Environmental microbiology / Eugene L. Madsen.

Includes bibliographical references and index.

1Significance, History, and Challenges of Environmental Microbiology, 00 1.1Core concepts can unify environmental microbiology, 00 1.2Synopsis of the significance of environmental microbiology, 00[JA1] 1.3A brief history of environmental microbiology 1.4Complexity of our world 1.5Many disciplines and their integration 2Formation of the Biosphere: Key Biogeochemical and Evolutionary Events, 00 2.1Issues and methods in Earth?s history and evolution 2.2Formation of early planet Earth 2.3Did life reach Earth from Mars? 2.4Plausible stages in the development of early life 2.5Mineral surfaces: the early iron/sulfur world could have driven biosynthesis 2.6Encapsulation: a key to cellular life 2.7A plausible definition of the tree of life?s ?last universal common ancestor? 2.8The rise of oxygen 2.9Evidence for oxygen and cellular life in the sedimentary record 2.10The evolution of oxygenic photosynthesis 2.11Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere and large pools of organic carbon 2.12Eukaryotic evolution: endosymbiotic theory and the blending of traits from Archaea and Bacteria 3Physiological Ecology: Resource Exploitation by Microorganisms, 00 3.1The cause of physiological diversity: diverse habitats provide selective pressures over evolutionary time 3.2Biological and evolutionary insights from genomics 3.3Fundamentals of nutrition: carbon- and energy-source utilization provide a foundation for physiological ecology 3.4Selective pressures: ecosystem nutrient fluxes regulate the physiological status and composition of microbial communities 3.5Cellular responses to starvation: resting stages, environmental sensing circuits, gene regulation, dormancy, and slow growth 3.6A planet of complex mixtures in chemical disequilibrium 3.7A thermodynamic hierarchy describing biosphere selective pressures, energy sources, and biogeochemical reactions 3.8Using the thermodynamic hierarchy of half reactions to predict biogeochemical reactions in time and space 3.9Overview of metabolism and the ?logic of electron transport? 310The flow of carbon and electrons in anaerobic food chains: syntrophy is the rule 3.11The diversity of lithotrophic reactions 4.A Survey of the Earth?s Microbial Habitats, 00 4.1Terrestrial biomes 4.2Soils: geographic features relevant to both vegetation and microorganisms 4.3Aquatic habitats 4.4Subsurface habitats: oceanic and terrestrial 4.5Defining the prokaryotic biosphere: where do prokaryotes occur on Earth? 4.6Life at the micron scale: an excursion into the microhabitat of soil microorganisms 4.7Extreme habitats for life and microbiological adaptations 5Microbial Diversity: Who is Here and How do we Know?, 000 5.1Defining cultured and uncultured microorganisms 5.2Approaching a census: an introduction to the environmental microbiological ?toolbox? 5.3Criteria for census taking: recognition of distinctive microorganisms (species) 5.4Proceeding toward census taking and measures of microbial diversity 5.5The tree of life: our view of evolution?s blueprint for biological diversity 5.6Sampling of key traits of cultured organisms from domains Eukarya, Bacteria, and Archaea 5.7Placing the ?uncultured majority? on the tree of life: what have nonculture-based investigations revealed? 5.8Viruses: an overview of biology, ecology, and diversity 5.9Microbial diversity illustrated by genomics, horizontal gene transfer, and cell size 6Generating and Interpreting Information in Environmental Microbiology: Methods and their Limitations, 000 6.1How do we know? 6.2Perspectives from a century of scholars and enrichment culturing procedures 6.3Constraints on knowledge imposed by ecosystem complexity 6.4Environmental microbiology?s ?Heisenberg uncertainty principle?: model systems and their risks 6.5Fieldwork: being sure sampling procedures are compatible with analyses and goals 6.6Blending and balancing disciplines from field geochemistry to pure cultures 6.7Overview of methods for determining the position and composition of microbial communities 6.8Methods for determining in situ biogeochemical activities and when they occur 6.9Metagenomics and related methods: procedures and insights 6.10Discovering the organisms responsible for particular ecological processes: linking identity with activity 7Microbial Biogeochemistry: a Grand Synthesis, 000 7.1Mineral connections: the roles of inorganic elements in life processes 7.2Greenhouse gases and lessons from biogeochemical modeling 7.3The ?stuff of life?: identifying the pools of biosphere materials whose microbiological transformations drive the biogeochemical cycles 7.4Elemental biogeochemical cycles: concepts and physiological processes 7.5Cellular mechanisms of microbial biogeochemical pathways 7.6Mass balance approaches to elemental cycles 8Special and Applied Topics in Environmental Microbiology, 000 8.1Other organisms as microbial habitats: ecological relationships 8.2Microbial residents of plants and humans 8.3Biodegradation and bioremediation 8.4Biofilms 8.5Evolution of catabolic pathways for organic contaminants 8.6Environmental biotechnology: overview and eight case studies 8.7Antibiotic resistance 9Future Frontiers in Environmental Microbiology, 000 9.1The influence of systems biology on environmental microbiology 9.2Ecological niches and their genetic basis 9.3Conceptualizations help define future progress in environmental microbiology

Significance, history, and challenges of environmental microbiology -- Formation of the biosphere : key biogeochemical and evolutionary events -- Physiological ecology : resource exploitation by microorganisms -- A survey of the earth\'s microbial habitats -- Microbial diversity : who is here and how do we know? -- Generating and interpreting information in environmental microbiology : methods and their limitations -- Microbial biogeochemistry : a grand synthesis -- Special and applied topics in environmental microbiology -- Future frontiers in environmental microbiology.

Eugene L. Madsen presents a state-of-the-art treatment of microbial diversity and 'cultured' versus 'non-cultured' microbial life. The text is filled with inquiry-driven facts, principles, and perspectives derived from genomics, earth science, and biotechnology.