Preface |
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xv | |
1 Introduction to Microorganisms and Their Activities |
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1 | (32) |
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1.1 Central Themes of Environmental Microbiology and Microbial Ecology |
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1 | (1) |
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1.2 Are the Terms Prokaryotes or Eukaryotes Relevant? |
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1 | (3) |
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1.2.1 Intracellular Membranes in Prokaryotes |
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2 | (1) |
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1.2.2 Compartmentalized Heterotrophic Bacterial Cells |
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3 | (1) |
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1.2.3 The Universal Tree of Life: Rooted or Unrooted |
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4 | (1) |
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1.2.4 What About the Giant Viruses? |
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4 | (1) |
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1.3 Major Approach to Study Microorganisms |
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4 | (3) |
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1.3.1 Application of Genomics, Metagenomics, and Proteomics |
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6 | (1) |
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1.3.2 Biochemical and Physiological Analysis |
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7 | (1) |
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1.4 The Impact of Horizontal Gene Transfer Between Microorganisms |
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7 | (5) |
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9 | (1) |
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1.4.2 Risks from Genetically Modified Organisms |
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10 | (1) |
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1.4.3 Microbial Viruses and Gene Transfer Agents |
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10 | (2) |
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1.5 What Determines Which Microorganisms are Present? |
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12 | (7) |
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1.5.1 Metabolism as a Basis of Selection |
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13 | (1) |
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1.5.2 Is Persistence of Microorganisms Dependent Only on Spore Production? |
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14 | (5) |
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1.6 Is the Size and Shape of a Prokaryotic Cell Important? |
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19 | (4) |
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19 | (2) |
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1.6.2 Ultramicroscopic Bacteria |
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21 | (1) |
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1.6.3 Very Large Bacteria |
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21 | (1) |
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1.6.4 Influence of Diffusion on Bacterial Cell Form |
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22 | (1) |
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1.6.5 Features of a Specific Cell Form |
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22 | (1) |
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22 | (1) |
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22 | (1) |
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1.6.5.3 Curved Rod or Spirochete Form |
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23 | (1) |
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23 | (1) |
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23 | (2) |
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23 | (1) |
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1.7.2 Bacteria as Trackers and Predators |
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24 | (1) |
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25 | (1) |
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25 | (1) |
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26 | (5) |
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31 | (2) |
2 Microbes in the Biosphere: Examination, Cultivation, and Communities |
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33 | (44) |
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33 | (1) |
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2.2 Microscopy to Study Environmental Microbes |
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33 | (8) |
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2.2.1 Light Supported Microscopy |
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34 | (1) |
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2.2.2 Fluorescence Microscopy |
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35 | (2) |
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2.2.3 Scanning Confocal Laser Microscopy |
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37 | (1) |
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2.2.4 High Resolution by Electron Microscopy |
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37 | (4) |
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2.3 Internal Structures in Prokaryotes |
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41 | (3) |
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41 | (1) |
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41 | (1) |
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2.3.3 Polymeric Carbon Reserves |
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42 | (1) |
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2.3.4 Polyphosphate Granules |
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43 | (1) |
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2.3.5 Metallic Nanoparticles |
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43 | (1) |
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2.4 Strategies for Culturing Microorganisms |
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44 | (5) |
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44 | (1) |
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2.4.2 Approaches for Isolation of Microorganisms |
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45 | (1) |
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2.4.3 Establishing Microbial Communities |
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45 | (1) |
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2.4.4 The iChip and Growing Uncultured Bacteria |
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46 | (3) |
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49 | (7) |
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2.5.1 Characterization of Microorganisms Using Genomics and Metagenomics |
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49 | (4) |
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2.5.2 Physiological Analysis Using Metatranscriptomics and Metaproteomics |
