Microbial Ecology

**This book covers the ecological activities of microbes in the biosphere with an emphasis on microbial interactions within their environments and communities**In thirteen concise and timely chapters, __Microbial Ecology__ presents a broad overview of this rapidly growing field, explaining the basic principles in an easy-to-follow manner. Using an integrative approach, it comprehensively covers traditional issues in ecology as well as cutting-edge content at the intersection of ecology, microbiology, environmental science and engineering, and molecular biology. Examining the microbial characteristics that enable microbes to grow in different environments, the book provides insights into relevant methodologies for characterization of microorganisms in the environment. The authors draw upon their extensive experience in teaching microbiology to address the latest hot-button topics in the field, such as: * Ecology of microorganisms in natural and engineered environments * Advances in molecular-based understanding of microbial phylogeny and interactions * Microbially driven biogeochemical processes and interactions among microbial populations and communities * Microbial activities in extreme or unusual environments * Ecological studies pertaining to animal, plant, and insect microbiology * Microbial processes and interactions associated with environmental pollution * Information boxes that highlight key microbial ecology issues * "Microbial Spotlights" that focus on how prominent microbial ecologists became interested in microbial ecology * Examples that illustrate the role of bacterial interaction with humans * Exercises to promote critical thinking * Selected reading lists * Chapter summaries and review questions for class discussion PowerPoint slides of figures from the book are available for download at: 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 This book covers the ecological activities of microbes in the biosphere with an emphasis on microbial interactions within their environments and communities In thirteen concise and timely chapters, Microbial Ecology presents a broad overview of this rapidly growing field, explaining the basic principles in an easy-to-follow manner. Using an integrative approach, it comprehensively covers traditional issues in ecology as well as cutting-edge content at the intersection of ecology, microbiology, environmental science and engineering, and molecular biology. Examining the microbial characteristics that enable microbes to grow in different environments, the book provides insights into relevant methodologies for characterization of microorganisms in the environment. The authors draw upon their extensive experience in teaching microbiology to address the latest hot-button topics in the field, such as: Ecology of microorganisms in natural and engineered environments Advances in molecular-based understanding of microbial phylogeny and interactions Microbially driven biogeochemical processes and interactions among microbial populations and communities Microbial activities in extreme or unusual environments Ecological studies pertaining to animal, plant, and insect microbiology Microbial processes and interactions associated with environmental pollution Designed for use in teaching, Microbial Ecology offers numerous special features to aid both students and instructors, including: Information boxes that highlight key microbial ecology issues'Microbial Spotlights'that focus on how prominent microbial ecologists became interested in microbial ecology Examples that illustrate the role of bacterial interaction with humans Exercises to promote critical thinking Selected reading lists Chapter summaries and review questions for class discussion Various microbial interactions and community structures are presented through examples and illustrations. Also included are mini case studies that address activities of microorganisms in specific environments, as well as a glossary and key words. All these features make this an ideal textbook for graduate or upper-level undergraduate students in biology, microbiology, ecology, or environmental science. It also serves as a highly useful reference for scientists and environmental professionals. "Microbial Ecology presents a broad overview of microbial ecology while providing numerous special features to assist students, teachers, and the professional reader. Information boxes in each of the sixteen chapters highlight specific microbial ecology issues of particular interest. Included in the text, also, is a glossary and key words. The book covers a selected reading list for each chapter; a special section in each chapter on "microbial spotlights" that focus on the latest work and findings of scientists from around the world; and exercises that promote critical thinking. "-- "Microbial Ecology is a text and reference book for upper-level undergraduate students and graduate students in microbiology, ecology, environmental science, and environmental engineering"-- “Microbial Ecology presents a broad overview of microbial ecology while providing numerous special features to assist students, teachers, and the professional reader. Information boxes in each of the sixteen chapters highlight specific microbial ecology issues of particular interest. Included in the text, also, is a glossary and key words. The book covers a selected reading list for each chapter; a special section in each chapter on "microbial spotlights" that focus on the latest work and findings of scientists from around the world; and exercises that promote critical thinking. PowerPoint slides of figures from the book are available for download at: ftp://ftp.wiley.com/public/sci_tech_med/microbial_ecology” "Microbial Ecology presents a broad overview of microbial ecology while providing numerous special features to assist students, teachers, and the professional reader. Information boxes in each of the sixteen chapters highlight specific microbial ecology issues of particular interest. Included in the text, also, is a glossary and key words. The book covers a selected reading list for each chapter; a special section in each chapter on "microbial spotlights" that focus on the latest work and findings of scientists from around the world; and exercises that promote critical thinking."-- Provided by publisher "Microbial Ecology presents a broad overview of microbial ecology while providing numerous special features to assist students, teachers, and the professional reader. Information boxes in each of the sixteen chapters highlight specific microbial ecology issues of particular interest. Included in the text, also, is a glossary and key words. The book covers a selected reading list for each chapter; a special section in each chapter on "microbial spotlights" that focus on the latest work and findings of scientists from around the world; and exercises that promote critical thinking."--Résumé de l'éditeur