Microbial Diversity in the Genomic Era

Functional Diversity and Community Analysis

2nd Edition - March 23, 2024
Editors: Surajit Das, Hirak Ranjan Dash
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 1 3 3 2 0 - 6
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 1 3 3 2 1 - 3

Microbial Diversity in the Genomic Era: Functional Diversity and Community Analysis, Second Edition presents techniques used for microbial taxonomy and phylogeny, along with th… Read more

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Microbial Diversity in the Genomic Era: Functional Diversity and Community Analysis, Second Edition presents techniques used for microbial taxonomy and phylogeny, along with their applications and respective strengths and challenges. The 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. Sections provide a broad overview of microbial genomics research and microbiome directed medicine and update 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. Step-by-step methodologies are provided for key techniques, along with applied case studies that break down recent research studies into practical components, thus illuminating pathways for new studies across the field.

Cover image
Title page
Table of Contents
Copyright
Contributors
Section I. Overview of Microbial Diversity
Chapter 1.1. Molecular Tools for Assessing Bacterial Diversity From Natural Environments
1.1.1. Introduction
1.1.2. Analysis of Microbial Communities Based on Cultured Approaches
1.1.3. Analysis of Microbial Communities Using Culture-Independent Approaches
1.1.4. Processing of NGS Data
1.1.5. Third-Generation Sequencers
1.1.6. “Omics”-Driven Metagenomics
Chapter 1.2. Importance of Microbial Diversity on Health: Perhaps the Best Tool to Intervene in Emerging and Continuing Diseases
1.2.1. Background
1.2.2. Introduction
1.2.3. Gut Microbial Composition (Abundance and Diversity) and Their Importance and Relation to Diseases
1.2.4. Molecular Basis of Microbiome Disease Correlation: In the Perspective of Conserved and Uniqueness of Metagenome and Metabolome Composition
1.2.5. Implication from the Perspective of Gut Microbiota
1.2.6. Prospective
Author Contributions
Conflict of Interest
Appendix
Chapter 1.3. Computational Tools for Whole Genome and Metagenome Analysis of NGS Data for Microbial Diversity Studies
1.3.1. Introduction
1.3.2. Computational Tools for Cultured-Dependent Whole Genome Analysis
1.3.3. Comparative Genomics and Pan-Genomic Analysis
1.3.4. Computational Tools for Microbial Community Analysis
1.3.5. Conclusion and Future Prospects
Chapter 1.4. Microbial Community Structure of the Sundarbans Mangrove Ecosystem
1.4.1. Introduction
1.4.2. Sustenance of Mangrove Ecosystems in Association with Microbiome
1.4.3. The Sundarbans: World’s Largest Mangrove Forest
1.4.4. Diversity and Distribution of Microbial Community Structure in the Mangrove Ecosystems of the Sundarbans
1.4.5. Culture-Independent Techniques Based on Next-Generation Sequencing Technology to Explore Microbial Community Structure
1.4.6. Study of Diversity from Sundarbans Mangrove-Associated Microorganisms
1.4.7. Conclusion and Future Perspective
Chapter 1.5. Understanding the Diversity and Evolution of Rhizobia from a Genomic Perspective
1.5.1. Diazotrophic Bacteria: Types of Interaction with Plants
1.5.2. Diversity, Evolution, and Taxonomy of Rhizobia: From the Classic Methods to the Genomic Era
1.5.3. State-of-The-Art in Current Rhizobial Classification
1.5.4. Symbiosis Genes: Insights About Their Evolution and Organization in the Genomes
1.5.5. Considerations About the Origin of the Symbiotic Nitrogen Fixation
Chapter 1.6. Role of Microbial Diversity in the Constructed Wetlands
1.6.1. Introduction
1.6.2. Classification, Design, and Property of the Constructed Wetlands