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53 | (1) |
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2.5.3 Lipid Biomarker Profiles |
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54 | (2) |
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2.6 Examining Bacteria that Do Not Grow as Pure Cultures in the Laboratory |
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56 | (3) |
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2.6.1 Host-dependent Microorganisms |
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56 | (2) |
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2.6.1.1 Bacteria as Obligate Pathogens |
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56 | (1) |
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2.6.1.2 Bacteria as Endosymbionts |
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57 | (1) |
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2.6.1.3 The Nanoarchaeum-Ignicoccus Relationship |
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58 | (1) |
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2.6.2 Molecular Analysis of Uncultivable Bacteria |
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58 | (1) |
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2.7 Microbial Community Structures |
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59 | (8) |
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2.7.1 Primary Production and Microbial Communities |
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59 | (3) |
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62 | (2) |
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2.7.3 Role of Quorum Sensing |
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64 | (3) |
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67 | (1) |
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68 | (1) |
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68 | (7) |
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75 | (2) |
3 Terrestrial Systems: Soil and Subsurface Environments |
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77 | (40) |
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77 | (1) |
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3.2 Soil: An Environment for Microorganisms |
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77 | (3) |
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78 | (1) |
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3.2.2 Soil Organic Matter (SOM) |
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78 | (2) |
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80 | (5) |
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80 | (2) |
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82 | (1) |
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83 | (1) |
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3.3.4 Soil Invertebrates and Burrowing Animals |
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83 | (1) |
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3.3.5 The Rhizosphere and Associated Bacteria |
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83 | (2) |
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3.4 Understanding Soil Ecosystems |
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85 | (5) |
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3.4.1 The Carbon: Nitrogen Ratio |
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85 | (1) |
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3.4.2 The Fungi: Bacteria Ratio |
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85 | (1) |
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3.4.3 SOM and Soil Food Webs |
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86 | (3) |
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3.4.4 Influence of Agricultural Management on the Soil Microbe Community |
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89 | (1) |
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3.4.5 Impact of Viruses on the Soil Microbiota |
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90 | (1) |
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3.5 Subsurface Microbiology |
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90 | (5) |
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90 | (2) |
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92 | (1) |
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3.5.3 Deep Subsurface Aquifers |
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92 | (3) |
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3.5.3.1 Aquifer in a Coal-bearing Basin |
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92 | (1) |
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3.5.3.2 Deep Granitic Aquifer |
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93 | (1) |
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3.5.3.3 Anaerobic, Alkaline Aquifer |
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94 | (1) |
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3.5.3.4 Saline Hydrothermal Aquifer |
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94 | (1) |
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3.6 Deep Subsurface Microbiology |
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95 | (8) |
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3.6.1 Marine Sediment Microbiology |
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96 | (1) |
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3.6.2 Deep Mines and Boreholes |
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97 | (1) |
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98 | (1) |
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3.6.4 Deep Subsurface Storage Sites |
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98 | (4) |
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3.6.4.1 Storage of Nuclear Fuel Waste |
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98 | (2) |
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3.6.4.2 Underground Storage for H2 and CH4 |
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100 | (1) |
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3.6.4.3 Underground Storage for CO2 |
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101 | (1) |
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3.6.4.4 Geothermal Energy Production |
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102 | (1) |
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3.6.5 Endolithic Microorganisms |
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102 | (1) |
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3.7 Life in Deep Subsurfaces |
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103 | (3) |
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3.7.1 Adjusting to a Subsurface Diet |
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103 | (1) |
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3.7.2 Energy Sources in the Deep Biosphere |
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103 | (2) |
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3.7.3 The Benefit of Living Together |
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105 | (1) |
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106 | (4) |
