Microbial Ecology

An Evolutionary Approach


  • J McArthur, Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, U.S.A.

Based on the thesis that insights into both evolution and ecology can be obtained through the study of microorganismsm, Microbial Ecology examines microbiology through the lens of evolutionary ecology. Measured from a microbial perspective, this text covers such topics as optimal foraging, genome, reduction, novel evolutionary mechanisms, bacterial speciation, and r and K selection. Numerous aspects of microbial existence are also discussed and include: species competition, predation, parasitism, mutualism, microbial communication through quorum sensing and other . The result is a context for understanding microbes in nature and a framework for microbiologists working in industry, medicine, and the environment.
View full description


Students in ecology of microorganisms. Prerequisite would be a general microbiology course. Readers of the following journals: Appllied and Environmental Microbiology, Microbial Ecology, Environmental Microbiology, Ecology, FEMS Microbial Ecology, Ecological Society of America, etc.


Book information

  • Published: February 2006
  • ISBN: 978-0-12-369491-1


"The author does an excellent job in describing fundamental concepts in evolutionary ecology and discussing how these concepts may apply to microorganisms in natural environments. It is unique in that it focuses on general ecological and evolutionary principles instead of rehashing information that could be found in current microbiology textbooks. This book would be most appropriate for readers that already have a solid background in microbiology and are interested in exploring the emerging field of microbial ecology." - Noah Fierer, University of Colorado, in ECOLOGY "Even medical microbiologists, who still isolate and study pathogens in pure culture, now, recognize that we can truly fathom microbial life only studying heterogeneous, evolving communities of microorganisms. Vaun McArthur set out to portray this wider reality, and has succeeded..." - Bernard Dixon in BIOLOGIST

