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Environmental Microbiology and Microbial Ecology

1. Aufl.

von: Larry L. Barton, Robert J. C. McLean
128,99 €
Verlag:	Wiley-Blackwell
Format:	PDF
Veröffentl.:	09.01.2019
ISBN/EAN:	9781118966273
Sprache:	englisch
Anzahl Seiten:	464

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Titelbeschreibung

An authoritative overview of the ecological activities of microbes in the biosphere Environmental Microbiology and Microbial Ecology presents a broad overview of microbial activity and microbes' interactions with their environments and communities. Adopting an integrative approach, this text covers both conventional ecological issues as well as cross-disciplinary investigations that combine facets of microbiology, ecology, environmental science and engineering, molecular biology, and biochemistry. Focusing primarily on single-cell forms of prokaryotes — and cellular forms of algae, fungi, and protozoans — this book enables readers to gain insight into the fundamental methodologies for the characterization of microorganisms in the biosphere. The authors draw from decades of experience to examine the environmental processes mediated by microorganisms and explore the interactions between microorganisms and higher life forms. Highly relevant to modern readers, this book examines topics including the ecology of microorganisms in engineered environments, microbial phylogeny and interactions, microbial processes in relation to environmental pollution, and many more. Now in its second edition, this book features updated references and major revisions to chapters on assessing microbial communities, community relationships, and their global impact. New content such as effective public communication of research findings and advice on scientific article review equips readers with practical real-world skills. <ul> <li>Explores the activities of microorganisms in specific environments with case studies and actual research data</li> <li>Highlights how prominent microbial biologists address significant microbial ecology issues</li> <li>Offers guidance on scientific communication, including scientific presentations and grant preparation</li> <li>Includes plentiful illustrations and examples of microbial interactions, community structures, and human-bacterial connections</li> <li>Provides chapter summaries, review questions, selected reading lists, a complete glossary, and critical thinking exercises</li> </ul> Environmental Microbiology and Microbial Ecology is an ideal textbook for graduate and advanced undergraduate courses in biology, microbiology, ecology, and environmental science, while also serving as a current and informative reference for microbiologists, cell and molecular biologists, ecologists, and environmental professionals.

