Microbes: Concepts and Applications

3.9.1 Immunodiagnostic Methods......Page 3
CONTENTS......Page 7
PREFACE......Page 15
ACKNOWLEDGMENTS......Page 17
1.2 Innovations in Microbiology for Human Welfare......Page 19
1.2.1 Impact of Microbes on the Human Genome Project......Page 20
1.2.2 Microbial Biosensors......Page 23
1.2.3 Molecular Diagnostics......Page 25
1.2.4 Nanomedicine......Page 31
1.2.5 Personalized Medicine......Page 34
1.2.6 Biowarfare......Page 39
1.3 The Microbial World......Page 42
1.3.1 Classification System......Page 43
1.3.2 Viruses, Viroids, and Prions......Page 44
1.3.3 Bacteria......Page 50
1.3.4 Eucarya......Page 53
1.3.5 Algae......Page 57
1.3.6 Fungi......Page 62
1.3.7 Protozoa......Page 65
1.3.8 Microscopic Invertebrates......Page 69
1.3.9 Microbial Interrelationships......Page 72
1.3.10 Probiotic Microbes......Page 74
1.4 Future Challenges: Metagenomics......Page 75
References......Page 78
2.2 Introduction to Gene Technology......Page 83
2.2.1 Genes and Bacteria......Page 85
2.2.2 Reporter Genes......Page 86
2.2.3 Recombinant DNA Pharmaceuticals......Page 87
2.2.4 In vitro DNA Selection......Page 91
2.3 Nucleic Acid Hybridization......Page 93
2.3.1 Colony Blot and Southern Blot......Page 94
2.3.2 Dot Blot and Zoo Blot......Page 95
2.3.3 In situ Hybridization......Page 97
2.3.4 Microarray Technology......Page 101
2.3.5 Molecular Diagnostic Research......Page 105
2.4 DNA Sequencing......Page 106
2.4.2 Automated DNA Sequencing......Page 108
2.4.3 Maxam and Gilbert Method......Page 110
2.4.4 Primer Walking......Page 114
2.4.6 Shotgun Sequencing......Page 115
2.5 Polymerase Chain Reaction......Page 117
2.6 Omics Technology and Microbes......Page 121
2.6.1 Genomics: A Tool for Understanding Genes......Page 122
2.6.2 Transcriptomics: A Tool for Deciphering Gene Function......Page 126
2.6.3 Proteomics: A Tool to Unravel the Mysteries of Protein......Page 130
2.6.4 Metabolomics: A Tool to Ultimately Understand the Whole Metabolome......Page 134
2.6.5 Integration of Omics......Page 139
2.7 Bioinformatics in Microbial Technology......Page 142
2.8 Future Challenges: The Biochips......Page 144
References......Page 155
3.1 Prologue......Page 169
3.2.1 Morphology and Nature of Microorganisms......Page 170
3.2.3 Bacterial Growth and Physiology......Page 172
3.2.4 Antimicrobial Agents......Page 174
3.2.6 Bacterial Pathogenecity......Page 176
3.2.7 Virus–Cell Interaction......Page 177
3.3.1 Overview of the Immune System......Page 178
3.3.2 The Organs of the Immune System......Page 179
3.3.3 Cells of the Immune System......Page 180
3.3.4 Innate Immunity......Page 182
3.3.5 Adaptive Immunity......Page 183
3.3.6 Hypersensitivity......Page 198
3.3.7 Immunity in Viral Infections......Page 201
3.4 Bacterial Pathogens and Associated Diseases......Page 203
3.4.1 Airborne Bacterial Infections......Page 204
3.4.2 Foodborne and Waterborne Diseases......Page 208
3.4.3 Soilborne Bacterial Infections......Page 216
3.4.4 Arthropodborne Bacterial Infections......Page 218
3.4.5 Sexually Transmitted Bacterial Infections......Page 219
3.4.6 Other Important Bacterial Diseases......Page 221
3.4.7 Actinomycetes Mycetoma......Page 222
3.5 Viral Pathogens and Associated Diseases......Page 227
3.5.3 Cytomegalovirus......Page 228
3.5.6 Hepatitis......Page 229
3.5.7 Respiratory Syncytial Virus......Page 231
3.5.8 Influenza Viruses......Page 232
3.5.11 Rhinoviruses......Page 233
3.5.14 Diarrheal Viruses......Page 234
3.5.18 Coxsackie......Page 235
3.5.21 Measles Virus......Page 236
3.5.23 Parvovirus B......Page 237
3.5.24 Human Immunodeficiency Viruses......Page 238
3.5.26 Papillomaviruses......Page 240
3.5.29 Smallpox......Page 241
3.5.33 Arthropodborne Viruses......Page 242
3.5.35 Filovirus......Page 244
3.6.2 Creutzfeldt–Jacob Disease (CJD)......Page 245
3.7 Parasitic Infections......Page 246
3.7.1 Nematoda......Page 247
3.7.2 Trematoda......Page 250
3.7.3 Cestoda......Page 252
3.7.4 Protozoan Parasites......Page 254
3.7.5 Skin Parasites......Page 266
3.8.1 Superficial Fungal Infections......Page 267
3.8.2 Systemic Fungal Infections......Page 268
3.9 Microbial Diagnostics......Page 271
