Preface xvii
Glossary xix
1 Microbial Ecology: Beginnings and the Road Forward 1
1.1 Central Themes 1
1.2 Introduction 2
1.2.1 Roots of Microbial Ecology 3
1.2.2 Current Perspectives 4
1.3 Timeline 5
1.4 Microfossils 7
1.5 Early Life 9
1.5.1 The Precellular World 9
1.5.2 The First Cell 10
1.5.3 Development of Cellular Biology 11
1.5.4 Evolution of Metabolic Pathways 12
1.6 Characteristics of Microbial Life 13
1.6.1 Structure and Evolution of Cell Shape 13
1.6.2 Metabolism and Use of Energy 16
1.6.3 Growth, Reproduction, and Development 17
1.6.4 Adaptations and Response to Stimuli 18
1.7 Classification and Taxonomy: The Species Concept 18
1.8 The Three Domains: Tree of Life 19
1.9 Relationship of Microbial Ecology to General Ecology 22
1.10 Changing Face of Microbial Ecology 23
1.10.1 Change in Focus 23
1.10.2 Diversity: From Culturing to Molecular Phylogeny 24
1.11 Summary 25
1.12 Delving Deeper: Critical Thinking Questions 26
2 Diversity of Microorganisms 29
2.1 Central Themes 29
2.2 The Ubiquity of Microorganisms 29
2.3 The Amazing Diversity of Morphologies 30
2.3.1 Comparison of the Three Domains 32
2.3.2 What’s in a Name: Prokaryotes 32
2.3.3 Winogradsky’s Experiments with Chemolithotrophs 32
2.4 Diversity of Bacterial Groups 33
2.4.1 Expansion of the Number of Bacterial Phyla 33
2.4.2 Bacterial Portrait Gallery: Processes and Players 35
2.5 Discovery of Archaea as a Separate Domain 38
2.6 Archaeal Diversity 39
2.6.1 Archaeal Portrait Gallery 39
2.7 Archaea–Bacteria Differences 45
2.8 Eukarya: A Changing Picture of Phylogenetic Diversity 46
2.9 Protist Diversity 46
2.9.1 Protist Gallery 49
2.10 Fungal Diversity 51
2.11 Algal Diversity 54
2.12 Viral Diversity 56
2.13 Summary 57
2.14 Delving Deeper: Critical Thinking Questions 58
3 Complexity and Simplicity of Cell Systems 61
3.1 Central Themes 61
3.2 Introduction 62
3.3 Cell Parameters 63
3.3.1 Life at the Lowest Level 64
3.3.2 Large Microorganisms 66
3.4 Cell Movement and Chemotaxis 68
3.5 Structures of Sporulation 71
3.6 Nutrient Reserves and Storage Materials 74
3.7 Cell–Cell Associations 75
3.7.1 Cell Attachment 76
3.7.2 Biofilms 78
3.7.3 Filamentous Growth 82
3.8 Cell Physiology and Metabolism 84
3.8.1 Sensory Response 84
3.8.2 Global Regulation 86
3.8.3 Internal Membranes in Bacteria 87
3.9 Energetics and Environment 88
3.9.1 Heterotrophs 88
3.9.2 Chemolithotrophs 91
3.9.3 Photophosphorylation 94
3.9.4 Bacteriorhodopsin Reaction 94
3.10 Bioelectrochemical Activities 97
3.11 Summary 99
3.12 Delving Deeper: Critical Thinking Questions 100
4 The Microbial Habitat: An Ecological Perspective 103
4.1 Central Themes 103
4.2 Habitats: An Overview 104
4.2.1 The Niche 105
4.3 Aquatic Habitats 105
4.3.1 Freshwater 107
4.3.2 Marine Habitats 110
4.4 Soil Habitats 111
4.4.1 Microbial Food Webs in the Soil Habitat 112
4.5 Rock and Subsurface Habitats 117
4.5.1 Rock Varnish 117
4.5.2 Cave Habitats 119
4.5.3 Groundwater 120
4.5.4 Deep Subsurface 120
4.6 Atmospheric Habitats 121
4.6.1 Atmospheric Microbial Diversity: African Dust 121
4.6.2 Mysteries Remain 122
4.7 Population Ecology Across Habitats 124
