Microbes: Concepts and Applications

An accessible introduction to the world of microbes frombasic microbe biology through industrial applications

Microbes affect our lives in a variety of ways playing animportant role in our health, food, agriculture, and environment.While some microbes are beneficial, others are pathogenic oropportunistic.

Microbes: Concepts and Applications describes basicmicrobe biology and identification and shows not only how theyoperate in the subfields of medicine, biotechnology, environmentalscience, bioengineering, agriculture, and food science, but howthey can be harnessed as a resource. It provides readers with asolid grasp of etiologic agents, pathogenic processes,epidemiology, and the role of microbes as therapeutic agents.

Placing a major emphasis on omics technology, the book coversrecent developments in the arena of microbes and discusses theirrole in industry and agriculture, as well as in related fields suchas immunology, cell biology, and molecular biology. It offerscomplete discussions of the major bacterial, viral, fungal, andparasitic pathogens; includes information on emerging infectiousdiseases, antibiotic resistance, and bioterrorism; and talks aboutthe future challenges in microbiology.

The most complete treatment of microbial biology available,Microbes features eye–opening chapters on:

Human and Microbial World Gene Technology: Application and Techniques Molecular Diagnostic and Medical Microbiology Identification and Classification of Microbes Diversity of Microorganisms Microbes in Agriculture Microbes as a Tool for Industry and Research

Complete with charts and figures, this book is an invaluabletextbook for university teachers, students, researchers, and peopleeverywhere who care about microorganisms.

PREFACE xiii

ACKNOWLEDGMENTS xv

1 HUMAN AND MICROBIAL WORLD 1
1.1 Prologue 1
1.2 Innovations in Microbiology for Human Welfare 1
1.3 The Microbial World 24
1.4 Future Challenges: Metagenomics 57

2 GENE TECHNOLOGY: APPLICATIONS AND TECHNIQUES 65
2.1 Prologue 65
2.2 Introduction to Gene Technology 65
2.3 Nucleic Acid Hybridization 75
2.4 DNA Sequencing 88
2.5 Polymerase Chain Reaction 99
2.6 Omics Technology and Microbes 103
2.7 Bioinformatics in Microbial Technology 124
2.8 Future Challenges: The Biochips 126

3 MEDICAL MICROBIOLOGY AND MOLECULAR DIAGNOSTICS 151
3.1 Prologue 151
3.2 Microbial Biology 152
3.3 Infection and Immunity 160
3.4 Bacterial Pathogens and Associated Diseases 185
3.5 Viral Pathogens and Associated Diseases 209
3.6 Prions 227
3.7 Parasitic Infections 228
3.8 Fungal Pathogen 249
3.9 Microbial Diagnostics 253
3.10 Future Challenges: Promises of Pharmacogenomics 265

4 IDENTIFICATION AND CLASSIFICATION OF MICROBES 275
4.1 Prologue 275
4.2 Principles of Taxonomy 276
4.3 Using Phenotypic Characteristics to Identify Microbes 281
4.4 Using Genotypic Character to Identify Microbes 299
4.5 Characterizing Strain Differences 306
4.6 Classification of Microbes on the Basis of Phenotypic Characteristics 319
4.7 Classification of Microbes on the Basis of Genotypic Characters 324
4.8 Future Challenges: Aptamers for Detection of Pathogens 333

5 DIVERSITY OF MICROORGANISMS 339
5.1 Prologue 339
5.2 Physiological Diversity of Microorganisms 339
5.3 Thriving in Terrestrial Environment 345
5.4 Aquatic Environment 353
5.5 Animals as Habitat 364
5.6 Archaea in Extreme Environments 368
5.7 Biogeochemical Cycles 373
5.8 Environmental Influence and Control of Microbial Growth 377
5.9 Microorganisms and Organic Pollutants 385
5.10 Microorganisms and Metal Pollutants 396
5.11 Environmentally Transmitted Pathogens 405
5.12 Microorganisms as Friends of Man 453
5.13 Microbes as a Disastrous Enemy 468
5.14 Future Challenges: Microbes in the Space 472

6 MICROBES IN AGRICULTURE 481
6.1 Prologue 481
6.2 The Soil Plant Microorganisms 482
6.3 Root Microbial Interaction 500
6.4 Pathogenic Microbes in Agriculture 508
6.5 Microbes as a Tool of Genetic Engineering 535
6.6 Future Challenges: Functional Genomics Approach for Improvement of Crops 557

7 MICROBES AS A TOOL FOR INDUSTRY AND RESEARCH 567
7.1 Prologue 567
7.2 Historical Development 567
7.3 Clinical Diagnostics in a New Era 578
7.4 Industrial Microorganisms and Product Formation 615
7.5 Major Industrial Products for Health and Industry 622
7.6 Food Diagnostics, Food Preservation, and Foodborne Microbial Diseases 649
7.7 Future Challenges: Next Generation Diagnostics Industry 680
References 681

INDEX 685

Dr. Mousumi Debnath received her BSx and MSc from CalcuttaUniversity and PhD from the Unversity of Rajasthan, Jaipur. Hermain research interest is in the field of abiotic stress onmedicinal plants using plant biotechnology tools. Presently sheisengaged in research on genomics and metabolomics of medicinalplants. She also holds a postgraduate degree in Business management(MBA) specialising in Human resource management. She presentlyserves as an Associate Professor in the Department ofBiotechnology, Jaipur Engineering College and Research centre,Affiliated to Rajasthan Technical University,India.

Professor Prakash Singh Bisen, PhD,D.Sc is an eminentscientist in the field of Biotechnology with over 32 years ofresearch and teaching experience. He has one US Patent and anIndian Patent on Tuberculosis to his credit. He is also an authorof over 130 research publicationsPresently, Professor Bisen is theChairman of Bisen Biotech and Biopharma (P) Ltd. a privateequity venture which focuses on diagnostic solutions for widespreaddiseases. Professor Bisen is also the Chairman of the VikrantGroup, which focuses on advancing technical education throughtechnical institutes at Gwalior and Indore, India.

Dr. G.B.K.S. Prasad is a Professor of Biochemistry atJiwaji University, India and possess over 25 yrs of experience as ateacher and researcher in the field of Medical Biotechnology. Heteaches Clinical Biochemistry and Medical Biotechnology toPostgraduate students at Jiwaji University and published over 50research papers in peer reviewed scientific journals. He was atLiverpool School of Tropical Medicine and Hygiene as a CommonwealthStaff Fellow. The focus of his research is Diagnostics andPharmaceutical Biotechnology.