Microbial Ecology

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.

Preface xvii Glossary xix

1 Microbial Ecology: Beginnings and the Road Forward 1

1.1 Central Themes 1

1.2 Introduction 2

1.2.1 Roots of Microbial Ecology 3

1.2.2 Current Perspectives 4

1.3 Timeline 5

1.4 Microfossils 7

1.5 Early Life 9

1.5.1 The Precellular World 9

1.5.2 The First Cell 10

1.5.3 Development of Cellular Biology 11

1.5.4 Evolution of Metabolic Pathways 12

1.6 Characteristics of Microbial Life 13

1.6.1 Structure and Evolution of Cell Shape 13

1.6.2 Metabolism and Use of Energy 16

1.6.3 Growth, Reproduction, and Development 17

1.6.4 Adaptations and Response to Stimuli 18

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

1.10.1 Change in Focus 23

1.10.2 Diversity: From Culturing to Molecular Phylogeny 24

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

2.3.1 Comparison of the Three Domains 32

2.3.2 What’s in a Name: Prokaryotes 32

2.3.3 Winogradsky’s Experiments with Chemolithotrophs 32

2.4 Diversity of Bacterial Groups 33

2.4.1 Expansion of the Number of Bacterial Phyla 33

2.4.2 Bacterial Portrait Gallery: Processes and Players 35

2.5 Discovery of Archaea as a Separate Domain 38

2.6 Archaeal Diversity 39

2.6.1 Archaeal Portrait Gallery 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

3.3.1 Life at the Lowest Level 64

3.3.2 Large Microorganisms 66

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

3.7.1 Cell Attachment 76

3.7.2 Biofilms 78

3.7.3 Filamentous Growth 82

3.8 Cell Physiology and Metabolism 84

3.8.1 Sensory Response 84

3.8.2 Global Regulation 86

 3.8.3 Internal Membranes in Bacteria 87

3.9 Energetics and Environment 88

3.9.1 Heterotrophs 88

3.9.2 Chemolithotrophs 91

3.9.3 Photophosphorylation 94

3.9.4 Bacteriorhodopsin Reaction 94

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

4.2.1 The Niche 105

4.3 Aquatic Habitats 105

4.3.1 Freshwater 107

4.3.2 Marine Habitats 110

4.4 Soil Habitats 111

4.4.1 Microbial Food Webs in the Soil Habitat 112

4.5 Rock and Subsurface Habitats 117

4.5.1 Rock Varnish 117

4.5.2 Cave Habitats 119

4.5.3 Groundwater 120

4.5.4 Deep Subsurface 120

4.6 Atmospheric Habitats 121

4.6.1 Atmospheric Microbial Diversity: African Dust 121

4.6.2 Mysteries Remain 122

4.7 Population Ecology Across Habitats 124

4.7.1 Population Growth and Dynamics 124

4.7.2 Horizontal Gene Transfer 125

4.7.3 Biogeograpy versus Everything is Everywhere; the Environment Selects 126

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 135

5.4.1 Gram Stains 135

5.4.2 Direct Count Procedures 135

5.4.3 Determining Actively Respiring Cells 136

5.4.4 Fluorescent in situ Hybridization (FISH) 137

5.4.5 Electron Microscopy 139

5.5 Cultivation of Microorganisms 139

5.5.1 Microbial Respiration 144

5.5.2 Microbial Biomass 144

5.5.3 Measuring Carbon Substrate Utilization 145

5.6 Molecular Phylogenetics 146

5.7 Culturing Versus Molecular Techniques: Comparisons from Soil Studies 148

5.8 Community Fingerprinting Methods 149

5.8.1 Denaturing Gradient Gel Electrophoresis 149

5.9 Metagenomics: A New Tool for Answering Community Ecology Questions 149

5.10 Environmental Proteomics 150