Inhaltsverzeichnis

Preface xv 1 Introduction to Microorganisms and Their Activities 1 1.1 Central Themes of Environmental Microbiology and Microbial Ecology 1 1.2 Are the Terms Prokaryotes or Eukaryotes Relevant? 1 1.2.1 Intracellular Membranes in Prokaryotes 2 1.2.2 Compartmentalized Heterotrophic Bacterial Cells 3 1.2.3 The Universal Tree of Life: Rooted or Unrooted 4 1.2.4 What About the Giant Viruses? 4 1.3 Major Approach to Study Microorganisms 5 1.3.1 Application of Genomics, Metagenomics, and Proteomics 6 1.3.2 Biochemical and Physiological Analysis 7 1.4 The Impact of Horizontal Gene Transfer Between Microorganisms 7 1.4.1 Genetic Islands 9 1.4.2 Risks from Genetically Modified Organisms 10 1.4.3 Microbial Viruses and Gene Transfer Agents 10 1.5 What Determines Which Microorganisms are Present? 12 1.5.1 Metabolism as a Basis of Selection 13 1.5.2 Is Persistence of Microorganisms Dependent Only on Spore Production? 14 1.6 Is the Size and Shape of a Prokaryotic Cell Important? 19 1.6.1 Nanobacteria 19 1.6.2 Ultramicroscopic Bacteria 21 1.6.3 Very Large Bacteria 21 1.6.4 Influence of Diffusion on Bacterial Cell Form 22 1.6.5 Features of a Specific Cell Form 22 1.6.5.1 Coccus Form 22 1.6.5.2 Rod Form 22 1.6.5.3 Curved Rod or Spirochete Form 23 1.6.5.4 Unusual Forms 23 1.7 Microbial Predation 23 1.7.1 Bacteria as Prey 23 1.7.2 Bacteria as Trackers and Predators 24 1.8 Summary 25 Discussion Questions 25 References 26 Further Reading 31 2 Microbes in the Biosphere: Examination, Cultivation, and Communities 33 2.1 Overview and Focus 33 2.2 Microscopy to Study Environmental Microbes 33 2.2.1 Light Supported Microscopy 34 2.2.2 Fluorescence Microscopy 35 2.2.3 Scanning Confocal Laser Microscopy 37 2.2.4 High Resolution by Electron Microscopy 37 2.3 Internal Structures in Prokaryotes 41 2.3.1 Gas Vacuoles 41 2.3.2 Sulfur Globules 41 2.3.3 Polymeric Carbon Reserves 42 2.3.4 Polyphosphate Granules 43 2.3.5 Metallic Nanoparticles 43 2.4 Strategies for Culturing Microorganisms 44 2.4.1 Overview 44 2.4.2 Approaches for Isolation of Microorganisms 45 2.4.3 Establishing Microbial Communities 45 2.4.4 The iChip and Growing Uncultured Bacteria 46 2.5 Molecular Detection 49 2.5.1 Characterization of Microorganisms Using Genomics and Metagenomics 49 2.5.2 Physiological Analysis Using Metatranscriptomics and Metaproteomics 53 2.5.3 Lipid Biomarker Profiles 54 2.6 Examining Bacteria that Do Not Grow as Pure Cultures in the Laboratory 56 2.6.1 Host‐dependent Microorganisms 56 2.6.1.1 Bacteria as Obligate Pathogens 56 2.6.1.2 Bacteria as Endosymbionts 57 2.6.1.3 The Nanoarchaeum–Ignicoccus Relationship 58 2.6.2 Molecular Analysis of Uncultivable Bacteria 58 2.7 Microbial Community Structures 59 2.7.1 Primary Production and Microbial Communities 59 2.7.2 Biofilms 62 2.7.3 Role of Quorum Sensing 64 2.8 Summary 67 Discussion Questions 68 References 68 Further Reading 75 3 Terrestrial Systems: Soil and Subsurface Environments 77 3.1 Overview and Focus 77 3.2 Soil: An Environment for Microorganisms 77 3.2.1 Soil Horizons 78 3.2.2 Soil Organic Matter (SOM) 78 3.3 Soil Microbiology 80 3.3.1 Soil Prokaryotes 80 3.3.2 Soil Fungi 82 3.3.3 Soil Crusts 83 3.3.4 Soil Invertebrates and Burrowing Animals 83 3.3.5 The Rhizosphere and Associated Bacteria 83 3.4 Understanding Soil Ecosystems 85 3.4.1 The Carbon : Nitrogen Ratio 85 3.4.2 The Fungi : Bacteria Ratio 85 3.4.3 SOM and Soil Food Webs 86 3.4.4 Influence of Agricultural Management on the Soil Microbe Community 89 3.4.5 Impact of Viruses on the Soil Microbiota 90 3.5 Subsurface Microbiology 90 3.5.1 Groundwater 90 3.5.2 Cave Water 92 3.5.3 Deep Subsurface Aquifers 92 3.5.3.1 Aquifer in a Coal‐bearing Basin 92 3.5.3.2 Deep Granitic Aquifer 93 3.5.3.3 Anaerobic, Alkaline Aquifer 94 3.5.3.4 Saline Hydrothermal Aquifer 94 3.6 Deep Subsurface