Omics for Environmental Engineering and Microbiology Systems

Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
Preface
Acknowledgments
Editors
Contributors
Chapter 1 Omics to Field Bioremediation: Current Status, Challenges, and Future Opportunities
1.1 Introduction
1.1.1 What Are Omics?
1.1.2 Different Tactics of Omics Studies
1.1.3 Applications of Omics in Various Fields
1.2 Bioremediation
1.2.1 What Is Bioremediation and Its Need
1.2.2 Means of Bioremediation
1.2.3 Phytoremediation
1.2.4 Limitations or Disadvantages of Bioremediation
1.3 Omics and Bioremediation: Current Status
1.3.1 Genomics and Metagenomics in Bioremediation
1.3.2 Proteomics in Bioremediation
1.3.3 Transcriptomics in Bioremediation
1.3.4 Metabolomics in Bioremediation
1.4 Future Prospects
1.5 Conclusions
References
Chapter 2 Role of Genomics, Metagenomics, and Other M eta-Omics Approaches for Expunging the Environmental Contaminants by Bioremediation
2.1 Introduction
2.2 Understanding Bioremediation
2.3 Molecular Biology of Microorganisms-Mediated Bioremediation
2.4 Microbial Enzyme Catalysis for Bioremediation
2.4.1 Oxygenases for Bioremediation
2.4.2 Oxidoreductases for Bioremediation
2.4.3 Peroxidases for Bioremediation
2.4.4 Hydrolases for Bioremediation
2.5 Exploring Genomes for Bioremediation
2.6 Metagenomics and Meta-Omics Approaches: A Boon to Bioremediation
2.6.1 Meta-transcriptomics
2.6.2 Meta-proteomics
2.6.3 Metabolomics
2.6.4 Metafluxomics
2.7 Computational Tools for Metagenomics-Mediated Bioremediation
2.7.1 MEGAN: MEtaGenome ANalyzer
2.7.2 MG-RAST: Metagenomic Rapid Annotations using Subsystems Technology
2.7.3 SMASHCommunity: Simple Metagenomics Analysis Shell for Microbial Communities
2.7.4 IMG/M:Integrated Microbial Genomes and Microbiomes
2.8 Drawbacks and Way Forward in Metagenomics-Mediated Bioremediation
2.9 Conclusions
References
Chapter 3 Functional Metagenomics: A Methodological Approach to View the Microbial World: A Review
3.1 Introduction
3.2 Functional Metagenomics
3.2.1 Isolation of Mobile Genetic Elements Using Functional Metagenomics
3.2.2 Consolidation of Genetic Elements without Independent Conjugal Transfer
3.2.3 Consolidation of Genetic Elements Proficient in Conciliating Their Own Transfer
3.2.4 Mobilizable Consolidative Elements
3.3 Types of Screening Strategies
3.3.1 Agar Plate Screening Method
3.3.2 Microarray-Based Screening
3.3.3 Microtiter Plate Screening
3.3.4 Fluorescence-Activated Cell Sorting
3.3.5 Microfluidics-Based Screening
3.4 Functional Metagenomic Libraries Screening
3.5 Functional Metagenomics: Methodological Approaches to Study Microbial World
3.5.1 Sequencing Depending on Strategies
3.5.2 Functional Depended Strategies
3.6 Applications of Functional Metagenomics
3.7 Conclusions and Future Objectives
Abbreviations
References
Chapter 4 Analysis of Emerging Microbial Contaminants through Next-Generation Sequencing ( NGS)
4.1 Introduction
4.2 Next-Generation Sequencing in the Clinical Aspect
4.3 Working Principle of NGS Technology
4.4 NGS Technology for Analyzing Microbial Contaminants
4.5 Advantages of Analyzing Microbial Contaminant through NGS
4.6 Applications of NGS in Microbial Contaminant Analysis Related to Human Health
