Microbial Ecology (eBook)

Front cover 1
Title page 4
Copyright page 5
Table of contents 6
Preface 12
Section I: Ecology and Evolution 14
1: Core Concepts in Studying Ecology and Evolution 16
The Beginnings of Microbiology 16
Viruses 18
Bacteria 19
Photosynthetic Bacteria 20
Gliding Bacteria 20
Sheathed Bacteria 20
Budding and Prosthecate Bacteria 22
Spirochetes 22
Spiral and Curved Bacteria 22
Strictly Aerobic Gram-Negative Rods 22
Facultative Anaerobic Gram-Negative Rods 22
Strictly Anaerobic Gram-Negative Rods 22
Nonphotosynthetic Autotrophic Bacteria 23
Gram-Negative Cocci 23
Gram-Positive Cocci 23
Endospore-Forming Bacteria 23
Non–Spore-Forming, Gram-Positive Rods 23
Branching Bacteria 23
Obligate Intracellular Bacteria 23
Ecology Becomes a Science 24
Evolution 26
Natural Selection 27
Patterns of Selection 28
Evolutionary Ecology 30
2: Molecules and Origins of Life 34
Chemistry of Life 35
Water 35
Biological Elements 36
Early Atmosphere and the Beginnings of Life 37
Miller Flask Experiment 37
Which Molecule Came First? 38
Genes-First Models 41
Proteins-First Models 42
Dual-Origin Models 43
3: Species Concepts and Speciation 48
Universal Species Concept 50
Biological Species Concept 51
Phenetic and Related Species Concepts 52
Evolutionary Species Concept 52
Phylogenetic Species Concept 52
Bacterial Taxonomy 53
Bacterial Species Concepts 54
Application of the Phenetic Species Concept to Bacteria 57
Application of the Phylogenetic Species Concept 58
Speciation 58
Bacterial Speciation 61
Mismatch Repair as a Speciation Mechanism 61
Rapid Speciation? 63
Operons 64
Genome Economization and Speciation 64
Hypermutation 65
Genome Reduction 66
Section II: Ecology of Individuals 68
4: The Individual 70
What Is an Individual? 70
Study of Individuals 72
Study of Individual Microorganisms 73
Genetic Individuals 74
Ramets 74
Ecological Individual 75
Niche 76
Abiotic Constraints 76
5: Growth and Feeding 96
Growth and Surface-to-Volume Ratios 96
Ecology of Feeding 98
Metabolic Energy 99
Role of Carbon 100
Microbial Feeding Strategies 101
Costs of Feeding 104
Generalists and Specialists 106
Optimal Foraging and Microbes 106
Cheating 109
Free-Living Microorganisms 110
Food Chains and Webs 114
Fermentations 118
6: Ecology of Sex 120
Reproductive Ecology 120
Microbial Reproduction 121
Conjugation 122
Transposons 123
Transformation 123
Transduction 125
Advantages and Disadvantages of Sex 125
Rate of Reproduction 129
Plasmids and Extrachromosomal DNA 130
When Would Plasmids Be Favorable? 132
Genes on Plasmids 133
Plasmids in Streams 135
Plasmids in Lakes 136
Hot Spots for Plasmid Transfer 137
Transformation in Nature 139
Section III: Living Together in Populations 142
7: Fundamentals of Microbial Population Ecology 144
Populations in Ecology 144
Properties of Populations 144
Density 145
Natality and Fecundity 145
Mortality, Longevity, and Senescence 145
Immigration and Emigration 145
Microbial Population Ecology 146
Population Growth 146
Density Dependence and Independence 152
r and K Selection 154
8: Metapopulations, Multicellularity, and Modular Growth 162
Metapopulations 162
Dispersal 164
Modularity 165
Source and Sinks 168
Population Ecology of Genes 172
Sources of Phenotypic and Genotypic Variation 173
Sources of Genic and Chromosomal Genetic Variation 174
Gene Ecology 181
9: Effects of Habitats, Genome Size, Diversity, and Bacterial Communication on Population Processes 184
Habitats 184
Genome Size and Genetic Diversity 188
Feeding Ecology and Modular Growth 195
Intercellular Communication 198
Clones or Sex? 200
Bacterial Sex 204
10: Population Spatial Stability 208
Uniformity of Populations 208
Adaptation 210
Populations in Time 212
Bacterial Communication: Do Microbes Talk to Each Other? 213
Quorum Sensing and Infections 216
Evolutionary Implication of Quorum Sensing 217
Cell–Cell Communication in Bacteria 217
Quorum Sensing and Evolution 220
Disruption or Manipulation of Quorum Sensing Response 222
Eavesdropping by Bacteria 223
Quorum Sensing: Final Thoughts 223
Cannibalism, Miniaturization, and Other Ways to Beat Tough Times 224
Oligotrophic State of Nature 227
Starvation-Survival 229
Aging, Senescence, and Death 229
Dormancy or Resting State and Miniaturization 230
Taxis: Light, Chemicals, Water, and Temperature 233
Section IV: Living Together in Communities 238
11: Characteristics of Communities and Diversity 240
Community Structure and Energetics 240
Species Diversity 242
Maintenance of Species Diversity 247
Origin and Maintenance of Communities 248
Effect of Diversity on Ecosystem Services 250
Molecular Techniques and Microbial Community Ecology 252
Methods Based on DNA or RNA 254
Methods Based on Fatty Acids or Lipids 257
Methods Based on Function or Physiology 258
Successional Theory 260
Abiotic Mechanisms of Dispersal 261
Community Development 262
Seasonality 265
12: Concepts in Community Ecology 266
Open-Water Communities 266
Biofilm Communities 270
Phylogenetics and Community Ecology 281
Soil Communities 282
Oral Communities 283
Functional Diversity 284
Niche Constructionists 287
13: Microbes and the Processing of Nutrients 290
Nutrient Cycling 290
Nitrogen Cycle 291
Fixation in Soils 296
Denitrification 299
Nitrification 300
Nitrogen Transformation Summary 301
Sulfur Biogeochemical Transformations 301
Carbon Cycling 302
Information Spiraling 304
Geostatistics and the Spatial Patterns of Microbes 308
14: Species Interactions and Processes 310
Species Interactions 310
Proliferation Hypothesis 311
Negative Relationships 316
Parasitism 317
Predation 319
Bacteria and Viral Interactions 337
Microbial Loop 337
Bacteria as Predators 338
Neutral Relationships 341
Positive Relationships 342
Metabiosis 342
Symbiosis 342
15: Additional Topics in Species Interactions 358
Cheating and Cheaters 358
Cooperation 361
Evolutionary Arms Races 364
Microbe Eukaryote Interactions 370
Biogeography 373
Bibliography 384
Glossary 408
Index 420