Microbiology 95 3.6.1 Marine Sediment Microbiology 96 3.6.2 Deep Mines and Boreholes 97 3.6.3 Deep Subsea Floor 98 3.6.4 Deep Subsurface Storage Sites 98 3.6.4.1 Storage of Nuclear Fuel Waste 98 3.6.4.2 Underground Storage for H 2 and CH 4 100 3.6.4.3 Underground Storage for CO 2 101 3.6.4.4 Geothermal Energy Production 102 3.6.5 Endolithic Microorganisms 102 3.7 Life in Deep Subsurfaces 103 3.7.1 Adjusting to a Subsurface Diet 103 3.7.2 Energy Sources in the Deep Biosphere 103 3.7.3 The Benefit of Living Together 105 3.8 Geomicrobiology 106 3.8.1 Rock and Mineral Weathering 106 3.8.2 Mineral Transformations 107 3.8.3 Microbial Metal Binding 109 3.8.4 Microbiota of Subsurface Crystals 109 3.9 Summary 110 Discussion Questions 111 References 111 Further Reading 116 4 Aquatic Surface Environments: Freshwater, Marine, and Wastewater 117 4.1 Overview and Focus 117 4.2 Water as Relevant to Microbial Growth 117 4.2.1 Water Activity 118 4.3 Marine Environments and Associated Microbiomes 119 4.3.1 Marine Primary Productivity 120 4.3.2 Marine Heterotrophs 122 4.3.3 Bacterial Symbionts and Marine Hosts 123 4.3.4 Microbial EPSs, Marine Snow, and Marine Gel Particles 125 4.3.5 Brackish Water and Intertidal Zones 127 4.3.6 Coral Reefs 128 4.4 Freshwater Environments and Associated Microbiomes 131 4.4.1 Lakes and Rivers 132 4.4.2 Wetlands 137 4.4.3 The Snow and Glacier Ice Ecosystems 139 4.4.4 Microbiota of Cold and Hot Springs 140 4.4.5 Microbial Mats 142 4.5 Maintaining Populations in Low Nutrient Environments 144 4.6 Aquaculture Wastewater 148 4.7 Hormone Degradation in Fresh Water 149 4.8 Human Activities and Influence on Microbial Ecology 150 4.9 Drinking Water 151 4.10 Municipal Water Treatment 151 4.11 Wastewater Treatment Systems 152 4.11.1 Septic Tanks 152 4.11.2 Municipal Wastewater Treatment 152 4.11.2.1 Primary Treatment 153 4.11.2.2 Secondary Treatment 153 4.12 Alternative Approaches for Wastewater Treatment 154 4.13 Coliforms and Other Indicator Organisms 155 4.14 Viruses in Aquatic Environments: Diversity and Activity 156 4.15 Summary 158 Discussion Questions 159 References 159 Further Reading 166 5 Life in Extreme Environments 167 5.1 Overview 167 5.2 Sampling in Extreme Environments 168 5.3 Extreme Temperature Environments 173 5.3.1 Psychrophiles 174 5.3.2 Thermophiles 176 5.3.2.1 Alpine Environment – Yellowstone National Park 176 5.3.2.2 Hydrothermal Vent Communities 179 5.3.2.3 The Guaymas Basin 180 5.4 Xerophiles 180 5.5 Piezophiles 182 5.6 Acidophiles 183 5.7 Alkaliphiles 187 5.8 Halophiles and Chaophiles 189 5.9 Radioresistant Microorganisms 194 5.10 Membrane Adaptations to Extreme Conditions 195 5.10.1 Low Temperatures 195 5.10.2 High Temperatures 196 5.10.3 pH Extremes: Low and High 196 5.11 Astrobiology 197 5.12 Nutrient Limited Environments 198 5.13 Volcanic Surfaces 200 5.14 Summary 202 Discussion Questions 202 References 202 Further Reading 209 6 Mutualism: Microorganisms and Terrestrial Plants 211 6.1 Overview and Focus 211 6.2 Cyanobacteria and the Chloroplast Ancestor 211 6.3 Lichens: Cyanobacteria/Algae–Fungi Mutualism 217 6.3.1 Distribution and Organization 217 6.3.2 Natural Products of Lichens 219 6.4 Mutualisms with Cyanobacteria as Intracellular or Epiphytic Organisms 220 6.4.1 Bryophytes 220 6.4.2 Mosses 221 6.4.3 Azolla 221 6.4.4 Gunnera 222 6.4.5 Cycads 222 6.4.6 Geosiphon 222 6.4.7 Diatoms 224 6.5 Rhizobia–Legume Symbiosis 224 6.5.1 Bacterial Species Involved 224 6.5.2 Rhizospheric Rhizobia 225 6.5.3 The Root Nodulation Process 226 6.5.4 Nodules on Plant Stems 230 6.6 Frankia and the Non‐legume Nitrogen‐fixing Nodule 231 6.7 Mycorrhizae 233 6.7.1 Arbuscular Mycorrhizae (AM) 235 6.7.2 Ectomycorrhiza (EcM) 236 6.8 Patterns of Regulation for Plant–Microbe Mutualism 237 6.9 Bacterial‐Fungal Interactions 238 6.9.1 Direct Effects 238 6.9.2 