Microbial Community Studies in Industrial Wastewater Treatment

Description

Focusing on microbial community structure in the field of wastewater treatment, this book highlights structural analyses in relation to changes in physico-chemical parameters. It further covers physiological analyses of microbial communities, enrichment of pure cultures of key species in relation to changes in physico-chemical parameters, and analyses and modelling of consequences of changes in microbial community structure. Based on 16S rRNA gene sequencing, groups of bacteria that perform nitrogen fixation, nitrification, ammonification and other biochemical processes are covered for an entire wastewater treatment plant bioreactor along with temporal dynamics of bacterial communities. Features: Describes the state-of-the-art techniques and the application of omics tools in wastewater treatment reactors (WWTRs). Includes both the theoretical and practical knowledge on the fundamental roles of microorganisms in WWTRs. Discusses environmental microbial community proteomics. Covers relating function and community structure of complex microbial systems using neural networks. Reviews the economics of wastewater treatment and the development of suitable alternatives in terms of performance and cost-effectiveness. This book is aimed at graduates and researchers in biological engineering, biochemical engineering, chemistry, environmental engineering, environmental microbiology, systems ecology and environmental biotechnology. 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