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