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3.8.1 Rock and Mineral Weathering |
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106 | (1) |
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3.8.2 Mineral Transformations |
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107 | (2) |
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3.8.3 Microbial Metal Binding |
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109 | (1) |
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3.8.4 Microbiota of Subsurface Crystals |
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109 | (1) |
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110 | (1) |
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111 | (1) |
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111 | (5) |
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116 | (1) |
4 Aquatic Surface Environments: Freshwater, Marine, and Wastewater |
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117 | (50) |
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117 | (1) |
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4.2 Water as Relevant to Microbial Growth |
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117 | (2) |
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118 | (1) |
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4.3 Marine Environments and Associated Microbiomes |
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119 | (12) |
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4.3.1 Marine Primary Productivity |
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120 | (2) |
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4.3.2 Marine Heterotrophs |
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122 | (1) |
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4.3.3 Bacterial Symbionts and Marine Hosts |
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123 | (2) |
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4.3.4 Microbial EPSs, Marine Snow, and Marine Gel Particles |
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125 | (2) |
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4.3.5 Brackish Water and Intertidal Zones |
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127 | (1) |
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128 | (3) |
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4.4 Freshwater Environments and Associated Microbiomes |
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131 | (13) |
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132 | (5) |
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137 | (2) |
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4.4.3 The Snow and Glacier Ice Ecosystems |
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139 | (1) |
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4.4.4 Microbiota of Cold and Hot Springs |
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140 | (2) |
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142 | (2) |
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4.5 Maintaining Populations in Low Nutrient Environments |
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144 | (4) |
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4.6 Aquaculture Wastewater |
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148 | (1) |
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4.7 Hormone Degradation in Fresh Water |
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149 | (1) |
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4.8 Human Activities and Influence on Microbial Ecology |
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150 | (1) |
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151 | (1) |
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4.10 Municipal Water Treatment |
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151 | (1) |
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4.11 Wastewater Treatment Systems |
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152 | (2) |
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152 | (1) |
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4.11.2 Municipal Wastewater Treatment |
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152 | (21) |
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4.11.2.1 Primary Treatment |
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153 | (1) |
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4.11.2.2 Secondary Treatment |
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153 | (1) |
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4.12 Alternative Approaches for Wastewater Treatment |
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154 | (1) |
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4.13 Coliforms and Other Indicator Organisms |
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155 | (1) |
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4.14 Viruses in Aquatic Environments: Diversity and Activity |
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156 | (2) |
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158 | (1) |
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159 | (1) |
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159 | (7) |
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166 | (1) |
5 Life in Extreme Environments |
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167 | (44) |
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167 | (1) |
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5.2 Sampling in Extreme Environments |
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168 | (5) |
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5.3 Extreme Temperature Environments |
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173 | (7) |
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174 | (2) |
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176 | (19) |
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5.3.2.1 Alpine Environment - Yellowstone National Park |
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176 | (3) |
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5.3.2.2 Hydrothermal Vent Communities |
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179 | (1) |
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5.3.2.3 The Guaymas Basin |
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180 | (1) |
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180 | (2) |
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182 | (1) |
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183 | (4) |
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187 | (2) |
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5.8 Halophiles and Chaophiles |
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189 | (5) |
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5.9 Radioresistant Microorganisms |
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194 | (1) |
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5.10 Membrane Adaptations to Extreme Conditions |
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195 | (2) |
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195 | (1) |
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196 | (1) |
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5.10.3 pH Extremes: Low and High |
