Preface |
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xv | |
The Authors |
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xvii | |
Contributing Authors |
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xix | |
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Introduction to Environmental Microbiology |
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1 | (1) |
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An Historical Perspective |
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1 | (3) |
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Modern Environmental Microbiology |
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4 | (1) |
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Purpose and Organization of This Text |
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5 | (2) |
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Microorganisms in the Environment |
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7 | (12) |
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Historical Outbreaks and Discovery |
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8 | (1) |
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Indigenous Virus Populations in the Environment |
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9 | (1) |
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Distinguishing Characteristics of Viruses and Their Evolution |
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10 | (2) |
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Structure and Classification |
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12 | (2) |
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Infective Nature of Viruses |
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14 | (2) |
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The Metabolic State of Viruses |
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16 | (1) |
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Methods of Virus Infection and Replication |
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16 | (3) |
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19 | (12) |
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19 | (1) |
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Size and Shape of Bacteria |
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19 | (1) |
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20 | (1) |
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Structure of the Bacterial Cell |
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21 | (4) |
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Plasmid-Chromosome Relationships |
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25 | (2) |
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27 | (4) |
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31 | (3) |
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31 | (1) |
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Taxonomic Diversity of Fungi |
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31 | (1) |
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32 | (1) |
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Structure of the Fungal Cell |
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32 | (2) |
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34 | (1) |
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34 | (1) |
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34 | (9) |
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35 | (1) |
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36 | (1) |
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36 | (1) |
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37 | (2) |
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39 | (1) |
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40 | (1) |
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References and Recommended Readings |
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40 | (3) |
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Growth in Pure Culture in a Flask |
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43 | (8) |
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44 | (1) |
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44 | (4) |
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48 | (1) |
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48 | (1) |
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Effect of Substrate Concentration on Growth |
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49 | (2) |
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51 | (1) |
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Growth under Aerobic Conditions |
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52 | (3) |
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Growth under Anaerobic Conditions |
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55 | (1) |
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Growth in the Environment |
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56 | (5) |
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56 | (2) |
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58 | (1) |
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The Stationary and Death Phases |
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58 | (1) |
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59 | (1) |
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References and Recommended Readings |
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59 | (2) |
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61 | (1) |
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61 | (9) |
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62 | (4) |
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66 | (2) |
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68 | (2) |
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70 | (1) |
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Soil and Subsurface Environments |
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70 | (4) |
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71 | (2) |
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73 | (1) |
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74 | (1) |
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General Characteristics of Microorganisms in Porous Media |
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74 | (3) |
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Distribution of Microorganisms in Porous Media |
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75 | (1) |
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Metabolic States of Bacteria in Porous Media |
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76 | (1) |
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Microbial Activities in Porous Media |
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77 | (2) |
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Role of Microorganisms in Surface Soil Formation |
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77 | (1) |
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Role of Microorganisms in Nutrient Cycling |
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78 | (1) |
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Role of Microorganisms in Pollution Abatement via Bioremediation |
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78 | (1) |
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Role of Microorganisms in Municipal Waste Disposal |
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79 | (1) |
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Microorganisms in Surface Soils |
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79 | (4) |
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79 | (1) |
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80 | (1) |
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81 | (1) |
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82 | (1) |
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Microorganisms in Shallow Subsurface Environments |
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83 | (2) |
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Microorganisms in Deep Subsurface Environments |
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85 | (6) |
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Microorganisms in the Deep Vadose Zone |
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86 | (1) |
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Microorganisms in the Deep Saturated Zone |
