MICROBES -- CONTENTS -- PREFACE -- ACKNOWLEDGMENTS -- 1 HUMAN AND MICROBIAL WORLD -- 1.1 Prologue -- 1.2 Innovations in Microbiology for Human Welfare -- 1.2.1 Impact of Microbes on the Human Genome Project -- 1.2.2 Microbial Biosensors -- 1.2.3 Molecular Diagnostics -- 1.2.4 Nanomedicine -- 1.2.5 Personalized Medicine -- 1.2.6 Biowarfare -- 1.3 The Microbial World -- 1.3.1 Classification System -- 1.3.2 Viruses, Viroids, and Prions -- 1.3.3 Bacteria -- 1.3.4 Eucarya -- 1.3.5 Algae -- 1.3.6 Fungi -- 1.3.7 Protozoa -- 1.3.8 Microscopic Invertebrates -- 1.3.9 Microbial Interrelationships -- 1.3.10 Probiotic Microbes -- 1.4 Future Challenges: Metagenomics -- References -- 2 GENE TECHNOLOGY: APPLICATIONS AND TECHNIQUES -- 2.1 Prologue -- 2.2 Introduction to Gene Technology -- 2.2.1 Genes and Bacteria -- 2.2.2 Reporter Genes -- 2.2.3 Recombinant DNA Pharmaceuticals -- 2.2.4 In vitro DNA Selection -- 2.3 Nucleic Acid Hybridization -- 2.3.1 Colony Blot and Southern Blot -- 2.3.2 Dot Blot and Zoo Blot -- 2.3.3 In situ Hybridization -- 2.3.4 Microarray Technology -- 2.3.5 Molecular Diagnostic Research -- 2.4 DNA Sequencing -- 2.4.1 Dideoxychain Termination Method -- 2.4.2 Automated DNA Sequencing -- 2.4.3 Maxam and Gilbert Method -- 2.4.4 Primer Walking -- 2.4.5 Contig Sequencing -- 2.4.6 Shotgun Sequencing -- 2.4.7 Importance of Sequencing -- 2.5 Polymerase Chain Reaction -- 2.6 Omics Technology and Microbes -- 2.6.1 Genomics: A Tool for Understanding Genes -- 2.6.2 Transcriptomics: A Tool for Deciphering Gene Function -- 2.6.3 Proteomics: A Tool to Unravel the Mysteries of Protein -- 2.6.4 Metabolomics: A Tool to Ultimately Understand the Whole Metabolome -- 2.6.5 Integration of Omics -- 2.7 Bioinformatics in Microbial Technology -- 2.8 Future Challenges: The Biochips -- References -- 3 MEDICAL MICROBIOLOGY AND MOLECULAR DIAGNOSTICS -- 3.1 Prologue.

3.2 Microbial Biology -- 3.2.1 Morphology and Nature of Microorganisms -- 3.2.2 Use of Bergey's Manual and Identibacter Interactus -- 3.2.3 Bacterial Growth and Physiology -- 3.2.4 Antimicrobial Agents -- 3.2.5 Bacterial Genetic Variations -- 3.2.6 Bacterial Pathogenecity -- 3.2.7 Virus-Cell Interaction -- 3.3 Infection and Immunity -- 3.3.1 Overview of the Immune System -- 3.3.2 The Organs of the Immune System -- 3.3.3 Cells of the Immune System -- 3.3.4 Innate Immunity -- 3.3.5 Adaptive Immunity -- 3.3.6 Hypersensitivity -- 3.3.7 Immunity in Viral Infections -- 3.4 Bacterial Pathogens and Associated Diseases -- 3.4.1 Airborne Bacterial Infections -- 3.4.2 Foodborne and Waterborne Diseases -- 3.4.3 Soilborne Bacterial Infections -- 3.4.4 Arthropodborne Bacterial Infections -- 3.4.5 Sexually Transmitted Bacterial Infections -- 3.4.6 Other Important Bacterial Diseases -- 3.4.7 Actinomycetes Mycetoma -- 3.5 Viral Pathogens and Associated Diseases -- 3.5.1 Herpes Simplex Viruses -- 3.5.2 Varicella Zoster Virus -- 3.5.3 Cytomegalovirus -- 3.5.4 Epstein-Barr Virus -- 3.5.5 Human Herpes Virus -- 3.5.6 Hepatitis -- 3.5.7 Respiratory Syncytial Virus -- 3.5.8 Influenza Viruses -- 3.5.9 Parainfluenza Viruses -- 3.5.10 Adenoviruses -- 3.5.11 Rhinoviruses -- 3.5.12 Coronaviruses -- 3.5.13 SARS Virus -- 3.5.14 Diarrheal Viruses -- 3.5.15 Calicivirus (Sapovirus) -- 3.5.16 Enterovirus -- 3.5.17 Poliomyelitis -- 3.5.18 Coxsackie -- 3.5.19 Echoviruses -- 3.5.20 Mumps -- 3.5.21 Measles Virus -- 3.5.22 Rubella -- 3.5.23 Parvovirus B -- 3.5.24 Human Immunodeficiency Viruses -- 3.5.25 Human T Cell Lymphotropic Viruses (HTLV) -- 3.5.26 Papillomaviruses -- 3.5.27 Polyomaviruses -- 3.5.28 Rabies -- 3.5.29 Smallpox -- 3.5.30 Monkeypox -- 3.5.31 Vaccinia -- 3.5.32 Cowpox -- 3.5.33 Arthropodborne Viruses -- 3.5.34 Lymphocytic Choriomenigitis Virus -- 3.5.35 Filovirus.