3.9.2 Molecular Diagnostic Approaches......Page 276
3.10 Future Challenges: Promises of Pharmacogenomics......Page 283
References......Page 285
4.1 Prologue......Page 293
4.2 Principles of Taxonomy......Page 294
4.2.1 Strategies Used to Identify Microbes......Page 298
4.3 Using Phenotypic Characteristics to Identify Microbes......Page 299
4.3.1 Microscopic Morphology......Page 301
4.3.2 Metabolic Differences......Page 306
4.3.3 Serology......Page 313
4.3.4 Fatty Acid Analysis (FAME)......Page 316
4.4 Using Genotypic Character to Identify Microbes......Page 317
4.4.1 Nucleic Acid Probes to Detect Specific Nucleotide Sequence......Page 318
4.4.2 Amplifying Specific DNA Sequences Using PCR......Page 319
4.4.3 Sequencing Ribosomal RNA Genes......Page 320
4.5.1 Phenotypic Typing Methods......Page 324
4.5.2 Molecular Typing Methods......Page 333
4.6 Classification of Microbes on the Basis of Phenotypic Characteristics......Page 337
4.6.2 Enzyme Production......Page 340
4.6.4 Motility......Page 341
4.7 Classification of Microbes on the Basis of Genotypic Characters......Page 342
4.7.1 DNA Base Ratio (G + C Ratio)......Page 343
4.7.2 DNA Hybridization......Page 344
4.7.3 Nucleotide Sequence Analysis......Page 348
4.7.4 Comparing the Sequence of 16S Ribosomal Nucleic Acid......Page 349
4.8 Future Challenges: Aptamers for Detection of Pathogens......Page 351
References......Page 352
5.2 Physiological Diversity of Microorganisms......Page 357
5.2.2 Anoxygenic Phototrophs......Page 358
5.2.3 Oxygenic Phototrophs......Page 360
5.2.4 Aerobic Chemolithotrophs......Page 361
5.2.5 Aerobic Chemoorganotrophs......Page 362
5.3 Thriving in Terrestrial Environment......Page 363
5.3.1 Microbial Population Counts in Soil......Page 364
5.3.2 Bacteria that Form a Resting Stage......Page 366
5.3.3 Bacteria that Associate with Plants......Page 367
5.3.4 Isolation of Antibiotic-Producing Bacteria from Soil......Page 369
5.4.1 Sheathed Bacteria......Page 371
5.4.2 Prosthecated Bacteria......Page 372
5.4.3 Bacteria that Derive their Nutrients from Other Organisms......Page 375
5.4.4 Bacteria that Move by Unusual Mechanisms......Page 376
5.4.5 Bacteria that Form Storage Granules......Page 377
5.4.6 Bacteriological Examination of Water—Qualitative Tests......Page 378
5.4.7 Membrane Filter Method......Page 379
5.4.8 Standard Plate Count—Quantitative Test......Page 381
5.5 Animals as Habitat......Page 382
5.5.1 Bacteria that Inhabit the Skin......Page 383
5.5.2 Bacteria that Inhabit the Mucous Membrane......Page 384
5.5.3 Obligate Intracellular Parasites......Page 385
5.6 Archaea in Extreme Environments......Page 386
5.6.1 Extreme Halophiles......Page 387
5.6.2 Extreme Thermophiles......Page 389
5.6.3 Thermophilic Extreme Acidophiles......Page 390
5.7 Biogeochemical Cycles......Page 391
5.7.2 Consequences of Biogeochemical Cycles Gone Wild......Page 394
5.8 Environmental Influence and Control of Microbial Growth......Page 395
5.8.1 Temperature......Page 396
5.8.2 Osmotic Pressure......Page 397
5.8.3 UV Light......Page 399
5.8.4 pH......Page 400
5.8.5 Oligodynamic Action......Page 402
5.9 Microorganisms and Organic Pollutants......Page 403
5.9.1 Environmental Law......Page 404
5.9.2 Process of Biodegradation......Page 405
5.9.3 Relationship between Contaminant Structure, Toxicity, and Biodegradability......Page 407
5.9.4 Environmental Factors......Page 409
5.9.5 Biodegradation of Organic Pollutants......Page 410
5.9.6 Bioremediation......Page 412
5.10 Microorganisms and Metal Pollutants......Page 414
5.10.1 Metals Defined......Page 416
5.10.2 Metal Toxicity Effect on Microbial Cells......Page 417
5.10.3 Mechanism of Microbial Metal Resistance and Detoxification......Page 418
5.10.4 Metal–Microbe Interaction......Page 420
5.10.5 Microbial Approaches in Remediation of Metal-Contaminated Soil and Sediments......Page 421
5.11.1 Transmission of Pathogen......Page 423
5.11.2 Indicator Organisms in Polluted Water......Page 449
5.11.3 Microbiology of Sewage Treatment......Page 467
5.12 Microorganisms as Friends of Man......Page 471
5.12.1 Microbes to Join the Oil Industry......Page 472
5.12.2 Microbes and Biodiesel: Production and Feedstocks......Page 473