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86 | (2) |
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88 | (1) |
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References and Recommended Readings |
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89 | (2) |
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91 | (1) |
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Important Airborne Pathogens |
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91 | (2) |
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Important Airborne Toxins |
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93 | (1) |
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93 | (1) |
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94 | (1) |
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Aeromicrobiological Pathway |
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95 | (5) |
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95 | (1) |
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96 | (2) |
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98 | (2) |
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100 | (3) |
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101 | (1) |
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102 | (1) |
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102 | (1) |
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Sampling Devices for the Collection of Bioaerosols |
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103 | (2) |
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103 | (1) |
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104 | (1) |
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104 | (1) |
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Filtration and Deposition |
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105 | (1) |
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Microbial Survival in the Air |
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105 | (2) |
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106 | (1) |
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106 | (1) |
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106 | (1) |
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107 | (1) |
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Extramural Aeromicrobiology |
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107 | (4) |
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107 | (2) |
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109 | (1) |
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109 | (2) |
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Intramural Aeromicrobiology |
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111 | (2) |
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111 | (1) |
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112 | (1) |
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113 | (1) |
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Hospitals and Laboratories |
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113 | (1) |
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113 | (2) |
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113 | (1) |
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114 | (1) |
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114 | (1) |
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114 | (1) |
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Biosafety in the Laboratory |
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115 | (5) |
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Biological Safety Cabinets |
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115 | (3) |
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118 | (1) |
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Biological Agent Classification |
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119 | (1) |
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120 | (3) |
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120 | (1) |
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References and Recommended Readings |
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121 | (2) |
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Aquatic and Extreme Environments |
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123 | (1) |
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Microbial Habitats in the Aquatic Environment |
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123 | (7) |
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123 | (2) |
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125 | (1) |
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126 | (2) |
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128 | (2) |
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130 | (10) |
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130 | (6) |
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136 | (1) |
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137 | (3) |
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140 | (1) |
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Environmental Determinants That Gover Extreme Environments |
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140 | (3) |
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140 | (1) |
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141 | (1) |
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141 | (1) |
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142 | (1) |
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142 | (1) |
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142 | (1) |
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Aquatic Microbes in the News |
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143 | (4) |
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143 | (1) |
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Aquatic Microbes: Food for the Future |
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143 | (2) |
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145 | (1) |
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References and Recommended Readings |
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145 | (2) |
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147 | (1) |
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Factors Affecting Microbial Transport |
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148 | (14) |
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148 | (1) |
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149 | (2) |
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Microbial Adhesion---The Influence of Cell Surface Properties |
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151 | (4) |
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Impact of pH on Microbial Transport |
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155 | (1) |
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Impact of Ionic Strength on Transport |
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156 | (1) |
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157 | (1) |
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158 | (1) |
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158 | (3) |
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Persistence and Activity of Introduced Microbes |
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161 | (1) |
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Factors Affecting Transport of DNA |
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162 | (1) |
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Novel Approaches to Facilitate Microbial Transport |
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163 | (3) |
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163 | (1) |
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163 | (1) |
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164 | (2) |
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166 | (1) |
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Methodology for Studying Transport |
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166 | (6) |
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166 | (2) |
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168 | (1) |
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169 | (2) |
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171 | (1) |
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Models for Microbial Transport |
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172 | (5) |
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Advection-Dispersion Models |
