Manual of Environmental Microbiology

by Hurst, Christon J.; Crawford, Ronald L.; Knudsen, Guy R.; McInerney, Michael J.; Stetzenbach, Linda D.

• ISBN13: 9781555811990
• ISBN10: 155581199X
• Edition: 2nd
• Format: Hardcover
• Copyright: 2002-01-01
• Publisher: Amer Society for Microbiology

Summary

The new second edition of this essential manual summarizes the information and knowledge of environmental microbiology in a single source. It details the natural fate of microorganisms in the environment as well as the intentional attempts to eliminate from the environment microorganisms that are pathogenic to humans or to plants and animals. The basic principles of environmental microbiology and general analytical methodologies, common across the range of the environments covered, are presented first. The core sections are structured with regard to the type of environmental medium being discussed. This landmark effort defines the study of environmental microbiology as we know it today and serves as an essential contribution to the literature.

Table of Contents

Editorial Board	p. xi
Contributors	p. xiii
Preface	p. xix
Introduction to Environmental Microbiology	p. 1
Introduction to Environmental Microbiology	p. 3
Neighborhoods and Community Involvement: No Microbe Is an Island	p. 6
Prokaryotic Diversity: Form, Ecophysiology, and Habitat	p. 19
General Methodology	p. 33
Overview: General Methodology	p. 35
Analytical Imaging and Microscopy Techniques	p. 39
Cultivation of Bacteria and Fungi	p. 62
Cultivation of Algae and Protozoa	p. 71
Cultivation and Assay of Animal Viruses	p. 84
Cultivation of Microbial Consortia and Communities
Biochemical Approaches to Biomass Measurements and Community Structure Analysis	p. 101
Molecular Approaches for the Measurement of Density, Diversity, and Phylogeny	p. 114
Application of Physiological Profiles to Assessment of Community Properties	p. 135
Emerging Technologies: Bioreporters, Biosensors, and Microprobes	p. 147
Quality Assurance	p. 158
Sampling and Data Analysis for Environmental Microbiology	p. 166
Water Microbiology in Public Health	p. 179
Overview of Water Microbiology as It Relates to Public Health	p. 181
Waterborne Transmission of Infectious Agents	p. 184
Detection of Microorganisms in Environmental Freshwaters and Drinking Waters	p. 205
Detection of Protozoan Parasites in Source and Finished Drinking Waters	p. 220
Microbial Indicators of Marine Recreational Water Quality	p. 234
Detection of Viruses in Environmental Waters, Sewage, and Sewage Sludges	p. 244
Detection of Bacterial Pathogens in Wastewater and Sludge	p. 254
Detection of Bacteria, Viruses, and Parasitic Protozoa in Shellfish	p. 264
Control of Microorganisms in Source Water and Drinking Water	p. 277
Assessing the Efficiency of Wastewater Treatment	p. 285
Modeling the Fate of Microorganisms in Water, Wastewater, and Soil	p. 300
Estimating the Risk of Infectious Disease Associated with Pathogens in Drinking Water	p. 309
Aquatic Environments	p. 321
Overview of Issues in Aquatic Microbial Ecology	p. 323
Primary Productivity and Producers	p. 329
Molecular Methods for Detecting and Characterizing Harmful Phytoplankton	p. 342
Bacterial Secondary Productivity	p. 354
Community Structure: Viruses	p. 364
Community Structure: Bacteria and Archaea	p. 371
Protistan Community Structure	p. 378
Biomass, Growth Rate, and Production of Filamentous Fungi in Plant Litter	p. 390
Phagotrophy in Aquatic Microbial Food Webs	p. 409
Radiotracer ([superscript 14]C and [superscript 3]H) Assays for Benthic Microbial Organic Matter Transformations	p. 419
Sulfur Cycling	p. 427
Microbial Nitrogen Cycling	p. 439
Phosphorus Cycling	p. 450
Metal Requirements and Tolerance	p. 456
Colonization, Adhesion, Aggregation, and Biofilms	p. 466