4.7 Conclusions
References
Chapter 5 Quorum Sensing: A Potential Mechanism Toward Microbial Activity and Biofilm Formation
5.1 Introduction
5.2 Mechanism of Quorum Sensing
5.2.1 Quorum Sensing in Gram-Negative Bacteria
5.2.2 Quorum Sensing in Gram-Positive Bacteria
5.2.3 Quorum Sensing in Cross-Species
5.3 Influence of Quorum Sensing on Biofilm Formation and Signal Transduction Pathway
5.3.1 Biofilm Formation
5.3.2 Signal Transduction Pathway
5.4 Bacterial Social Behavior and QS in Switching the EPS Production
5.5 Quorum Sensing in Microbial Colony-Wide Functions
5.5.1 Sporulation
5.5.2 Bioluminescence
5.5.3 Virulence
5.5.4 Competence
5.6 Effects of Quorum Sensing on Microenvironment
5.7 Regulatory Mechanism Maintaining the Biofilm Activity
5.7.1 Regulation of Quorum Sensing in Gram-Positive Bacteria
5.7.2 Regulation of Quorum Sensing in Gram-Negative Bacteria
5.7.3 Mechanism of Quorum Quenching in Subduing Biofilm Formation
5.8 Quorum Sensing in Dispersal and Upregulation of Biofilm Surfactant Molecules
5.8.1 Upregulation of Virulence
5.8.2 Dispersal of Members of the Colony
5.9 Conclusions
References
Chapter 6 Integrated Omics Approaches to Understand and Improve Wastewater Remediation
6.1 Introduction
6.2 Wastewater and Wastewater Treatment Plants (WWTPs)
6.3 A Glance at the Major Pollutants of Wastewater and The Need for Remediation
6.4 Bioremediation: A Brief Introduction
6.5 Omics Approaches in Wastewater Remediation
6.5.1 Genomics
6.5.2 Metagenomics
6.5.3 Meta-transcriptomics
6.5.4 Metaproteomics
6.5.5 Metabolomics
6.5.6 Fluxomics
6.6 Bioinformatics Tools for Omics Data Analysis
6.7 Conclusions
References
Chapter 7 Omics Insights into Quorum Sensing and Biofilm Formation
7.1 Introduction
7.2 Transcriptomic Insights into Quorum Sensing Within Biofilm
7.3 Proteomic Insights into the QS Regulation for Biofilms Formation
7.3.1 Environmental Adaptation of Biofilms
7.4 Metabolomic Insights into the QS Within the Biofilm
7.5 Drawbacks and Future Perspectives of the Omics Technologies for Understanding Quorum Sensing for Biofilm Formation
References
Chapter 8 Genome Editing Tools: Increasing Efficiency of Microbes for Remediating Contaminated Environment
8.1 Introduction
8.2 Bioremediation of Environmental Pollutants
8.3 Pre-genomics Techniques for Bioremediation
8.3.1 Non-molecular Techniques
8.3.2 The 16S rRNA-Based Approach
8.3.3 Analysis of Functional Genes in Bioremediation
8.4 Genome Editing Tools
8.4.1 Zinc-Finger Nucleases
8.4.2 Transcription Activator-Like Effector Nucleases
8.4.3 CRISPR-Cas9 System
8.4.3.1 Genome Editing Using CRISPR-Cas System
8.4.3.2 Programmable Base Editing Using CRISPR-Cas
8.4.3.3 Transcriptional Modulation of Gene Expression through CRISPR-Cas
8.5 Computational Tools Used for Metabolic Engineering
8.6 Bacterial Genome Editing for Enhanced Phytoremediation
8.7 Risks Associated with Genetically Modified Organisms
8.8 Conclusions
References
Chapter 9 Recent Advancements in Microbial Degradation of Xenobiotics by Using Proteomics Approaches
9.1 Introduction
9.2 Xenobiotic Compounds
9.2.1 Different Classes of Xenobiotic Compounds
9.2.1.1 Halocarbons
9.2.1.2 Polychlorinated Biphenyls (PCBs)
9.2.1.3 Synthetic Polymers
9.2.1.4 Alkylbenzene Sulphonates
