine 394

16.6 Technological Gaps in Therapeutic Product Development Using Extremophiles 396

16.7 Conclusions 397

Acknowledgment 398

References 398

Index 403