Microbial ecology/ Barton,Larry L.

PREFACE xvii GLOSSARY xix 1 MICROBIAL ECOLOGY: BEGINNINGS AND THE ROAD FORWARD 1 1.1 Central Themes 1 1.2 Introduction 2 1.3 Timeline 5 1.4 Microfossils 7 1.5 Early Life 9 1.6 Characteristics of Microbial Life 13 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 1.11 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 2.4 Diversity of Bacterial Groups 33 2.5 Discovery of Archaea as a Separate Domain 38 2.6 Archaeal Diversity 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 3.4 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 3.8 Cell Physiology and Metabolism 84 3.9 Energetics and Environment 88 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 4.3 Aquatic Habitats 105 4.4 Soil Habitats 111 4.5 Rock and Subsurface Habitats 117 4.6 Atmospheric Habitats 121 4.7 Population Ecology Across Habitats 124 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 135scopy 139 5.5 Cultivation of Microorganisms 139 5.6 Molecular Phylogenetics 146 5.7 Culturing Versus Molecular Techniques: Comparisons from Soil Studies 148 5.8 Community Fingerprinting Methods 149 5.9 Metagenomics: A New Tool for Answering Community Ecology Questions 149 5.10 Environmental Proteomics 150 5.11 Stable-Isotope Studies 152 5.12 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 6.4 Symbiotic Associations 168 6.5 Fungus Bacterium Symbiosis 174 6.6 Prokaryote Prokaryote Interactions 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 7.6 Nitrogen-Fixing Bacteria and Higher Plants 195 7.7 Bacteria Supporting Plant Growth 202 7.8 Leaf Surfaces and Microorganisms 205 7.9 Detrimental Activities of Microorganisms on Plants 206 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 8.5 Microbe Animal Interactions: Mutualism 225 8.6 Lessons from the Deep: Evolutionary and Ecosystem Insights from Deep-Sea Vents Symbioses 230 8.7 Microbial Vertebrate Interactions 233 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 9.3 Metagenomics: A New Tool for Answering Community Ecology Questions 246 9.4 Biomats and Biofilms 247 9.5 Formation of Organized Communities: Quorum Sensing 249 9.6 Colonization and Recolonization by Microorganisms 251 9.7 Dispersal, Succession, and Stability 253 9.8 Species Diversity 256 9.9 Food Webs 259 9.10 Primary Production and Energy Flow 261 9.11 Microbial Community Examples 262 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 10.6 Sulfur Cycling 284 10.7 Phosphorus Cycling 286 10.8 Iron Cycling 287 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 11.3 Cell Characteristics and Metal Binding 303 11.4 Energy Flow: Shuffling Electrons; Redox Reactions 304 11.5 Dissolution Versus Precipitation 305 11.6 Formation of Ores and Minerals 306 11.7 Microbial Participation in Silicification 312 11.8 Biomineralization of Ferromanganese Deposits 314 11.9 Microbial Carbonate Microbialites 317 11.10 Stromatolites 319 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 12.5 Starch Hydrolysis 336 12.6 Inulin Hydrolysis 336 12.7 Decomposition of Diverse Biopolymers Including Animal Fibrous Proteins 337 12.8 Ecology of Fermented Foods 341 12.9 Ecology of Bioenergy Production 343 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 13.6 Bioremediation of Organic Compounds 365 13.7 Degradation of Hydrocarbons 365 13.8 Degradation of Xenobiotics 373 13.9 Bioremediation with Inorganic Pollutants 380 13.10 Summary 389 13.11 Delving Deeper: Critical Thinking Questions 390 Bibliographic Material 390 INDEX 395