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196 | (1) |
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197 | (1) |
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5.12 Nutrient Limited 'Environments |
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198 | (2) |
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200 | (2) |
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202 | (1) |
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202 | (1) |
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202 | (7) |
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209 | (2) |
6 Mutualism: Microorganisms and Terrestrial Plants |
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211 | (38) |
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211 | (1) |
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6.2 Cyanobacteria and the Chloroplast Ancestor |
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211 | (6) |
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6.3 Lichens: Cyanobacteria/Algae-Fungi Mutualism |
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217 | (3) |
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6.3.1 Distribution and Organization |
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217 | (2) |
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6.3.2 Natural Products of Lichens |
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219 | (1) |
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6.4 Mutualisms with Cyanobacteria as Intracellular or Epiphytic Organisms |
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220 | (4) |
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220 | (1) |
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221 | (1) |
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221 | (1) |
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222 | (1) |
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222 | (1) |
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222 | (2) |
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224 | (1) |
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6.5 Rhizobia-Legume Symbiosis |
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224 | (7) |
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6.5.1 Bacterial Species Involved |
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224 | (1) |
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6.5.2 Rhizospheric Rhizobia |
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225 | (1) |
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6.5.3 The Root Nodulation Process |
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226 | (4) |
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6.5.4 Nodules on Plant Stems |
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230 | (1) |
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6.6 Frankia and the Non-legume Nitrogen-fixing Nodule |
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231 | (2) |
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233 | (4) |
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6.7.1 Arbuscular Mycorrhizae (AM) |
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235 | (1) |
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6.7.2 Ectomycorrhiza (EcM) |
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236 | (1) |
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6.8 Patterns of Regulation for Plant-Microbe Mutualism |
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237 | (1) |
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6.9 Bacterial-Fungal Interactions |
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238 | (2) |
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238 | (1) |
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6.9.2 Plant Growth-promoting Bacteria |
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239 | (1) |
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6.9.3 Systemic Induction of Plant Immunity |
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239 | (1) |
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6.10 Endophytic Microorganisms |
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240 | (1) |
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6.11 Microbiology of the Phyllosphere |
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241 | (1) |
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242 | (1) |
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243 | (1) |
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243 | (4) |
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247 | (2) |
7 Mutualism: Microorganisms and Animals |
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249 | (48) |
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249 | (1) |
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7.2 Building a Microbial Community - The Role of the Host |
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249 | (2) |
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7.2.1 Microbiology and Innate Immunity |
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249 | (1) |
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7.2.2 Microbiology and Adaptive Immunity |
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250 | (1) |
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7.3 Host Models to Study Parasite Relationships |
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251 | (1) |
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251 | (1) |
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7.3.2 Caenorhabditis elegans |
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251 | (1) |
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7.3.3 Drosophila melanogaster |
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252 | (1) |
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7.3.4 Galleria mellonella |
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252 | (1) |
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7.4 Digestive Tract Environment |
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252 | (8) |
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253 | (1) |
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254 | (1) |
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255 | (5) |
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7.4.3.1 Bacteria and Archaea |
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257 | (1) |
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7.4.3.2 Anaerobic Protozoa |
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257 | (1) |
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258 | (2) |
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7.4.3.4 Probiotics and Methane Mitigation Strategies |
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260 | (1) |
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260 | (9) |
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260 | (1) |
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7.5.2 Oral Microorganisms |
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261 | (2) |
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7.5.3 Intestinal Microbiome |
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263 | (6) |