Plant Growth‐promoting Bacteria 239 6.9.3 Systemic Induction of Plant Immunity 239 6.10 Endophytic Microorganisms 240 6.11 Microbiology of the Phyllosphere 241 6.12 Summary 242 Discussion Questions 243 References 243 Further Reading 247 7 Mutualism: Microorganisms and Animals 249 7.1 Overview and Focus 249 7.2 Building a Microbial Community – The Role of the Host 249 7.2.1 Microbiology and Innate Immunity 249 7.2.2 Microbiology and Adaptive Immunity 250 7.3 Host Models to Study Parasite Relationships 251 7.3.1 Germ‐free Animals 251 7.3.2 Caenorhabditis elegans 251 7.3.3 Drosophila melanogaster 252 7.3.4 Galleria mellonella 252 7.4 Digestive Tract Environment 252 7.4.1 Omnivores 253 7.4.2 Carnivores 254 7.4.3 Herbivores 255 7.4.3.1 Bacteria and Archaea 257 7.4.3.2 Anaerobic Protozoa 257 7.4.3.3 Anaerobic Fungi 258 7.4.3.4 Probiotics and Methane Mitigation Strategies 260 7.5 The Human Microbiome 260 7.5.1 Skin 260 7.5.2 Oral Microorganisms 261 7.5.3 Intestinal Microbiome 263 7.5.3.1 Establishment of Intestinal Flora 263 7.5.3.2 The Healthy Gut 264 7.5.3.3 Influence of the Intestine on Human Health 265 7.5.3.4 Obesity, Diabetes, and Health Issues 266 7.5.3.5 Probiotics 269 7.6 Gut Microbiota across the Animal World 269 7.6.1 Systems of Maternal Transmission 270 7.6.2 Microbiota of Ruminates and Hindgut Fermenters 270 7.6.3 Gut Microbiota of Bears 275 7.6.4 Microbiota of Birds 275 7.6.5 Intestinal Bacteria of Fish 278 7.7 Insect–Fungus Symbiosis 279 7.7.1 Scale Insects and Septobasidium 279 7.7.2 Attine Ant–Fungus Symbiosis 279 7.7.3 Woodwasp–Fungus Symbiosis 280 7.7.4 Ambrosia Beetles–Fungus 281 7.7.5 Termite–Fungus 281 7.8 Mutualisms Involving Insects and Bacteria 282 7.8.1 Aphids–Buchnera and Endosymbionts 282 7.8.2 Wolbachia–Insects 283 7.8.3 Mealybug–Bacteria 283 7.8.4 Termite Gut–Bacteria 284 7.9 Mutualisms Involving Invertebrates 285 7.9.1 Microbiome of Marine Worms 285 7.9.2 Squid (Euprymna)–Vibrio fischeri Symbiosis 286 7.9.3 Medicinal Leech–Aeromonas sp. and Rikenella‐like Bacteria 287 7.9.4 Nematode–Bacteria 288 7.10 Summary 288 Discussion Questions 289 References 290 Further Reading 295 8 Microbes Driving the Nutrient Cycles 297 8.1 Overview and Focus 297 8.2 Nutrient Cycles and What Drives Them 297 8.3 The Aerobic Environment 299 8.3.1 The “Great Oxidation Event” 299 8.3.2 Oxygen Cycle 300 8.3.3 Hydrogen Peroxide and ROS 303 8.4 Carbon – A Renewable Resource 304 8.4.1 Carbon Dioxide Fixation and Carbonate Reduction 305 8.4.2 Methanogenesis, Methanotrophy, and Methylotrophy 306 8.4.3 Mineralization of Carbon Compounds 308 8.4.4 Production and Utilization of CO 311 8.4.5 Production and Utilization of Hydrogen Cyanide 312 8.5 Nitrogen for Biosynthesis and Energy 312 8.5.1 Nitrification 314 8.5.2 Denitrification 314 8.5.3 Nitrate Reduction 315 8.5.4 Nitrite Reductase 316 8.5.5 Metabolism of NO and N 2 O 316 8.5.6 Production of NO by NOS 317 8.5.7 Respiratory Ammonification 317 8.5.8 Anammox Reaction 318 8.5.9 Assimilation of Nitrogen 318 8.5.10 Dinitrogen Fixation 318 8.6 Sulfur Cycling 319 8.6.1 Oxidation of Hydrogen Sulfide 320 8.6.2 Oxidation of Elemental Sulfur 321 8.6.3 Dissimilative S 0 Reduction 321 8.6.4 Dissimilative Sulfate Reduction 322 8.6.5 Assimilatory Sulfate Reduction 322 8.6.6 Production of H 2 S and Dimethyl Sulfide 322 8.6.6.1 Hydrogen Sulfide 322 8.6.6.2 Dimethyl Sulfide 323 8.7 Cycling of Trace Elements 324 8.7.1 Iron 324 8.7.2 Manganese 326 8.8 Phosphorus Cycling 328 8.9 Selenium Cycling 330 8.10 Cycling Toxic Elements 331 8.10.1 Mercury 331 8.10.2 Arsenic 332 8.11 Summary 335 Discussion Questions 335 References 336 Further Reading 340 9 Bioremediation Using Microorganisms 341 9.1 Overview and Focus 341 9.2 Microbial Bioremediation: Strategies and Applications 341 9.2.1 Biostimulation 343 9.2.2 Bioaugmentation 344 9.2.2.1 Indigenous