Microbial Ecology

MICROBIAL ECOLOGY......Page 3
CONTENTS......Page 9
PREFACE......Page 19
GLOSSARY......Page 21
1.1 Central Themes......Page 29
1.2 Introduction......Page 30
1.2.1 Roots of Microbial Ecology......Page 31
1.2.2 Current Perspectives......Page 32
1.3 Timeline......Page 33
1.4 Microfossils......Page 35
1.5.1 The Precellular World......Page 37
1.5.2 The First Cell......Page 38
1.5.3 Development of Cellular Biology......Page 39
1.5.4 Evolution of Metabolic Pathways......Page 40
1.6.1 Structure and Evolution of Cell Shape......Page 41
1.6.2 Metabolism and Use of Energy......Page 44
1.6.3 Growth, Reproduction, and Development......Page 45
1.7 Classification and Taxonomy: The Species Concept......Page 46
1.8 The Three Domains: Tree of Life......Page 47
1.9 Relationship of Microbial Ecology to General Ecology......Page 50
1.10.1 Change in Focus......Page 51
1.10.2 Diversity: From Culturing to Molecular Phylogeny......Page 52
1.11 Summary......Page 53
Bibliographic Material......Page 54
2.2 The Ubiquity of Microorganisms......Page 57
2.3 The Amazing Diversity of Morphologies......Page 58
2.3.3 Winogradsky’s Experiments with Chemolithotrophs......Page 60
2.4.1 Expansion of the Number of Bacterial Phyla......Page 61
2.4.2 Bacterial Portrait Gallery: Processes and Players......Page 63
2.5 Discovery of Archaea as a Separate Domain......Page 66
2.6.1 Archaeal Portrait Gallery......Page 67
2.7 Archaea–Bacteria Differences......Page 73
2.9 Protist Diversity......Page 74
2.9.1 Protist Gallery......Page 77
2.10 Fungal Diversity......Page 79
2.11 Algal Diversity......Page 82
2.12 Viral Diversity......Page 84
2.13 Summary......Page 85
Bibliographic Material......Page 86
3.1 Central Themes......Page 89
3.2 Introduction......Page 90
3.3 Cell Parameters......Page 91
3.3.1 Life at the Lowest Level......Page 92
3.3.2 Large Microorganisms......Page 94
3.4 Cell Movement and Chemotaxis......Page 96
3.5 Structures of Sporulation......Page 99
3.6 Nutrient Reserves and Storage Materials......Page 102
3.7 Cell–Cell Associations......Page 103
3.7.1 Cell Attachment......Page 104
3.7.2 Biofilms......Page 106
3.7.3 Filamentous Growth......Page 110
3.8.1 Sensory Response......Page 112
3.8.2 Global Regulation......Page 114
3.8.3 Internal Membranes in Bacteria......Page 115
3.9.1 Heterotrophs......Page 116
3.9.2 Chemolithotrophs......Page 119
3.9.4 Bacteriorhodopsin Reaction......Page 122
3.10 Bioelectrochemical Activities......Page 125
3.11 Summary......Page 127
Bibliographic Material......Page 128
4.1 Central Themes......Page 131
4.2 Habitats: An Overview......Page 132
4.3 Aquatic Habitats......Page 133
4.3.1 Freshwater......Page 135
4.3.2 Marine Habitats......Page 138
4.4 Soil Habitats......Page 139
4.4.1 Microbial Food Webs in the Soil Habitat......Page 140
4.5.1 Rock Varnish......Page 145
4.5.2 Cave Habitats......Page 147
4.5.4 Deep Subsurface......Page 148
4.6.1 Atmospheric Microbial Diversity: African Dust......Page 149
4.6.2 Mysteries Remain......Page 150
4.7.1 Population Growth and Dynamics......Page 152
4.7.2 Horizontal Gene Transfer......Page 153
4.7.3 Biogeograpy versus Everything is Everywhere; the Environment Selects......Page 154
4.8 Summary......Page 156
Bibliographic Material......Page 157
5.1 Central Themes......Page 159
5.2 Introduction......Page 160
5.3 Sampling and Sample Storage......Page 162
5.4.2 Direct Count Procedures......Page 163
5.4.3 Determining Actively Respiring Cells......Page 164
5.4.4 Fluorescent in situ Hybridization (FISH)......Page 165
5.5 Cultivation of Microorganisms......Page 167
5.5.2 Microbial Biomass......Page 172
5.5.3 Measuring Carbon Substrate Utilization......Page 173
5.6 Molecular Phylogenetics......Page 174