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7.5.3.1 Establishment of Intestinal Flora |
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263 | (1) |
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264 | (1) |
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7.5.3.3 Influence of the Intestine on Human Health |
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265 | (1) |
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7.5.3.4 Obesity, Diabetes, and Health Issues |
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266 | (3) |
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269 | (1) |
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7.6 Gut Microbiota across the Animal World |
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269 | (10) |
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7.6.1 Systems of Maternal Transmission |
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270 | (1) |
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7.6.2 Microbiota of Ruminates and Hindgut Fermenters |
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270 | (5) |
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7.6.3 Gut Microbiota of Bears |
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275 | (1) |
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7.6.4 Microbiota of Birds |
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275 | (3) |
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7.6.5 Intestinal Bacteria of Fish |
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278 | (1) |
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7.7 Insect-Fungus Symbiosis |
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279 | (3) |
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7.7.1 Scale Insects and Septobasidium |
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279 | (1) |
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7.7.2 Attine Ant-Fungus Symbiosis |
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279 | (1) |
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7.7.3 Woodwasp-Fungus Symbiosis |
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280 | (1) |
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7.7.4 Ambrosia Beetles-Fungus |
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281 | (1) |
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281 | (1) |
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7.8 Mutualisms Involving Insects and Bacteria |
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282 | (3) |
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7.8.1 Aphids-Buchnera and Endosymbionts |
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282 | (1) |
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283 | (1) |
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283 | (1) |
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7.8.4 Termite Gut-Bacteria |
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284 | (1) |
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7.9 Mutualisms Involving Invertebrates |
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285 | (3) |
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7.9.1 Microbiome of Marine Worms |
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285 | (1) |
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7.9.2 Squid (Euprymna)-Vibrio fischeri Symbiosis |
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286 | (1) |
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7.9.3 Medicinal Leech-Aeromonas sp. and Rikenella-like Bacteria |
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287 | (1) |
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288 | (1) |
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288 | (1) |
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289 | (1) |
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290 | (5) |
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295 | (2) |
8 Microbes Driving the Nutrient Cycles |
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297 | (44) |
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297 | (1) |
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8.2 Nutrient Cycles and What Drives Them |
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297 | (2) |
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8.3 The Aerobic Environment |
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299 | (5) |
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8.3.1 The "Great Oxidation Event" |
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299 | (1) |
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300 | (3) |
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8.3.3 Hydrogen Peroxide and ROS |
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303 | (1) |
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8.4 Carbon - A Renewable Resource |
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304 | (8) |
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8.4.1 Carbon Dioxide Fixation and Carbonate Reduction |
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305 | (1) |
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8.4.2 Methanogenesis, Methanotrophy, and Methylotrophy |
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306 | (2) |
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8.4.3 Mineralization of Carbon Compounds |
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308 | (3) |
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8.4.4 Production and Utilization of CO |
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311 | (1) |
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8.4.5 Production and Utilization of Hydrogen Cyanide |
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312 | (1) |
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8.5 Nitrogen for Biosynthesis and Energy |
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312 | (7) |
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314 | (1) |
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314 | (1) |
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315 | (1) |
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316 | (1) |
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8.5.5 Metabolism of NO and N2O |
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316 | (1) |
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8.5.6 Production of NO by NOS |
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317 | (1) |
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8.5.7 Respiratory Ammonification |
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317 | (1) |
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318 | (1) |
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8.5.9 Assimilation of Nitrogen |
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318 | (1) |
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8.5.10 Dinitrogen Fixation |
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318 | (1) |
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319 | (5) |
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8.6.1 Oxidation of Hydrogen Sulfide |
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320 | (1) |
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8.6.2 Oxidation of Elemental Sulfur |