9.2.1.5 Oil Mixtures
9.2.1.6 Other Xenobiotic Compounds
9.2.2 Harmful Impacts of Xenobiotic Compounds
9.3 Strategies for Removing Xenobiotic Compounds
9.3.1 Different Methods
9.3.2 Antioxidant Mechanism for Remediation of Xenobiotic Compounds
9.4 Major Metabolic Pathways
9.5 Proteomics
9.6 Other Omics Approaches
9.7 Conclusions and Future Perspectives
References
Chapter 10 Importance of Genetically Engineered Microbes (GEMs) in Bioremediation of Environmental Pollutants: Recent Advances and Challenges
10.1 Introduction
10.2 Recent Genetic Engineering Progress in the Use of GEMs for the Bioremediation of Pollutants
10.2.1 Modification of Genes for the Biodegradative Enzymes
10.2.2 Gene Transfer and/or Pathways to the Heterologous Host
10.2.3 Bacterial Haemoglobin Technology for Pollutants
10.2.4 Tracking of GEMs with the Aid of Molecular Tools and Techniques
10.3 The Prominence of Environmental Pollutants Rescue Using GEMs
10.3.1 Heavy Metals
10.3.2 Dyes
10.3.3 Xenobiotics
10.3.4 Pesticides
10.3.5 Organic Compounds
10.3.6 Oil Components
10.3.7 Radioactive Compounds
10.4 Field Applications of GEMs
10.5 Stability and Risk Assessment of GEMs in the Field
10.6 Conclusions
Acknowledgements
References
Chapter 11 Role of Indigenous Microbial Community in Bioremediation: Recent Advances, Challenges, and Future Outlook
11.1 Introduction
11.2 Effects of Pollution on Indigenous Microbial Community
11.3 Analysis of Microbial Community Composition and Structure
11.4 Microbial Diversity and Composition in Response to Pollution
11.5 Potential of Indigenous Microbial Community for Bioremediation
11.6 Bioremediation Strategies of Indigenous Microbial Community
11.7 Functional Gene Analysis of Microbial Community
11.8 Biostimulation of Indigenous Microbial Community
11.9 Bioaugmentation
11.10 Challenges Associated with the Bioremediation by Indigenous Microbial Community
11.11 Future Prospects of Utilizing Indigenous Microbial Community for Bioremediation Purpose
Abbreviations
References
Chapter 12 Functional Metagenomics in Environmental Bioremediation: Recent Advances, Challenges and Future Outlook
12.1 Functional Metagenomics and Its Importance in Environmental Engineering
12.2 Metagenomic Libraries Constructed from Different Environmental Samples (Recent Advances)
12.3 Challenges in Functional Metagenomics and Library Construction
12.4 Applications of Functional Metagenomics in Environmental Bioremediation
12.5 Strategies for Improvement in Functional Metagenomics Approach and Future Prospects
12.6 Conclusions
References
Chapter 13 The Use of Microalgae and Cyanobacteria for Wastewater Treatment and the Sustainable Production of Biomass
13.1 Introduction
13.2 Microalgae and Cyanobacteria in Wastewaters
13.2.1 Development of a Culture of Microalgae and Cyanobacteria
13.2.2 Use of Microalgae and Cyanobacteria for Wastewater Treatment
13.3 Cultivation and Harvesting
13.3.1 Harvest by Flocculation of Chlorella vulgaris
13.3.1.1 pH-Induced Autoflocculation of Chlorella vulgaris
13.3.2 Effect of pH on Chemical Flocculation Efficiency of Chlorella vulgaris
13.4 Bioproducts of High Commercial Value
13.5 Future Trends
13.6 Conclusions
References
