Dedication
Preface
The Authors
Contributing Authors
Part I: Review of Basic Microbiological Concepts
Chapter 1. Introduction to Environmental Microbiology
1.1 Environmental Microbiology as a Discipline
1.2 Microbial Influences on our Daily Lives
1.3 Environmental Microbiology in 2014
Questions and Problems
References and Recommended Reading
Chapter 2. Microorganisms Found in the Environment
2.1 Classification of Organisms
2.2 Prokaryotes
2.3 Eukaryotes
2.4 Viruses
2.5 Other Biological Entities
Questions and Problems
References and Recommended Reading
Chapter References
Chapter 3. Bacterial Growth
3.1 Growth in Pure Culture in a Flask
3.2 Continuous Culture
3.3 Growth in the Environment
3.4 Mass Balance of Growth
Questions and Problems
References and Recommended Reading
Part II: Microbial Environments
Chapter 4. Earth Environments
4.1 Earth’s Living Skin
4.2 Physicochemical Characteristics of the Earth Environment
4.3 Soil as a Microbial Environment
4.4 Microorganisms in Surface Soils
4.5 Distribution of Microorganisms in Soil
4.6 Microorganisms in Subsurface Environments
References and Recommended Reading
Chapter References
Chapter 5. Aeromicrobiology
5.1 Introduction
5.2 Aerosols
5.3 Nature of Bioaerosols
5.4 Aeromicrobiological Pathway
5.5 Microbial Survival in the Air
5.6 Extramural Aeromicrobiology
5.7 Intramural Aeromicrobiology
5.8 Bioaerosol Control
5.9 Biosafety in the Laboratory
Questions and Problems
References and Recommended Reading
Chapter 6. Aquatic Environments
6.1 Introduction
6.2 Microbial Habitats in the Aquatic Environment
6.3 Microbial Lifestyles in Aquatic Environments
6.4 Marine Environments
6.5 Freshwater Environments
6.6 Other Notable Aquatic Environments
Questions and Problems
References and Recommended Reading
Chapter 7. Extreme Environments
7.1 Low Temperature Environments
7.2 High Temperature Environments
7.3 Desiccation and UV Stress
7.4 Aphotic Environments Based on Chemolithoautotrophy
Questions and Problems
References and Recommended Reading
Part III: Detection, Enumeration, and Identification
Chapter 8. Environmental Sample Collection and Processing
8.1 Soils and Sediments
8.2 Water
8.3 Air
8.4 Detection of Microorganisms on Fomites
Questions and Problems
References and Recommended Reading
Chapter 9. Microscopic Techniques
9.1 History of Microscopy
9.2 Theory of Microscopy
9.3 Visible Light Microscopy
9.4 Fluorescence Microscopy
9.5 Electron Microscopy
9.6 Scanning Probe Microscopy
9.7 Imaging
Questions and Problems
References and Recommended Reading
Chapter References
Chapter 10. Cultural Methods
10.1 Introduction
10.2 Extraction and Isolation Techniques
10.3 Plating Methods
10.4 Culture Media for Bacteria
10.5 Cultural Methods for Fungi
10.6 Cultural Methods for Algae and Cyanobacteria
10.7 Cell Culture-Based Detection Methods for Viruses
Questions and Problems
References and Recommended Reading
Chapter 11. Physiological Methods
11.1 Introduction
11.2 Measuring Microbial Activity in Pure Culture
11.3 Choosing the Appropriate Activity Measurement for Environmental Samples
11.4 Carbon Respiration
11.5 Incorporation of Radiolabeled Tracers into Cellular Macromolecules
11.6 Adenylate Energy Charge
11.7 Enzyme Assays
11.8 Stable Isotope Probing
Questions and Problems
References and Recommended Reading
Chapter 12. Immunological Methods
12.1 Introduction
12.2 What is an Antibody?
12.3 Immunoassays
12.4 Immunosensors
Questions and Problems
References and Recommended Reading
Chapter 13. Nucleic Acid-Based Methods of Analysis
13.1 Structure and Complementarity of Nucleic Acids
13.2 Obtaining Microbial Nucleic Acids from the Environment
13.3 Hybridization-Based Assays
13.4 Amplification-Based Assays
13.5 DNA Fingerprinting
13.6 Recombinant DNA Techniques
13.7 Sequence Analysis
13.8 Choosing the Appropriate Nucleic Acid-Based Method
Questions and Problems
References and Recommended Reading
Part IV: Microbial Communication, Activities, and Interactions with Environment and Nutrient Cycling
Chapter 14. Microbial Source Tracking
14.1 Water Quality and Fecal Contamination
14.2 Microbial Source Tracking Methods
14.3 Common Bacteria Used in Source Tracking Studies: Bacteroides
14.4 Application of Source Tracking
Questions and Problems
References and Recommended Reading
Chapter 15. Microbial Transport in the Subsurface
15.1 Factors Affecting Microbial Transport
15.2 Factors Affecting Transport of DNA
15.3 Novel Approaches to Facilitate Microbial Transport
15.4 Microbial Transport Studies
15.5 Models for Microbial Transport
Questions and Problems
References and Recommended Reading
Chapter 16. Biogeochemical Cycling
16.1 Introduction
16.2 Carbon Cycle
16.3 Nitrogen Cycle
16.4 Sulfur Cycle
16.5 Iron Cycle
Questions and Problems
References and Recommended Reading
Part V: Remediation of Organic and Metal Pollutants
Chapter 17. Microorganisms and Organic Pollutants
17.1 Introduction
17.2 Environmental Law
17.3 The Overall Process of Biodegradation
17.4 Contaminant Structure, Toxicity and Biodegradability
17.5 Environmental Factors Affecting Biodegradation
17.6 Biodegradation of Organic Pollutants
