Manual of Environmental Microbiology

Editors: Christon J. Hurst, Xavier University and Universidad del Valle, USA Ronald L. Crawford, University of Idaho, USA Jay L. Garland, Dynamac Corporation, USA David A. Lipson, San Diego State University, USA Aaron L. Mills, University of Virginia, USA Linda D. Stetzenbach, University of Nevada, Las Vegas, USA

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