Manual of Environmental Microbiology

Contents I. Introduction to Environmental Microbiology Volume editor: Michael J. McInerney 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, Edward R. Leadbetter II. General Methodology Volume editor: Michael J. McInerney Section editor: David A. Stahl 4. Overview: General Methodology, Michael J. McInerney and David A. Stahl 5. Analytical Imaging and Microscopy Techniques, J. R. Lawrence, D. R. Korber, G. M. Wolfaardt, D. E. Caldwell, and T. R. Neu 6. Cultivation of Bacteria and Fungi, Ralph S. Tanner 7. Cultivation of Algae and Protozoa, Alan Warren, John G. Day, and Susan Brown 8. Cultivation and Assay of Animal Viruses, Pierre Payment 9. Cultivation of Microbial Consortia and Communities, Douglas E. Caldwell, Gideon M. Wolfaardt, Darren R. Korber, Subramanian Karthikeyan, John R. Lawrence, and Daniel K. Brannan 10. Biochemical Approaches to Biomass Measurements and Community Structure Analysis, Holly C. Pinkart, David B. Ringelberg, Yvette M. Piceno, Sarah J. Macnaughton, and David C. White 11. Molecular Approaches for the Measurement of Density, Diversity, and Phylogeny, Wen-Tso Liu and David Stahl 12. Application of Physiological Profiles to Assessment of Community Properties, Aaron L. Mills and Jay L. Garland 13. Emerging Technologies: Bioreporters, Biosensors, and Microprobes, Robert S. Burlage 14. Quality Assurance, A. J. Cross-Smiecinski 15. Sampling and Data Analysis for Environmental Microbiology, Christopher J. Murray III. Water Microbiology in Public Health Volume editor: Christon J. Hurst Section editor: Gary A. Toranzos 16. Overview of Water Microbiology as It Relates to Public Health, Christon J. Hurst 17. Waterborne Transmission of Infectious Agents, Christine L. Moe 18. Detection of Microorganisms in Environmental Freshwaters and Drinking Waters, Gary A. Toranzos, Gordon A. McFeters, and Juan J. Borrego 19. Detection of Protozoan Parasites in Source and Finished Drinking Waters, Frank W. Schaefer III 20. Microbial Indicators of Marine Recreational Water Quality, Roger S. Fujioka 21. Detection of Viruses in Environmental Waters, Sewage, and Sewage Sludges, Christon J. Hurst and Kelly A. Reynolds 22. Detection of Bacterial Pathogens in Wastewater and Sludge, Robert C. Cooper and Richard E. Danielson 23. Detection of Bacteria, Viruses, and Parasitic Protozoa in Shellfish, Lee-Ann Jaykus, Ricardo De Leon, and Gary A. Toranzos 24. Control of Microorganisms in Source Water and Drinking Water, Aaron B. Margolin 25. Assessing the Efficiency of Wastewater Treatment, Wesley O. Pipes and James T. Zmuda 26. Modeling the Fate of Microorganisms in Water, Wastewater, and Soil, Christon J. Hurst 27. Estimating the Risk of Infectious Disease Associated with Pathogens in Drinking Water, Christon J. Hurst IV. Aquatic Environments Volume editor: Christon J. Hurst Section editors: Steven Y. Newell and Robert R. Christian 28. Overview of Issues in Aquatic Microbial Ecology, Robert R. Christian and Douglas G. Capone 29. Primary Productivity and Producers, Hans W. Paerl 30. Molecular Methods for Detecting and Characterizing Harmful Phytoplankton, R. Wayne Litaker and Patricia A. Tester 31. Bacterial Secondary Productivity, Gerardo Chin-Leo 32. Community Structure: Viruses, Curtis A. Suttle *Community Structure: Bacteria and Archaea, Jed A. Fuhrman 34. Protistan Community Structure, David A. Caron 35. Biomass, Growth Rate, and Production of Filamentous Fungi in Plant Litter, Mark O. Gessner and Steven Y. Newell 36. Phagotrophy in Aquatic Microbial Food Webs, Evelyn B. Sherr and Barry F. Sherr 37. Radiotracer (14C and 3H) Assays for Benthic Microbial Organic Matter Transformations, Gary M. King 38. Sulfur Cycling, Mark E. Hines, Pieter T. Visscher, and Richard Devereux 39. Microbial Nitrogen Cycling, Douglas G. Capone 40. Phosphorus Cycling, Ronald D. Jones 41. Metal Requirements and Tolerance, Aaron L. Mills 42. Colonization, Adhesion, Aggregation, and Biofilms, John R. Lawrence, Thomas R. Neu, and Kevin C. Marshall 43. Unusual or Extreme High-Pressure Marine Environments, Jody W. Deming 44. Field and Laboratory Methods for Meiofaunal Research, Paul A. Montagna V. Soil, Rhizosphere, and Phyllosphere Volume editor: Guy R. Knudsen Section editor: Linda S. Thomashow 45. Introduction and Overview: Soil, Rhizosphere, and Phyllosphre, Guy R. Knudsen 46. Methods for Sampling Soil Microbes, J. D. van Elsas, K. Smalla, A. K. Lilley, and M. J. Bailey 47. Sampling Microbes from the Rhizosphere and Phyllosphere, Louise-Marie C. Dandurand and Guy R. Knudsen 48. Sampling Viruses from Soil, Christon J. Hurst and Kelly A. Reynolds 49. Isolation, Culture, and Detection of Arbuscular Mycorrhizal Fungi, Amiel G. Jarstfer and David M. Sylvia 50. Isolation, In Planta Detection, and Culture of Endophytic Bacteria and Fungi, Charles W. Bacon, Anthony E. Glenn, and Dorothy M. Hinton 51. Methods of Soil Microbial Community Analysis, Andrew Ogram and Kanika Sharma 52. Isolation and Purification of Microbial Community Nucleic Acids from Environmental Samples, Mary Ann Bruns and Daniel H. Buckley 53. PCR Applications for Plant and Soil Microbes, Ian L. Pepper and Scot E. Dowd 54. Quantification of Nitrogen Transformations, David D. Myrold 55. Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes, Guy R. Knudsen 56. Assessment of Extracellular Enzymatic Activity in Soil, Matthew J. Morra 57. Antibiotic, Chromogenic, and Luminescent Markers for Bacteria, J. K. Jansson 58. Use of Fluorescent Antibodies for Studying the Ecology of Soil- and Plant-Associated Microbes, Timothy R. McDermott and Frank B. Dazzo 59. Reporter Gene Systems Useful in Evaluating In Situ Gene Expression by Soil- and Plant-Associated Bacteria, Joyce E. Loper and Steven E. Lindow 60. Antibiotic Production by Soil and Rhizosphere Microbes In Situ, Linda S. Thomashow, Robert F. Bonsall, and David M. Weller 61. Quantification of Gene Transfer in Soil and the Phytosphere, T. M. Timms-Wilson, L. S. Van Overbeek, J. T. Trevors, M. J. Bailey, and J. D. van Elsas 62. Research Methods for Microorganisms Interacting with Arthropods in Soil, James R. Fuxa, Yasuhisa Kunimi, and Madoka Nakai VI. Subsurface and Landfills Volume editor: Michael J. McInerney 63. Overview of Issues in Subsurface and Landfill Microbiology, Ronald W. Harvey, Joseph M. Suflita, and Michael J. McInerney 64. Drilling, Coring, and Sampling Subsurface Environments, Tommy J. Phelps and James K. Fredrickson 65. Anaerobic Decomposition of Refuse in Landfills and Methane Oxidation in Landfill Cover Soils, Helene H. Hilger and Morton A. Barlaz 66. The Biogeochemistry of Aquifer Systems, John D. Coates and Laurie A. Achenbach 67. Stable Carbon Isotopes as Indicators of Microbial Activity in Aquifers, Ethan L. Grossman 68. Determining the Terminal Electron-Accepting Reaction in the Saturated Subsurface, Richard L. Smith 69. Transport of Microorganisms in the Terrestrial Subsurface: In Situ and Laboratory Methods, Ronald W. Harvey and Hauke Harms 70. Oil Field Microbiology, Michael J. McInerney and Kerry L. Sublette 71. Placement of Drinking Water Wells and Their Protection, Marylynn V. Yates VII. Aerobiology Volume editor: Linda D. Stetzenbach Section editor: Mark P. Buttner 72. Introduction to Aerobiology, Linda D. Stetzenbach 73. Sampling and Analysis of Airborne Microorganisms, Mark P. Buttner, Klaus Willeke, and Sergey A. Grinshpun 74. Fate and Transport of Microorganisms in Air, Alan Jeff Mohr 75. Airborne Fungi and Mycotoxins, Chin S. Yang and Eckardt Johanning 76. Airborne Endotoxin, Stephen A. Olenchock 77. Legionellae and Legionnaires' Disease, Barry S. Fields 78. Airborne Viruses, Syed A. Sattar and M. Khalid Ijaz 79. Aerobiology of Agricultural Pathogens, Estelle Levetin VIII. Biotransformation and Biodegradation Volume editor: Ronald L. Crawford 80. Overview: Biotransformation and Biodegradation, Ronald L. Crawford 81. Methods for Determining Biodegradability, Eugene L. Madsen 82. Measuring and Modeling Physicochemical Limitations to Bioavailability and Biodegradation, Anuradha Ramaswami and Richard G. Luthy 83. Lignocellulose Biodegradation, Lee A. Deobald and Don L. Crawford 84. Methods for Measuring Hydrocarbon Biodegradation in Soils, Ingeborg D. Bossert, Leslie M. Shor, and David S. Kosson 85. Soil Bioventilation and Modeling of Airflow in Soil, Stephen J. Cullen and Mark Lupo 86. Bioaugmentation, Timothy M. Vogel and Michael V. Walter 87. Use of Fungi in Biodegradation, J. W. Bennett, K. G. Wunch, and B. D. Faison 88. Assessment of Various Methods for the Isolation of Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Microorganisms and the Procedures for the Determination of Biodegradation Intermediates and Environmental Monitoring of PAHs, Carl E. Cerniglia and Kay L. Shuttleworth 89. Biodegradation, Transformation, and Bioremediation of Nitroaromatic Compounds, Shirley F. Nishino and Jim C. Spain 90. Biodegradation of Halogenated Solvents, Kevin H. Mitchell and Brian G. Fox 91. Methods for Assessing Anaerobic Biodegradation Potential, D. J. Roberts 92. The Ecology of Iron-Reducing Bacteria in Pristine and Contaminated Environments, David E. Cummings, Stefan Spring, and R. Frank Rosenzweig 93. Biotransformations of Polychlorinated Biphenyls, D. D. Focht and W. Reineke 94. Biodegradation of Agricultural Chemicals, David A. Newcombe, Stephen N. Bradley, Terry B. Hammill, David E. Crowley, and Ronald L. Crawford 95. Use of Bioreactors and Microcosms To Assess the Biodegradation Potential of Soils, Steven Schmidt and Kate Scow 96. Microbiology for the Metal Mining Industry, Corale L. Brierley and James A. Brierley 97. Microbiologically Influenced Corrosion: Perspectives and Approaches, Joanne Horn and Denny Jones 98. Scale-Up of Processes for Bioremediation, Roger A.