Microbial Community Studies in Industrial Wastewater Treatment

Cover
Half Title
Title Page
Copyright Page
Table of Contents
Preface
Editor
Chapter 1 Metagenomics: A Powerful Lens Viewing the Microbial World
1.1 Introduction
1.2 Background of Metagenomics
1.3 Classification of Metagenomics
1.3.1 Shotgun Metagenomic Sequencing
1.3.2 16 S Sequencing
1.4 Investigation of Metagenome
1.4.1 Shotgun Metagenomic Sequencing Analysis
1.4.2 Construction of Metagenomic Athenaeum
1.4.3 Rendering Vectors
1.4.4 Investigation of Metagenomics
1.4.5 Construction of Clones
1.4.6 Investigation of G+C Content
1.4.7 Examination of Genomes
1.4.8 16 S rRNA Quality Analysis
1.4.9 PCR-Based Examination Method
1.5 Hereditary Fingerprinting Procedure
1.5.1 16 S rRNA Quality Check
1.5.2 LH-PCR and TRFLP Investigations
1.5.3 RAPD Method
1.6 DDH-Based Microarray
1.6.1 Construction of rDNA Microarray
1.6.2 Steps in Gene Array Construction
1.7 Massive Parallel Sequencing Technology
1.8 Metaproteomics
1.8.1 Proteogenomics Approach
1.9 Conclusion
References
Chapter 2 Microbial Response to Lead Exposure
2.1 Introduction
2.1.1 Lead and Its Toxicity
2.1.2 Mechanism of Lead Survival by Microbes
2.1.3 Microbes Identified for Lead Resistance
2.2 Cellular and Molecular Responses
2.3 Case Study
2.4 Future Scope
2.5 Conclusions
References
Chapter 3 Metagenomics and Metatranscriptomic Analysis of Wastewater
3.1 Introduction
3.2 Opportunities and Challenges with Biological Treatment of Wastewater
3.3 Metagenomics: A Technological Drift
3.3.1 Metagenomic Approaches
3.3.1.1 Metatranscriptomics
3.3.1.2 Metaproteomics
3.3.1.3 Metabolomics
3.3.1.4 Fluxomics
3.4 Importance of Metagenomics, Transcriptomics, Proteomics and Metabolomics in Optimising Wastewater Treatment
3.5 Application of the Omics Approach in Wastewater Treatment
3.5.1 Computational and Bioinformatics Tools for Metagenomic
Data Analysis
3.5.2 Advantages and Limitations of the Omics Approach in Wastewater Treatment
3.6 Conclusion
References
Chapter 4 Environmental Metaproteomics: Tools to Study Microbial Communities
4.1 Introduction
4.1.1 Microbial Ecology
4.1.2 Historical Retrospective of ‘‘Omics’’ Technologies
4.1.3 Terminology of Environmental Proteomics
4.1.4 Potential Applications of Environmental Proteomics
4.1.5 Does Microbial Composition Affect Ecosystem Processes?
4.1.6 Proteomics in the Postgenomic Era
4.2 What Is Proteomics?
4.3 Environmental Proteomics
4.3.1 Optimisation of Sample Preparation Protocols
4.3.2 Community Proteomics of Marine Symbionts of R. pachyptila
4.3.3 Proteome Studies of WasteWater Management Plants and Activated Sludge
4.3.4 Community Proteogenomics of Phyllosphere Bacteria
4.3.5 Community Proteomics of Animal Intestinal Tracts
4.3.6 Community Proteomics of Human Intestinal Tracts
4.3.7 Metaproteome Analyses of Ocean Water
4.3.8 Metaproteome Studies of Highly Complex Groundwater and Soil Environments
4.4 Future Perspectives
4.4.1 Improvements in Mass Spectrometer Sensitivity and Accuracy
4.4.2 Quantitative Environmental Proteomics
4.5 Conclusion
References
Chapter 5 Events and Hazards in Biotransformation of Contaminants
5.1 Introduction
5.2 Types of Water Contaminants
5.2.1 Organic Contaminants