1.6.3. The Factors That Affect Microbial Growth in the CW
1.6.4. Microbial Distribution in the Constructed Wetland
1.6.5. The Microbial Associated With Pollutant Removal in Constructed Wetland
1.6.6. Plant–Microbe Synergism in the CW for the Treatment of Various Wastewater
1.6.7. Conclusion
Section II. Molecular Tools in Microbial Diversity
Chapter 2.1. Deriving Microbial Community Fingerprints From Environmental Samples Using Advanced Molecular Fingerprinting Techniques
2.1.1. Introduction
2.1.2. Culture-Dependent Approaches: Advantages and Limitations
2.1.3. Molecular Approaches to Derive Microbial Community Fingerprint from Environmental Samples
2.1.4. Limitations of Molecular Community Analysis Techniques
2.1.5. Conclusion
Chapter 2.2. Planktonic and Benthic Archaea in Brackish Coastal Lagoons; a Case Study using High-throughput Amplicon Sequencing from Chilika Lagoon, Odisha, India
2.2.1. Introduction
2.2.2. Biogeochemical Roles of Archaea
2.2.3. Biology and Ecology of Archaea through Application of High-throughput Sequencing
2.2.4. Microbial Ecology of Archaea from Chilika Lagoon
2.2.5. Concluding Remarks and Perspective
Chapter 2.3. Molecular Tools in Microbial Diversity: Functional Assessment for Genomes and Metagenomes by Genomaple
2.3.1. Introduction
2.3.2. Development of a New Method for Evaluating the Potential Functionome
2.3.3. Overview of the Genomaple System
2.3.4. User's Guide for Genomaple Version 2.4.0
2.3.5. Conclusion and Future Prospects
Chapter 2.4. Exploration of Bacterial Alkaline Protease Diversity in Chilika Lake Wetland Ecosystem
2.4.1. Introduction
2.4.2. Bioprospecting for Alkaline Protease in Chilika Lake
2.4.3. Bioprospecting of Novel Bacterial Alkaline Proteases From Chilika Lake by Culture-Dependent Approach
2.4.4. Bioprospecting of Novel Bacterial Alkaline Proteases From Chilika Lake by Culture-Independent Approach
2.4.5. Limitations to Study Microbial Diversity From Natural Ecosystems
2.4.6. Conclusion and Future Perspectives
Chapter 2.5. Metabolic Reprogramming Triggered by Abiotic Stress: A Treasure-Trove of Bio-Based Technologies
2.5.1. Introduction
2.5.2. Nutrient Stress and Metabolic Reprogramming
2.5.3. Sulfur Stress and Enhanced Production of α-Ketoglutarate
2.5.4. Conclusions
Chapter 2.6. Recent Molecular Tools for Analyzing Microbial Diversity in Rhizosphere Ecosystem
2.6.1. Introduction
2.6.2. Polyphasic Taxonomy: Approaches to Study Microbial Diversity
2.6.3. Phenotypic Approaches for Microbial Diversity Analysis
2.6.4. Molecular-Based Techniques for Analyzing Microbial Diversity
2.6.5. PCR-Independent Techniques
2.6.6. Conclusion
Section III. Extremophilic Microbial Diversity
Chapter 3.1. Gut Microorganisms and Caenorhabditis elegans: A Model for Microbiome Research
3.1.1. Introduction
3.1.2. C. elegans and its Microbiome
3.1.3. Effect of the Microbiota on C. elegans Physiology
3.1.4. Microbial Pathogens and Impact on C. elegans Microbiome
3.1.5. Conclusion and Future Direction
Chapter 3.2. Assessment of Microbial Diversity in Hot Springs for Sustainable Industrial Applications
3.2.1. Microbes, Microbial Diversity, and Microbial Evolution
3.2.2. Extreme Environments and Diversity of Extremophiles
3.2.3. Unique Characteristics of Thermophiles
3.2.4. Habitats of Thermophiles
3.2.5. Microbial Diversity of Hot Springs
3.2.6. Industrial Applications of Thermophiles
3.2.7. Future Prospects of Hot Spring Microbiota
Chapter 3.3. Disentangling the Autotrophic Thermophiles: Concepts, Diversity, and Emerging Trends
3.3.1. Introduction
3.3.2. Autotrophic Carbon-Fixation Cycles
3.3.3. Carbon Fixation in Thermophiles
3.3.4. Assessing the Thermophilic Autotrophic Diversity
3.3.5. Emerging Trends in the Biotechnological Potential of Autotrophic Thermophiles
3.3.6. Final Remarks