17.7 Bioremediation
Questions and Problems
References and Recommended Reading
Chapter 18. Microorganisms and Metal Pollutants
18.1 Metals in the Environment
18.2 Cause for Concern
18.3 Metals Defined
18.4 Metal Sources
18.5 Metal Solubility, Bioavailability and Speciation
18.6 Metal Toxicity Effects on the Microbial Cell
18.7 Mechanisms of Microbial Metal Resistance and Detoxification
18.8 Methods for Studying Metal–Microbial Interactions
18.9 Microbial Metal Transformations
18.10 Physicochemical Methods of Metal Remediation
18.11 Microbial Approaches in the Remediation of Metal-Contaminated Soils and Sediments
18.12 Microbial Approaches in the Remediation of Metal-Contaminated Aquatic Systems
Questions and Problems
Chapter References
References and Recommended Reading
Chapter 19. Microbial Diversity and Interactions in Natural Ecosystems
19.1 Microbial Communities
19.2 Microbial Diversity in Natural Systems
19.3 Microbial Interactions
19.4 Microbial Diversity and Natural Products
Questions and Problems
References and Recommended Reading
Chapter 20. Microbial Communication: Bacteria/Bacteria and Bacteria/Host
20.1 Introduction
20.2 Signaling Via Quorum Sensing in Gram-Negative Bacteria
20.3 Signaling in Gram-Positive Bacteria
20.4 Other Types of Signaling
20.5 Summary and Core Concepts
Questions and Problems
References and Recommended Reading
Chapter 21. Bioinformation and ’Omic Approaches for Characterization of Environmental Microorganisms
21.1 Introduction
21.2 Genomics and Comparative Genomics
21.3 Metagenomics
21.4 Transcriptomics
21.5 Proteomics
21.6 Metabolomics
21.7 Bioinformation
Questions and Problems
References and Recommended Reading
Part VI: Water- and Foodborne Pathogens
Chapter 22. Environmentally Transmitted Pathogens
22.1 Environmentally Transmitted Pathogens
22.2 Bacteria
22.3 Parasitology
22.4 Viruses
22.5 Fate and Transport of Enteric Pathogens in the Environment
Questions and Problems
References and Recommended Reading
Chapter 23. Indicator Microorganisms
23.1 The Concept of Indicator Organisms
23.2 Total Coliforms
23.3 Fecal Coliforms and Escherichia Coli
23.4 Fecal Streptococci (Enterococci)
23.5 Clostridium Perfringens
23.6 Bacteroides and Bifidobacterium
23.7 Heterotrophic Plate Count
23.8 Bacteriophages
23.9 Other Potential Indicator Organisms
23.10 Standards and Criteria for Indicators
Questions and Problems
References and Recommended Reading
Chapter 24. Risk Assessment
24.1 The Concept of Risk Assessment
24.2 Elements of Risk Analysis
24.3 The Process of Risk Assessment
24.4 Microbial Risk Assessment
Questions and Problems
References and Recommended Reading
Part VII: Wastewater Treatment and Disinfection
Chapter 25. Municipal Wastewater Treatment
25.1 The Nature of Wastewater (Sewage)
25.2 Conventional Wastewater Treatment
25.3 Oxidation Ponds
25.4 Septic Tanks
25.5 Land Application of Wastewater
25.6 Wetlands Systems
25.7 Sludge Processing
Questions and Problems
References and Recommended Reading
Chapter 26. Land Application of Organic Residuals: Municipal Biosolids and Animal Manures
26.1 Introduction to Organic Residuals
26.2 Land Application of Biosolids and Animal Wastes: A Historical Perspective and Current Outlook
26.3 Potential Microbial Hazards Associated with Class B Biosolids, Animal Manures and Land Application
26.4 Pathogens of Concern in Organic Residuals
26.5 Quantitative Microbial Risk Assessment of Pathogens in Organic Residuals
Questions and Problems
References and Recommended Reading
Chapter 27. Recycled Water Treatment and Reuse
27.1 Recycled Water Reuse
27.2 Treatment Technologies to Produce Recycled Water
27.3 Recycled Water Application in the U.S.
27.4 Recycled Water Regulations
27.5 Microbial Water Quality Aspects of Recycled Water
27.6 Influence of Residence Time in Distribution Systems on Microbial Water Quality
Questions and Problems
References and Recommended Reading
Chapter 28. Drinking Water Treatment and Distribution
28.1 Water Treatment Processes
28.2 Water Treatment Requirements
28.3 Water Distribution Systems
28.4 Real-Time Monitoring of Microbial Contaminants in Water Distribution Systems
Questions and Problems
References and Recommended Reading
Chapter 29. Disinfection
29.1 Thermal Destruction
29.2 Kinetics of Disinfection
29.3 Factors Affecting Disinfectants
29.4 Halogens
29.5 Ozone
29.6 Metal Ions
29.7 Ultraviolet Disinfection
29.8 Photodynamic Inactivation and Photocataylysts
29.9 Other Chemical Disinfectants
29.10 Gamma and High-Energy Irradiation
Questions and Problems
References and Recommended Reading
Part VIII: Urban Microbiology
Chapter 30. Domestic and Indoor Microbiology
30.1 Household Sources of Pathogens
30.2 Fomites: Role in Disease Spread
30.3 Transfer of Pathogens
30.4 Questions and Problems
References and Recommended Reading
Chapter 31. Global Emerging Microbial Issues in the Anthropocene Era
31.1 Microbial Contributions to Climate Change
31.2 Global Change and Microbial Infectious Disease
31.3 Microbial Remediation of Marine Oil Spills
31.4 Antibiotic-Resistant Bacteria
Questions and Problems
References and Recommended Reading
Index
