Manual of environmental microbiology/ Christon J. Hurst & Ronald L. Crawford

Table of ContentsI. Introduction to Environmental MicrobiologyVolume Editor: Jay L. Garland1. Introduction to Environmental Microbiology, Christon J. Hurst2. Neighborhoods and Community Involvement: No Microbe Is an Island, Christon J. Hurst3. Prokaryotic Diversity: Form, Ecophysiology, and Habitat, Frederick S. Colwell and Edward R. LeadbetterII. General MethodologyVolume Editor: Jay L. GarlandSection Editor: Sean P. O'Connell4. Overview: General Methodology, Jay L. Garland and Sean P. O'Connell5. Analytical Imaging and Microscopy Techniques, J. R. Lawrence, D. R. Korber, and T. R. Neu6. Cultivation of Bacteria and Fungi, Ralph S. Tanner7. Cultivation of Algae and Protozoa, John G. Day, Undine Achillles-Day, Susan Brown, and Alan Warren8. Cultivation and Assay of Animal Viruses, Pierre Payment9. Cultivation of Microbial Consortia and Communities, Gideon M. Wolfaardt, Darren R. Korber, and John R. Lawrence10. Lipid Analyses for Viable Microbial Biomass, Community Composition, Metabolic Status, and In Situ Metabolism, David B. Hedrick, Aaron D. Peacock, and David C. White11. Physiological Profiling of Microbial Communities, Jay L. Garland, Colin D. Campbell, and Aaron L. Mills12. Molecular Approaches for the Measurement of Density, Diversity, and Phylogeny, Wen-Tso Liu and David A. Stahl13. Phylogenetic and Genomic Analysis, Dirk Gevers and Tom Coenye14. Bioreporters, Biosensors, and Microprobes, Robert S. Burlage15. Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems, John E. Hobbie, Michele Bahr, and Anna-Louise Reysenbach16. Quality Assurance, A. J. Cross-Smiecinski17. Issues of Study Design and Statistical Analysis for Environmental Microbiology, Kenneth M. Portier and Ronald CorstanjeIII. Water Microbiology in Public HealthVolume Editor: Christon J. HurstSection Editor: Gary A. Toranzos18. Overview of Water Microbiology as It Relates to Public Health, Christon J. Hurst19. Waterborne Transmission of Infectious Agents, Christine L. Moe20. Detection of Microorganisms in Environmental Freshwaters and Drinking Waters, Gary A. Toranzos, Gordon A. McFeters, Juan Jose Borrego, and Marion Savill21. Detection of Protozoan Parasites in Source and Finished Drinking Water, Frank W. Schaefer III22. Microbial Indicators of Marine Recreational Water Quality, Stephen B. Weisberg, Rachel T. Noble, and John F. Griffith23. Detection of Viruses in Environmental Waters, Sewage, and Sewage Sludges, Christon J. Hurst and Kelly A. Reynolds24. Detection of Bacterial Pathogens in Wastewater and Sludge, Richard E. Danielson and Robert C. Cooper25. Detection of Pathogenic Bacteria, Viruses, and Parasitic Protozoa in Shellfish, Lee-Ann Jaykus26. Control of Microorganisms in Source Water and Drinking Water, Morteza Abbaszadegan and Aaron B. Margolin27. Assessing the Efficiency of Wastewater Treatment, Wesley O. Pipes and James T. Zmuda28. Modeling the Fate of Microorganisms in Water, Wastewater, and Soil, Christon J. Hurst29. Estimating the Risk of Infectious Disease Associated with Pathogens in Drinking Water, Christon J. Hurst30. Toxic Photosynthetic Microbes, Wesley Clinton Jackson, Jr.IV. Aquatic EnvironmentsVolume Editor: Christon J. HurstSection Editor: Meredith A. J. Hullar31. An Overview of Methodologies in Aquatic Microbial Ecology, Meredith A. J. Hullar32. 