Chapter 14 Bioprospecting of Microbial Diversity for Sustainable Agriculture and Environment
14.1 Introduction
14.2 Microbial Interactions and Their Potential Roles in Plant Growth
14.2.1 Nutrients Availability for Plant
14.2.1.1 Nitrogen Fixation
14.2.1.2 Phosphorus Solubilization and Mobilization
14.2.1.3 Potassium Solubilization
14.2.1.4 Iron Uptake
14.2.2 Phytohormones for Plant Growth
14.2.3 Combating Abiotic Stress
14.2.4 Protection against Phytopathogen
14.3 Extremophiles for Sustainable Agriculture
14.4 Arbuscular Mycorrhizal Fungi (AMF)
14.5 Role of Microbial Cell Signalling and Communication
14.5.1 Quorum Sensing
14.5.2 Volatile Organic Compounds
14.6 Tools and Techniques for Screening and Trait Alteration
14.7 Microbiome Screening of Important Agricultural Crops
14.8 Conclusions and Future Prospects
References
Chapter 15 A Consortium of Sulfate-Reducing Bacteria Used for Lead, Copper, and Cadmium Bioremediation
15.1 Introduction
15.2 Heavy Metal Contamination
15.3 Sources of PTEs Generation in Water
15.4 Lead, Cadmium, and Copper Toxicity
15.5 Sulfate-Reducing Bacteria
15.6 Hydrogen Sulfide Production Kinetics in the Presence of Peat Moss
15.7 Production of Hydrogen Sulfide in the Presence of Cadmium, Copper, and Lead
15.8 Effect of the Cu, Cd, and Pb Mixture in the Production of Hydrogen Sulfide
15.9 Future Trends
15.10 Conclusion
References
Chapter 16 Omics Reflection on the Bacterial Escape from the Toxic Trap of Metal(loid)s: Cracking the Code of Contaminants Stress, Resistance Repertoire, and Remediation
16.1 Metal(loid)s Contamination
16.1.1 Natural
16.1.2 Anthropogenic
16.2 Metal(loid)s Stress on Bacteria
16.3 Metal(loid)s Resistance Mechanisms in Bacteria
16.3.1 Exclusion of TMs by Permeability Barrier
16.3.2 Extracellular Sequestration of TMs by Protein/Chelator Binding
16.3.3 Intracellular Sequestration of TMs by Protein/Chelator Binding
16.3.4 Enzymatic Detoxification of TMs to the Less Toxic Form
16.3.5 Active Transport of TMs
16.3.6 Passive Tolerance
16.3.7 Reduction in TMs Sensitivity of Cellular Targets
16.4 Applications
16.4.1 Bioremediation
16.4.1.1 Bioaugmentation
16.4.1.2 Biostimulation
16.4.1.3 Bioattenuation
16.4.2 Bioleaching
16.4.3 Phytoremediation Assisted by TMs-Resistant Bacteria
16.4.4 Plant Growth Promotion by TMs-Resistant Bacteria
16.5 Conclusions and Future Prospects
References
Chapter 17 Omics Approaches for Microalgal Remediation of Wastewater: Recent Advances, Challenges, and Future Outlook
17.1 Introduction
17.2 Omics Technologies Applied in Wastewater Treatment
17.2.1 Genomics of Microalgae for Wastewater Treatment
17.2.2 Microalgae Metagenomics in Wastewater Treatment
17.2.3 Transcriptomics of Microalgae for Wastewater Treatment
17.2.4 Proteomics of Microalgae for Wastewater Treatment
17.2.5 Metabolomics of Microalgae for Wastewater Treatment
17.2.6 Interactomics of Microalgae for Wastewater Treatment
17.2.7 Epigenomics of Microalgae for Wastewater Treatment
17.3 Drawbacks and Future Perspectives
17.4 Recent Advances, Challenges, and Future Outlook
References
Chapter 18 Disturbance and Stress in Coastal Ecosystems: Quantifying Responses at Multiple Levels of Biological Organization
18.1 Introduction
18.1.1 Environmental Impacts on Coastal Ecosystems