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173 | (1) |
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173 | (1) |
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173 | (1) |
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References and Recommended Readings |
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174 | (3) |
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Environmental Sample Collection and Processing |
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177 | (9) |
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Sampling Strategies and Methods for Surface Soils |
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177 | (2) |
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Sampling Strategies and Methods for the Subsurface |
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179 | (2) |
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Sample Processing and Storage |
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181 | (5) |
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186 | (4) |
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Sampling Strategies and Methods for Water |
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186 | (1) |
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Processing of Water Samples for Virus Analysis |
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186 | (2) |
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Processing Water Samples for Detection of Bacteria |
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188 | (1) |
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Processing Water Samples for Detection of Protozoan Parasites |
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189 | (1) |
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Detection of Microorganisms on Fomites |
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190 | (5) |
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194 | (1) |
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References and Recommended Readings |
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194 | (1) |
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195 | (1) |
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195 | (2) |
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Basic Microscopic Techniques |
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197 | (3) |
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197 | (2) |
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Preparation of Samples for Microscopic Observation |
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199 | (1) |
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200 | (1) |
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In Situ Detection with Molecular Probes and Epifluoresence Microscopy |
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201 | (1) |
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202 | (2) |
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Estimation of Biomass Using Microscopic Counts |
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204 | (1) |
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Advanced Microscopic Techniques |
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204 | (9) |
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204 | (1) |
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205 | (4) |
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Confocal Scanning Microscopy |
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209 | (1) |
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209 | (1) |
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210 | (1) |
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211 | (1) |
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References and Recommended Readings |
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211 | (2) |
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Cultural Methods for Enumeration of Bacteria |
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213 | (5) |
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Enumeration and Isolation Techniques |
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213 | (1) |
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214 | (3) |
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Most Probable Number Technique |
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217 | (1) |
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Cultural Media for Bacteria |
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218 | (6) |
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General Media Used for Culturing Bacteria |
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218 | (6) |
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Cultural Methods for Fungi |
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224 | (1) |
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Cultural Methods for Algae and Cyanobacteria |
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225 | (2) |
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Cell Culture-Based Detection Methods for Viruses |
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227 | (8) |
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232 | (1) |
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References and Recommended Readings |
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232 | (3) |
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235 | (1) |
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Measuring Microbial Activity in Pure Culture |
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236 | (7) |
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236 | (3) |
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Terminal Electron Acceptors |
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239 | (3) |
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242 | (1) |
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242 | (1) |
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Choosing the Appropriate Activity Measurement for Environmental Samples |
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243 | (1) |
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243 | (14) |
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Measurement of Respiration Gases, CO2 and O2, in Laboratory and Field Studies |
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245 | (3) |
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The Application of Respiration Measurements in Environmental Microbiology |
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248 | (6) |
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Tracer Studies to Determine Heterotrophic Potential |
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254 | (2) |
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Anaerobic Respiration as an Indicator of Microbial Activity |
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256 | (1) |
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Incorporation of Radiolabeled Tracers into Cellular Macromolecules |
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257 | (1) |
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Incorporation of Thymidine into DNA |
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257 | (1) |
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Incorporation of Leucine into Protein |
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258 | (1) |
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258 | (1) |
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259 | (8) |
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261 | (2) |
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263 | (1) |
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263 | (1) |
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References and Recommended Readings |
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263 | (4) |
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267 | (1) |
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267 | (6) |
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268 | (1) |
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269 | (1) |
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269 | (1) |
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Polyclonal and Monoclonal Antibodies |
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270 | (2) |
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272 | (1) |
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273 | (14) |