Unusual or Extreme High-Pressure Marine Environments	p. 478
Field and Laboratory Methods for Meiofaunal Research	p. 491
Soil, Rhizosphere, and Phyllosphere	p. 500
Introduction and Overview: Soil, Rhizosphere, and Phyllosphere	p. 503
Methods for Sampling Soil Microbes	p. 505
Sampling Microbes from the Rhizosphere and Phyllosphere	p. 516
Sampling Viruses from Soil	p. 527
Isolation, Culture, and Detection of Arbuscular Mycorrhizal Fungi	p. 535
Isolation, In Planta Detection, and Culture of Endophytic Bacteria and Fungi	p. 543
Methods of Soil Microbial Community Analysis	p. 554
Isolation and Purification of Microbial Community Nucleic Acids from Environmental Samples	p. 564
PCR Applications for Plant and Soil Microbes	p. 573
Quantification of Nitrogen Transformations	p. 583
Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes	p. 591
Assessment of Extracellular Enzymatic Activity in Soil	p. 597
Antibiotic, Chromogenic, and Luminescent Markers for Bacteria	p. 604
Use of Fluorescent Antibodies for Studying the Ecology of Soil- and Plant-Associated Microbes	p. 615
Reporter Gene Systems Useful in Evaluating In Situ Gene Expression by Soil-and Plant-Associated Bacteria	p. 627
Antibiotic Production by Soil and Rhizosphere Microbes In Situ	p. 638
Quantification of Gene Transfer in Soil and the Phytosphere	p. 648
Research Methods for Microorganisms Interacting with Arthropods in Soil	p. 660
Subsurface and Landfills	p. 673
Overview of Issues in Subsurface and Landfill Microbiology	p. 675
Drilling, Coring, and Sampling Subsurface Environments	p. 679
Anaerobic Decomposition of Refuse in Landfills and Methane Oxidation in Landfill Cover Soils	p. 696
The Biogeochemistry of Aquifer Systems	p. 719
Stable Carbon Isotopes as Indicators of Microbial Activity in Aquifers	p. 728
Determining the Terminal Electron-Accepting Reaction in the Saturated Subsurface	p. 743
Transport of Microorganisms in the Terrestrial Subsurface: In Situ and Laboratory Methods	p. 753
Oil Field Microbiology	p. 777
Placement of Drinking Water Wells and Their Protection	p. 788
Aerobiology	p. 799
Introduction to Aerobiology	p. 801
Sampling and Analysis of Airborne Microorganisms	p. 814
Fate and Transport of Microorganisms in Air	p. 827
Airborne Fungi and Mycotoxins	p. 839
Airborne Endotoxin	p. 853
Legionellae and Legionnaires' Disease	p. 860
Airborne Viruses	p. 871
Aerobiology of Agricultural Pathogens	p. 884
Biotransformation and Biodegranation	p. 898
Overview: Biotransformation and Biodegradation	p. 901
Methods for Determining Biodegradability	p. 903
Measuring and Modeling Physicochemical Limitations to Bioavailability and Biodegradation	p. 916
Lignocellulose Biodegradation	p. 925
Methods for Measuring Hydrocarbon Biodegradation in Soils	p. 934
Soil Bioventilation and Modeling of Airflow in Soil	p. 944
Bioaugmentation
Use of Fungi in Biodegradation	p. 960
Methods for Isolation of Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Microorganisms and Procedures for Determination of Biodegradation Intermediates and Environmental Monitoring of PAHs	p. 972
Biodegradation, Transformation, and Bioremediation of Nitroaromatic Compounds	p. 987
Biodegradation of Halogenated Solvents	p. 997
Methods for Assessing Anaerobic Biodegradation Potential	p. 1008
The Ecology of Iron-Reducing Bacteria in Pristine and Contaminated Environments
Biotransformations of Polychlorinated Biphenyls	p. 1028
Biodegradation of Agricultural Chemicals	p. 1038
Use of Bioreactors and Microcosms To Assess the Biodegradation Potential of Soils	p. 1049
Microbiology for the Metal Mining Industry
Microbiologically Influenced Corrosion: Perspectives and Approaches	p. 1072
Scale-Up of Processes for Bioremediation	p. 1084
Author Index	p. 1095
Subject Index	p. 1097
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