Chapter 3.4. Exploring the Microbial Diversity in Extreme Acidic Environment Using Molecular Techniques
3.4.1. Introduction
3.4.2. Molecular Approaches in Microbial Diversity
3.4.3. Molecular Approaches in Acidic Environment Microbial Diversity
3.4.4. Case Studies About Acidophiles Diversity Determined by Using Molecular Approaches
3.4.5. Conclusion
Chapter 3.5. Microbial Communities Sustain Indigo Reduction Under Anaerobic Alkaline Conditions in the Indigo Fermentation Fluids
3.5.1. Introduction
3.5.2. Background of Indigo Fermentation
3.5.3. Mechanisms of Indigo Reduction
3.5.4. Microbial Community in Indigo Dye Fermentation
3.5.5. Microbial Community in Woad Fermentation
3.5.6. Transitional Changes During Indigo Fermentation Using Sukumo
3.5.7. Effects of Additives in Indigo Fermentation Using Sukumo
3.5.8. Isolation of Indigo-Reducing Bacteria
3.5.9. Indigo-Reducing Bacteria Isolated from Fermentation Fluid for Indigo Dyeing
3.5.10. Conclusion and Perspectives
Chapter 3.6. Diversity of Extreme Electroactive Microorganisms and Their Bioelectrochemical Applications
3.6.1. Introduction
3.6.2. Diversity of Extremophilic Electroactive Microorganisms
3.6.3. Bioelectrochemical Applications of Extremophilic Electroactive Microorganisms
3.6.4. A Case Study of a Well-Studied Thermophilic Electroactive Microorganism Thermincola ferriacetica
3.6.5. Conclusions
Section IV. Functional Microbial Diversity
Chapter 4.1. Functional Microbial Diversity in the Study of Soils of Various Ecosystems
4.1.1. Introduction
4.1.2. Human Activity and Microbial Diversity
4.1.3. Biolog Method
4.1.4. Assessment of the Metabolic Diversity of Microorganisms According to EcoPlate as an Indicators of Soil Quality on Various Ecosystems
4.1.5. Conclusion
Chapter 4.2. Advanced Molecular Tools in Microbial Community Profiling in the Context of Bioremediation Applications
4.2.1. Introduction
4.2.2. Microbial Community Profiling
4.2.3. Functional Microbial Diversity
4.2.4. PostGenomic Application
4.2.5. Functional Microbial Diversity and Bioremediation
4.2.6. Conclusion
Chapter 4.3. Molecular Structure and Stress Response Diversity of Ciliate Metallothioneins
4.3.1. Introduction: Reviewing the Metallothionein Concept and its General Features
4.3.2. Ciliate Metallothionein Structural Diversity: Variations on the Same Topic
4.3.3. Metal Binding (Metalation)
4.3.4. Are Metallothioneins Multifunctional or Multistress Proteins?
4.3.5. Microbial Metallothionein Gene Expression Regulation
4.3.6. Biotechnological Applications of Ciliate Metallothionein Genes
4.3.7. Summary and Concluding Remarks
Chapter 4.4. Functional Diversity of Bacterial Systems for Metal Homeostasis
4.4.1. The Metals
4.4.2. Metals and Bacteria
4.4.3. Metal-Dedicated Resistance Systems
4.4.4. Metals Interplay
4.4.5. Case Study—Impact of the Environment on Caulobacter crescentus Cu Tolerance
4.4.6. Conclusion
Chapter 4.5. Functional Microbial Diversity: Functional Genomics and Metagenomics Using Genomaple
4.5.1. Introduction
4.5.2. Functional Classification of Uncultivated Archaea Within Aigarchaeota
4.5.3. Metabolic and Physiological Potential of “Ca. C. subterraneum” Deduced by Genomaple Analysis
4.5.4. Functional Diversity of Lysobacter Species Producing Antimicrobial Enzymes
4.5.5. Functional Diversity of Anammox Bioreactor Revealed by Omics
4.5.6. Conclusion and Future Prospects
Chapter 4.6. Carbapenem-Resistant Enterobacteriaceae: A Clinical and Environmental Perspective in the Amazon Region
4.6.1. Introduction
4.6.2. Antibiotic Resistance Mechanisms
4.6.3. Currently Relevant Beta-Lactamases in Enterobacteriaceae
4.6.4. Role of Mobile Genetic Elements in the Antibiotic Resistance Dissemination
4.6.5. A Systematic Review on Multidrug-Resistant Enterobacteriaceae in the Amazon Region