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Fluorescent Immunolabeling |
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274 | (2) |
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Enzyme-Linked Immunosorbent Assays |
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276 | (1) |
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277 | (1) |
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Immunomagnetic Separation Assays |
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278 | (1) |
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Western Immunoblotting Assays |
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279 | (1) |
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Immunoaffinity Chromatography Assays |
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280 | (2) |
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Immunocytochemical Assays |
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282 | (1) |
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Immunoprecipitation Assays |
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282 | (2) |
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284 | (1) |
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References and Recommended Readings |
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284 | (3) |
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Nucleic Acid-Based Methods of Analysis |
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Structure and Complementarity of Nucleic Acids |
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287 | (2) |
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Obtaining Microbial Nucleic Acids from the Environment |
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289 | (1) |
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Extracting Community Bacterial DNA from Soil Samples |
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289 | (1) |
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Nucleic Acid-Based Methods |
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290 | (29) |
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290 | (4) |
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Polymerase Chain Reaction |
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294 | (10) |
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Recombinant DNA Techniques |
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304 | (3) |
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Restriction Fragment Length Polymorphism Analysis |
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307 | (3) |
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Denaturing/Temperature Gradient Gel Electrophoresis |
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310 | (1) |
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311 | (1) |
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312 | (3) |
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315 | (1) |
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References and Recommended Readings |
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316 | (3) |
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319 | (2) |
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319 | (1) |
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319 | (2) |
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321 | (10) |
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321 | (1) |
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Carbon Fixation and Energy Flow |
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322 | (1) |
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322 | (9) |
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331 | (9) |
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332 | (1) |
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332 | (1) |
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Ammonium Assimilation (Immobilization) and Ammonification (Mineralization) |
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333 | (2) |
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335 | (1) |
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336 | (4) |
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340 | (7) |
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340 | (1) |
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Assimilatory Sulfate Reduction and Sulfur Mineralization |
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341 | (1) |
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342 | (2) |
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344 | (1) |
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345 | (1) |
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References and Recommended Readings |
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345 | (2) |
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Consequences of Biogeochemical Cycles Gone Wild |
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347 | (1) |
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Microbially Influenced Corrosion |
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347 | (3) |
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347 | (2) |
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349 | (1) |
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Acid Mine Drainage and Metal Recovery |
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350 | (2) |
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350 | (1) |
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Metal Recovery and Desulfurization of Coal |
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351 | (1) |
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Biomethylation of Metals and Metalloids |
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352 | (2) |
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Nitrous Oxide and Earth's Atmosphere |
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354 | (2) |
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Nitrate Contamination of Groundwater |
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356 | (2) |
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Biogenesis of Halomethanes and Other Organohalogens |
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358 | (1) |
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358 | (5) |
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360 | (1) |
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References and Recommended Readings |
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360 | (3) |
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Microorganisms and Organic Pollutants |
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363 | (1) |
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364 | (1) |
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The Overall Process of Biodegradation |
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365 | (3) |
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Relationship between Contaminant Structure, Toxicity, and Biodegradability |
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368 | (7) |
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370 | (1) |
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370 | (2) |
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372 | (1) |
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373 | (2) |
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Environmental Factors Affecting Biodegradation |
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375 | (2) |
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375 | (1) |
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375 | (1) |
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376 | (1) |
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Other Environmental Factors |
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376 | (1) |
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Biodegradation of Organic Pollutants |
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377 | (17) |
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Pollutant Sources and Types |
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377 | (1) |
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377 | (12) |
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389 | (5) |
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394 | (9) |
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Addition of Oxygen or Other Gases |
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396 | (1) |
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396 | (3) |