18.1.2 Ecological Disturbance Theory
18.1.3 Eco-evolutionary Implications of Disturbances in Coastal Ecosystems
18.1.4 Detecting Stress at Different Levels of Biological Organization
18.2 Measurement of Stress and Disturbance in Coastal Ecosystems
18.2.1 Analysis of Environmental Quality in Laguna Madre, Tamaulipas, Mexico
18.2.2 A Quantitative Research Framework for Analyzing Ecosystem Data in the Context of Disturbance Ecology
18.2.3 Measuring Ecosystem Response: Resistance and Resilience
18.2.3.1 Quantifying Resistance and Resilience in a Time Series: A Big-Data, Remote Sensing Approach
18.2.4 Resistance and Resilience Metrics: GPP Response of a Salt Marsh in Galveston Bay, Texas
18.3 Conclusions and Future Outlooks
References
Chapter 19 Impact of Cadmium Toxicity on Environment and Its Remedy
19.1 Introduction
19.2 Exposure and Absorption of Cadmium
19.3 Impact on Human Health
19.3.1 Intervention in the DNA Repair Pathway
19.3.2 Oxidative Damage to Cells
19.3.3 Reproductive Toxicity
19.3.4 Rheumatoid Arthritis
19.3.5 Effect on Kidneys
19.3.6 Development of Cancer
19.3.7 Breast Cancer
19.3.8 Lung Cancer
19.3.9 Impact on various Cell Types
19.3.10 Cadmium-Induced Cell Death
19.4 Remediation of Cadmium Intoxication
19.4.1 Use of Chelating Agents
19.4.2 Use of Antioxidants
19.4.3 Biological Methods
19.4.3.1 Bioremediation
19.4.3.2 Phytoremediation
19.4.3.3 Detoxification through Selenium
19.5 Conclusions
Abbreviations
References
Chapter 20 Metal(loid)-Microbe Interactions: Trading on Tolerance and Transformation for Environmental Remediation
20.1 Introduction
20.2 Environmental Contamination and (Eco)toxicity of Toxic Metals and Metalloids
20.3 Resistance and Tolerance against Metal(loid)s: Coping with Toxicity
20.4 Bioremediation: A Product of Microbial Wisdom and Tolerance
20.4.1 Bacteria
20.4.2 Fungi
20.4.3 Microalgae
20.4.4 Factors Influencing Bioremediation of Metal(loid)s
20.5 Microbial-Mediated Mechanisms for Remediation of Metal(loid)s
20.5.1 Biosorption
20.5.2 Biosequestration
20.5.2.1 Intracellular Sequestration
20.5.2.2 Extracellular Sequestration
20.5.3 Outer Cytoplasmic Structures Preventing Metal Entry into Microbial Cell
20.5.4 Biotransformation
20.5.5 Reducing Bacterial Sensitivity to Metal Ions
20.6 Future Perspectives
20.7 Conclusions
References
Chapter 21 Insights into Pathways of Biodegradation of Endocrine Disrupting Chemicals by Microbes
21.1 Introduction
21.2 Microbial Removal of EDCs
21.2.1 Bacterial Degradation of EDCs
21.2.2 Fungal Degradation of EDCs
21.2.3 Degradation of EDCs by Microalgae
21.3 Biodegradation Pathways of EDCs by Microbes
21.4 Conclusions
References
Chapter 22 New Insights into Horizontal Gene Transfer among Bacterial Pathogens to Acquire Antibiotic Resistance and Culture- Independent Techniques to Study ARG Dissemination
22.1 Introduction
22.2 Horizontal Gene Transfer (HGT) Mechanisms
22.2.1 Methods of HGT
22.2.1.1 Transformation
22.2.1.2 Membrane Vesicles
22.2.1.3 Transduction
22.2.1.4 Conjugation
22.3 Modes of Antibiotic Resistance Dissemination in the Environment
22.3.1 Insertion Sequences
22.3.2 Transposons
22.3.3 Integrons
22.3.4 Plasmids
22.4 Bacterial Efflux Pumps and Their Role in Antibiotic Resistance