4.6.6. Conclusion
Chapter 4.7. Functional Gene Diversity and Metabolic Potential of Uncultured Bacteria
4.7.1. Introduction
4.7.2. General Concept of Functional Gene Diversity
4.7.3. Metabolic Potential of Uncultivated Bacteria
4.7.4. Limitations of Metagenome-Derive Microbial Isolation
4.7.5. Conclusion
4.7.6. Future Perspective
Chapter 4.8. Changes in Microbial Communities Throughout the Body Decomposition Process and Its Potential Application in Forensic Casework
4.8.1. Introduction
4.8.2. Postmortem Microbial Changes
4.8.3. Conclusions
Section V. Microbial Diversity and Infectious Diseases
Chapter 5.1. Viral Genome Sequencing and Its Significance in Latest Clinical and Research Findings
5.1.1. Introduction
5.1.2. Evolution of Sequencing
5.1.3. Use of Sequencing in Healthcare and Clinical Setups
5.1.4. Whole Genome Sequencing in Virology
5.1.5. Deep Sequencing in Virology
5.1.6. Approaches to Virological Sequencing
5.1.7. Challenges Faced in Analysis and Interpretation in Viral Genome Sequencing
5.1.8. Case Study
Chapter 5.2. Prevalence of Multidrug Resistance Efflux Pumps (MDREPs) in Environmental Communities
5.2.1. Introduction
5.2.2. Multidrug Resistance Superfamilies
5.2.3. Genomic Prevalence of Multidrug Resistance Efflux Pumps
5.2.4. Genetic Methods to Study Multidrug Resistance
5.2.5. Hydrocarbon Biodegradation Environments
5.2.6. Corrosion Environments
5.2.7. Agricultural and Aquatic Environments
5.2.8. Summary
Chapter 5.3. Pathogenic Microbial Genetic Diversity With Reference to Significant Medical and Public Health
5.3.1. Introduction
5.3.2. Microbial Pathogenicity and Diseases
5.3.3. ESKAPE Pathogens
5.3.4. Genetic Heterogenicity Among Pathogenic Microbial Populations
5.3.5. Molecular Evolution and Genetic Diversity of Pathogenic Microbes
5.3.6. Molecular Techniques to Study Pathogenic Microbial Genetic Diversity
5.3.7. Application/Implication on Public Health
5.3.8. Conclusions
Chapter 5.4. Functional Applications of Human Microbiome Diversity Studies
5.4.1. Introduction
5.4.2. Global Microbiome Profiling Studies
5.4.3. Functional Profiling of the Human Microbiome
5.4.4. Gut–Organ Axes
5.4.5. Gut Microbiome and Other Human Pathologies
5.4.6. Functional Applications of Microbiome Research and Therapies
5.4.7. Future Perspectives
Chapter 5.5. Exploring Plant–Microbe Interaction in the Postgenomic Era: Insight From Diseases in Rice and Beyond
5.5.1. Introduction
5.5.2. Genomic Era
5.5.3. Detection of Pathogen Effector Sequences
5.5.4. Applications of Genomics in Disease Analysis
5.5.5. Genomics Era: An Approach to Enhance Disease Resistance
5.5.6. Plant and Microbes Interactions, the Basic Defense Mechanism, and Signaling
5.5.7. Salicylic Acid Role in Plant Defense
5.5.8. Jasmonic Acid Role in Plant Defense
5.5.9. Ethylene Role in Plant Defense
5.5.10. Chemical Communication Between Rice and Microbes
5.5.11. Rice–Microbe Beneficial Interactions and Rice Immune Response Basic Signaling Mechanisms
5.5.12. Postgenomic Era: Transgenic and Clones
5.5.13. Transgenic and Microbial Community
5.5.14. Transgenic and Symbiotic Interactions
5.5.15. Conclusion
Chapter 5.6. Quorum Sensing Directed Microbial Diversity in Infectious Bacteria
5.6.1. Introduction
5.6.2. Infectivity and Pathogenesis
5.6.3. Special Virulence Factors
5.6.4. Quorum Sensing
5.6.5. Diversity of Bacteria with Their Infectivity
5.6.6. Regulation Mechanism
5.6.7. Future Aspects and Strategies
Chapter 5.7. Insights Into Bacterial Vaginosis: A Metagenomic Case-Controlled Study
5.7.1. Introduction
5.7.2. The Microenvironment of Human vagina
5.7.3. Gardnerella vaginalis: The Etiological Agent of Bacterial Vaginosis
5.7.4. Cellular Composition of Gardnerella vaginalis
5.7.5. Virulence Factors of G. vaginalis
5.7.6. Pathogenicity of Bacterial Vaginosis