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321 | (1) |
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8.6.3 Dissimilative S° Reduction |
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321 | (1) |
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8.6.4 Dissimilative Sulfate Reduction |
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322 | (1) |
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8.6.5 Assimilatory Sulfate Reduction |
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322 | (1) |
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8.6.6 Production of H2S and Dimethyl Sulfide |
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322 | (2) |
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322 | (1) |
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323 | (1) |
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8.7 Cycling of Trace Elements |
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324 | (4) |
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324 | (2) |
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326 | (2) |
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328 | (2) |
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330 | (1) |
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8.10 Cycling Toxic Elements |
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331 | (4) |
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331 | (1) |
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332 | (3) |
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335 | (1) |
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335 | (1) |
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336 | (4) |
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340 | (1) |
9 Bioremediation Using Microorganisms |
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341 | (30) |
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341 | (1) |
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9.2 Microbial Bioremediation: Strategies and Applications |
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341 | (6) |
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343 | (1) |
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344 | (1) |
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9.2.2.1 Indigenous Bacteria |
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344 | (1) |
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9.2.2.2 Genetically Modified Organisms |
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344 | (1) |
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9.2.3 Intrinsic Bioremediation |
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345 | (1) |
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9.2.4 Microbial Consortium |
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345 | (1) |
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346 | (1) |
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9.3 Organic Compounds and Xenobiotics Degraded |
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347 | (15) |
|
|
347 | (1) |
|
9.3.2 Chlorinated Organic Compounds |
|
|
348 | (4) |
|
|
349 | (1) |
|
|
350 | (1) |
|
9.3.2.3 Polychlorinated Biphenyl Compounds |
|
|
351 | (1) |
|
9.3.3 Population Dynamics in Degradation of Hydrocarbons |
|
|
352 | (5) |
|
|
352 | (1) |
|
9.3.3.2 Fuel Hydrocarbons |
|
|
353 | (2) |
|
9.3.3.3 Polyaromatic Hydrocarbons |
|
|
355 | (2) |
|
|
357 | (1) |
|
|
357 | (2) |
|
|
357 | (2) |
|
|
359 | (1) |
|
|
359 | (1) |
|
9.3.5 Bioremediation and Detoxification of Metal(loid)s |
|
|
359 | (3) |
|
9.3.5.1 Dissimilatory Metal(loid) Reduction |
|
|
360 | (1) |
|
9.3.5.2 Methylation Reactions |
|
|
361 | (1) |
|
9.4 Design of Systems for Bioremediation |
|
|
362 | (2) |
|
|
362 | (1) |
|
|
363 | (1) |
|
|
363 | (1) |
|
9.4.4 Permeable Reactive Barriers |
|
|
363 | (1) |
|
9.4.5 Groundwater and Lagoon Treatment |
|
|
363 | (1) |
|
|
364 | (1) |
|
|
364 | (1) |
|
|
364 | (1) |
|
|
365 | (5) |
|
|
370 | (1) |
10 Biocorrosion and Geomicrobiology |
|
371 | (28) |
|
|
371 | (1) |
|
10.2 Microbially Influenced Corrosion (MIC) of Ferrous Metals |
|
|
371 | (5) |
|
10.2.1 Current Theories of Biocorrosion |
|
|
371 | (4) |
|
|
373 | (1) |
|
|
374 | (1) |
|
10.2.1.3 Iron Sulfide Crusts |
|
|
374 | (1) |
|
10.2.1.4 Biofilms and Extracellular Matrix |
|
|
374 | (1) |
|
10.2.2 Biocorrosion of Nonferrous Materials |
|
|
375 | (1) |
|
10.2.3 Control of Biocorrosion |
|
|
376 | (1) |
|
10.3 Bioalteration of Rocks, Monuments, and Other Surfaces |
|
|
376 | (4) |
|
10.3.1 Biofilms on Rocks and Buildings |
|
|
376 | (1) |
|
10.3.2 Biodegradation of Art Objects |
|
|
377 | (1) |
|
10.3.2.1 Marble Statues in Italy |
|
|
377 | (1) |
|
10.3.2.2 Paintings in the Lascaux Cave in France |
|
|
377 | (1) |
|
10.3.2.3 Mogao Grottoes in China |
|
|
378 | (1) |
|
10.3.2.4 Damage to Frescoes |
|
|
378 | (1) |
|
10.3.3 Biotechnology for Restoration of Artworks and Historic Stones |
|
|
378 | (2) |
|
10.4 Biodeterioration of Concrete |
|
|
380 | (2) |
|
10.5 Mineral Interaction and Biomineralization |
|
|
382 | (5) |
|
|
382 | (1) |
|
10.5.2 Magnetic Mineral Crystals |
|
|
383 | (1) |
|
|
383 | (1) |
|
|
384 | (1) |
|
|
384 | (1) |
|
|
385 | (1) |
|
|
385 | (1) |
|
|
385 | (1) |
|
10.5.9 Uranium Precipitate and Crystals |
|
|
386 | (1) |
|
|
386 | (1) |
|
10.6 Interactions with Transition and Rare Earth Elements |
|
|
387 | (2) |
|
10.6.1 Transition Elements |
|
|
387 | (1) |
|
10.6.2 Rare Earth Elements |
|
|
388 | (1) |
|
|
389 | (2) |
|
|
389 | (1) |
|
|
389 | (1) |
|
|
390 | (1) |
|
|
390 | (1) |
|
10.8 Metallic and Metalloid Nanoparticles of Microbial Origin |
|
|
391 | (2) |
|
|
393 | (1) |
|
|
393 | (1) |
|
|
394 | (4) |
|
|
398 | (1) |
11 Microbial Communities and Metabolic Networks |
|
399 | (36) |
|
|
399 | (1) |
|
11.2 Examples of Succession of Populations |
|
|
399 | (4) |
|
11.2.1 Development of Coral Black Band Disease |
|
|
400 | (1) |
|
11.2.2 Population Succession in Production of Dairy Products |
|
|
400 | (1) |
|
11.2.3 Population Dynamics in Fermentation of Non-dairy Foods |
|
|
401 | (2) |
|
|
401 | (1) |
|
|
401 | (1) |
|
|
402 | (1) |
|
11.2.3.4 Chinese Soy Sauce |
|
|
402 | (1) |
|
11.2.4 Composting Plant Material |
|
|
403 | (1) |
|
11.3 Impact of Climate Change on Microorganisms |
|
|
403 | (3) |
|
11.3.1 Marine Environment |
|
|
403 | (1) |
|
|
404 | (2) |
|
11.4 Syntrophy and Co-metabolism |
|
|
406 | (2) |
|
11.5 Ecosystem Created by Hydraulic Fracturing in Shale |
|
|
408 | (1) |
|
11.6 Extracellular Electron Transport |
|
|
408 | (2) |
|
11.6.1 Membrane-bound Proteins |
|
|
409 | (1) |
|
11.6.2 Electron Shuttling |
|
|
409 | (1) |
|
|
410 | (1) |
|
11.6.4 Extracellular Electron Movement in Biofilms |
|
|
410 | (1) |
|
11.7 Cross-talk: Interkingdom Signaling |
|
|
410 | (2) |
|
11.7.1 Microbial Endocrinology |
|
|
411 | (1) |
|
11.7.2 Cross-signaling in Nonhuman Systems |
|
|
412 | (1) |
|
11.8 Evolving Systems of Interest |
|
|
412 | (12) |
|
11.8.1 Polyploidy in Bacteria |
|
|
412 | (2) |
|
11.8.2 Impact of Viruses and CRISPR-cas Systems |
|
|
414 | (2) |
|
11.8.3 Impact of Outer Membrane Vesicles |
|
|
416 | (4) |
|
11.8.4 Atmospheric Microbiology |
|
|
420 | (3) |
|
11.8.5 Long-distance Electron Transfer |
|
|
423 | (1) |
|
|
424 | (1) |
|
|
425 | (1) |
|
|
425 | (8) |
|
|
433 | (2) |
Index |
|
435 | |