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 variation
8.7 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 sensing
10.5.2 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 miniaturization
10.7 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 Interactions
15.1 Cheating and cheaters
15.2 Cooperation
15.3 Evolutionary Arms Races
15.4 Microbe Eukaryote Interactions
15.5 Biogeography
Bibliography
Glossary
Figure Legends