22.5 Co-selection of ARGs and MRGs in Bacterial Pathogens
22.6 Molecular Techniques Used to Study Horizontal Gene Transfer in Bacterial Community
22.6.1 Molecular Experimental Techniques
22.6.1.1 Flow Cytometry Using gfp-Encoding Protein
22.6.1.2 Population Genetic Model Prediction Method
22.6.1.3 MetaCHIP
22.6.1.4 MetaCherchant
22.6.1.5 Computational Binning Using DNA Methylation
22.6.1.6 In vivo Experimental Studies
22.6.1.7 Culturomics Using MALDI-TOF
22.6.1.8 Fluorescent Reporter Systems
22.6.1.9 epicPCR
22.6.1.10 meta3C Approach
22.6.1.11 Hi-C Sequencing Technique
22.6.1.12 CRISPR Recorder
22.7 Conclusions
Acknowledgements
References
Chapter 23 Genetically Engineered Microorganisms: A Promising Approach for Bioremediation
23.1 Introduction
23.2 GEMs for Environmental Rescue against Pollutants
23.2.1 Bioremediation of Inorganic Pollutants by GEMs
23.2.2 Bioremediation of Organic Pollutants by GEMs
23.3 Suicidal Genetically Engineered Microorganisms (S-GEMs)
23.4 Various Approaches for the Development of GEMs
23.5 Use of GEMs for Bioremediation: From Laboratory to Field
23.6 Advantages and Obstacles of GEMs
23.6.1 Advantages of GEMs Application
23.6.2 Obstacles in the GEMs Application
23.7 Conclusions and Future Challenges
References
Chapter 24 Microbial Biofilm in Remediation of Environmental Contaminants from Wastewater: Mechanisms, Opportunities, Challenges, and Future Perspectives
24.1 Introduction
24.2 Sources of Industrial Wastewater
24.2.1 Industrial Effluents
24.2.2 Inorganic Source
24.2.3 Organic Source
24.3 Biofilm
24.3.1 Extracellular Polymeric Substances
24.3.2 Biofilm Formation Process
24.4 Approaches to Characterize Biofilm Community
24.4.1 Traditional Methods
24.4.1.1 Weight Determination
24.4.1.2 Optical Density Determination
24.4.1.3 Microscopic Biofilm Analysis
24.4.1.4 Biofilm Activity Determination
24.4.2 Advanced Methods
24.4.2.1 Clone Library Technique
24.4.2.2 DNA Microarray Technology
24.4.2.3 Next-Generation Sequencing (NGS) Technology
24.5 Biofilm in Wastewater Treatment
24.5.1 Types of Reactors Used in Secondary Treatment of Wastewater
24.5.1.1 Rotating Biological Contactor (RBC)
24.5.1.2 Membrane Bioreactor (MBR)
24.5.1.3 Membrane Biofilm Reactor
24.5.1.4 Nutrient Removal Using Biofilm Process
24.5.1.5 Moving Bed Biofilm Reactor (MBBR)
24.5.1.6 Nanotechnology Applications of Biofilm
24.6 Remediation of Chemicals and Heavy Metals through Biofilm
24.7 Challenges of Microbial Biofilm in Wastewater Remediation
24.7.1 Challenges in Biofilm-Based Processes
24.7.2 Challenges Faced in Aerobic/Anaerobic Treatment
24.7.3 Challenges Faced in Different Bioreactors
24.7.3.1 Challenges in Membrane Biofilm Reactors
24.7.3.2 Challenges in Moving-Bed Biofilm Reactors
24.7.3.3 Challenges in Trickling Filter in Biofilm Reactors
24.7.3.4 Challenges in Microbial Fuel Cells
24.8 Opportunities of Biofilms in Wastewater Treatment Technology
24.9 Conclusions
24.10 Future Perspectives
References
Chapter 25 Artificial Intelligence in Waste Management/ Wastewater Treatment
25.1 Introduction
25.2 Neural Networks
25.3 Heuristic Algorithms
25.4 Applications of AI Tools on Optimization and Modelling of Pollutant Removal Process
25.5 Conclusions
References
Index