4.7.1 Population Growth and Dynamics 124
4.7.2 Horizontal Gene Transfer 125
4.7.3 Biogeograpy versus Everything is Everywhere; the Environment Selects 126
4.8 Summary 128
4.9 Delving Deeper: Critical Thinking Questions 129
5 The How of Microbial Ecology Studies 131
5.1 Central Themes 131
5.2 Introduction 132
5.3 Sampling and Sample Storage 134
5.4 Microscopy 135
5.4.1 Gram Stains 135
5.4.2 Direct Count Procedures 135
5.4.3 Determining Actively Respiring Cells 136
5.4.4 Fluorescent in situ Hybridization (FISH) 137
5.4.5 Electron Microscopy 139
5.5 Cultivation of Microorganisms 139
5.5.1 Microbial Respiration 144
5.5.2 Microbial Biomass 144
5.5.3 Measuring Carbon Substrate Utilization 145
5.6 Molecular Phylogenetics 146
5.7 Culturing Versus Molecular Techniques: Comparisons from Soil Studies 148
5.8 Community Fingerprinting Methods 149
5.8.1 Denaturing Gradient Gel Electrophoresis 149
5.9 Metagenomics: A New Tool for Answering Community Ecology Questions 149
5.10 Environmental Proteomics 150
5.11 Stable-Isotope Studies 152
5.11.1 Using Stable Isotopes: Movile Cave Food Web Case Study 153
5.12 Summary 154
5.13 Delving Deeper: Critical Thinking Questions 155
6 Microbe–Microbe Interactions 159
6.1 Central Themes 159
6.2 Introduction 160
6.3 Classification of Microbial Interactions 161
6.3.1 Neutralism 162
6.3.2 Commensalism 162
6.3.3 Competition 162
6.3.4 Parasitism 163
6.3.5 Predation 164
6.3.6 Antagonism (Amensalism) 164
6.3.7 Syntrophism 167
6.4 Symbiotic Associations 168
6.4.1 Diatoms 168
6.4.2 Lichen 169
6.4.3 Hatena 171
6.4.4 Symbiosis between Bacteria and Protozoa 173
6.5 Fungus–Bacterium Symbiosis 174
6.6 Prokaryote–Prokaryote Interactions 174
6.6.1 Two-Member Mutualism 174
6.6.2 Examples of Parasites and Predators 174
6.7 Establishing a Symbiosis: The Nostoc–Geosiphon Association 176
6.8 Sexual Interactions 176
6.9 Summary 178
6.10 Delving Deeper: Critical Thinking Questions 180
7 Interactions Between Microorganisms and Plants 183
7.1 Central Themes 183
7.2 Introduction 184
7.3 Symbiotic Associations with Cyanobacteria 186
7.4 Interactions in the Rhizosphere 187
7.5 Mycorrhizae 189
7.5.1 Ectomycorrhizae 190
7.5.2 Endomycorrhizae 193
7.5.3 Other Mycorrhizal Associations 193
7.6 Nitrogen-Fixing Bacteria and Higher Plants 195
7.6.1 Root Associations 195
7.6.2 Stem Associations 202
7.7 Bacteria Supporting Plant Growth 202
7.7.1 Production of Hormones 202
7.7.2 Growth-Promoting Rhizobacteria 202
7.7.3 Cactus Symbiosis 204
7.8 Leaf Surfaces and Microorganisms 205
7.9 Detrimental Activities of Microorganisms on Plants 206
7.9.1 Fungal Parasites 206
7.9.2 Bacterial Pathogens 207
7.9.3 Rhizosphere Activities and Plant Diseases 209
7.10 Fungi Promoting Increased Heat Tolerance in Plants 211
7.11 Biocontrol of Pests and Pathogens 211
7.12 Summary 214
7.13 Delving Deeper: Critical Thinking Questions 214
8 Interactions Between Microorganisms and Animals 217
8.1 Central Themes 217
8.2 Introduction 218
8.3 Primary and Secondary Symbionts 222
8.4 Microbe–Animal Interactions: Parasitism 223
8.4.1 Parasitism Introduction 223