Bacteria 344 9.2.2.2 Genetically Modified Organisms 344 9.2.3 Intrinsic Bioremediation 345 9.2.4 Microbial Consortium 345 9.2.5 Co‐metabolism 346 9.3 Organic Compounds and Xenobiotics Degraded 347 9.3.1 Pesticides 347 9.3.2 Chlorinated Organic Compounds 348 9.3.2.1 Chloroethylenes 349 9.3.2.2 Chloromethanes 350 9.3.2.3 Polychlorinated Biphenyl Compounds 351 9.3.3 Population Dynamics in Degradation of Hydrocarbons 352 9.3.3.1 Oil Spills 352 9.3.3.2 Fuel Hydrocarbons 353 9.3.3.3 Polyaromatic Hydrocarbons 355 9.3.3.4 Azo Dyes 357 9.3.4 Explosives 357 9.3.4.1 Trinitrotoluene 357 9.3.4.2 RDX and HMX 359 9.3.4.3 Perchlorate 359 9.3.5 Bioremediation and Detoxification of Metal(loid)s 359 9.3.5.1 Dissimilatory Metal(loid) Reduction 360 9.3.5.2 Methylation Reactions 361 9.4 Design of Systems for Bioremediation 362 9.4.1 In Situ vs Ex Situ 362 9.4.2 Bioreactors 363 9.4.3 Biofarming 363 9.4.4 Permeable Reactive Barriers 363 9.4.5 Groundwater and Lagoon Treatment 363 9.4.6 Bioventing 364 9.5 Summary 364 Discussion Questions 364 References 365 Further Reading 370 10 Biocorrosion and Geomicrobiology 371 10.1 Overview and Focus 371 10.2 Microbially Influenced Corrosion (MIC) of Ferrous Metals 371 10.2.1 Current Theories of Biocorrosion 371 10.2.1.1 Emic 373 10.2.1.2 Cmic 374 10.2.1.3 Iron Sulfide Crusts 374 10.2.1.4 Biofilms and Extracellular Matrix 374 10.2.2 Biocorrosion of Nonferrous Materials 375 10.2.3 Control of Biocorrosion 376 10.3 Bioalteration of Rocks, Monuments, and Other Surfaces 376 10.3.1 Biofilms on Rocks and Buildings 376 10.3.2 Biodegradation of Art Objects 377 10.3.2.1 Marble Statues in Italy 377 10.3.2.2 Paintings in the Lascaux Cave in France 377 10.3.2.3 Mogao Grottoes in China 378 10.3.2.4 Damage to Frescoes 378 10.3.3 Biotechnology for Restoration of Artworks and Historic Stones 378 10.4 Biodeterioration of Concrete 380 10.5 Mineral Interaction and Biomineralization 382 10.5.1 Iron Hydroxides 382 10.5.2 Magnetic Mineral Crystals 383 10.5.3 Manganese Oxides 383 10.5.4 Carbonates 384 10.5.5 Phosphates 384 10.5.6 Sulfates 385 10.5.7 Sulfides 385 10.5.8 Clays 385 10.5.9 Uranium Precipitate and Crystals 386 10.5.10 Gold Grains 386 10.6 Interactions with Transition and Rare Earth Elements 387 10.6.1 Transition Elements 387 10.6.2 Rare Earth Elements 388 10.7 Toxic Elements 389 10.7.1 Mercury 389 10.7.2 Chromium 389 10.7.3 Arsenic 390 10.7.4 Selenium 390 10.8 Metallic and Metalloid Nanoparticles of Microbial Origin 391 10.9 Summary 393 Discussion Questions 393 References 394 Further Reading 398 11 Microbial Communities and Metabolic Networks 399 11.1 Overview and Focus 399 11.2 Examples of Succession of Populations 399 11.2.1 Development of Coral Black Band Disease 400 11.2.2 Population Succession in Production of Dairy Products 400 11.2.3 Population Dynamics in Fermentation of Non‐dairy Foods 401 11.2.3.1 Kimchi 401 11.2.3.2 Coffee 401 11.2.3.3 Cocoa 402 11.2.3.4 Chinese Soy Sauce 402 11.2.4 Composting Plant Material 403 11.3 Impact of Climate Change on Microorganisms 403 11.3.1 Marine Environment 403 11.3.2 Soil Environment 404 11.4 Syntrophy and Co‐metabolism 406 11.5 Ecosystem Created by Hydraulic Fracturing in Shale 408 11.6 Extracellular Electron Transport 408 11.6.1 Membrane‐bound Proteins 409 11.6.2 Electron Shuttling 409 11.6.3 Nanowires 410 11.6.4 Extracellular Electron Movement in Biofilms 410 11.7 Cross‐talk: Interkingdom Signaling 410 11.7.1 Microbial Endocrinology 411 11.7.2 Cross‐signaling in Nonhuman Systems 412 11.8 Evolving Systems of Interest 412 11.8.1 Polyploidy in Bacteria 412 11.8.2 Impact of Viruses and CRISPR‐cas Systems 414 11.8.3 Impact of Outer Membrane Vesicles 416 11.8.4 Atmospheric Microbiology 420 11.8.5 Long‐distance Electron Transfer 423 11.9 Summary 424 Discussion Questions 425 References 425 Further Reading 433 Index 435

