An Historical Perspective -- Modern Environmental Microbiology -- Purpose and Organization of This Text -- Microorganisms in the Environment / Kelly A. Reynolds, Ian L. Pepper -- Viruses -- Bacteria -- Fungi -- Alage -- Protozoa -- Bacterial Growth / Raina M. Maier -- Growth in Pure Culture in a Flask -- Continuous Culture -- Growth under Aerobic Conditions -- Growth under Anaerobic Conditions -- Growth in the Environment -- Terrestrial Environments / Raina M. Maier, Ian L. Pepper -- Porous Media -- Soil and Subsurface Environments -- General Characteristics of Microorganisms in Porous Media -- Microbial Activities in Porous Media -- Microorganisms in Surface Soils -- Microorganisms in Shallow Subsurface Environments -- Microorganisms in Deep Subsurface Environments -- Aeromicrobiology / Scot E. Dowd, Raina M. Maier -- Important Airborne Pathogens -- Important Airborne Toxins -- Nature of Bioaerosols -- The Atmosphere -- Aeromicrobiological Pathway -- Mathematical Modeling -- Sampling Devices for the Collection of Bioaerosols -- Microbial Survival in the Air -- Extramural Aeromicrobiology -- Intramural Aeromicrobiology -- Bioaerosol Control -- Biosafety in the Laboratory -- Other Areas of Interest -- Aquatic and Extreme Environments / Scot E. Dowd, David C. Herman, Raina M. Maier -- Microbial Habitats in the Aquatic Environment -- Aquatic Environments -- Environmental Determinants That Govern Extreme Environments -- Aquatic Microbes in the News -- Microbial Transport / Deborah T. Newby, Ian L. Pepper, Raina M. Maier -- Factors Affecting Microbial Transport -- Factors Affecting Transport of DNA -- Novel Approaches to Facilitate Microbial Transport -- Methodology for Studying Transport -- Models for Microbial Transport -- Environmental Sample Collection and Processing / Ian L. Pepper, Charles P. Gerba, Raina M. Maier -- Soils and Sediments -- Water -- Detection of Microorganisms on Fomites -- Microscopic Techniques / Timberley M. Roane, Ian L. Pepper -- History of Microscopy -- Theory of Microscopy -- Basic Microscopic Techniques -- In Situ Soil Microscopy -- In Situ Detection with Molecular Probes and Epifluoresence Microscopy -- Direct Bacterial Counts -- Estimation of Biomass Using Microscopic Counts -- Advanced Microscopic Techniques -- Cultural Methods / Karen C. Josephson, Charles P. Gerba, Ian L. Pepper -- Cultural Methods for Enumeration of Bacteria -- Cultural Media for Bacteria -- Cultural Methods for Fungi -- Cultural Methods for Algae and Cyanobacteria -- Cell Culture-Based Detection Methods for Viruses -- Physiological Methods / David C. Herman, Raina M. Maier -- Measuring Microbial Activity in Pure Culture -- Choosing the Appropriate Activity Measurement for Environmental Samples -- Carbon Respiration -- Incorporation of Radiolabeled Tracers into Cellular Macromolecules -- Adenylate Energy Charge -- Enzyme Assays -- Immunological Methods / Scot E. Dowd, Raina M. Maier -- What Is an Antibody? -- Immunoassays -- Nucleic Acid-Based Methods of Analysis / Elizabeth M. Marlowe, Karen L. Josephson, Ian L. Pepper -- Structure and Complementarity of Nucleic Acids -- Obtaining Microbial Nucleic Acids from the Environment -- Nucleic Acid-Based Methods -- Biogeochemical Cycling / Raina M. Maier -- Carbon Cycle -- Nitrogen Cycle -- Sulfur Cycle -- Consequences of Biogeochemical Cycles Gone Wild / David C. Herman, Raina M. Maier -- Microbially Influenced Corrosion -- Acid Mine Drainage and Metal Recovery -- Biomethylation of Metals and Metalloids -- Nitrous Oxide and Earth's Atmosphere -- Nitrate Contamination of Groundwater -- Biogenesis of Halomethanes and Other Organohalogens -- Composting -- Microorganisms and Organic Pollutants / Raina M. Maier -- Environmental Law -- The Overall Process of Biodegradation -- Relationship between Contaminant Structure, Toxicity, and Biodegradability -- Environmental Factors Affecting Biodegradation -- Biodegradation of Organic Pollutants -- Bioremediation -- Microorganisms and Metal Pollutants / Timberley M. Roane, Ian L. Pepper -- Cause for Concern -- Metals Defined -- Sources of Metals -- Metal Bioavailability in the Environment -- Metal Toxicity Effects on the Microbial Cell -- Mechanisms of Microbial Metal Resistance and Detoxification -- Methods for Studying Metal-Microbial Interactions -- Adverse Effects of Microbial Metal Transformations -- The Benefits of Metal-Microbial Interactions -- Physical/Chemical Methods of Metal Remediation -- Innovative Microbial Approaches in the Remediation of Metal-Contaminated Soils and Sediments -- Innovative Microbial Approaches in the Remediation of Metal-Contaminated Aquatic Systems -- Beneficial and Pathogenic Microbes in Agriculture / Ian L. Pepper -- Beneficial Root-Microbial Interactions -- Pathogenic Microbes in Agriculture -- Environmentally Transmitted Pathogens / Patricia Rusin, Carlos E. Enriquez, Dana Johnson, Charles P. Gerba -- Environmental Transmitted Pathogens -- Bacteria -- Parasitology -- Viruses -- Indicator Microorganisms / Charles P. Gerba -- The Concept of Indicator Organisms -- Total Coliforms -- Fecal Coliforms -- Fecal Streptococci -- Clostridium perfringens -- Heterotrophic Plate Count -- Bacteriophage -- Other Indicator Organisms -- Standards and Criteria for Indicators -- Domestic Wastes and Waste Treatment / Charles P. Gerba -- Domestic Wastewater -- Modern Wastewater Treatment -- Oxidation Ponds -- Septic Tanks -- Land Application of Wastewater -- Wetlands and Aquaculture Systems -- Solid Waste -- Drinking Water Treatment and Distribution / Charles P. Gerba -- Water Treatment Processes -- Water Distribution Systems -- Assimilable Organic Carbon -- Disinfection / Charles P. Gerba -- Thermal Destruction -- Kinetics of Disinfection -- Factors Affecting Disinfectants -- Halogens -- Ozone -- Metal Ions -- Ultraviolet Disinfection -- Photodynamic Inactivation -- Gamma and High-Energy Irradiation -- Risk Assessment / Charles P. Gerba -- The Concept of Risk Assessment -- Elements of Risk Assessment -- The Process of Risk Assessment -- Microbial Risk Assessment