Manual of 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: Seán P. O’Connell.

4. Overview: General Methodology, Jay L. Garland and Seán 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 José 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. Rappé.

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 Bärlocher.

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 Córdova-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 Schüler 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