Table of Contents I. Introduction to Environmental Microbiology Volume Editor: Jay L. Garland 1. Introduction to Environmental Microbiology, Christon J. Hurst 2. Neighborhoods and Community Involvement: No Microbe Is an Island, Christon J. Hurst 3. Prokaryotic Diversity: Form, Ecophysiology, and Habitat, Frederick S. Colwell and Edward R. Leadbetter II. General Methodology Volume Editor: Jay L. Garland Section Editor: Sean P. O'Connell 4. Overview: General Methodology, Jay L. Garland and Sean P. O'Connell 5. Analytical Imaging and Microscopy Techniques, J. R. Lawrence, D. R. Korber, and T. R. Neu 6. Cultivation of Bacteria and Fungi, Ralph S. Tanner 7. Cultivation of Algae and Protozoa, John G. Day, Undine Achillles-Day, Susan Brown, and Alan Warren 8. Cultivation and Assay of Animal Viruses, Pierre Payment 9. Cultivation of Microbial Consortia and Communities, Gideon M. Wolfaardt, Darren R. Korber, and John R. Lawrence 10. Lipid Analyses for Viable Microbial Biomass, Community Composition, Metabolic Status, and In Situ Metabolism, David B. Hedrick, Aaron D. Peacock, and David C. White 11. Physiological Profiling of Microbial Communities, Jay L. Garland, Colin D. Campbell, and Aaron L. Mills 12. Molecular Approaches for the Measurement of Density, Diversity, and Phylogeny, Wen-Tso Liu and David A. Stahl 13. Phylogenetic and Genomic Analysis, Dirk Gevers and Tom Coenye 14. Bioreporters, Biosensors, and Microprobes, Robert S. Burlage 15. Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems, John E. Hobbie, Michele Bahr, and Anna-Louise Reysenbach 16. Quality Assurance, A. J. Cross-Smiecinski 17. Issues of Study Design and Statistical Analysis for Environmental Microbiology, Kenneth M. Portier and Ronald Corstanje III. Water Microbiology in Public Health Volume Editor: Christon J. Hurst Section Editor: Gary A. Toranzos 18. Overview of Water Microbiology as It Relates to Public Health, Christon J. Hurst 19. Waterborne Transmission of Infectious Agents, Christine L. Moe 20. Detection of Microorganisms in Environmental Freshwaters and Drinking Waters, Gary A. Toranzos, Gordon A. McFeters, Juan Jose Borrego, and Marion Savill 21. Detection of Protozoan Parasites in Source and Finished Drinking Water, Frank W. Schaefer III 22. Microbial Indicators of Marine Recreational Water Quality, Stephen B. Weisberg, Rachel T. Noble, and John F. Griffith 23. Detection of Viruses in Environmental Waters, Sewage, and Sewage Sludges, Christon J. Hurst and Kelly A. Reynolds 24. Detection of Bacterial Pathogens in Wastewater and Sludge, Richard E. Danielson and Robert C. Cooper 25. Detection of Pathogenic Bacteria, Viruses, and Parasitic Protozoa in Shellfish, Lee-Ann Jaykus 26. Control of Microorganisms in Source Water and Drinking Water, Morteza Abbaszadegan and Aaron B. Margolin 27. Assessing the Efficiency of Wastewater Treatment, Wesley O. Pipes and James T. Zmuda 28. Modeling the Fate of Microorganisms in Water, Wastewater, and Soil, Christon J. Hurst 29. Estimating the Risk of Infectious Disease Associated with Pathogens in Drinking Water, Christon J. Hurst 30. Toxic Photosynthetic Microbes, Wesley Clinton Jackson, Jr. IV. Aquatic Environments Volume Editor: Christon J. Hurst Section Editor: Meredith A. J. Hullar 31. An Overview of Methodologies in Aquatic Microbial Ecology, Meredith A. J. Hullar 32. Cultivating Microorganisms from Dilute Aquatic Environments: Melding Traditional Methodology with New Cultivation Techniques and Molecular Methods, Jamie W. Becker, Marina L. Brandon, and Michael S. Rappe 33. Primary Productivity and Producers, Hans W. Paerl 34. Bacterial Secondary Productivity, Gerardo Chin-Leo and Colleen T. Evans 35. Community Structure: Bacteria