Autorenportrait

Larry L. Barton is Professor Emeritus, Department of Biology, University of New Mexico. He is author or co-editor of eight books on microbiology and is founding editor of the journal Anaerobe. Dr. Barton studies the physiological activities of microorganisms, focusing on energetics of anaerobic bacteria and bacterial inorganic metabolism. R.J.C. McLean is Regents’ Professor, Department of Biology, Texas State University. His research include biofilm growth and development as well as microbial mineral formation and nanobacteria.

Back cover copy

An authoritative overview of the ecological activities of microbes in the biosphere Environmental Microbiology and Microbial Ecology presents a broad overview of microbial activity and microbes' interactions with their environments and communities. Adopting an integrative approach, this text covers both conventional ecological issues as well as cross-disciplinary investigations that combine facets of microbiology, ecology, environmental science and engineering, molecular biology, and biochemistry. Focusing primarily on single-cell forms of prokaryotes — and cellular forms of algae, fungi, and protozoans — this book enables readers to gain insight into the fundamental methodologies for the characterization of microorganisms in the biosphere. The authors draw from decades of experience to examine the environmental processes mediated by microorganisms and explore the interactions between microorganisms and higher life forms. Highly relevant to modern readers, this book examines topics including the ecology of microorganisms in engineered environments, microbial phylogeny and interactions, microbial processes in relation to environmental pollution, and many more. Now in its second edition, this book features updated references and major revisions to chapters on assessing microbial communities, community relationships, and their global impact. New content such as effective public communication of research findings and advice on scientific article review equips readers with practical real-world skills. <ul> <li>Explores the activities of microorganisms in specific environments with case studies and actual research data</li> <li>Highlights how prominent microbial biologists address significant microbial ecology issues</li> <li>Offers guidance on scientific communication, including scientific presentations and grant preparation</li> <li>Includes plentiful illustrations and examples of microbial interactions, community structures, and human-bacterial connections</li> <li>Provides chapter summaries, review questions, selected reading lists, a complete glossary, and critical thinking exercises</li> </ul> Environmental Microbiology and Microbial Ecology is an ideal textbook for graduate and advanced undergraduate courses in biology, microbiology, ecology, and environmental science, while also serving as a current and informative reference for microbiologists, cell and molecular biologists, ecologists, and environmental professionals.

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