Manual of Environmental Microbiology

Editorial Board
Contributors
1.1.1 Introduction
General Methodology
2.1.1 Detection of Specific Taxa Using Chromogenic and Fluorogenic Media
2.1.2 Anaerobic Cultivation
2.1.3 New Devices for Cultivation
2.2.1 Gold-Based In Situ Hybridization for Phylogenetic Single-Cell Detection of Prokaryotes in Environmental Samples
2.2.2 Assessment of Prokaryotic Biological Activity at the Single-Cell Level by Combining Microautoradiography and Fluorescence in situ Hybridization
2.3.1 Antibody-Based Technologies for Environmental Biodetection
2.3.2 PCR, Real-Time PCR, Digital PCR, and Isothermal Amplification
2.3.3 Microarray-Based Environmental Diagnostics
2.3.4 Field Application of Pathogen Detection Technologies
2.4.1 Introduction to Microbial Community Analysis of Environmental Samples with Next-Generation Sequencing
2.4.2 Microbial Community Analysis Using High-Throughput Amplicon Sequencing
2.4.3 Functional Metagenomics: Procedures and Progress
2.4.4 Metagenomics: Assigning Functional Status to Community Gene
2.4.5 Generation and Analysis of Microbial Metatranscriptomes
2.5.1 Introduction to Principles of Quality Assurance
2.5.2 General Quality Control
2.5.3 Quality Control for Bacteriological Analyses
2.5.4 Quality Control for Virological Analyses
2.5.5 Quality Control for USEPA Method 1623 Protozoan Analysis and PCR Analyses
2.5.6 The Role of Statistical Thinking in Environmental Microbiology
2.5.7 Study Design
2.6.1 Water Sampling and Processing Techniques for Public Health–Related Microbes
2.6.2 Surface Sampling
2.6.3 Soil Sampling for Microbial Analyses
2.6.4 Microbiological Sampling of Wastewater and Biosolids
Environmental Public Health Microbiology
3.1.1 Current and Developing Methods for the Detection of Microbial Indicators in Environmental Freshwaters and Drinking Waters
3.1.2 Best Practices for Cyanobacterial Harmful Algal Bloom Monitoring
3.1.3 Assessing the Efficiency of Wastewater Treatment
3.1.4 Epidemiologic Aspects of Waterborne Infectious Disease
3.1.5 Waterborne Enteric Viruses: Diversity, Distribution, and Detection
3.1.6 Detection of Protozoa in Surface and Finished Waters
3.1.7 Drinking Water Microbiology
3.2.1 Introduction to Aerobiology
3.2.2 Sampling for Airborne Microorganisms
3.2.3 Analysis of Bioaerosol Samples
3.2.4 Fate and Transport of Microorganisms in Air
3.2.5 Airborne Fungi and Mycotoxins
3.2.6 Airborne Bacteria, Archaea, and Endotoxin
3.2.7 Airborne Viruses
3.2.8 Aerobiology of Agricultural Pathogens
3.2.9 Legionellae and Legionnaires’ Disease
3.3.1 Pathogenic Viruses and Protozoa Transmitted by Soil
3.3.2 Natural Soil Reservoirs for Human Pathogenic and Fecal Indicator Bacteria
3.4.1 The Evolving Science of Microbial Source Tracking
3.4.2 Validation of Microbial Source Tracking Markers and Detection Protocols: Considerations for Effective Interpretation
3.4.3 Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources
3.4.4 Methods of Targeting Animal Sources of Fecal Pollution in Water
3.4.5 Microbial Source Tracking: Field Study Planning and Implementation
3.4.6 Fecal Indicator Organism Modeling and Microbial Source Tracking in Environmental Waters
3.5.1 Risk Assessment Framework
3.5.2 Exposure Assessment
3.5.3 Dose-Response Modeling and Use: Challenges and Uncertainties in Environmental Exposure
Microbial Ecology
4.1.1 Phylogenomic Networks of Microbial Genome Evolution
4.1.2 Evolutionary Ecology of Microorganisms: From the Tamed to the Wild
4.2.1 The Microbial Ecology of Benthic Environments
4.2.2 Heterotrophic Planktonic Microbes: Virus, Bacteria, Archaea, and Protozoa
4.2.3 Aquatic Biofilms: Development, Cultivation, Analyses, and Applications
4.3.1 The Microbiology of Extremely Acidic Environments
4.3.2 Life in High-Salinity Environments
4.3.3 Microbial Life in Extreme Low-Biomass Environments: A Molecular Approach
4.3.4 Life in High-Temperature Environments
4.4.1 Invertebrate Gut Associations
4.4.2 Studying the Mammalian Intestinal Microbiome Using Animal Models
4.4.3 Animal Gut Microbiomes
Biodegradation and Biotransformation
5.1.1 Genomic Features and Genome-Wide Analysis of Dioxin-Like Compound Degraders
5.1.2 Biodegradation of Organochlorine Pesticides
5.1.3 Anaerobic Degradation of Aromatic Compounds
5.1.4 Microbial Electrochemical Technologies Producing Electricity and Valuable Chemicals from Biodegradation of Waste Organic Matters
5.1.5 A Basic Introduction to Aerobic Biodegradation of Petroleum Aromatic Compounds
5.1.6 Environmental Systems Microbiology of Contaminated Environments
5.2.1 Breathing Iron: Molecular Mechanism of Microbial Iron Reduction by Shewanella oneidensis
5.2.2 Experimental Geomicrobiology: From Field to Laboratory
5.2.3 Microbial Uses in the Remediation of Metal-Impacted Soils
Index