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. Rappe33. Primary Productivity and Producers, Hans W. Paerl34. Bacterial Secondary Productivity, Gerardo Chin-Leo and Colleen T. Evans35. Community Structure: Bacteria and Archaea, Jed A. Fuhrman36. Viral Community Structure, Alexander I. Culley and Curtis A. Suttle37. Protistan Community Structure, David A. Caron and Astrid Schnetzer38. Decomposition and Fungal Community Structure in Aquatic Environments, Felix Barlocher39. Bacterial Organic Carbon Cycling in Aquatic Environments, Matthew T. Cottrell40. Environmental Genomics of C1 Metabolism, Marina G. Kalyuzhnaya, Olivier Nercessian, Mary E. Lidstrom, and Ludmila Chistoserdova41. Sulfur Cycling, Mark E. Hines, Pieter T. Visscher, Andreas P. Teske, and Richard Devereux42. Nitrogen Cycling in Aquatic Environments, Bess B. Ward43. The Marine Phosphorus Cycle, David M. Karl44. Microbial Metal Cycling in Aquatic Environments, Eric E. Roden and David Emerson45. Biofilms on Living Surfaces, Jeremy S. Webb, Michael W. Taylor, Scott Rice, Torsten Thomas, Dhana Rao, Diane McDougald, and Staffan Kjelleberg46. Extreme High-Pressure Marine Environments, Jody W. DemingV. Soil, Rhizosphere, and PhyllosphereVolume Editor: David A. Lipson47. Introduction and Overview: Soil, Rhizosphere, and Phyllosphere, David Lipson48. Surface Soil Microbial Sampling Methods, David B. Knaebel49. Application of Phylogenetic Techniques in Studies of Soil Microbial Communities, Ryan T. Jones, Elizabeth K. Costello, and Andrew P. Martin50. Sampling Viruses from Soil, Christon J. Hurst and Kelly A. Reynolds51. Isolation, Culture, and Detection of Arbuscular Mycorrhizal Fungi, David G. Sylvia, Wittaya Kaonongbua, and James D. Bever52. Isolation, In Planta Detection, and Uses of Endophytic Bacteria for Plant Protection, Charles W. Bacon and Dorothy M. Hinton53. Methods of Soil Microbial Community Analysis, Andrew Ogram, Hector Castro, and Ashvini Chauhan54. Microarrays: Design and Use for Agricultural and Environmental Applications, Scot E. Dowd, Hiroshi Ishizaki, and Jeanette Thurston Enriquez55. PCR: Agricultural and Environmental Applications for Soil Microbes, Scot E. Dowd and Ian L. Pepper56. Quantification of Nitrogen Transformations, David D. Myrold57. Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes, Guy R. Knudsen58. Soil Enzymes: Linking Proteomics and Ecological Processes, Steven D. Allison, Tracy B. Gartner, Keri Holland, Michael Weintraub, and Robert L. Sinsabaugh59. 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 Hartmann60. 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. Lindow61. 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 Yin62. Mobile Gene Elements in Environmental Microbial Communities, Diana R. Nemergut, Tamar Barkay, and Jonna Coombs63. Microorganisms Associated with Soil Arthropods, Ann E. Hajek, James R. Fuxa, and Yasuhisa Kunimi64. Lipid Fingerprinting of Soil Microbial Communities, Ana Lucia Cordova-Kreylos and Kate M. ScowVI. Subsurface and LandfillsVolume Editor: Aaron L. Mills65. Overview of Issues in Subsurface and Landfill Microbiology, Ronald W. Harvey, Joseph M. Suflita, Michael J. McInerney, and Aaron L. Mills66. Drilling, Coring, and Sampling Subsurface Environments, Thomas L. Kieft, Tommy J. Phelps, and James K. Fredrickson67. Anaerobic Decomposition of Refuse in Landfills and Methane Oxidation in Landfill Covers, Helene H. Hilger and Morton A. Barlaz68. Biogeochemistry of Aquifer Systems, Isabelle M. Cozzarelli and Johanna V. Weiss69. 