5.12.3 Genetic Modification of Lignin Biosynthesis for Improved Biofuel Production......Page 475
5.12.4 Microbes and Biogas Production......Page 477
5.12.5 Biosensors for Environmental Monitoring......Page 478
5.12.6 Microbes as Mining Agents......Page 480
5.12.7 Microbial Fuel Cells......Page 482
5.12.8 Microbes as a Source of Bioenergy......Page 484
5.13 Microbes as a Disastrous Enemy......Page 486
5.13.1 Microbes as Biowarfare Agents......Page 488
5.14 Future Challenges: Microbes in the Space......Page 490
References......Page 493
6.1 Prologue......Page 499
6.2 The Soil Plant Microorganisms......Page 500
6.2.1 Soil Fertility......Page 501
6.2.2 Rhizosphere Environment......Page 506
6.2.3 Ammonification in Soil......Page 509
6.2.4 Nitrification in Soil......Page 511
6.2.6 Nitrogen-Fixing Bacteria......Page 513
6.3 Root Microbial Interaction......Page 518
6.3.1 Biological Dinitrogen Fixation......Page 522
6.3.2 Free-Living Dinitrogen Fixation......Page 523
6.3.3 Associative Nitrogen Fixation......Page 524
6.3.5 Mycorrhizal Association......Page 525
6.4 Pathogenic Microbes in Agriculture......Page 526
6.4.1 Microbes and Agriculture......Page 528
6.4.2 Biopesticides......Page 530
6.4.3 Commercial Microbial Pesticides......Page 532
6.4.4 Bioweedicides......Page 536
6.4.5 Diseases Caused by Bacteria......Page 537
6.4.6 Diseases Caused by Virus......Page 543
6.4.7 Soil Biological Control and Plant Diseases......Page 546
6.5 Microbes as a Tool of Genetic Engineering......Page 553
6.5.1 Agrobacterium: The Friendly Bacteria......Page 554
6.5.2 Transformation Technology: Refined Tools for Genetic Transformation......Page 555
6.5.3 Transgenic Cellulosic Biofuel Crops......Page 559
6.5.4 Expression of Microbial Enzymes in Crops......Page 563
6.5.5 Genetic Transformation for Crop Improvement: Biotic Stress Tolerance......Page 565
6.5.6 Genetic Transformation for Crop Improvement: Altering Plant Development......Page 570
6.5.7 Genomics: Gene Mining and Gene Expression Profiling......Page 572
6.6 Future Challenges: Functional Genomics Approach for Improvement of Crops......Page 575
References......Page 578
7.2 Historical Development......Page 585
7.2.1 Era of Pasteur and Fermentation......Page 586
7.2.2 Discovery of Antibiotics......Page 590
7.2.3 Growth of Industrial Fermentation......Page 591
7.2.4 Production of Strains......Page 594
7.2.5 Strain Development......Page 595
7.3 Clinical Diagnostics in a New Era......Page 596
7.3.1 Genes and Diseases......Page 597
7.3.2 Biomedical Research in the Postgenomic Era......Page 600
7.3.3 Molecular Diagnostics Technology and Health Care Industries......Page 604
7.3.4 Therapeutic Applications of rDNA Pharmaceuticals......Page 611
7.3.5 Aptamers as Therapeutics......Page 613
7.3.6 Immunodiagnostics......Page 617
7.3.7 Reporter Genes in Molecular Diagnostics......Page 620
7.3.8 Human Genome Project and Health Services......Page 622
7.3.9 Prognostics, Diagnostics, and Therapeutics of Disease-Causing Pathogens......Page 625
7.3.10 Promise of Pharmacogenomics......Page 629
7.4 Industrial Microorganisms and Product Formation......Page 633
7.4.1 Microorganisms and Their Products......Page 634
7.4.2 Primary and Secondary Metabolites......Page 635
7.4.3 Characteristics of Large-Scale Fermentation......Page 637
7.4.4 Fermentation Scale-Up......Page 639
7.5 Major Industrial Products for Health and Industry......Page 640
7.5.1 Immobilized Enzymes......Page 641
7.5.2 Antibiotics......Page 644
7.5.3 Organic Acids......Page 650
7.5.4 Enzymes......Page 653
7.5.5 Solvents......Page 655
7.5.6 Amino Acids......Page 656
7.5.7 Vitamins......Page 658
7.5.8 Yeast......Page 659
7.5.9 Single Cell Protein......Page 661
7.5.10 Fermented Food......Page 663
7.5.12 Beverages......Page 665
7.6 Food Diagnostics, Food Preservation, and Foodborne Microbial Diseases......Page 667
7.6.1 Food Preservation and Microbial Growth......Page 668
7.6.2 Microbial Sampling and Food Poisoning......Page 680
7.6.3 Food Diagnostics......Page 684
7.7 Future Challenges: Next Generation Diagnostics Industry......Page 698
References......Page 699
INDEX......Page 703