Microbial Diversity in the Genomic Era, Second Edition presents techniques used for microbial taxonomy and phylogeny, along with their applications and respective strengths and challenges. Though many advanced techniques for the identification of unknown bacterium are available in the genomic era, a far fewer number of the total microbial species have been discovered and identified to date. With that in mind, this book incorporates recently developed biosystematics methods and approaches to assess microbial taxonomy, with suitable recommendations for where to apply them across the range of bacterial identification and infectious disease research. Here, international researchers in the field first provide a broad overview of microbial genomics research and microbiome directed medicine, followed by sections on molecular tools for microbial diversity research, extremophilic microbial diversity, functional microbial diversity across application areas, microbial diversity and infectious disease research, and future directions for research. Step-by-step methodologies are provided for key techniques, along with applied case studies breaking down recent research studies into the practical components, illuminating pathways for new studies across the field. This new edition has been fully updated to address advances in the field of microbiome directed medicine, and whole genome sequencing for studying microbial diversity, considering both recent technological advances and new applications areas, from extremophile studies to the latest approaches in human microbiome analysis.
1. Microbial Diversity in the Genomic Era - p. i 2. Cover - p. i 3. Title Page - p. ii 4. Copyright Page - p. iv 5. Table of Contents - p. xx 6. Contributors - p. xxi 7. Chapter 1.1 Molecular Tools for Assessing Bacterial Diversity From Natural Environments - p. 3 8. Chapter 1.2 Importance of Microbial Diversity on Health - p. 19 9. Chapter 1.3 Computational Tools for Whole Genome and Metagenome Analysis of NGS Data for Microbial Diversity Studies - p. 43 10. Chapter 1.4 Microbial Community Structure of the Sundarbans Mangrove Ecosystem - p. 74 11. Chapter 1.5 Understanding the Diversity and Evolution of Rhizobia from a Genomic Perspective - p. 89 12. Chapter 1.6 Role of Microbial Diversity in the Constructed Wetlands - p. 118 13. Chapter 2.1 Deriving Microbial Community Fingerprints From Environmental Samples Using Advanced Molecular Fingerprinting Techniques - p. 133 14. Chapter 2.2 Planktonic and Benthic Archaea in Brackish Coastal Lagoons; a Case Study using High-throughput Amplicon Sequencing from Chilika Lagoon, Odisha, India - p. 147 15. Chapter 2.3 Molecular Tools in Microbial Diversity - p. 171 16. Chapter 2.4 Exploration of Bacterial Alkaline Protease Diversity in Chilika Lake Wetland Ecosystem - p. 195 17. Chapter 2.5 Metabolic Reprogramming Triggered by Abiotic Stress - p. 218 18. Chapter 2.6 Recent Molecular Tools for Analyzing Microbial Diversity in Rhizosphere Ecosystem - p. 234 19. Chapter 3.1 Gut Microorganisms and Caenorhabditis elegans: A Model for Microbiome Research - p. 249 20. Chapter 3.2 Assessment of Microbial Diversity in Hot Springs for Sustainable Industrial Applications - p. 263 21. Chapter 3.3 Disentangling the Autotrophic Thermophiles - p. 281 22. Chapter 3.4 Exploring the Microbial Diversity in Extreme Acidic Environment Using Molecular Techniques - p. 301 23. Chapter 3.5 Microbial Communities Sustain Indigo Reduction Under Anaerobic Alkaline Conditions in the Indigo Fermentation Fluids - p. 313 24. Chapter 3.6 Diversity of Extreme Electroactive Microorganisms and Their Bioelectrochemical Applications - p. 335 25. Chapter 4.1 Functional Microbial Diversity in the Study of Soils of Various Ecosystems - p. 355 26. Chapter 4.2 Advanced