5.2.2 Inorganic Pollutants
5.3 Biodegradation
5.4 Biotransformation
5.5 Microorganism Flora Involved in the Biodegradation of Organic and Inorganic Pollutants
5.6 Microorganisms Involved in Biotransformation
5.7 Conclusion
References
Chapter 6 Microbial Community Analysis of Contaminated Soils
6.1 Introduction
6.2 Application of Novel Techniques for Evaluation of Taxonomic and Functional Properties That Could Lead to Remediation of Heavy Metal-Polluted Soil
6.3 The Process Involved in the Microbial Community Analysis of Contaminated Soils
6.3.1 Phytoremediation
6.3.2 Phytoextraction
6.3.3 Phytostabilisation
6.3.4 Phytostimulation
6.3.5 Phytovolatilisation
6.3.6 Immobilisation Technique
6.3.7 Soil Washing
6.4 Numerous Techniques for Taxonomic Profiling of the Soil Microcosms
6.5 Conclusion and Prospects
References
Chapter 7 Microbe Performance and Dynamics in Activated Sludge Digestion
7.1 Introduction
7.2 Processes Involved in Correlating the Population Dynamics of Pathogens Such as Mesophilic Sludge Digesters with Several Process Parameters
7.3 Specific Examples of Mesophilic Sludge Digesters and Archaeal
Methanogens
7.4 Different Types of Bioreactors Used in Waste-Activated Sludge for Anaerobic Digestion
7.5 Types of Bioreactors for Treatment of Anaerobic Wastes
7.5.1 Stirred-Tank Bioreactors
7.5.2 Packed-Bed Biofilm
7.5.3 Moving Bed Reactor with Biofilm
7.5.4 Fluidised-Bed Reactor
7.5.5 Semifluidised Bed Biofilm
7.6 Conclusion and Prospects
References
Chapter 8 Genomic Analysis of Heavy Metal-Resistant Genes in Wastewater Treatment Plants
8.1 Introduction
8.2 HMRGs in the Environment
8.3 Application of High-Throughput Sequencing-Based Metagenomic Approach for the Assessment of Diversity, Occurrence, and the Level of Assessment of Mobile Genetic Elements and Antibiotic Resistance Genes in Aerobic and Anaerobic Sludge
8.4 Relevant Information on the Genes Coding for Antibiotic Resistance in Numerous Communities as well as the Application of BLAST Analysis against Antibiotic Resistance
8.5 Mechanisms of Antimicrobial Resistance
8.6 Conclusion and Prospects
References
Chapter 9 Molecular Characterization of Multidrug-Resistant Genes in Wastewater Treatment Plants
9.1 Introduction
9.2 Application of PCR and Other Relevant Molecular Techniques Such as 16S rDNA Sequencing and PCR Genotyping
9.3 Utilization of Phenotypic Susceptibility Patterns Using the Kirby–Bauer
Disk Diffusion Technique and Some Other Relevant Techniques
9.4 Role of Beta-Lactamase Resistance to Beta-Lactam Antibiotics as well as a New Type of Beta-Lactamase Enzyme, Which Entails AmpC Beta- Lactamase and Extended-Spectrum Beta-Lactamase
9.5 Conclusion and Prospects
References
Chapter 10 Microbes and Events in Contaminant Biotransformation
10.1 Introduction
10.2 Mechanism of Bioremediation
10.2.1 Bioremediation by Bacteria
10.2.2 Phycoremediation
10.2.3 Mycoremediation
10.2.4 Bioaccumulation and Biosorption
10.3 Strategies of Microbial Bioremediation
10.3.1 In Situ Bioremediation Strategy
10.3.1.1 Biostimulation
10.3.1.2 Bioattenuation/Natural Attenuation
10.3.1.3 Bioaugmentation
10.3.1.4 Bioventing
10.3.1.5 Biosparging
10.3.2 Ex Situ Bioremediation Strategies
10.3.2.1 Biopile
10.3.2.2 Windrows