8.4.2 Nematode Parasitism of Insects 223
8.4.3 Effects of Multiple Parasitic Infections on Virulence 224
8.4.4 A Widespread Endosymbiosis: Wolbachia —Parasitism or Mutualism? 224
8.5 Microbe–Animal Interactions: Mutualism 225
8.5.1 Gut Animal–Microbe Mutualistic Interactions 225
8.5.2 Case Study: Unique Bacterial–Polychaete Endosymbiosis 227
8.5.3 Case Study: Beetles Cultivating Fungal Gardens 228
8.5.4 Mealybug Mutualisms 229
8.5.5 Luminescent Bacteria in Fish and Squid:Turning on the Lights 230
8.6 Lessons from the Deep: Evolutionary and Ecosystem Insights from Deep-Sea Vents Symbioses 230
8.7 Microbial–Vertebrate Interactions 233
8.7.1 Bacteria and Birds 235
8.7.2 Microorganisms and Humans 236
8.8 Grazing and Predation by Animals 236
8.9 Summary 239
8.10 Delving Deeper: Critical Thinking Questions 239
9 Living Together: Microbial Communities 243
9.1 Central Themes 243
9.2 Introduction 244
9.2.1 Dominant Issues and Questions in Microbial Community Ecology 245
9.3 Metagenomics: A New Tool for Answering Community Ecology Questions 246
9.4 Biomats and Biofilms 247
9.4.1 Changes in Community Structure during Biofilm Succession 249
9.5 Formation of Organized Communities: Quorum Sensing 249
9.6 Colonization and Recolonization by Microorganisms 251
9.6.1 Case Study: Colonization of the Sterile Newborn Gut 252
9.6.2 Case Study: Undesirable Colonization—Factors in Disease 253
9.6.3 Case Study: Recolonization and Early Succession in Intertidal Sediments 253
9.7 Dispersal, Succession, and Stability 253
9.7.1 Case Study: Dispersal and Succession in the Oceans—Whale Falls as Dispersal Agents between Vents 254
9.7.2 Competition as a Structuring Force in Succession 254
9.7.3 Stability in Microcosm Studies 255
9.8 Species Diversity 256
9.8.1 Diversity Indices 257
9.8.2 Connections between Metazoans and Microorganisms: Co-ocurrence Patterns 258
9.8.3 Disturbance and Diversity 258
9.9 Food Webs 259
9.9.1 Structure of Microbial Food Webs 260
9.9.2 Keystone Species Effects on Food Webs and Diversity 261
9.10 Primary Production and Energy Flow 261
9.10.1 Cycling of Nutrients 261
9.11 Microbial Community Examples 262
9.11.1 Plankton in Marine Ecosystems 263
9.11.2 Hot Springs 264
9.11.3 Wine and Cheese 266
9.12 Summary 269
9.13 Delving Deeper: Critical Thinking Questions 270
10 Microbial Processes Contributing to Biogeochemical Cycles 273
10.1 Central Themes 273
10.2 Introduction 274
10.3 Energy Flow 276
10.4 Oxygen and Carbon Cycling 278
10.5 Nitrogen Cycling 281
10.5.1 Nitrogen Fixation 282
10.5.2 Nitrogen Assimilation 283
10.5.3 Nitrification 283
10.5.4 Denitrification 284
10.6 Sulfur Cycling 284
10.6.1 Organic Sulfur Metabolism 285
10.6.2 Inorganic Sulfur Metabolism 285
10.7 Phosphorus Cycling 286
10.8 Iron Cycling 287
10.8.1 Siderophores 288
10.8.2 Ferritin and Magnetosomes 289
10.9 Cycling of Manganese and Selenium 290
10.10 Cycling of Hydrogen 293
10.11 Transformation of Mercury 294
10.12 Closed Systems 295
10.13 Summary 296
10.14 Delving Deeper: Critical Thinking Questions 297
11 Microbes at Work In Nature: Biomineralization and Microbial Weathering 299