Molecular Tools in Microbial Community Profiling in the Context of Bioremediation Applications - p. 371 27. Chapter 4.3 Molecular Structure and Stress Response Diversity of Ciliate Metallothioneins - p. 408 28. Chapter 4.4 Functional Diversity of Bacterial Systems for Metal Homeostasis - p. 422 29. Chapter 4.5 Functional Microbial Diversity - p. 440 30. Chapter 4.6 Carbapenem-Resistant Enterobacteriaceae - p. 467 31. Chapter 4.7 Functional Gene Diversity and Metabolic Potential of Uncultured Bacteria - p. 481 32. Chapter 4.8 Changes in Microbial Communities Throughout the Body Decomposition Process and Its Potential Application in Forensic Casework - p. 493 33. Chapter 5.1 Viral Genome Sequencing and Its Significance in Latest Clinical and Research Findings - p. 517 34. Chapter 5.2 Prevalence of Multidrug Resistance Efflux Pumps (MDREPs) in Environmental Communities - p. 541 35. Chapter 5.3 Pathogenic Microbial Genetic Diversity With Reference to Significant Medical and Public Health - p. 562 36. Chapter 5.4 Functional Applications of Human Microbiome Diversity Studies - p. 589 37. Chapter 5.5 Exploring Plant–Microbe Interaction in the Postgenomic Era - p. 610 38. Chapter 5.6 Quorum Sensing Directed Microbial Diversity in Infectious Bacteria - p. 626 39. Chapter 5.7 Insights Into Bacterial Vaginosis - p. 641 40. Chapter 6.1 Understanding the Structure and Function of Landfill Microbiome Through Genomics - p. 670 41. Chapter 6.2 Significance of Upcoming Technologies and Their Potential Applications in Understanding Microbial Diversity - p. 697 42. Chapter 6.3 Extremophiles-Mediated Carbon Dioxide Sequestration - p. 714 43. Chapter 6.4 Molecular Evolution of Xenobiotic-Degrading Genes and Mobile Genetic Elements in Soil Bacteria - p. 732 44. Chapter 6.5 Deciphering the Microbial Dark Matter Using Metagenome-Assembled Genomes, Culturomics, and Seqcode - p. 748 45. Chapter 6.6 Cultural and Molecular Approaches to Analyse Antimicrobial Resistant Bacteria from Environmental Samples - p. 759 46. Chapter 6.7 Microbial Communities Driving Pollution Degradation in Contaminated Environments - p. 778 47. Index - p. 791 48. Index - continued - p. 801 49. Index - continued - p. 811
Microbial Diversity in the Genomic Era, Second Edition presents techniques used for microbial taxonomy and phylogeny, along with their applications and respective strengths and challenges. Though many advanced techniques for the identification of unknown bacterium are available in the genomic era, a far fewer number of the total microbial species have been discovered and identified to date. With that in mind, this book incorporates recently developed biosystematics methods and approaches to assess microbial taxonomy, with suitable recommendations for where to apply them across the range of bacterial identification and infectious disease research. Here, international researchers in the field first provide a broad overview of microbial genomics research and microbiome directed medicine, followed by sections on molecular tools for microbial diversity research, extremophilic microbial diversity, functional microbial diversity across application areas, microbial diversity and infectious disease research, and future directions for research. Step-by-step methodologies are provided for key techniques, along with applied case studies breaking down recent research studies into the practical components, illuminating pathways for new studies across the field. This new edition has been fully updated to address advances in the field of microbiome directed medicine, and whole genome sequencing for studying microbial diversity, considering both recent technological advances and new applications areas, from extremophile studies to the latest approaches in human microbiome analysis.