and Archaea, Jed A. Fuhrman 36. Viral Community Structure, Alexander I. Culley and Curtis A. Suttle 37. Protistan Community Structure, David A. Caron and Astrid Schnetzer 38. Decomposition and Fungal Community Structure in Aquatic Environments, Felix Barlocher 39. Bacterial Organic Carbon Cycling in Aquatic Environments, Matthew T. Cottrell 40. Environmental Genomics of C1 Metabolism, Marina G. Kalyuzhnaya, Olivier Nercessian, Mary E. Lidstrom, and Ludmila Chistoserdova 41. Sulfur Cycling, Mark E. Hines, Pieter T. Visscher, Andreas P. Teske, and Richard Devereux 42. Nitrogen Cycling in Aquatic Environments, Bess B. Ward 43. The Marine Phosphorus Cycle, David M. Karl 44. Microbial Metal Cycling in Aquatic Environments, Eric E. Roden and David Emerson 45. Biofilms on Living Surfaces, Jeremy S. Webb, Michael W. Taylor, Scott Rice, Torsten Thomas, Dhana Rao, Diane McDougald, and Staffan Kjelleberg 46. Extreme High-Pressure Marine Environments, Jody W. Deming V. Soil, Rhizosphere, and Phyllosphere Volume Editor: David A. Lipson 47. Introduction and Overview: Soil, Rhizosphere, and Phyllosphere, David Lipson 48. Surface Soil Microbial Sampling Methods, David B. Knaebel 49. Application of Phylogenetic Techniques in Studies of Soil Microbial Communities, Ryan T. Jones, Elizabeth K. Costello, and Andrew P. Martin 50. Sampling Viruses from Soil, Christon J. Hurst and Kelly A. Reynolds 51. Isolation, Culture, and Detection of Arbuscular Mycorrhizal Fungi, David G. Sylvia, Wittaya Kaonongbua, and James D. Bever 52. Isolation, In Planta Detection, and Uses of Endophytic Bacteria for Plant Protection, Charles W. Bacon and Dorothy M. Hinton 53. Methods of Soil Microbial Community Analysis, Andrew Ogram, Hector Castro, and Ashvini Chauhan 54. Microarrays: Design and Use for Agricultural and Environmental Applications, Scot E. Dowd, Hiroshi Ishizaki, and Jeanette Thurston Enriquez 55. PCR: Agricultural and Environmental Applications for Soil Microbes, Scot E. Dowd and Ian L. Pepper 56. Quantification of Nitrogen Transformations, David D. Myrold 57. Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes, Guy R. Knudsen 58. Soil Enzymes: Linking Proteomics and Ecological Processes, Steven D. Allison, Tracy B. Gartner, Keri Holland, Michael Weintraub, and Robert L. Sinsabaugh 59. Use of Immunofluorescence Microscopy and Fluorescence In Situ Hybridization Combined with CMEIAS and Other Image Analysis Tools To Study the Autecology of Soil- and Plant-Associated Microbes, Frank B. Dazzo, Michael Schmid, and Anton Hartmann 60. Reporter Gene Systems Useful in Evaluating In Situ Gene Expression by Soil- and Plant-Associated Bacteria, H. J. Leveau, Joyce E. Loper, and Steven E. Lindow 61. Identifying Microorganisms Involved in Specific In Situ Functions: Experimental Design Considerations for rRNA Gene-Based Population Studies and Sequence-Selective PCR Assays, James Borneman, J. Ole Becker, Elizabeth Bent, Brian Lanoil, Brian McSpadden Gardener, Rabiu Olatinwo, Laura Presley, Alexandra J. Scupham, Lea Valinsky, and Bei Yin 62. Mobile Gene Elements in Environmental Microbial Communities, Diana R. Nemergut, Tamar Barkay, and Jonna Coombs 63. Microorganisms Associated with Soil Arthropods, Ann E. Hajek, James R. Fuxa, and Yasuhisa Kunimi 64. Lipid Fingerprinting of Soil Microbial Communities, Ana Lucia Cordova-Kreylos and Kate M. Scow VI. Subsurface and Landfills Volume Editor: Aaron L. Mills 65. Overview of Issues in Subsurface and Landfill Microbiology, Ronald W. Harvey, Joseph M. Suflita, Michael J. McInerney, and Aaron L. Mills 66. Drilling, Coring, and Sampling Subsurface Environments, Thomas L. Kieft, Tommy J. Phelps, and James K. Fredrickson 67. Anaerobic Decomposition