5.11 Stable-Isotope Studies 152

5.11.1 Using Stable Isotopes: Movile Cave Food Web Case Study 153

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

6.3.1 Neutralism 162

6.3.2 Commensalism 162

6.3.3 Competition 162

6.3.4 Parasitism 163

6.3.5 Predation 164

6.3.6 Antagonism (Amensalism) 164

6.3.7 Syntrophism 167

6.4 Symbiotic Associations 168

6.4.1 Diatoms 168

6.4.2 Lichen 169

6.4.3 Hatena 171

6.4.4 Symbiosis between Bacteria and Protozoa 173

 6.5 Fungus–Bacterium Symbiosis 174

6.6 Prokaryote–Prokaryote Interactions 174

6.6.1 Two-Member Mutualism 174

6.6.2 Examples of Parasites and Predators 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

7.5.1 Ectomycorrhizae 190

7.5.2 Endomycorrhizae 193

7.5.3 Other Mycorrhizal Associations 193

7.6 Nitrogen-Fixing Bacteria and Higher Plants 195

7.6.1 Root Associations 195

7.6.2 Stem Associations 202

7.7 Bacteria Supporting Plant Growth 202

7.7.1 Production of Hormones 202

7.7.2 Growth-Promoting Rhizobacteria 202

7.7.3 Cactus Symbiosis 204

7.8 Leaf Surfaces and Microorganisms 205

7.9 Detrimental Activities of Microorganisms on Plants 206

7.9.1 Fungal Parasites 206

7.9.2 Bacterial Pathogens 207

7.9.3 Rhizosphere Activities and Plant Diseases 209

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

8.4.1 Parasitism Introduction 223

8.4.2 Nematode Parasitism of Insects 223

8.4.3 Effects of Multiple Parasitic Infections on Virulence 224

8.4.4 A Widespread Endosymbiosis: Wolbachia —Parasitism or Mutualism? 224

8.5 Microbe–Animal Interactions: Mutualism 225

8.5.1 Gut Animal–Microbe Mutualistic Interactions 225

8.5.2 Case Study: Unique Bacterial–Polychaete Endosymbiosis 227

8.5.3 Case Study: Beetles Cultivating Fungal Gardens 228

8.5.4 Mealybug Mutualisms 229

8.5.5 Luminescent Bacteria in Fish and Squid:Turning on the Lights 230

8.6 Lessons from the Deep: Evolutionary and Ecosystem Insights from Deep-Sea Vents Symbioses 230

8.7 Microbial–Vertebrate Interactions 233

8.7.1 Bacteria and Birds 235

8.7.2 Microorganisms and Humans 236

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

9.2.1 Dominant Issues and Questions in Microbial Community Ecology 245

9.3 Metagenomics: A New Tool for Answering Community Ecology Questions 246

9.4 Biomats and Biofilms 247

9.4.1 Changes in Community Structure during Biofilm Succession 249

9.5 Formation of Organized Communities: Quorum Sensing 249

9.6 Colonization and Recolonization by Microorganisms 251

9.6.1 Case Study: Colonization of the Sterile Newborn Gut 252

9.6.2 Case Study: Undesirable Colonization—Factors in Disease 253

9.6.3 Case Study: Recolonization and Early Succession in Intertidal Sediments 253

9.7 Dispersal, Succession, and Stability 253

 9.7.1 Case Study: Dispersal and Succession in the Oceans—Whale Falls as Dispersal Agents between Vents 254

9.7.2 Competition as a Structuring Force in Succession 254

9.7.3 Stability in Microcosm Studies 255

9.8 Species Diversity 256

9.8.1 Diversity Indices 257

9.8.2 Connections between Metazoans and Microorganisms: Co-ocurrence Patterns 258

9.8.3 Disturbance and Diversity 258

9.9 Food Webs 259

9.9.1 Structure of Microbial Food Webs 260

9.9.2 Keystone Species Effects on Food Webs and Diversity 261

