Microbial Ecology

by Barton, Larry L.; Northup, Diana E.

• ISBN13: 9780470048177
• ISBN10: 0470048174
• Edition: 1st
• Format: Hardcover
• Copyright: 2011-10-04
• Publisher: Wiley-Blackwell

Summary

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.

Author Biography

Larry L. Barton studies the physiological activities of environmentally important microorganisms, focusing on energetics of bacterial inorganic metabolism and bacterial bioremediation. Larry has been the instructor of the course in General Microbiology for over 30 years. The author of five previous books, he was the founding editor and the initial editor-in chief of the international journal Anerobe, begun in 1995 and now published by Academic Press. Most recently, he published a college textbook on bacterial physiology.

Diana E. Northup investigates the microorganisms that inhabit caves throughout the world. Her research was featured on the Nova episode, "Mysterious Life of Caves." Within the Department of Biology at UNM, she gives lectures, directs undergraduate students in research, supervises a postdoctoral fellow, and, currently, she is mentoring a doctoral student in microbial ecology of a cave in southern New Mexico.

Table of Contents

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