of Refuse in Landfills and Methane Oxidation in Landfill Covers, Helene H. Hilger and Morton A. Barlaz 68. Biogeochemistry of Aquifer Systems, Isabelle M. Cozzarelli and Johanna V. Weiss 69. Determining the Terminal Electron-Accepting Reaction in the Saturated Subsurface, Richard L. Smith and Steve H. Harris, Jr. 70. Transport of Microorganisms in the Terrestrial Subsurface: In Situ and Laboratory Methods, Ronald W. Harvey, Hauke Harms, and Lee Landkamer 71. Oil Field Microbiology, Michael J. McInerney, Gerrit Voordouw, Gary E. Jenneman, and Kerry L. Sublette 72. Placement of Drinking Water Wells and Their Protection, Marylynn V. Yates VII. Aerobiology Volume Editor: Linda D. Stetzenbach Section Editor: Mark P. Buttner 73. Introduction to Aerobiology, Linda D. Stetzenbach 74. Sampling for Airborne Microorganisms, Sergey A. Grinshpun, Mark P. Buttner, and Klaus Willeke 75. Analysis of Bioaerosol Samples, Patricia Cruz and Mark P. Buttner 76. Fate and Transport of Microorganisms in Air, Alan Jeff Mohr 77. Airborne Fungi and Mycotoxins, Chin S. Yang and Eckhardt Johanning 78. Airborne Bacteria and Endotoxin, Peter S. Thorne and Caroline Duchaine 79. Legionellae and Legionnaires' Disease, Barry S. Fields 80. Airborne Viruses, Syed A. Sattar and M. Khalid Ijaz 81. Aerobiology of Agricultural Pathogens, Estelle Levetin VIII. Biotransformation and Biodegradation Volume Editor: Ronald L. Crawford Section Editor: Jonathan R. Lloyd and Ming Tien 82. Overview: Biotransformation and Biodegradation, Ronald L. Crawford 83. Functional Gene Arrays for Microbial Community Analysis, Terry J. Gentry, Christopher W. Schadt, Zhili He, and Jizhong Zhou 84. Methods for Soil Metagenomics: Extraction and Cloning of Soil DNA, Christian S. Riesenfeld, Lynn L. Williamson, and Jo Handelsman 85. Using Genetic Algorithms To Optimize Functions of Microbial Ecosystems, Frederik P. J. Vandecasteele, Thomas F. Hess, and Ronald L. Crawford 86. Metagenomic Methods for the Identification of Active Microorganisms and Genes in Biodegradation Processes, Don Cowan and William Stafford 87. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, Feng Liu, Hasan Koc, and Ming Tien 88. Current Progress in the Application of Mycoremediation to Soil Cleanup, Richard T. Lamar and R. B. White 89. Fungal Solid-State Fermentation Systems for Bioconversion of Lignocellulosic Biomass: Process Protocol and Applications, Chundakkadu Krishna 90. Characterization of Microeukaryota in Natural Environments, Janice L. Strap 91. Methods Useful in Assessing Biological and Chemical Activity of Low-Molecular-Weight Brown Rot Fungal Metabolites, Jody Jellison, Barry Goodell, and Yuhui Qian 92. Techniques for Studying Uncultured and Cultured Magnetotactic Bacteria, Dirk Schuler and Dennis A. Bazylinski 93. Growth of Electrode-Reducing Bacteria, Daniel R. Bond 94. Microbially Mediated Anaerobic Iron (II) Oxidation at Circumneutral pH, Karrie A. Weber and John D. Coates 95. Isolation, Enumeration, Growth, and Preservation of Acidophilic Prokaryotes, Kevin B. Hallberg and D. Barrie Johnson 96. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, Jon L. Hobman 97. Synchrotron-Based Techniques for Monitoring Metal Transformations, Kenneth M. Kemner and Shelly D. Kelly 98. Techniques for Studying Microbial Transformations of Metals and Radionuclides, Jonathan R. Lloyd, Terry J. Beveridge, Katherine Morris, David A. Polya, and David J. Vaughan 99. Arsenate-Respiring Bacteria, Chad W. Saltikov and Davin Malasarn 100. Biotransformations of Manganese, Bradley M. Tebo, Brian G. Clement, and Gregory J. Dick 101. Microbial Fe (III) Reduction: Ecological and Physiological Considerations, David E. Cummings and Timothy S. Magnuson