5.7.7. Detection and Biotyping of G. vaginalis
5.7.8. Biofilm Formation: An Essential Phase of BV
5.7.9. Synchronism Between BV and Other STIs
5.7.10. Adverse Outcomes of BV During Pregnancy
5.7.11. Spread of Viral Infections During BV
5.7.12. Association of Men with Bacterial Vaginosis and Its Consequences
5.7.13. Therapeutic Interventions to Control BV
5.7.14. A Metagenomic Case Controlled Study on Bacterial Vaginosis
5.7.15. Results and Discussion
Section VI. Future Directions of Microbial Diversity Studies
Chapter 6.1. Understanding the Structure and Function of Landfill Microbiome Through Genomics
6.1.1. Introduction
6.1.2. Landfill Environment
6.1.3. Microbiology of Landfill
6.1.4. Microbial Metabolism in Plastics Bioremediation
6.1.5. Biotechnological Application of Landfill Microbiome
6.1.6. Challenges of Utilizing Landfills as Reservoirs for Bioremediating Microorganisms
6.1.7. Conclusion
Chapter 6.2. Significance of Upcoming Technologies and Their Potential Applications in Understanding Microbial Diversity
6.1.1. Introduction
6.1.2. Importance of Microbial Diversity in Various Potential Fields
6.2.3. Earlier Methods Used to Study Microbial Diversity
6.2.4. Overall Steps to Follow to Understand Microbial Diversity Using NGS
6.2.5. Bioinformatics Tools Focused on Quantitative and Functional Analysis of Metagenomics and Microbial Diversity
6.2.6. Application of Next-Generation Sequencing in Determining Microbial Diversity in Various Fields
6.2.7. Upcoming Technologies of Third-Generation Sequencing
6.2.8. Summary
Chapter 6.3. Extremophiles-Mediated Carbon Dioxide Sequestration
6.3.1. Introduction
6.3.2. Preferred Conditions for Carbon Sequestration
6.3.3. Urease-Aided Microbial-Induced Carbonate Precipitation
6.3.4. Carbonic Anhydrase Enzyme in Microbial-Induced Carbonate Precipitation
6.3.5. Role of Extremophiles in Subsurface Carbon Mineralization
6.3.6. Conclusions and Prospects
Chapter 6.4. Molecular Evolution of Xenobiotic-Degrading Genes and Mobile Genetic Elements in Soil Bacteria
6.4.1. Classification of Xenobiotics
6.4.2. Potential Xenobiotics in Soil and Their Impacts
6.4.3. Organisms Involved in Xenobiotics Degradation
6.4.4. Recent Technologies for the Characterization of Xenobiotic Degrading Microorganisms
6.4.5. Methods for Identification of Xenobiotic Degrading Genes
6.4.6. Quantification of Xenobiotic-Degrading Genes
6.4.7. Molecular Mechanism of Xenobiotics Degradation
6.4.8. Mobile DNA Elements Involved in Xenobiotics Degradation
Chapter 6.5. Deciphering the Microbial Dark Matter Using Metagenome-Assembled Genomes, Culturomics, and Seqcode
6.5.1. Introduction
6.5.2. Microbial Dark Matter: the Need for Metagenomics
6.5.3. Metagenome-Assembled Genomes (MAGs): Putting Light on the Microbial Dark Matter
6.5.4. Procedure for MAG Reconstruction
6.5.5. Advantages of Metagenome-Assembled Genomes
6.5.6. Limitations of Metagenome-Assembled Genomes
6.5.7. SeqCode: Prokaryotic Nomenclature Code Described from Sequence Data
6.5.8. Blending Culturomics with Metagenomics
6.5.9. Future Prospects
6.5.10. Conclusions
Acknowledgments
Chapter 6.6. Cultural and Molecular Approaches to Analyse Antimicrobial Resistant Bacteria from Environmental Samples
6.6.1. Introduction
6.6.2. Culture-Based Methods
6.6.3. Culture-Independent Methods
6.6.4. Case Studies on Analysis of ARB from Wastewaters and Sediments
6.6.5. Conclusions and Future Perspectives
Chapter 6.7. Microbial Communities Driving Pollution Degradation in Contaminated Environments: Metagenomic Insights
6.7.1. Introduction
6.7.2. Microbial Diversity at the Contaminated Site
6.7.3. Metagenomics in Microbial Bioremediation
6.7.4. Metagenomic Sequencing Tools and Strategies
6.7.5. Bioinformatic Tools in Metagenomics
6.7.6. Challenges and Prospects
6.7.7. Conclusions
Index

