Front cover -- Title page -- Copyright page -- Table of contents -- Preface -- Section I: Ecology and Evolution -- 1: Core Concepts in Studying Ecology and Evolution -- The Beginnings of Microbiology -- Viruses -- Bacteria -- Photosynthetic Bacteria -- Gliding Bacteria -- Sheathed Bacteria -- Budding and Prosthecate Bacteria -- Spirochetes -- Spiral and Curved Bacteria -- Strictly Aerobic Gram-Negative Rods -- Facultative Anaerobic Gram-Negative Rods -- Strictly Anaerobic Gram-Negative Rods -- Nonphotosynthetic Autotrophic Bacteria -- Gram-Negative Cocci -- Gram-Positive Cocci -- Endospore-Forming Bacteria -- Non-Spore-Forming, Gram-Positive Rods -- Branching Bacteria -- Obligate Intracellular Bacteria -- Ecology Becomes a Science -- Evolution -- Natural Selection -- Patterns of Selection -- Evolutionary Ecology -- 2: Molecules and Origins of Life -- Chemistry of Life -- Water -- Biological Elements -- Early Atmosphere and the Beginnings of Life -- Miller Flask Experiment -- Which Molecule Came First? -- Genes-First Models -- Proteins-First Models -- Dual-Origin Models -- 3: Species Concepts and Speciation -- Universal Species Concept -- Biological Species Concept -- Phenetic and Related Species Concepts -- Evolutionary Species Concept -- Phylogenetic Species Concept -- Bacterial Taxonomy -- Bacterial Species Concepts -- Application of the Phenetic Species Concept to Bacteria -- Application of the Phylogenetic Species Concept -- Speciation -- Bacterial Speciation -- Mismatch Repair as a Speciation Mechanism -- Rapid Speciation? -- Operons -- Genome Economization and Speciation -- Hypermutation -- Genome Reduction -- Section II: Ecology of Individuals -- 4: The Individual -- What Is an Individual? -- Study of Individuals -- Study of Individual Microorganisms -- Genetic Individuals -- Ramets -- Ecological Individual -- Niche -- Abiotic Constraints.

5: Growth and Feeding -- Growth and Surface-to-Volume Ratios -- Ecology of Feeding -- Metabolic Energy -- Role of Carbon -- Microbial Feeding Strategies -- Costs of Feeding -- Generalists and Specialists -- Optimal Foraging and Microbes -- Cheating -- Free-Living Microorganisms -- Food Chains and Webs -- Fermentations -- 6: Ecology of Sex -- Reproductive Ecology -- Microbial Reproduction -- Conjugation -- Transposons -- Transformation -- Transduction -- Advantages and Disadvantages of Sex -- Rate of Reproduction -- Plasmids and Extrachromosomal DNA -- When Would Plasmids Be Favorable? -- Genes on Plasmids -- Plasmids in Streams -- Plasmids in Lakes -- Hot Spots for Plasmid Transfer -- Transformation in Nature -- Section III: Living Together in Populations -- 7: Fundamentals of Microbial Population Ecology -- Populations in Ecology -- Properties of Populations -- Density -- Natality and Fecundity -- Mortality, Longevity, and Senescence -- Immigration and Emigration -- Microbial Population Ecology -- Population Growth -- Density Dependence and Independence -- r and K Selection -- 8: Metapopulations, Multicellularity, and Modular Growth -- Metapopulations -- Dispersal -- Modularity -- Source and Sinks -- Population Ecology of Genes -- Sources of Phenotypic and Genotypic Variation -- Sources of Genic and Chromosomal Genetic Variation -- Gene Ecology -- 9: Effects of Habitats, Genome Size, Diversity, and Bacterial Communication on Population Processes -- Habitats -- Genome Size and Genetic Diversity -- Feeding Ecology and Modular Growth -- Intercellular Communication -- Clones or Sex? -- Bacterial Sex -- 10: Population Spatial Stability -- Uniformity of Populations -- Adaptation -- Populations in Time -- Bacterial Communication: Do Microbes Talk to Each Other? -- Quorum Sensing and Infections -- Evolutionary Implication of Quorum Sensing.

Cell-Cell Communication in Bacteria -- Quorum Sensing and Evolution -- Disruption or Manipulation of Quorum Sensing Response -- Eavesdropping by Bacteria -- Quorum Sensing: Final Thoughts -- Cannibalism, Miniaturization, and Other Ways to Beat Tough Times -- Oligotrophic State of Nature -- Starvation-Survival -- Aging, Senescence, and Death -- Dormancy or Resting State and Miniaturization -- Taxis: Light, Chemicals, Water, and Temperature -- Section IV: Living Together in Communities -- 11: Characteristics of Communities and Diversity -- Community Structure and Energetics -- Species Diversity -- Maintenance of Species Diversity -- Origin and Maintenance of Communities -- Effect of Diversity on Ecosystem Services -- Molecular Techniques and Microbial Community Ecology -- Methods Based on DNA or RNA -- Methods Based on Fatty Acids or Lipids -- Methods Based on Function or Physiology -- Successional Theory -- Abiotic Mechanisms of Dispersal -- Community Development -- Seasonality -- 12: Concepts in Community Ecology -- Open-Water Communities -- Biofilm Communities -- Phylogenetics and Community Ecology -- Soil Communities -- Oral Communities -- Functional Diversity -- Niche Constructionists -- 13: Microbes and the Processing of Nutrients -- Nutrient Cycling -- Nitrogen Cycle -- Fixation in Soils -- Denitrification -- Nitrification -- Nitrogen Transformation Summary -- Sulfur Biogeochemical Transformations -- Carbon Cycling -- Information Spiraling -- Geostatistics and the Spatial Patterns of Microbes -- 14: Species Interactions and Processes -- Species Interactions -- Proliferation Hypothesis -- Negative Relationships -- Parasitism -- Predation -- Bacteria and Viral Interactions -- Microbial Loop -- Bacteria as Predators -- Neutral Relationships -- Positive Relationships -- Metabiosis -- Symbiosis -- 15: Additional Topics in Species Interactions.

Cheating and Cheaters -- Cooperation -- Evolutionary Arms Races -- Microbe Eukaryote Interactions -- Biogeography -- Bibliography -- Glossary -- Index.