10.3.2.3 Bioreactor
10.3.2.4 Landfarming
10.4 Microbes with Biofilm-Associated Remediation
10.4.1 Biofilm-Mediated Bioremediation
10.5 Analysis of Remediating Microbial Communities by Metagenomic Approaches
10.5.1 Metagenomic Approaches
10.5.1.1 Function-Based Metagenomic Approach
10.5.1.2 Sequence-Based Metagenomic Approach
10.5.2 Major Steps in Metagenomic Approaches
10.5.2.1 Study Site Selection
10.5.2.2 Collection of Samples and Extraction of Nucleic Acids
10.5.2.3 Enrichment of Genome and Gene
10.5.2.4 Metagenomic Library Construction
10.5.3 Use of Metagenomics in Bioremediation
10.6 Conclusion
References
Chapter 11 Metagenomics for Studying Microbes in Wastewater
Treatment Plants
11.1 Introduction
11.2 Methods Involved in Metagenomic Data Analysis
11.2.1 Sampling from WWTPs
11.2.2 Total Genomic DNA Extraction, Confirmation, and Storage
11.2.3 Construction of the Metagenomic Library
11.2.4 NGS Method
11.2.4.1 Solexa (Illumina) Genome Sequencing
11.2.4.2 Pyrosequencing
11.2.4.3 Sequencing by Oligonucleotide Ligation and Detection (SOLiD)
11.2.4.4 Ion Torrent Semiconductor Sequencing
11.2.4.5 Nanopore Sequencing
11.2.5 Analysis of Sequenced Metagenomic Data
11.3 Application of Metagenomics in Diversified Fields
11.4 Application of Metagenomics in Wastewater Treatment Plants
References
Chapter 12 Diversity and Interaction of Microbes in Biodegradation
12.1 Introduction
12.2 Microbial Diversity in Bioremediation Techniques
12.2.1 Bioaugmentation
12.2.2 Biostimulation
12.2.3 Biosparging
12.2.4 Bioventing
12.2.5 Bioreactor Bioremediation
12.2.6 Biofiltration
12.2.7 Land Farming
12.3 Interactions and Degradation of Organic Contaminants
12.3.1 Physical Methods
12.3.2 Chemical Methods
12.3.3 Biological Methods
12.3.3.1 Microbial Diversity
12.3.3.2 Interactions of Microbes
12.3.3.3 Degradation Pathways
12.3.3.4 Genomics Involved in Microbial Degradation
12.4 Interaction and Degradation of Inorganic Contaminants
12.4.1 Physical Methods
12.4.2 Chemical Methods
12.4.3 Biological Methods
12.4.3.1 Microbial Diversity
12.4.3.2 Interactions of Microbes
12.4.3.3 Degradation Pathways
12.4.3.4 Genomics Involved in Microbial Degradation
12.5 Future Perspective
12.6 Conclusion
References
Chapter 13 Metagenomics: A Pathway for Searching in Microbial Contexts
13.1 Introduction
13.2 Operation of Activated Sludge
13.3 Evolution in AS Procedures
13.3.1 Conventional Complete Mix AS Process
13.4 Microbial Composition of ASP
13.5 Metagenomics
13.6 Timeline
13.7 Techniques Used in Metagenomics
13.7.1 Sequencing Technology
13.7.1.1 First-Generation Sequencing
13.7.1.2 Second-Generation Sequencing (SGS)
13.7.1.3 Third-Generation Sequencing (TGS)
13.7.2 RAPD
13.7.3 Ribosomal RNA Intergenic Spacer Analysis (RISA)
13.7.4 Fluorescence In Situ Hybridisation (FISH)
13.7.5 Terminal Restriction Fragment Length Polymorphism (T-RFLP)
13.7.6 Quantitative PCR Q-PCR
13.7.7 Pulsed-Field Gel Electrophoresis (PFGE)
13.8 Metatranscriptomics
13.8.1 Denaturing Gradient Gel Electrophoresis (DGGE)
13.8.2 Microarray
13.8.3 Temperature Gradient Gel Electrophoresis (TGGE)
13.8.4 Length Heterogeneity PCR (LH-PCR)
13.9 Techniques Used for Analysis of Microbiome Found in Waste Water
References
Index