Surajit Das

Prof. Surajit Das is currently working at the Department of Life Science, National Institute of Technology Rourkela, India. He received his doctoral degree in Marine Biology with specialization in microbiology from the Centre of Advanced Study in Marine Biology, Annamalai University, Tamil Nadu, India. He has been awarded the Endeavour Research Fellowship by the Australian Government to conduct postdoctoral research on marine microbial technology at the University of Tasmania. He has more than 15 years of research experience in environmental biotechnology, marine microbiology, bacterial biofilm, waste water treatment, and bioremediation. Prof. Das has maintained a strong commitment to explore the diversity of marine microorganisms from tropical, coastal, mangrove, and deep-sea environments using taxonomic and molecular tools. The main goal of his research is to understand the genetic regulation of bacterial biofilm for the improvement and development of biofilm-mediated bioremediation, thereby restoring the deteriorating environment as an eco-friendly approach.

Affiliations and expertise

Professor, Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology Rourkela, India

Hirak Ranjan Dash

Dr. Hirak Ranjan Dash is an Assistant Professor of Forensic Biotechnology at the National Forensic Sciences University, Delhi Campus, India. He obtained his PhD degree in Life Science from the National Institute of Technology, Rourkela, India. Previously, he served as a DNA expert at Forensic Science Laboratory, Madhya Pradesh, India. His research interests include forensic microbiology, microbial phylogeny, forensic DNA analysis, genetic markers, and next generation sequencing. He has published 50 research papers and 9 books. He has previously received a research fellowship from the Indian Academy of Science. He is a pioneer in India working on NGS-based forensic DNA analysis. He is a life member of the Association of Microbiologists of India, International Society of Forensic Geneticists, and Asian Federation of Biotechnologists.

Affiliations and expertise

Assistant Professor, Department of Forensic Science, National Forensic Sciences University, Delhi Campus, New Delhi, India

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