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| Preface | |
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| Ecology and Evolution | |
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| Core Concepts in Studying Ecology and Evolution | |
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| The Beginnings of Microbiology | |
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| Viruses | |
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| Bacteria | |
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| Photosynthetic Bacteria | |
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| Gliding Bacteria | |
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| Sheathed Bacteria | |
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| Budding and Prosthecate Bacteria | |
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| Spirochetes | |
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| Spiral and Curved Bacteria | |
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| Strictly Aerobic Gram-Negative Rods | |
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| Facultative Anaerobic Gram-Negative Rods | |
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| Strictly Anaerobic Gram-Negative Rods | |
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| Nonphotosynthetic Autotrophic Bacteria | |
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| Gram-Negative Cocci | |
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| Gram-Positive Cocci | |
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| Endospore-Forming Bacteria | |
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| Non-Spore-Forming, Gram-Positive Rods | |
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| Branching Bacteria | |
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| Obligate Intracellular Bacteria | |
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| Ecology Becomes a Science | |
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| Evolution | |
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| Natural Selection | |
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| Patterns of Selection | |
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| Evolutionary Ecology | |
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| Molecules and Origins of Life | |
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| Chemistry of Life | |
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| Water | |
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| Biological Elements | |
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| Early Atmosphere and the Beginnings of Life | |
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| Miller Flask Experiment | |
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| Which Molecule Came First? | |
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| Genes-First Models | |
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| Proteins-First Models | |
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| Dual-Origin Models | |
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| Species Concepts and Speciation | |
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| Universal Species Concept | |
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| Biological Species Concept | |
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| Phenetic and Related Species Concepts | |
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| Evolutionary Species Concept | |
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| Phylogenetic Species Concept | |
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| Bacterial Taxonomy | |
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| Bacterial Species Concepts | |
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| Application of the Phenetic Species Concept to Bacteria | |
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| Application of the Phylogenetic Species Concept | |
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| Speciation | |
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| Bacterial Speciation | |
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| Mismatch Repair as a Speciation Mechanism | |
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| Rapid Speciation? | |
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| Operons | |
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| Genome Economization and Speciation | |
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| Hypermutation | |
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| Genome Reduction | |
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| Ecology of Individuals | |
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| The Individual | |
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| What Is an Individual? | |
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| Study of Individuals | |
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| Study of Individual Microorganisms | |
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| Genetic Individuals | |
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| Ramets | |
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| Ecological Individual | |
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| Niche | |
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| Abiotic Constraints | |
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| Growth and Feeding | |
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| Growth and Surface-to-Volume Ratios | |
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| Ecology of Feeding | |
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| Metabolic Energy | |
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| Role of Carbon | |
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| Microbial Feeding Strategies | |
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| Costs of Feeding | |
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| Generalists and Specialists | |
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| Optimal Foraging and Microbes | |
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| Cheating | |
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| Free-Living Microorganisms | |
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| Food Chains and Webs | |
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| Fermentations | |
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| Ecology of Sex | |
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| Reproductive Ecology | |
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| Microbial Reproduction | |
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| Conjugation | |
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| Transposons | |
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| Transformation | |
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| Transduction | |
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| Advantages and Disadvantages of Sex | |
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| Rate of Reproduction | |
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| Plasmids and Extrachromosomal DNA | |
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| When Would Plasmids Be Favorable? | |
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| Genes on Plasmids | |
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| Plasmids in Streams | |
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| Plasmids in Lakes | |
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| Hot Spots for Plasmid Transfer | |
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| Transformation in Nature | |
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| Living Together in Populations | |
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| Fundamentals of Microbial Population Ecology | |
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| Populations in Ecology | |
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| Properties of Population | |
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| Density | |
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| Natality and Fecundity | |
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| Mortality, Longevity, and Senescence | |
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| Immigration and Emigration | |
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| Microbial Population Ecology | |
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| Population Growth | |
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| Density Dependence and Independence | |
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| r and K Selection | |
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| Metapopulations, Multicellularity, and Modular Growth | |
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| Metapopulations | |
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| Dispersal | |
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| Modularity | |
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| Source and Sinks | |
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| Population Ecology of Genes | |
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| Sources of Phenotypic and Genotypic Variation | |
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| Sources of Genic and Chromosomal Genetic Variation | |
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| Gene Ecology | |
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| Effects of Habitats, Genome Size, Diversity, and Bacterial Communication on Population Processes | |
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| Habitats | |
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| Genome Size and Genetic Diversity | |
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| Feeding Ecology and Modular Growth | |
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| Intercellular Communication | |
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| Clones or Sex? | |
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| Bacterial Sex | |
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| Population Spatial Stability | |
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| Uniformity of Populations | |
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| Adaptation | |
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| Populations in Time | |
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| Bacterial Communication: Do Microbes Talk to Each Other? | |
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| Quorum Sensing and Infections | |
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| Evolutionary Implication of Quorum Sensing | |
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| Cell-Cell Communication in Bacteria | |
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| Quorum Sensing and Evolution | |
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| Disruption or Manipulation of Quorum Sensing Response | |
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| Eavesdropping by Bacteria | |
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| Quorum Sensing: Final Thoughts | |
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| Cannibalism, Miniaturization, and Other Ways to Beat Tough Times | |
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| Oligotrophic State of Nature | |
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| Starvation-Survival | |
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| Aging, Senescence, and Death | |
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| Dormancy or Resting State and Miniaturization | |
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| Taxis: Light, Chemicals, Water, and Temperature | |
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| Living Together in Communities | |
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| Characteristics of Communities and Diversity | |
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| Community Structure and Energetics | |
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| Species Diversity | |
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| Maintenance of Species Diversity | |
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| Origin and Maintenance of Communities | |
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| Effect of Diversity on Ecosystem Services | |
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| Molecular Techniques and Microbial Community Ecology | |
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| Methods Based on DNA or RNA | |
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| Methods Based on Fatty Acids or Lipids | |
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| Methods Based on Function or Physiology | |
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| Successional Theory | |
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| Abiotic Mechanisms of Dispersal | |
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| Community Development | |
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| Seasonality | |
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| Concepts in Community Ecology | |
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| Open-Water Communities | |
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| Biofilm Communities | |
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| Phylogenetics and Community Ecology | |
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| Soil Communities | |
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| Oral Communities | |
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| Functional Diversity | |
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| Niche Constructionists | |
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| Microbes and the Processing of Nutrients | |
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| Nutrient Cycling | |
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| Nitrogen Cycle | |
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| Fixation in Soils | |
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| Denitrification | |
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| Nitrification | |
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| Nitrogen Transformation Summary | |
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| Sulfur Biogeochemcial Transformations | |
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| Carbon Cycling | |
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| Information Spiraling | |
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| Geostatistics and the Spatial Patterns of Microbes | |
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| Species Interactions and Processes | |
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| Species Interactions | |
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| Proliferation Hypothesis | |
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| Negative Relationships | |
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| Parasitism | |
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| Predation | |
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| Bacteria and Viral Interactions | |
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| Microbial Loop | |
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| Bacteria as Predators | |
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| Neutral Relationships | |
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| Positive Relationships | |
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| Metabiosis | |
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| Symbiosis | |
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| Additional Topics in Species Interactions | |
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| Cheating and Cheaters | |
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| Cooperation | |
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| Evolutionary Arms Races | |
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| Microbe Eukaryote Interactions | |
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| Biogeography | |
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| Bibliography | |
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| Glossary | |
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| Index | |