9.10 Primary Production and Energy Flow 261

9.10.1 Cycling of Nutrients 261

9.11 Microbial Community Examples 262

9.11.1 Plankton in Marine Ecosystems 263

9.11.2 Hot Springs 264

9.11.3 Wine and Cheese 266

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

10.5.1 Nitrogen Fixation 282

10.5.2 Nitrogen Assimilation 283

10.5.3 Nitrification 283

10.5.4 Denitrification 284

10.6 Sulfur Cycling 284

10.6.1 Organic Sulfur Metabolism 285

10.6.2 Inorganic Sulfur Metabolism 285

10.7 Phosphorus Cycling 286

10.8 Iron Cycling 287

10.8.1 Siderophores 288

10.8.2 Ferritin and Magnetosomes 289

 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

11.2.1 Passive versus Active Biomineralization 302

11.3 Cell Characteristics and Metal Binding 303

11.3.1 Passive Metal Adsorption 303

11.3.2 Active Metal Adsorption 303

11.4 Energy Flow: Shuffling Electrons; Redox Reactions 304

11.5 Dissolution Versus Precipitation 305

11.6 Formation of Ores and Minerals 306

11.6.1 Biomining 307

11.6.2 Recovery of Petroleum 307

11.6.3 Sulfuric Acid–Driven Speleologenesis 310

11.7 Microbial Participation in Silicification 312

11.7.1 Silica Formation in Diatoms, Radiolarians, and Sponges 312

11.7.2 Geyserites 313

11.8 Biomineralization of Ferromanganese Deposits 314

11.8.1 Magnetite Formation 314

11.8.2 Rock Varnish 315

11.9 Microbial Carbonate Microbialites 317

11.10 Stromatolites 319

11.10.1 Thrombolites 320

11.10.2 Travertines and Tufas 321

11.10.3 Coccolithophores and Foraminifera: Biologically Controlled Mineralization 323

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

12.4.1 Protopectinase and Pectinase Activities 333

12.4.2 Microbial Decomposition of Lignin 333

12.4.3 Degradation of Hemicelllose 334

12.4.4 Enzymatic Degradation of Cellulose 335

12.5 Starch Hydrolysis 336

12.6 Inulin Hydrolysis 336

12.7 Decomposition of Diverse Biopolymers Including Animal Fibrous Proteins 337

12.7.1 Chitin Digestion 337

12.7.2 Decomposition of Keratin 337

12.7.3 Fibroin Decomposition 338

12.7.4 Collagen Breakdown 339

12.8 Ecology of Fermented Foods 341

12.9 Ecology of Bioenergy Production 343

12.9.1 Alcohol Production 345

12.9.2 H2 Production 346

12.9.3 Methane Production 347

12.9.4 Biodiesel Production by Algae 348

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

13.5.1 Bioreactors 362

13.5.2 Biofarming 363

13.5.3 Permeable Reactive Barriers 363

13.5.4 Optimizing Bioremediation 363

13.6 Bioremediation of Organic Compounds 365

13.7 Degradation of Hydrocarbons 365

13.7.1 Oil Spills 366

13.7.2 Methane Utilization 366

13.7.3 Fuel Hydrocarbons 368

13.7.4 Polyaromatic Hydrocarbons 372

13.8 Degradation of Xenobiotics 373

13.8.1 Detoxification of Chlorinated Organic Compounds 375

13.8.2 Herbicides and Pesticides 376

13.8.3 Biodegradation of Explosives 377

13.8.4 Decomposition of Textile Dyes 378

13.9 Bioremediation with Inorganic Pollutants 380

13.9.1 Microbe–Toxic Metal Interactions 381

13.9.2 Detoxification of Selenium 384

13.9.3 Reactions with Arsenic 385

13.9.4 Bioremediation of Perchlorate Sites 387

13.9.5 Bioremediation of Nitrate Pollution 387

13.10 Summary 389

13.11 Delving Deeper: Critical Thinking Questions 390

index 395