The field of environmental microbiology addresses one of the world’s most important areas of scientific research: the roles that microbes play in all planetary environments. The Manual of Environmental Microbiology is the only book to offer a comprehensive analysis of these critical environments. Thoroughly updated and revised, this third edition assembles in a single volume the most definitive information on microbes in air, water, and soil and their impact on human health and welfare.
In accessible, clear prose, the Manual describes the natural activities and fate of microorganisms in the environment. This wealth of information is divided into 101 chapters, each written by experts. Five general areas detailed throughout this volume are: basic principles of environmental microbiology, general analytical methodologies, detection of microbial activity, the impact of microbial activity on the environment, and detection and control of pathogens in the environment.
The Manual will serve as an indispensable reference for environmental microbiologists, microbial ecologists, and environmental engineers, as well as those interested in human diseases, water and wastewater treatment, and biotechnology.
Key Features of the third edition:
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Provides the single most comprehensive discussion of environmental microbiology
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Incorporates a summary of the latest methodology used to study the activity and fate of microorganisms in various environments
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Synthesizes the latest information on the assessment of microbial presence and microbial activity in natural and artificial environments
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Contains a completely revamped section covering biotransformation and biodegradation
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Incorporates an international perspective with contributions from acknowledged experts in their respective fields throughout the world
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: 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