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Contents Preface Section 1 Ecology and Evolution Chapter 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 Chapter 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 Chapter 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 2 Ecology of Individuals Chapter 4 The Individual What Is an Individual? Study of Individuals Study of Individual Microorganisms Genetic Individuals Ramets Ecological Individual Niche Abiotic Constraints Chapter 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 Chapter 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 3 Living Together in Populations Chapter 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 Chapter 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 Chapter 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 Chapter 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 4 Living Together in Communities Chapter 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/RNA Methods Based on Fatty Acids or Lipids Methods Based on Function/Physiology Successional Theory Abiotic Mechanisms of Dispersal Community Development Seasonality Chapter 12 Concepts in Community Ecology Open Water Communities Biofilm Communities Phylogenetics and Community Ecology Soil Communities Oral Communities Functional Diversity Niche Constructionists Chapter 13 Microbes and the Processing of Nutrients Nutrient Cycling Nitrogen Cycle Fixation in Soils Denitrification Nitrification Nitrogen Transformation Summary Sulfur Biogechemcial Transformations Carbon Cycling Information Spiraling Geostatistics and the Spatial Patterns of Microbes Chapter 14 Species Interactions and Processes Species Interactions Proliferation Hypothesis Negative Relationships Parasitism Predation Satiating the Predator Bacteria and Viral Interactions Microbial Loop Bacteria as Predators Neutral Relationships Positive Relationships Metabiosis Symbiosis Chapter 15 Additional Topics in Species Interactions Cheating and Cheaters Cooperation Evolutionary Arms Races Microbe Eukaryote Interactions Biogeography Bibliography Glossary Index
Library of Congress Subject Headings for this publication:
Microbial ecology.
Surface chemistry.
Microbiology.
Ecology.
Evolution.