Environmental Microbiology

Ian L. Pepper is currently the Chair of the Undergraduate Program in Environmental Sciences at the University of Arizona.

For microbiology and environmental microbiology courses, this leading textbook builds on the academic success of the previous edition by including a comprehensive and up-to-date discussion of environmental microbiology as a discipline that has grown in scope and interest in recent years. From environmental science and microbial ecology to topics in molecular genetics, this edition relates environmental microbiology to the work of a variety of life science, ecology, and environmental science investigators. The authors and editors have taken the care to highlight links between environmental microbiology and topics important to our changing world such as bioterrorism and national security with sections on practical issues such as bioremediation, waterborne pathogens, microbial risk assessment, and environmental biotechnology.WHY ADOPT THIS EDITION? New chapters on: Urban Environmental Microbiology Bacterial Communities in Natural Ecosystems Global Change and Microbial Infectious Disease Microorganisms and Bioterrorism Extreme Environments (emphasizing the ecology of these environments) Aquatic Environments (now devoted to its own chapter- was combined with Extreme Environments) Updates to Methodologies: Nucleic Acid -Based Methods: microarrays, phyloarrays, real-time PCR, metagomics, and comparative genomics Physiological Methods: stable isotope fingerprinting and functional genomics and proteomics-based approaches Microscopic Techniques: FISH (fluorescent in situ hybridization) and atomic force microscopy Cultural Methods: new approaches to enhanced cultivation of environmental bacteria Environmental Sample Collection and Processing: added section on air sampling

For microbiology and environmental microbiology courses, this leading textbook builds on the academic success of the previous edition by including a comprehensive and up-to-date discussion of environmental microbiology as a discipline that has grown in scope and interest in recent years. From environmental science and microbial ecology to topics in molecular genetics, this edition relates environmental microbiology to the work of a variety of life science, ecology, and environmental science investigators. The authors and editors have taken the care to highlight links between environmental microbiology and topics important to our changing world such as bioterrorism and national security with sections on practical issues such as bioremediation, waterborne pathogens, microbial risk assessment, and environmental biotechnology.WHY ADOPT THIS EDITION? New chapters on: Urban Environmental Microbiology Bacterial Communities in Natural Ecosystems Global Change and Microbial Infectious Disease Microorganisms and Bioterrorism Extreme Environments (emphasizing the ecology of these environments) Aquatic Environments (now devoted to its own chapter- was combined with Extreme Environments) Updates to Methodologies: Nucleic Acid -Based Methods: microarrays, phyloarrays, real-time PCR, metagomics, and comparative genomics Physiological Methods: stable isotope fingerprinting and functional genomics and proteomics-based approaches Microscopic Techniques: FISH (fluorescent in situ hybridization) and atomic force microscopy Cultural Methods: new approaches to enhanced cultivation of environmental bacteria Environmental Sample Collection and Processing: added section on air sampling

