ENVIRONMENTAL MICROBIOLOGY FROM GENOMES TO BIOGEOCHEMISTRY【2025|PDF|Epub|mobi|kindle电子书版本百度云盘下载】

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1 Significance, History, and Challenges of Environmental Microbiology1

1.1 Core concepts can unify environmental microbiology1

1.2 Synopsis of the significance of environmental microbiology2

1.3 A brief history of environmental microbiology6

1.4 Complexity of our world10

1.5 Many disciplines and their integration12

2 Formation of the Biosphere: Key Biogeochemical and Evolutionary Events23

2.1 Issues and methods in Earth′s history and evolution24

2.2 Formation of early planet Earth24

2.3 Did life reach Earth from Mars?26

2.4 Plausible stages in the development of early life29

2.5 Mineral surfaces: the early iron/sulfur world could have driven biosynthesis33

2.6 Encapsulation: a key to cellular life34

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

2.8 The rise of oxygen36

2.9 Evidence for oxygen and cellular life in the sedimentary record37

2.10 The evolution of oxygenic photosynthesis38

2.11 Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere and large pools of organic carbon43

2.12 Eukaryotic evolution: endosymbiotic theory and the blending of traits from Archaea and Bacteria45

3 Physiological Ecology: Resource Exploitation by Microorganisms52

3.1 The cause of physiological diversity: diverse habitats provide selective pressures over evolutionary time53

3.2 Biological and evolutionary insights from genomics53

3.3 Fundamentals of nutrition: carbon- and energy-source utilization provide a foundation for physiological ecology62

3.4 Selective pressures: ecosystem nutrient fluxes regulate the physiological status and composition of microbial communities64

3.5 Cellular responses to starvation: resting stages, environmental sensing circuits,gene regulation, dormancy, and slow growth69

3.6 A planet of complex mixtures in chemical disequilibrium77

3.7 A thermodynamic hierarchy describing biosphere selective pressures, energy sources, and biogeochemical reactions82

3.8 Using the thermodynamic hierarchy of half reactions to predict biogeochemical reactions in time and space85

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 rule97

3.11 The diversity of lithotrophic reactions100

4 A Survey of the Earth′s Microbial Habitats106

4.1 Terrestrial biomes107

4.2 Soils: geographic features relevant to both vegetation and microorganisms109

4.3 Aquatic habitats113

4.4 Subsurface habitats: oceanic and terrestrial121

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 microorganisms135

4.7 Extreme habitats for life and microbiological adaptations140

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

5.1 Defining cultured and uncultured microorganisms151

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 diversity162

5.5 The tree of life: our view of evolution′s blueprint for biological diversity169

5.6 A sampling of key traits of cultured microorganisms from domains Eukarya,Bacteria, and Archaea172

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 diversity194

5.9 Microbial diversity illustrated by genomics, horizontal gene transfer, and cell size199

6 Generating and Interpreting Information in Environmental Microbiology: Methods and their Limitations208

6.1 How do we know?209

6.2 Perspectives from a century of scholars and enrichment-culturing procedures209

6.3 Constraints on knowledge imposed by ecosystem complexity213

6.4 Environmental microbiology′s "Heisenberg uncertainty principle": model systems and their risks215

6.5 Fieldwork: being sure sampling procedures are compatible with analyses and goals217

6.6 Blending and balancing disciplines from field geochemistry to pure cultures223

6.7 Overview of methods for determining the position and composition of microbial communities226

6.8 Methods for determining in situ biogeochemical activities and when they occur243

6.9 Metagenomics and related methods: procedures and insights245

6.10 Discovering the organisms responsible for particular ecological processes:linking identity with activity255

7 Microbial Biogeochemistry: a Grand Synthesis281

7.1 Mineral connections: the roles of inorganic elements in life processes282

7.2 Greenhouse gases and lessons from biogeochemical modeling286

7.3 The "stuff of life": identifying the pools of biosphere materials whose microbiological transformations drive the biogeochemical cycles293

7.4 Elemental biogeochemical cycles: concepts and physiological processes313

7.5 Cellular mechanisms of microbial biogeochemical pathways329

7.6 Mass balance approaches to elemental cycles335

8 Special and Applied Topics in Environmental Microbiology346

8.1 Other organisms as microbial habitats: ecological relationships346

8.2 Microbial residents of plants and humans363

8.3 Biodegradation and bioremediation373

8.4 Biofilms399

8.5 Evolution of catabolic pathways for organic contaminants403

8.6 Environmental biotechnology: overview and eight case studies410

8.7 Antibiotic resistance423

9 Future Frontiers in Environmental Microbiology442

9.1 The influence of systems biology on environmental microbiology442

9.2 Ecological niches and their genetic basis448

9.3 Concepts help define future progress in environmental microbiology453

Glossary460

Index467