5.7 Culturing Versus Molecular Techniques: Comparisons from Soil Studies......Page 176
5.9 Metagenomics: A New Tool for Answering Community Ecology Questions......Page 177
5.10 Environmental Proteomics......Page 178
5.11 Stable-Isotope Studies......Page 180
5.12 Summary......Page 182
Bibliographic Sources......Page 183
6.1 Central Themes......Page 187
6.2 Introduction......Page 188
6.3 Classification of Microbial Interactions......Page 189
6.3.3 Competition......Page 190
6.3.4 Parasitism......Page 191
6.3.6 Antagonism (Amensalism)......Page 192
6.3.7 Syntrophism......Page 195
6.4.1 Diatoms......Page 196
6.4.2 Lichen......Page 197
6.4.3 Hatena......Page 199
6.4.4 Symbiosis between Bacteria and Protozoa......Page 201
6.6.2 Examples of Parasites and Predators......Page 202
6.8 Sexual Interactions......Page 204
6.9 Summary......Page 206
6.10 Delving Deeper: Critical Thinking Questions......Page 208
Bibliographic Material......Page 209
7.1 Central Themes......Page 211
7.2 Introduction......Page 212
7.3 Symbiotic Associations with Cyanobacteria......Page 214
7.4 Interactions in the Rhizosphere......Page 215
7.5 Mycorrhizae......Page 217
7.5.1 Ectomycorrhizae......Page 218
7.5.3 Other Mycorrhizal Associations......Page 221
7.6.1 Root Associations......Page 223
7.7.2 Growth-Promoting Rhizobacteria......Page 230
7.7.3 Cactus Symbiosis......Page 232
7.8 Leaf Surfaces and Microorganisms......Page 233
7.9.1 Fungal Parasites......Page 234
7.9.2 Bacterial Pathogens......Page 235
7.9.3 Rhizosphere Activities and Plant Diseases......Page 237
7.11 Biocontrol of Pests and Pathogens......Page 239
7.13 Delving Deeper: Critical Thinking Questions......Page 242
Bibliographic Material......Page 243
8.1 Central Themes......Page 245
8.2 Introduction......Page 246
8.3 Primary and Secondary Symbionts......Page 250
8.4.2 Nematode Parasitism of Insects......Page 251
8.4.4 A Widespread Endosymbiosis: Wolbachia—Parasitism or Mutualism?......Page 252
8.5.1 Gut Animal–Microbe Mutualistic Interactions......Page 253
8.5.2 Case Study: Unique Bacterial–Polychaete Endosymbiosis......Page 255
8.5.3 Case Study: Beetles Cultivating Fungal Gardens......Page 256
8.5.4 Mealybug Mutualisms......Page 257
8.6 Lessons from the Deep: Evolutionary and Ecosystem Insights from Deep-Sea Vents Symbioses......Page 258
8.7 Microbial–Vertebrate Interactions......Page 261
8.7.1 Bacteria and Birds......Page 263
8.8 Grazing and Predation by Animals......Page 264
8.10 Delving Deeper: Critical Thinking Questions......Page 267
Bibliographic Material......Page 268
9.1 Central Themes......Page 271
9.2 Introduction......Page 272
9.2.1 Dominant Issues and Questions in Microbial Community Ecology......Page 273
9.3 Metagenomics: A New Tool for Answering Community Ecology Questions......Page 274
9.4 Biomats and Biofilms......Page 275
9.5 Formation of Organized Communities: Quorum Sensing......Page 277
9.6 Colonization and Recolonization by Microorganisms......Page 279
9.6.1 Case Study: Colonization of the Sterile Newborn Gut......Page 280
9.7 Dispersal, Succession, and Stability......Page 281
9.7.2 Competition as a Structuring Force in Succession......Page 282
9.7.3 Stability in Microcosm Studies......Page 283
9.8 Species Diversity......Page 284
9.8.1 Diversity Indices......Page 285
9.8.3 Disturbance and Diversity......Page 286
9.9 Food Webs......Page 287
9.9.1 Structure of Microbial Food Webs......Page 288
9.10.1 Cycling of Nutrients......Page 289
9.11 Microbial Community Examples......Page 290
9.11.1 Plankton in Marine Ecosystems......Page 291
9.11.2 Hot Springs......Page 292
9.11.3 Wine and Cheese......Page 294
9.12 Summary......Page 297
Bibliographic Material......Page 298
