Environmental Microbiology: From Genomes to Biogeochemistry

Editor/Author Madsen, Eugene L.
Publication Year: 2015
Publisher: Wiley

Single-User Purchase Price: $130.00
Unlimited-User Purchase Price: $195.00
ISBN: 978-1-118-43963-0
Category: Science - Biology
Image Count: 208
Book Status: Available
Table of Contents

Environmental Microbiology: From Genomes to Biogeochemistry, Second Edition, offers a coherent and comprehensive treatment of this dynamic, emerging field, building bridges between basic biology, evolution, genomics, ecology, biotechnology, climate change, and the environmental sciences.

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Table of Contents

  • Preface
  • Chapter 1: Significance, History, and Challenges of Environmental Microbiology
  • 1.1 Core concepts can unify environmental microbiology
  • 1.2 Synopsis of the significance of environmental microbiology
  • 1.3 A brief history of environmental microbiology
  • 1.4 Complexity of our world
  • 1.5 Many disciplines and their integration
  • Study questions
  • References
  • Chapter 2: Formation of the Biosphere: Key Biogeochemical and Evolutionary Events
  • 2.1 Issues and methods in Earth's history and evolution
  • 2.2 Formation of early planet Earth
  • 2.3 Did life reach Earth from Mars?
  • 2.4 Plausible stages in the development of early life
  • 2.5 Mineral surfaces in marine hydrothermal vents: the early iron/sulfur world could have driven biosynthesis
  • 2.6 Encapsulation (a key to cellular life) and an alternative (nonmarine) hypothesis for the habitat of precellular life
  • 2.7 A plausible definition of the tree of life's “Last universal common ancestor” (LUCA)
  • 2.8 The rise of oxygen
  • 2.9 Evidence for oxygen and cellular life in the sedimentary record
  • 2.10 The evolution of oxygenic photosynthesis
  • 2.11 Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere and large pools of organic carbon
  • 2.12 Eukaryotic evolution: endosymbiotic theory and the blending of traits from Archaea and Bacteria
  • Study questions
  • References
  • Further reading
  • Chapter 3: Physiological Ecology: Resource Exploitation by Microorganisms
  • 3.1 The cause of physiological diversity: diverse habitats provide selective pressures over evolutionary time
  • 3.2 Biological and evolutionary insights from genomics
  • 3.3 Fundamentals of nutrition: carbon- and energy-source utilization provide a foundation for physiological ecology
  • 3.4 Selective pressures: ecosystem nutrient fluxes regulate the physiological status and composition of microbial communities
  • 3.5 Cellular responses to starvation: resting stages, environmental sensing circuits, gene regulation, dormancy, and slow growth
  • 3.6 A planet of complex mixtures in chemical disequilibrium
  • 3.7 A thermodynamic hierarchy describing biosphere selective pressures, energy sources, and biogeochemical reactions
  • 3.8 Using the thermodynamic hierarchy of half reactions to predict biogeochemical reactions in time and space
  • 3.9 Overview of metabolism and the “logic of electron transport”
  • 3.10 The flow of carbon and electrons in anaerobic food chains: syntrophy is the rule
  • 3.11 The diversity of lithotrophic reactions
  • Study questions
  • References
  • Further reading
  • Chapter 4: A Survey of the Earth's Microbial Habitats
  • 4.1 Terrestrial biomes
  • 4.2 Soils: geographic features relevant to both vegetation and microorganisms
  • 4.3 Aquatic habitats
  • 4.4 Subsurface habitats: oceanic and terrestrial
  • 4.5 Defining the prokaryotic biosphere: where do prokaryotes occur on Earth?
  • 4.6 Life at the micron scale: an excursion into the microhabitat of soil microorganisms
  • 4.7 Extreme habitats for life and microbiological adaptations
  • Study questions
  • References
  • Chapter 5: Microbial Diversity: Who is Here and How do we Know?
  • 5.1 Defining cultured and uncultured microorganisms
  • 5.2 Approaching a census: an introduction to the environmental microbiological “toolbox”
  • 5.3 Criteria for census taking: recognition of distinctive microorganisms (species)
  • 5.4 Proceeding toward census taking and measures of microbial diversity
  • 5.5 The tree of life: our view of evolution's blueprint for biological diversity
  • 5.6 A Sampling of key traits of cultured microorganisms from the domains Eukarya, Bacteria, and Archaea
  • 5.7 Placing the “uncultured majority” on the tree of life: what have nonculture-based investigations revealed?
  • 5.8 Viruses: an overview of biology, ecology, and diversity
  • 5.9 Microbial diversity illustrated by genomics, horizontal gene transfer, and cell size
  • 5.10 Biogeography of microorganisms
  • Study questions
  • References
  • Further reading
  • Chapter 6: Generating and Interpreting Information in Environmental Microbiology: Methods and Their Limitations1
  • 6.1 How do we know?
  • 6.2 Perspectives from a century of scholars and enrichment-cultivation procedures
  • 6.3 Constraints on knowledge imposed by ecosystem complexity
  • 6.4 Environmental microbiology's “Heisenberg uncertainty principle”: model systems and their risks
  • 6.5 Fieldwork: being sure sampling procedures are compatible with analyses and goals
  • 6.6 Blending and balancing disciplines from field geochemistry to pure cultures
  • 6.7 Overview of methods for determining the position and composition of microbial communities
  • 6.8 Methods for determining in situ biogeochemical activities and when they occur
  • 6.9 Cloning-based Metagenomics and related methods: procedures and insights
  • 6.10 Cloning-free, next-generation sequencing and omics methods: procedures and insights
  • 6.11 Discovering the organisms responsible for particular ecological processes: linking identity with activity
  • Study questions
  • References
  • Further reading
  • Chapter 7: Microbial Biogeochemistry: A Grand Synthesis
  • 7.1 Mineral connections: the roles of inorganic elements in life processes
  • 7.2 Greenhouse gases and lessons from biogeochemical modeling
  • 7.3 The “stuff of life”: identifying the pools of biosphere materials whose microbiological transformations drive the biogeochemical cycles
  • 7.4 Elemental biogeochemical cycles: concepts and physiological processes
  • 7.5 Cellular mechanisms of microbial biogeochemical pathways
  • 7.6 Mass balance approaches to elemental cycles
  • Study questions
  • References
  • Further reading
  • Chapter 8: Special and Applied Topics in Environmental Microbiology
  • 8.1 Other organisms as microbial habitats: ecological relationships
  • 8.2 Microbial residents of plants and humans
  • 8.3 Biodegradation and bioremediation
  • 8.4 BioFilms
  • 8.5 Evolution of catabolic pathways for organic contaminants
  • 8.6 Environmental biotechnology: overview and nine case studies
  • 8.7 Antibiotic resistance
  • Study questions
  • References
  • Chapter 9: Future Frontiers in Environmental Microbiology
  • 9.1 The influence of systems biology on environmental microbiology
  • 9.2 Ecological niches and their genetic basis
  • 9.3 Concepts help define future progress in environmental microbiology
  • Study questions
  • References
  • Glossary