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1 Significance, History, and Challenges of Environmental Microbiology 1

1.1 Core concepts can unify environmental microbiology 1

1.2 Synopsis of the significance of environmental microbiology 2

1.3 A brief history of environmental microbiology 6

1.4 Complexity of our world 10

1.5 Many disciplines and their integration 12

2 Formation of the Biosphere: Key Biogeochemical and Evolutionary Events 23

2.1 Issues and methods in Earth′s history and evolution 24

2.2 Formation of early planet Earth 24

2.3 Did life reach Earth from Mars? 26

2.4 Plausible stages in the development of early life 29

2.5 Mineral surfaces: the early iron/sulfur world could have driven biosynthesis 33

2.6 Encapsulation: a key to cellular life 34

2.7 A plausible definition of the tree of life′s "last universal common ancestor" 35

2.8 The rise of oxygen 36

2.9 Evidence for oxygen and cellular life in the sedimentary record 37

2.10 The evolution of oxygenic photosynthesis 38

2.11 Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere and large pools of organic carbon 43

2.12 Eukaryotic evolution: endosymbiotic theory and the blending of traits from Archaea and Bacteria 45

3 Physiological Ecology: Resource Exploitation by Microorganisms 52

3.1 The cause of physiological diversity: diverse habitats provide selective pressures over evolutionary time 53

3.2 Biological and evolutionary insights from genomics 53

3.3 Fundamentals of nutrition: carbon- and energy-source utilization provide a foundation for physiological ecology 62

3.4 Selective pressures: ecosystem nutrient fluxes regulate the physiological status and composition of microbial communities 64

3.5 Cellular responses to starvation: resting stages, environmental sensing circuits,gene regulation, dormancy, and slow growth 69

3.6 A planet of complex mixtures in chemical disequilibrium 77

3.7 A thermodynamic hierarchy describing biosphere selective pressures, energy sources, and biogeochemical reactions 82

3.8 Using the thermodynamic hierarchy of half reactions to predict biogeochemical reactions in time and space 85

3.9 Overview of metabolism and the "logic of electron transport" 95

3.10 The flow of carbon and electrons in anaerobic food chains: syntrophy is the rule 97

3.11 The diversity of lithotrophic reactions 100

4 A Survey of the Earth′s Microbial Habitats 106

4.1 Terrestrial biomes 107

4.2 Soils: geographic features relevant to both vegetation and microorganisms 109

4.3 Aquatic habitats 113

4.4 Subsurface habitats: oceanic and terrestrial 121

4.5 Defining the prokaryotic biosphere: where do prokaryotes occur on Earth? 131

4.6 Life at the micron scale: an excursion into the microhabitat of soil microorganisms 135

4.7 Extreme habitats for life and microbiological adaptations 140

5 Microbial Diversity: Who is Here and How do we Know? 150

5.1 Defining cultured and uncultured microorganisms 151

5.2 Approaching a census: an introduction to the environmental microbiological "toolbox" 155

5.3 Criteria for census taking: recognition of distinctive microorganisms （species） 158

5.4 Proceeding toward census taking and measures of microbial diversity 162

5.5 The tree of life: our view of evolution′s blueprint for biological diversity 169

5.6 A sampling of key traits of cultured microorganisms from domains Eukarya,Bacteria, and Archaea 172

5.7 Placing the "uncultured majority" on the tree of life: what have nonculture-based investigations revealed? 189

5.8 Viruses: an overview of biology, ecology, and diversity 194

5.9 Microbial diversity illustrated by genomics, horizontal gene transfer, and cell size 199

6 Generating and Interpreting Information in Environmental Microbiology: Methods and their Limitations 208

6.1 How do we know? 209

6.2 Perspectives from a century of scholars and enrichment-culturing procedures 209

6.3 Constraints on knowledge imposed by ecosystem complexity 213

6.4 Environmental microbiology′s "Heisenberg uncertainty principle": model systems and their risks 215

6.5 Fieldwork: being sure sampling procedures are compatible with analyses and goals 217

6.6 Blending and balancing disciplines from field geochemistry to pure cultures 223

6.7 Overview of methods for determining the position and composition of microbial communities 226

6.8 Methods for determining in situ biogeochemical activities and when they occur 243

6.9 Metagenomics and related methods: procedures and insights 245

6.10 Discovering the organisms responsible for particular ecological processes:linking identity with activity 255

7 Microbial Biogeochemistry: a Grand Synthesis 281

7.1 Mineral connections: the roles of inorganic elements in life processes 282

7.2 Greenhouse gases and lessons from biogeochemical modeling 286

7.3 The "stuff of life": identifying the pools of biosphere materials whose microbiological transformations drive the biogeochemical cycles 293

7.4 Elemental biogeochemical cycles: concepts and physiological processes 313

7.5 Cellular mechanisms of microbial biogeochemical pathways 329

7.6 Mass balance approaches to elemental cycles 335

8 Special and Applied Topics in Environmental Microbiology 346

8.1 Other organisms as microbial habitats: ecological relationships 346

8.2 Microbial residents of plants and humans 363

8.3 Biodegradation and bioremediation 373

8.4 Biofilms 399

8.5 Evolution of catabolic pathways for organic contaminants 403

8.6 Environmental biotechnology: overview and eight case studies 410

8.7 Antibiotic resistance 423

9 Future Frontiers in Environmental Microbiology 442

9.1 The influence of systems biology on environmental microbiology 442

9.2 Ecological niches and their genetic basis 448

9.3 Concepts help define future progress in environmental microbiology 453

Glossary 460

Index 467