1;Front Cover;12;Environmental Microbiology;43;Copyright Page;54;Contents;85;Preface;166;Acknowledgments;187;The Authors;208;Contributing Authors;229;Part I: Review of Basic Microbiological Concepts;249.1;Chapter 1. Introduction to Environmental Microbiology;269.1.1;1.1 Introduction;269.1.2;1.2 An Historical Perspective;269.1.3;1.3 Modern Environmental Microbiology;299.1.4;1.4 Purpose and Organization of This Text;309.2;Chapter 2. Microorganisms;329.2.1;2.1 Classification of Organisms;339.2.2;2.2 Eubacteria;339.2.2.1;2.2.1 Cell Envelope;349.2.2.2;2.2.2 Cytoplasm;379.2.2.3;2.2.3 Glycocalyx;399.2.2.4;2.2.4 Appendages;399.2.2.5;2.2.5 Endospores;399.2.2.6;2.2.6 Information Transfer;409.2.2.7;2.2.7 Metabolism;419.2.3;2.3 The Archaea;439.2.3.1;2.3.1 Archaean Habitats;449.2.3.2;2.3.2 Archaean Function;449.2.4;2.4 Fungi;459.2.4.1;2.4.1 Fungal Structure;459.2.4.2;2.4.2 Fungal Diversity;469.2.4.3;2.4.3 Ecological Considerations;479.2.5;2.5 Slime Molds;489.2.6;2.6 Protozoa;489.2.6.1;2.6.1 Structure and Function;489.2.6.2;2.6.2 Physiological and Ecological Considerations;499.2.7;2.7 Algae;499.2.7.1;2.7.1 Cell Structure;509.2.7.2;2.7.2 Physiological and Ecological Considerations;509.2.8;2.8 Viruses;519.2.8.1;2.8.1 Infective Nature of Viruses;529.2.8.2;2.8.2 Procaryotic Viruses;539.2.8.3;2.8.3 Eucaryotic Viruses;559.2.9;2.9 Other Biological Entities;569.2.9.1;2.9.1 Viroids;569.2.9.2;2.9.2 Prions;569.2.10;References;579.3;Chapter 3. Bacterial Growth;609.3.1;3.1 Growth in Pure Culture in a Flask;619.3.1.1;3.1.1 The Lag Phase;619.3.1.2;3.1.2 The Exponential Phase;629.3.1.3;3.1.3 The Stationary Phase;639.3.1.4;3.1.4 The Death Phase;649.3.1.5;3.1.5 Effect of Substrate Concentration on Growth;659.3.2;3.2 Continuous Culture;679.3.3;3.3 Growth in the Environment;699.3.3.1;3.3.1 The Lag Phase;709.3.3.2;3.3.2 The Exponential Phase;709.3.3.3;3.3.3 The Stationary and Death Phases;709.3.4;3.4 Mass Balance of Growth;729.3.4.1;3.4.1 Aerobic Conditions;739.3.4.2;3.4.2 Anaerobic Conditions;759.3.5;Questions and Problems;769.3.6;References and Recommended Readings;7710;Part II: Microbial Environments;7810.1;Chapter 4. Earth Environments;8010.1.1;4.1 Earth's Living Skin;8010.1.2;4.2 Physicochemical Characteristics of the Earth Environment;8110.1.2.1;4.2.1 Earth Environments;8110.1.2.2;4.2.2 The Solid Phase;8210.1.2.3;4.2.3 The Liquid Phase;9010.1.2.4;4.2.4 Soil Atmosphere;9210.1.3;4.3 Soil as a Microbial Environment;9310.1.3.1;4.3.1 Biotic Stresses;9310.1.3.2;4.3.2 Abiotic Stresses;9310.1.4;4.4 Microorganisms in Surface Soils;9410.1.4.1;4.4.1 Bacteria;9410.1.4.2;4.4.2 Actinomycetes;9410.1.4.3;4.4.3 Fungi;9610.1.4.4;4.4.4 Algae;9710.1.4.5;4.4.5 Protozoa;9710.1.5;4.5 Distribution of Microorganisms in Soil;9810.1.6;4.6 Microorganisms in Subsurface Environments;9910.1.6.1;4.6.1 Microorganisms in Shallow Subsurface Environments;10010.1.6.2;4.6.2 Microorganisms in Deep Subsurface Environments;10010.1.7;Questions and Problems;10410.1.8;References and Recommended Readings;10410.2;Chapter 5. Aeromicrobiology;10610.2.1;5.1 Introduction;10610.2.2;5.2 Important Airborne Pathogens;10610.2.3;5.3 Important Airborne Toxins;10710.2.4;5.4 Aerosols;10810.2.5;5.5 Nature of Bioaerosols;11010.2.6;5.6 Aeromicrobiological Pathway;11010.2.6.1;5.6.1 Launching;11110.2.6.2;5.6.2 Transport;11110.2.6.3;5.6.3 Deposition;11210.2.7;5.7 Microbial Survival in the Air;11410.2.7.1;5.7.1 Relative Humidity;11410.2.7.2;5.7.2 Temperature;11510.2.7.3;5.7.3 Radiation;11510.2.7.4;5.7.4 Oxygen, OAFs, and Ions;11510.2.8;5.8 Extramural Aeromicrobiology;11510.2.8.1;5.8.1 Agriculture;11510.2.8.2;5.8.2 Waste Disposal;11710.2.9;5.9 Intramural Aeromicrobiology;11810.2.9.1;5.9.1 Buildings;11810.2.9.2;5.9.2 Public Health;11910.2.9.3;5.9.3 Hospitals and Laboratories;11910.2.10;5.10 Bioaerosol Control;12010.2.10.1;5.10.1 Ventilation;12010.2.10.2;5.10.2 Filtration;12010.2.10.3;5.10.3 Biocidal Control;1201