11.1 Central Themes 299
11.2 Introduction 300
11.2.1 Passive versus Active Biomineralization 302
11.3 Cell Characteristics and Metal Binding 303
11.3.1 Passive Metal Adsorption 303
11.3.2 Active Metal Adsorption 303
11.4 Energy Flow: Shuffling Electrons; Redox Reactions 304
11.5 Dissolution Versus Precipitation 305
11.6 Formation of Ores and Minerals 306
11.6.1 Biomining 307
11.6.2 Recovery of Petroleum 307
11.6.3 Sulfuric Acid–Driven Speleologenesis 310
11.7 Microbial Participation in Silicification 312
11.7.1 Silica Formation in Diatoms, Radiolarians, and Sponges 312
11.7.2 Geyserites 313
11.8 Biomineralization of Ferromanganese Deposits 314
11.8.1 Magnetite Formation 314
11.8.2 Rock Varnish 315
11.9 Microbial Carbonate Microbialites 317
11.10 Stromatolites 319
11.10.1 Thrombolites 320
11.10.2 Travertines and Tufas 321
11.10.3 Coccolithophores and Foraminifera: Biologically Controlled Mineralization 323
11.11 Summary 324
11.12 Delving Deeper: Critical Thinking Questions 324
12 Decomposition of Natural Compounds 327
12.1 Central Themes 327
12.2 Introduction 328
12.3 Decomposition of Wood 329
12.4 Digestion of Plant Cell Wall Structures 331
12.4.1 Protopectinase and Pectinase Activities 333
12.4.2 Microbial Decomposition of Lignin 333
12.4.3 Degradation of Hemicelllose 334
12.4.4 Enzymatic Degradation of Cellulose 335
12.5 Starch Hydrolysis 336
12.6 Inulin Hydrolysis 336
12.7 Decomposition of Diverse Biopolymers Including Animal Fibrous Proteins 337
12.7.1 Chitin Digestion 337
12.7.2 Decomposition of Keratin 337
12.7.3 Fibroin Decomposition 338
12.7.4 Collagen Breakdown 339
12.8 Ecology of Fermented Foods 341
12.9 Ecology of Bioenergy Production 343
12.9.1 Alcohol Production 345
12.9.2 H2 Production 346
12.9.3 Methane Production 347
12.9.4 Biodiesel Production by Algae 348
12.10 Waste Treatment Systems 349
12.11 Composting of Plant Organic Matter 350
12.12 Impact of Microbial Degradation on Humans 352
12.13 Summary 354
12.14 Delving Deeper: Critical Thinking Questions 355
13 Microbes at Work: Bioremediation 359
13.1 Central Themes 359
13.2 Introduction 360
13.3 Bioremediation as a Technology 361
13.4 Genetic Engineering 362
13.5 Design and Implementation of Bioremediation 362
13.5.1 Bioreactors 362
13.5.2 Biofarming 363
13.5.3 Permeable Reactive Barriers 363
13.5.4 Optimizing Bioremediation 363
13.6 Bioremediation of Organic Compounds 365
13.7 Degradation of Hydrocarbons 365
13.7.1 Oil Spills 366
13.7.2 Methane Utilization 366
13.7.3 Fuel Hydrocarbons 368
13.7.4 Polyaromatic Hydrocarbons 372
13.8 Degradation of Xenobiotics 373
13.8.1 Detoxification of Chlorinated Organic Compounds 375
13.8.2 Herbicides and Pesticides 376
13.8.3 Biodegradation of Explosives 377
13.8.4 Decomposition of Textile Dyes 378
13.9 Bioremediation with Inorganic Pollutants 380
13.9.1 Microbe–Toxic Metal Interactions 381
13.9.2 Detoxification of Selenium 384
13.9.3 Reactions with Arsenic 385
13.9.4 Bioremediation of Perchlorate Sites 387
13.9.5 Bioremediation of Nitrate Pollution 387
13.10 Summary 389
13.11 Delving Deeper: Critical Thinking Questions 390
index 395
