Manual of environmental microbiology/ edited by Christon J. Hurst

SECTION I INTRODUCTION TO ENVIRONMENTAL MICROBIOLOGY
VOLUME EDITOR: JAY L. GARLAND
1. Introduction to Environmental Microbiology Christon J. Hurst
2. Neighborhoods and Communities: No Microbe Is an Island Christon J. Hurst
3. Prokaryotic Diversity: Form, Ecophysiology, and Habitat Frederick S.
Colwell and Edward R. Leadbetter
SECTION II GENERAL METHODOLOGY
VOLUME EDITOR: JAY L. GARLAND, SECTION EDITOR: SEAN O'CONNELL
4. Overview: General Methodology Jay L. Garland
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 Achilles-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
SECTION 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, Wastewater, and Wastewater
Biosolids 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.
SECTION IV AQUATIC ENVIRONMENTS
VOLUME EDITOR: CHRISTON J. HURST, SECTION EDITOR: MEREDITH A. J. HULLAR
31. Advances in Aquatic Microbial Ecology Meredith 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
45. Biofilms on Living Surfaces Jeremy S. Webb, Mike Taylor, Scott Rice,
Torsten Thomas, Dhana Rao, Diane
McDougald, and Staffan Kjelleberg
46. Extreme High-Pressure Marine Environments Jody W. Deming
SECTION 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 Process 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 Johan
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. A Review of Mobile Gene Elements and Methods To Study Horizontal Gene
Transfer in Environmental Microbial
Communities Diana R. Nemergut, Tamar Barkay, and Jonna Coombs
63. Research Methods for Microorganisms Interacting with Arthropods in Soil
Ann E. Hajek
64. Lipid Fingerprinting of Soil Microbial Communities Ana Lucia Cordova-
Kreylos and Kate M. Scow
SECTION 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
Harris
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
SECTION 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 Eckardt Johanning
78. Airborne Bacteria and Endotoxin Peter S. Thorne
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
SECTION VIII BIOTRANSFORMATION AND BIODEGRADATION
VOLUME EDITOR: RONALD L. CRAWFORD, SECTION EDITORS: 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 Ming Tien, Feng Liu, and Hasan
Koc
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