1. Microbial Diversity in the Genomic Era - p. i 2. Cover - p. i 3. Title Page - p. ii 4. Copyright Page - p. iv 5. Table of Contents - p. xx 6. Contributors - p. xxi 7. Chapter 1.1 Molecular Tools for Assessing Bacterial Diversity From Natural Environments - p. 3 8. Chapter 1.2 Importance of Microbial Diversity on Health - p. 19 9. Chapter 1.3 Computational Tools for Whole Genome and Metagenome Analysis of NGS Data for Microbial Diversity Studies - p. 43 10. Chapter 1.4 Microbial Community Structure of the Sundarbans Mangrove Ecosystem - p. 74 11. Chapter 1.5 Understanding the Diversity and Evolution of Rhizobia from a Genomic Perspective - p. 89 12. Chapter 1.6 Role of Microbial Diversity in the Constructed Wetlands - p. 118 13. Chapter 2.1 Deriving Microbial Community Fingerprints From Environmental Samples Using Advanced Molecular Fingerprinting Techniques - p. 133 14. Chapter 2.2 Planktonic and Benthic Archaea in Brackish Coastal Lagoons; a Case Study using High-throughput Amplicon Sequencing from Chilika Lagoon, Odisha, India - p. 147 15. Chapter 2.3 Molecular Tools in Microbial Diversity - p. 171 16. Chapter 2.4 Exploration of Bacterial Alkaline Protease Diversity in Chilika Lake Wetland Ecosystem - p. 195 17. Chapter 2.5 Metabolic Reprogramming Triggered by Abiotic Stress - p. 218 18. Chapter 2.6 Recent Molecular Tools for Analyzing Microbial Diversity in Rhizosphere Ecosystem - p. 234 19. Chapter 3.1 Gut Microorganisms and Caenorhabditis elegans: A Model for Microbiome Research - p. 249 20. Chapter 3.2 Assessment of Microbial Diversity in Hot Springs for Sustainable Industrial Applications - p. 263 21. Chapter 3.3 Disentangling the Autotrophic Thermophiles - p. 281 22. Chapter 3.4 Exploring the Microbial Diversity in Extreme Acidic Environment Using Molecular Techniques - p. 301 23. Chapter 3.5 Microbial Communities Sustain Indigo Reduction Under Anaerobic Alkaline Conditions in the Indigo Fermentation Fluids - p. 313 24. Chapter 3.6 Diversity of Extreme Electroactive Microorganisms and Their Bioelectrochemical Applications - p. 335 25. Chapter 4.1 Functional Microbial Diversity in the Study of Soils of Various Ecosystems - p. 355 26. Chapter 4.2 Advanced Molecular Tools in Microbial Community Profiling in the Context of Bioremediation Applications - p. 371 27. Chapter 4.3 Molecular Structure and Stress Response Diversity of Ciliate Metallothioneins - p. 408 28. Chapter 4.4 Functional Diversity of Bacterial Systems for Metal Homeostasis - p. 422 29. Chapter 4.5 Functional Microbial Diversity - p. 440 30. Chapter 4.6 Carbapenem-Resistant Enterobacteriaceae - p. 467 31. Chapter 4.7 Functional Gene Diversity and Metabolic Potential of Uncultured Bacteria - p. 481 32. Chapter 4.8 Changes in Microbial Communities Throughout the Body Decomposition Process and Its Potential Application in Forensic Casework - p. 493 33. Chapter 5.1 Viral Genome Sequencing and Its Significance in Latest Clinical and Research Findings - p. 517 34. Chapter 5.2 Prevalence of Multidrug Resistance Efflux Pumps (MDREPs) in Environmental Communities - p. 541 35. Chapter 5.3 Pathogenic Microbial Genetic Diversity With Reference to Significant Medical and Public Health - p. 562 36. Chapter 5.4 Functional Applications of Human Microbiome Diversity Studies - p. 589 37. Chapter 5.5 Exploring Plant–Microbe Interaction in the Postgenomic Era - p. 610 38. Chapter 5.6 Quorum Sensing Directed Microbial Diversity in Infectious Bacteria - p. 626 39. Chapter 5.7 Insights Into Bacterial Vaginosis - p. 641 40. Chapter 6.1 Understanding the Structure and Function of Landfill Microbiome Through Genomics - p. 670 41. Chapter 6.2 Significance of Upcoming Technologies and Their Potential Applications in Understanding Microbial Diversity - p. 697 42. Chapter 6.3 Extremophiles-Mediated Carbon Dioxide Sequestration - p. 714 43. Chapter 6.4 Molecular Evolution of Xenobiotic-Degrading Genes and Mobile Genetic Elements in Soil Bacteria - p. 732 44. Chapter 6.5 Deciphering the Microbial Dark Matter Using Metagenome-Assembled Genomes, Culturomics, and Seqcode - p. 748 45. Chapter 6.6 Cultural and Molecular Approaches to Analyse Antimicrobial Resistant Bacteria from Environmental Samples - p. 759 46. Chapter 6.7 Microbial Communities Driving Pollution Degradation in Contaminated Environments - p. 778 47. Index - p. 791 48. Index - continued - p. 801 49. Index - continued - p. 811