Table of Contents

Section 1 Ecology and Evolution Chapter 1 Core Concepts in Studying Ecology and Evolution 1.1 The beginnings of microbiology 1.2 Viruses 1.3 Bacteria 1.3.1. Photosynthetic Bacteria 1.3.2 Gliding bacteria 1.3.3 Sheathed Bacteria 1.3.4 Budding and Prosthecate Bacteria 1.3.5 Spirochetes 1.3.6 Spiral and Curved Bacteria 1.3.7 Strictly Aerobic Gram-negative Rods 1.3.8 Facultative Anaerobic Gram-negative Rods 1.3.9 Strictly Anaerobic Gram-negative Rods 1.3.10 Nonphotosynthetic Autotrophic Bacteria 1.3.11 Gram-negative Cocci 1.3.12 Gram-positive Cocci 1.3.13 Endospore forming Bacteria 1.3.14 Nonspore-forming Gram-Positive Rods 1.3.15 Branching bacteria 1.3.16 Obligate Intracellular Bacteria 1..4 Ecology becomes a science 1.5 Evolution 1.5.1 Natural selection 1.5.2 Patterns of Selection 1.6 Evolutionary ecology Chapter 2 Molecules and origins of life 2.1 Chemistry of life 2.1.1 Water 2.1.2 Biological Elements 2.2 Early Atmosphere and the beginnings of life 2.2.1 Miller Flask Experiment 2.2.2 Which molecule came first? 2.2.3 Genes first models 2.2.4 Proteins first models 2.2.5 Dual origin models Chapter 3 Species concepts and speciation 3.1 Universal Species Concept 3.2 Biological Species Concept 3.3 Phenetic and Related Species Concepts 3.4 Evolutionary Species Concept 3.5 Phylogenetic Species Concept 3.6 Bacterial Taxonomy 3.7 Bacterial Species Concepts 3.7.1 Application of the Phenetic Species concept to bacteria 3.7.2 Application of the phylogenetic species concept 3.8 Speciation 3.9 Bacterial Speciation 3.10 Mismatch Repair as a speciation mechanism 3.11 Rapid Speciation? 3.12 Operons 3.12 Genome economization and speciation 3.13 Hypermutation 3.14 Genome Reduction Section 2 Ecology of Individuals Chapter 4 The individual 4.1 What is an individual? 4.2 Study of Individuals 4.3 Study of Individual Microorganisms 4.4 Genetic Individuals 4.5 Ramets 4.6 Ecological Individual 4.7 Niche 4.7.1 Abiotic Constraints Chapter 5 Growth and Feeding 5.1 Growth and surface to volume ratios 5.2 Ecology of Feeding 5.3 Metabolic Energy 5.4 Role of Carbon 5.5 Microbial Feeding Strategies 5.6 Costs of Feeding 5.7 Generalists and Specialists 5.8 Optimal Foraging and Microbes 5.9 Cheating 5.10 Free-living microorganisms 5.11 Food Chains and Webs 5.12 Fermentations Chapter 6 Ecology of Sex 6.1 Reproductive Ecology 6.2 Microbial Reproduction 6.2.1 Conjugation 6.2.2 Transposons 6.2.3 Transformation 6.2.4 Transduction 6.3 Advantages and Disadvantages of Sex 6.4 Rate of Reproduction 6.5 Plasmids and extra-chromosomal DNA 6.6 When would plasmids be favorable? 6.6.1 Genes on Plasmids 6.6.2 Plasmids in streams 6.6.3 Plasmids in lakes 6.6.4 Hot spots for plasmids transfer 6.7 Transformation in nature Section 3 Living Together in Populations Chapter 7 Fundamentals of microbial population ecology 7.1 Introduction 7. 2 Properties of populations 7.2.1 Density 7.2.2 Natality and fecundity 7.2.3 Mortality, longevity and senescence 7.2.4 Immigration and emigration 7. 3 Microbial population ecology 7.3.1 Population growth 7.3.2 Density dependence and independence 7.3.3 r and K selection Chapter 8 Metapopulations, Multicellularity, and Modular Growth 8.1 Metapopulations 8.2 Dispersal 8.3 Modularity 8.4 Source and Sinks 8.5 Population ecology of genes 8.6 Sources of phenotypic and genotypic variation8.7 Sources of genic and chromosomal genetic variation 8.8 Gene Ecology Chapter 9 Effects of Habitats, Genome size, Diversity and Bacterial Communication on population processes 9.1 Habitats 9.2 Genome Size and Genetic Diversity 9.3 Feeding ecology and Modular growth 9.4 Intercellular Communication 9.5 Clones or sex? 9.6 Bacterial Sex Chapter 10 Population Spatial Stability 10.1 Uniformity of Populations 10.2 Adaptation 10.3 Populations in Time 10.4 Bacterial communication: Do microbes talk to each other? 10.5 Quorum Sensing and Infections 10.5.1 Evolutionary implication of Quorum sensing10.5.2 Cell-cell communication in bacteria 10.5.3 Quorum sensing and evolution 10.5.4 Disruption or manipulation of quorum sensing response 10.5.5 Eavesdropping by bacteria 10.5.6 Quorum sensing – final thoughts 10.6 Cannibalism, miniaturization and other ways to beat tough times 10.6.1 Oligotrophic state of nature 10.6.2 Starvation-survival 10.6.3 Ageing and senescence and death 10.6.4 Dormancy or resting state and miniaturization10.7 Taxis – light, chemicals, water, and temperature Section 4 Living Together in Communities Chapter 11 Characteristics of Communities and Diversity 11.1 Community Structure and Energetics 11.2 Species Diversity 11.3 Maintenance of Species Diversity 11.4 Origin and Maintenance of Communities 11.5 Effect of diversity on ecosystem services 11.6 Molecular Techniques and Microbial Community Ecology 11.6.1 Methods based on DNA/RNA 11.6.2 Methods based on Fatty Acids or Lipids 11.6.3 Methods based on Function/Physiology 11.7 Successional Theory 11.8 Abiotic Mechanisms of Dispersal 11.9 Community Development 11.10 Seasonality Chapter 12 Concepts in Community Ecology 12.1 Open Water Communities 12.2 Biofilm Communities 12.3 Phylogenetics and community ecology 12.4 Soil Communities 12.5 Oral Communities 12.6 Functional Diversity 12.7 Niche Constructionists Chapter 13 Microbes and the processing of Nutrients 13.1 Nutrient Cycling 13.2 Nitrogen Cycle 13.2.1 Fixation in Soils 13.2.2 Denitrification 13.2.3 Nitrification 13.2.4. Nitrogen transformation summary 13.3 Sulfur Biogechemcial Transformations 13.4 Carbon Cycling 13.5 Information Spiraling 13.6 Geostatistics and the spatial patterns of microbes Chapter 14 Species Interactions and Processes 14.1 Species Interactions 14.2 Proliferation Hypothesis 14.3 Negative relationships 14.3.1 Parasitism 14.3.2 Predation Satiating the Predator 14.3.4 Bacteria and viral interactions 14.3.5 Microbial Loop 14.3.6 Bacteria as Predators 14.4 Neutral Relationships 14.5 Positive relationships 14.5.1 Metabiosis 14.5.2 Symbiosis Chapter 15 Additional Topics in Species Interactions15.1 Cheating and cheaters 15.2 Cooperation 15.3 Evolutionary Arms Races 15.4 Microbe Eukaryote Interactions 15.5 Biogeography Bibliography Glossary Figure Legends