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Stimulation of Anaerobic Degradation Using Alternative Electron Acceptors |
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399 | (1) |
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399 | (1) |
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Addition of Microorganisms or DNA |
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399 | (1) |
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400 | (1) |
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References and Recommended Readings |
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400 | (3) |
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Microorganisms and Metal Pollutants |
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403 | (1) |
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404 | (1) |
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405 | (1) |
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Metal Bioavailability in the Environment |
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406 | (2) |
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407 | (1) |
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407 | (1) |
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408 | (1) |
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408 | (1) |
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Metal Toxicity Effects on the Microbial Cell |
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408 | (1) |
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Mechanisms of Microbial Metal Resistance and Detoxification |
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408 | (5) |
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General Mechanisms of Metal Resistance |
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410 | (1) |
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Metal-Dependent Mechanisms of Resistance |
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411 | (2) |
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Methods for Studying Metal-Microbial Interactions |
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413 | (2) |
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Adverse Effects of Microbial Metal Transformations |
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415 | (1) |
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The Benefits of Metal-Microbial Interactions |
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416 | (2) |
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Physical/Chemical Methods of Metal Remediation |
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418 | (1) |
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Innovative Microbial Approaches in the Remediation of Metal-Contaminated Soils and Sediments |
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418 | (3) |
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Innovative Microbial Approaches in the Remediation of Metal-Contaminated Aquatic Systems |
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421 | (4) |
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422 | (1) |
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References and Recommended Readings |
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423 | (2) |
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Beneficial and Pathogenic Microbes in Agriculture |
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425 | (4) |
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The Soil-Plant-Microorganism System |
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425 | (1) |
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The Rhizosphere Environment |
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425 | (1) |
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Organic Compounds Released by Plants |
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426 | (3) |
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429 | (1) |
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Beneficial Root-Microbial Interactions |
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429 | (10) |
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Biological Dinitrogen Fixation |
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430 | (2) |
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Free-Living Dinitrogen Fixation |
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432 | (1) |
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Associative Dinitrogen Fixation |
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432 | (1) |
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The Legume-Rhizobia Symbioses |
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433 | (5) |
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438 | (1) |
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Pathogenic Microbes in Agriculture |
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439 | (8) |
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Plant Disease Caused by Fungi |
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440 | (1) |
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Diseases Caused by Bacteria |
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440 | (2) |
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Plant Diseases Caused by Viruses |
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442 | (1) |
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Soil Biological Control of Plant Diseases |
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443 | (2) |
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445 | (1) |
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References and Recommended Readings |
|
|
445 | (2) |
|
Environmentally Transmitted Pathogens |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Environmental Transmitted Pathogens |
|
|
447 | (2) |
|
|
449 | (10) |
|
|
449 | (1) |
|
Escherichia coli and Shigella |
|
|
450 | (1) |
|
|
451 | (1) |
|
|
452 | (1) |
|
|
452 | (1) |
|
|
453 | (1) |
|
|
453 | (2) |
|
Opportunistic Bacterial Pathogens |
|
|
455 | (2) |
|
|
457 | (2) |
|
|
459 | (13) |
|
|
460 | (4) |
|
|
464 | (2) |
|
Cestodes (Taenia saginata) |
|
|
466 | (1) |
|
Trematodes (Schistosoma mansoni) |
|
|
467 | (2) |
|
|
469 | (3) |
|
|
472 | (19) |
|
|
472 | (9) |
|
|
481 | (3) |
|
|
484 | (1) |
|
References and Recommended Readings |
|
|
485 | (6) |
|
|
|
|
|
|
|
The Concept of Indicator Organisms |
|
|
491 | (1) |
|
|
491 | (5) |
|
The Most Probable Number (MPN) Test |
|
|
493 | (1) |
|
The Membrane Filter (MF) Test |
|
|
493 | (1) |
|
The Presence-Absence (P-A) Test |
|
|
493 | (3) |
|
|
496 | (1) |
|
|
496 | (1) |
|
|
497 | (1) |
|
Heterotrophic Plate Count |
|
|
497 | (2) |
|
|
499 | (1) |
|
Other Indicator Organisms |
|
|
500 | (1) |
|
Standards and Criteria for Indicators |
|
|
500 | (5) |
|
|
502 | (1) |
|
References and Recommended Readings |
|
|
503 | (2) |
|
Domestic Wastes and Waste Treatment |
|
|
|
|
|
|
|
|
505 | (3) |
|
Modern Wastewater Treatment |
|
|
508 | (12) |
|
|
508 | (1) |
|
|
508 | (4) |
|
|
512 | (1) |
|
Removal of Pathogens by Sewage Treatment Processes |
|
|
512 | (3) |
|
|
515 | (1) |
|
Pathogen Occurrence and Fate in Biosolids |
|
|
516 | (2) |
|
An Example of a Modern Sewage Treatment Plant |
|
|
518 | (2) |
|
|
520 | (1) |
|
|
521 | (1) |
|
Land Application of Wastewater |
|
|
522 | (2) |
|
Wetlands and Aquaculture Systems |
|
|
524 | (4) |
|
|
528 | (7) |
|
|
528 | (1) |
|
Modern Sanitary Landfills |
|
|
528 | (2) |
|
Composting of Biosolids and Domestic Solid Waste |
|
|
530 | (2) |
|
|
532 | (1) |
|
References and Recommended Readings |
|
|
533 | (2) |
|
Drinking Water Treatment and Distribution |
|
|
|
|
|
|
|
Water Treatment Processes |
|
|
535 | (3) |
|
Water Distribution Systems |
|
|
538 | (1) |
|
Assimilable Organic Carbon |
|
|
539 | (4) |
|
|
541 | (1) |
|
References and Recommended Readings |
|
|
541 | (2) |
|
|
|
|
|
|
|
|
543 | (1) |
|
|
544 | (2) |
|
Factors Affecting Disinfectants |
|
|
546 | (1) |
|
|
547 | (3) |
|
|
547 | (1) |
|
|
548 | (1) |
|
|
549 | (1) |
|
|
550 | (1) |
|
|
550 | (1) |
|
|
551 | (1) |
|
|
552 | (2) |
|
Photodynamic Inactivation |
|
|
554 | (1) |
|
Gamma and High-Energy Irradiation |
|
|
554 | (3) |
|
|
555 | (1) |
|
References and Recommended Readings |
|
|
555 | (2) |
|
|
|
|
|
|
|
The Concept of Risk Assessment |
|
|
557 | (1) |
|
Elements of Risk Assessment |
|
|
557 | (3) |
|
The Process of Risk Assessment |
|
|
560 | (4) |
|
|
560 | (1) |
|
|
560 | (2) |
|
|
562 | (1) |
|
|
563 | (1) |
|
Microbial Risk Assessment |
|
|
564 | (6) |
|
|
570 | (1) |
|
References and Recommended Readings |
|
|
570 | |