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 Landkamer71. Oil Field Microbiology, Michael J. McInerney, Gerrit Voordouw, Gary E. Jenneman, and Kerry L. Sublette72. Placement of Drinking Water Wells and Their Protection, Marylynn V. YatesVII. AerobiologyVolume Editor: Linda D. StetzenbachSection Editor: Mark P. Buttner73. Introduction to Aerobiology, Linda D. Stetzenbach74. Sampling for Airborne Microorganisms, Sergey A. Grinshpun, Mark P. Buttner, and Klaus Willeke75. Analysis of Bioaerosol Samples, Patricia Cruz and Mark P. Buttner76. Fate and Transport of Microorganisms in Air, Alan Jeff Mohr77. Airborne Fungi and Mycotoxins, Chin S. Yang and Eckhardt Johanning78. Airborne Bacteria and Endotoxin, Peter S. Thorne and Caroline Duchaine79. Legionellae and Legionnaires' Disease, Barry S. Fields80. Airborne Viruses, Syed A. Sattar and M. Khalid Ijaz81. Aerobiology of Agricultural Pathogens, Estelle LevetinVIII. Biotransformation and BiodegradationVolume Editor: Ronald L. CrawfordSection Editor: Jonathan R. Lloyd and Ming Tien82. Overview: Biotransformation and Biodegradation, Ronald L. Crawford83. Functional Gene Arrays for Microbial Community Analysis, Terry J. Gentry, Christopher W. Schadt, Zhili He, and Jizhong Zhou84. Methods for Soil Metagenomics: Extraction and Cloning of Soil DNA, Christian S. Riesenfeld, Lynn L. Williamson, and Jo Handelsman85. Using Genetic Algorithms To Optimize Functions of Microbial Ecosystems, Frederik P. J. Vandecasteele, Thomas F. Hess, and Ronald L. Crawford86. Metagenomic Methods for the Identification of Active Microorganisms and Genes in Biodegradation Processes, Don Cowan and William Stafford87. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, Feng Liu, Hasan Koc, and Ming Tien88. Current Progress in the Application of Mycoremediation to Soil Cleanup, Richard T. Lamar and R. B. White89. Fungal Solid-State Fermentation Systems for Bioconversion of Lignocellulosic Biomass: Process Protocol and Applications, Chundakkadu Krishna90. Characterization of Microeukaryota in Natural Environments, Janice L. Strap91. Methods Useful in Assessing Biological and Chemical Activity of Low-Molecular-Weight Brown Rot Fungal Metabolites, Jody Jellison, Barry Goodell, and Yuhui Qian92. Techniques for Studying Uncultured and Cultured Magnetotactic Bacteria, Dirk Schuler and Dennis A. Bazylinski93. Growth of Electrode-Reducing Bacteria, Daniel R. Bond94. Microbially Mediated Anaerobic Iron (II) Oxidation at Circumneutral pH, Karrie A. Weber and John D. Coates95. Isolation, Enumeration, Growth, and Preservation of Acidophilic Prokaryotes, Kevin B. Hallberg and D. Barrie Johnson96. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, Jon L. Hobman97. Synchrotron-Based Techniques for Monitoring Metal Transformations, Kenneth M. Kemner and Shelly D. Kelly98. Techniques for Studying Microbial Transformations of Metals and Radionuclides, Jonathan R. Lloyd, Terry J. Beveridge, Katherine Morris, David A. Polya, and David J. Vaughan99. Arsenate-Respiring Bacteria, Chad W. Saltikov and Davin Malasarn100. Biotransformations of Manganese, Bradley M. Tebo, Brian G. Clement, and Gregory J. Dick101. Microbial Fe (III) Reduction: Ecological and Physiological Considerations, David E. Cummings and Timothy S. Magnuson