3.5.36 Hantaviruses -- 3.6 Prions -- 3.6.1 Kuru -- 3.6.2 Creutzfeldt-Jacob Disease (CJD) -- 3.6.3 Gerstmann-Straussler Syndrome (GSS) -- 3.7 Parasitic Infections -- 3.7.1 Nematoda -- 3.7.2 Trematoda -- 3.7.3 Cestoda -- 3.7.4 Protozoan Parasites -- 3.7.5 Skin Parasites -- 3.8 Fungal Pathogen -- 3.8.1 Superficial Fungal Infections -- 3.8.2 Systemic Fungal Infections -- 3.9 Microbial Diagnostics -- 3.9.1 Immunodiagnostic Methods -- 3.9.2 Molecular Diagnostic Approaches -- 3.10 Future Challenges: Promises of Pharmacogenomics -- References -- 4 IDENTIFICATION AND CLASSIFICATION OF MICROBES -- 4.1 Prologue -- 4.2 Principles of Taxonomy -- 4.2.1 Strategies Used to Identify Microbes -- 4.2.2 Methods for Bacterial Identification -- 4.3 Using Phenotypic Characteristics to Identify Microbes -- 4.3.1 Microscopic Morphology -- 4.3.2 Metabolic Differences -- 4.3.3 Serology -- 4.3.4 Fatty Acid Analysis (FAME) -- 4.4 Using Genotypic Character to Identify Microbes -- 4.4.1 Nucleic Acid Probes to Detect Specific Nucleotide Sequence -- 4.4.2 Amplifying Specific DNA Sequences Using PCR -- 4.4.3 Sequencing Ribosomal RNA Genes -- 4.5 Characterizing Strain Differences -- 4.5.1 Phenotypic Typing Methods -- 4.5.2 Molecular Typing Methods -- 4.6 Classification of Microbes on the Basis of Phenotypic Characteristics -- 4.6.1 Carbohydrate Utilization -- 4.6.2 Enzyme Production -- 4.6.3 Mode of Growth -- 4.6.4 Motility -- 4.6.5 Antigen and Phage Susceptibility -- 4.7 Classification of Microbes on the Basis of Genotypic Characters -- 4.7.1 DNA Base Ratio (G + C Ratio) -- 4.7.2 DNA Hybridization -- 4.7.3 Nucleotide Sequence Analysis -- 4.7.4 Comparing the Sequence of 16S Ribosomal Nucleic Acid -- 4.8 Future Challenges: Aptamers for Detection of Pathogens -- References -- 5 DIVERSITY OF MICROORGANISMS -- 5.1 Prologue -- 5.2 Physiological Diversity of Microorganisms.