10.1 Central Themes......Page 301
10.2 Introduction......Page 302
10.3 Energy Flow......Page 304
10.4 Oxygen and Carbon Cycling......Page 306
10.5 Nitrogen Cycling......Page 309
10.5.1 Nitrogen Fixation......Page 310
10.5.3 Nitrification......Page 311
10.6 Sulfur Cycling......Page 312
10.6.2 Inorganic Sulfur Metabolism......Page 313
10.7 Phosphorus Cycling......Page 314
10.8 Iron Cycling......Page 315
10.8.1 Siderophores......Page 316
10.8.2 Ferritin and Magnetosomes......Page 317
10.9 Cycling of Manganese and Selenium......Page 318
10.10 Cycling of Hydrogen......Page 321
10.11 Transformation of Mercury......Page 322
10.12 Closed Systems......Page 323
10.13 Summary......Page 324
Bibliographic Material......Page 325
11.1 Central Themes......Page 327
11.2 Introduction......Page 328
11.2.1 Passive versus Active Biomineralization......Page 330
11.3.2 Active Metal Adsorption......Page 331
11.4 Energy Flow: Shuffling Electrons; Redox Reactions......Page 332
11.5 Dissolution Versus Precipitation......Page 333
11.6 Formation of Ores and Minerals......Page 334
11.6.2 Recovery of Petroleum......Page 335
11.6.3 Sulfuric Acid–Driven Speleologenesis......Page 338
11.7.1 Silica Formation in Diatoms, Radiolarians, and Sponges......Page 340
11.7.2 Geyserites......Page 341
11.8.1 Magnetite Formation......Page 342
11.8.2 Rock Varnish......Page 343
11.9 Microbial Carbonate Microbialites......Page 345
11.10 Stromatolites......Page 347
11.10.1 Thrombolites......Page 348
11.10.2 Travertines and Tufas......Page 349
11.10.3 Coccolithophores and Foraminifera: Biologically Controlled Mineralization......Page 351
11.12 Delving Deeper: Critical Thinking Questions......Page 352
Bibliographic Material......Page 353
12.1 Central Themes......Page 355
12.2 Introduction......Page 356
12.3 Decomposition of Wood......Page 357
12.4 Digestion of Plant Cell Wall Structures......Page 359
12.4.2 Microbial Decomposition of Lignin......Page 361
12.4.3 Degradation of Hemicelllose......Page 362
12.4.4 Enzymatic Degradation of Cellulose......Page 363
12.6 Inulin Hydrolysis......Page 364
12.7.2 Decomposition of Keratin......Page 365
12.7.3 Fibroin Decomposition......Page 366
12.7.4 Collagen Breakdown......Page 367
12.8 Ecology of Fermented Foods......Page 369
12.9 Ecology of Bioenergy Production......Page 371
12.9.1 Alcohol Production......Page 373
12.9.2 H2 Production......Page 374
12.9.3 Methane Production......Page 375
12.9.4 Biodiesel Production by Algae......Page 376
12.10 Waste Treatment Systems......Page 377
12.11 Composting of Plant Organic Matter......Page 378
12.12 Impact of Microbial Degradation on Humans......Page 380
12.13 Summary......Page 382
Bibliographic Material......Page 383
13.1 Central Themes......Page 387
13.2 Introduction......Page 388
13.3 Bioremediation as a Technology......Page 389
13.5.1 Bioreactors......Page 390
13.5.4 Optimizing Bioremediation......Page 391
13.7 Degradation of Hydrocarbons......Page 393
13.7.2 Methane Utilization......Page 394
13.7.3 Fuel Hydrocarbons......Page 396
13.7.4 Polyaromatic Hydrocarbons......Page 400
13.8 Degradation of Xenobiotics......Page 401
13.8.1 Detoxification of Chlorinated Organic Compounds......Page 403
13.8.2 Herbicides and Pesticides......Page 404
13.8.3 Biodegradation of Explosives......Page 405
13.8.4 Decomposition of Textile Dyes......Page 406
13.9 Bioremediation with Inorganic Pollutants......Page 408
13.9.1 Microbe–Toxic Metal Interactions......Page 409
13.9.2 Detoxification of Selenium......Page 412
13.9.3 Reactions with Arsenic......Page 413
13.9.5 Bioremediation of Nitrate Pollution......Page 415
13.10 Summary......Page 417
Bibliographic Material......Page 418
INDEX......Page 423