5.2.1 Anaerobic Chemotrophs -- 5.2.2 Anoxygenic Phototrophs -- 5.2.3 Oxygenic Phototrophs -- 5.2.4 Aerobic Chemolithotrophs -- 5.2.5 Aerobic Chemoorganotrophs -- 5.3 Thriving in Terrestrial Environment -- 5.3.1 Microbial Population Counts in Soil -- 5.3.2 Bacteria that Form a Resting Stage -- 5.3.3 Bacteria that Associate with Plants -- 5.3.4 Isolation of Antibiotic-Producing Bacteria from Soil -- 5.4 Aquatic Environment -- 5.4.1 Sheathed Bacteria -- 5.4.2 Prosthecated Bacteria -- 5.4.3 Bacteria that Derive their Nutrients from Other Organisms -- 5.4.4 Bacteria that Move by Unusual Mechanisms -- 5.4.5 Bacteria that Form Storage Granules -- 5.4.6 Bacteriological Examination of Water-Qualitative Tests -- 5.4.7 Membrane Filter Method -- 5.4.8 Standard Plate Count-Quantitative Test -- 5.5 Animals as Habitat -- 5.5.1 Bacteria that Inhabit the Skin -- 5.5.2 Bacteria that Inhabit the Mucous Membrane -- 5.5.3 Obligate Intracellular Parasites -- 5.6 Archaea in Extreme Environments -- 5.6.1 Extreme Halophiles -- 5.6.2 Extreme Thermophiles -- 5.6.3 Thermophilic Extreme Acidophiles -- 5.7 Biogeochemical Cycles -- 5.7.1 Various Cycles -- 5.7.2 Consequences of Biogeochemical Cycles Gone Wild -- 5.8 Environmental Influence and Control of Microbial Growth -- 5.8.1 Temperature -- 5.8.2 Osmotic Pressure -- 5.8.3 UV Light -- 5.8.4 pH -- 5.8.5 Oligodynamic Action -- 5.9 Microorganisms and Organic Pollutants -- 5.9.1 Environmental Law -- 5.9.2 Process of Biodegradation -- 5.9.3 Relationship between Contaminant Structure, Toxicity, and Biodegradability -- 5.9.4 Environmental Factors -- 5.9.5 Biodegradation of Organic Pollutants -- 5.9.6 Bioremediation -- 5.10 Microorganisms and Metal Pollutants -- 5.10.1 Metals Defined -- 5.10.2 Metal Toxicity Effect on Microbial Cells -- 5.10.3 Mechanism of Microbial Metal Resistance and Detoxification -- 5.10.4 Metal-Microbe Interaction.

5.10.5 Microbial Approaches in Remediation of Metal-Contaminated Soil and Sediments -- 5.11 Environmentally Transmitted Pathogens -- 5.11.1 Transmission of Pathogen -- 5.11.2 Indicator Organisms in Polluted Water -- 5.11.3 Microbiology of Sewage Treatment -- 5.12 Microorganisms as Friends of Man -- 5.12.1 Microbes to Join the Oil Industry -- 5.12.2 Microbes and Biodiesel: Production and Feedstocks -- 5.12.3 Genetic Modification of Lignin Biosynthesis for Improved Biofuel Production -- 5.12.4 Microbes and Biogas Production -- 5.12.5 Biosensors for Environmental Monitoring -- 5.12.6 Microbes as Mining Agents -- 5.12.7 Microbial Fuel Cells -- 5.12.8 Microbes as a Source of Bioenergy -- 5.13 Microbes as a Disastrous Enemy -- 5.13.1 Microbes as Biowarfare Agents -- 5.14 Future Challenges: Microbes in the Space -- References -- 6 MICROBES IN AGRICULTURE -- 6.1 Prologue -- 6.2 The Soil Plant Microorganisms -- 6.2.1 Soil Fertility -- 6.2.2 Rhizosphere Environment -- 6.2.3 Ammonification in Soil -- 6.2.4 Nitrification in Soil -- 6.2.5 Organic Compounds Released by Plants -- 6.2.6 Nitrogen-Fixing Bacteria -- 6.3 Root Microbial Interaction -- 6.3.1 Biological Dinitrogen Fixation -- 6.3.2 Free-Living Dinitrogen Fixation -- 6.3.3 Associative Nitrogen Fixation -- 6.3.4 Legume-Rhizobia Symbioses -- 6.3.5 Mycorrhizal Association -- 6.4 Pathogenic Microbes in Agriculture -- 6.4.1 Microbes and Agriculture -- 6.4.2 Biopesticides -- 6.4.3 Commercial Microbial Pesticides -- 6.4.4 Bioweedicides -- 6.4.5 Diseases Caused by Bacteria -- 6.4.6 Diseases Caused by Virus -- 6.4.7 Soil Biological Control and Plant Diseases -- 6.5 Microbes as a Tool of Genetic Engineering -- 6.5.1 Agrobacterium: The Friendly Bacteria -- 6.5.2 Transformation Technology: Refined Tools for Genetic Transformation -- 6.5.3 Transgenic Cellulosic Biofuel Crops.

6.5.4 Expression of Microbial Enzymes in Crops.