Environmental microbiology and microbial ecology / Larry L. Barton and Robert J. C. McLean.

Includes bibliographical references and index

2.3 Internal Structures in Prokaryotes -- 2.3.1 Gas Vacuoles -- 2.3.2 Sulfur Globules -- 2.3.3 Polymeric Carbon Reserves -- 2.3.4 Polyphosphate Granules -- 2.3.5 Metallic Nanoparticles -- 2.4 Strategies for Culturing Microorganisms -- 2.4.1 Overview -- 2.4.2 Approaches for Isolation of Microorganisms -- 2.4.3 Establishing Microbial Communities -- 2.4.4 The iChip and Growing Uncultured Bacteria -- 2.5 Molecular Detection -- 2.5.1 Characterization of Microorganisms Using Genomics and Metagenomics -- 2.5.2 Physiological Analysis Using Metatranscriptomics and Metaproteomics -- 2.5.3 Lipid Biomarker Profiles -- 2.6 Examining Bacteria that Do Not Grow as Pure Cultures in the Laboratory -- 2.6.1 Host-dependent Microorganisms -- 2.6.1.1 Bacteria as Obligate Pathogens -- 2.6.1.2 Bacteria as Endosymbionts -- 2.6.1.3 The Nanoarchaeum-Ignicoccus Relationship -- 2.6.2 Molecular Analysis of Uncultivable Bacteria -- 2.7 Microbial Community Structures -- 2.7.1 Primary Production and Microbial Communities -- 2.7.2 Biofilms -- 2.7.3 Role of Quorum Sensing -- 2.8 Summary -- Discussion Questions -- References -- Further Reading -- Web Sites -- Chapter 3 Terrestrial Systems: Soil and Subsurface Environments -- 3.1 Overview and Focus -- 3.2 Soil: An Environment for Microorganisms -- 3.2.1 Soil Horizons -- 3.2.2 Soil Organic Matter (SOM) -- 3.3 Soil Microbiology -- 3.3.1 Soil Prokaryotes -- 3.3.2 Soil Fungi -- 3.3.3 Soil Crusts -- 3.3.4 Soil Invertebrates and Burrowing Animals -- 3.3.5 The Rhizosphere and Associated Bacteria -- 3.4 Understanding Soil Ecosystems -- 3.4.1 The Carbon : Nitrogen Ratio -- 3.4.2 The Fungi : Bacteria Ratio -- 3.4.3 SOM and Soil Food Webs -- 3.4.4 Influence of Agricultural Management on the Soil Microbe Community -- 3.4.5 Impact of Viruses on the Soil Microbiota -- 3.5 Subsurface Microbiology -- 3.5.1 Groundwater -- 3.5.2 Cave Water.

3.5.3 Deep Subsurface Aquifers -- 3.5.3.1 Aquifer in a Coal-bearing Basin -- 3.5.3.2 Deep Granitic Aquifer -- 3.5.3.3 Anaerobic, Alkaline Aquifer -- 3.5.3.4 Saline Hydrothermal Aquifer -- 3.6 Deep Subsurface Microbiology -- 3.6.1 Marine Sediment Microbiology -- 3.6.2 Deep Mines and Boreholes -- 3.6.3 Deep Subsea Floor -- 3.6.4 Deep Subsurface Storage Sites -- 3.6.4.1 Storage of Nuclear Fuel Waste -- 3.6.4.2 Underground Storage for H2 and CH4 -- 3.6.4.3 Underground Storage for CO2 -- 3.6.4.4 Geothermal Energy Production -- 3.6.5 Endolithic Microorganisms -- 3.7 Life in Deep Subsurfaces -- 3.7.1 Adjusting to a Subsurface Diet -- 3.7.2 Energy Sources in the Deep Biosphere -- 3.7.3 The Benefit of Living Together -- 3.8 Geomicrobiology -- 3.8.1 Rock and Mineral Weathering -- 3.8.2 Mineral Transformations -- 3.8.3 Microbial Metal Binding -- 3.8.4 Microbiota of Subsurface Crystals -- 3.9 Summary -- Discussion Questions -- References -- Further Reading -- Web Sites -- Chapter 4 Aquatic Surface Environments: Freshwater, Marine, and Wastewater -- 4.1 Overview and Focus -- 4.2 Water as Relevant to Microbial Growth -- 4.2.1 Water Activity -- 4.3 Marine Environments and Associated Microbiomes -- 4.3.1 Marine Primary Productivity -- 4.3.2 Marine Heterotrophs -- 4.3.3 Bacterial Symbionts and Marine Hosts -- 4.3.4 Microbial EPSs, Marine Snow, and Marine Gel Particles -- 4.3.5 Brackish Water and Intertidal Zones -- 4.3.6 Coral Reefs -- 4.4 Freshwater Environments and Associated Microbiomes -- 4.4.1 Lakes and Rivers -- 4.4.2 Wetlands -- 4.4.3 The Snow and Glacier Ice Ecosystems -- 4.4.4 Microbiota of Cold and Hot Springs -- 4.4.5 Microbial Mats -- 4.5 Maintaining Populations in Low Nutrient Environments -- 4.6 Aquaculture Wastewater -- 4.7 Hormone Degradation in Fresh Water -- 4.8 Human Activities and Influence on Microbial Ecology -- 4.9 Drinking Water.

4.10 Municipal Water Treatment -- 4.11 Wastewater Treatment Systems -- 4.11.1 Septic Tanks -- 4.11.2 Municipal Wastewater Treatment -- 4.11.2.1 Primary Treatment -- 4.11.2.2 Secondary Treatment -- 4.12 Alternative Approaches for Wastewater Treatment -- 4.13 Coliforms and Other Indicator Organisms -- 4.14 Viruses in Aquatic Environments: Diversity and Activity -- 4.15 Summary -- Discussion Questions -- References -- Further Reading -- Chapter 5 Life in Extreme Environments -- 5.1 Overview -- 5.2 Sampling in Extreme Environments -- 5.3 Extreme Temperature Environments -- 5.3.1 Psychrophiles -- 5.3.2 Thermophiles -- 5.3.2.1 Alpine Environment - Yellowstone National Park -- 5.3.2.2 Hydrothermal Vent Communities -- 5.3.2.3 The Guaymas Basin -- 5.4 Xerophiles -- 5.5 Piezophiles -- 5.6 Acidophiles -- 5.7 Alkaliphiles -- 5.8 Halophiles and Chaophiles -- 5.9 Radioresistant Microorganisms -- 5.10 Membrane Adaptations to Extreme Conditions -- 5.10.1 Low Temperatures -- 5.10.2 High Temperatures -- 5.10.3 pH Extremes: Low and High -- 5.11 Astrobiology -- 5.12 Nutrient Limited Environments -- 5.13 Volcanic Surfaces -- 5.14 Summary -- Discussion Questions -- References -- Further Reading -- Web Sites -- Chapter 6 Mutualism: Microorganisms and Terrestrial Plants -- 6.1 Overview and Focus -- 6.2 Cyanobacteria and the Chloroplast Ancestor -- 6.3 Lichens: Cyanobacteria/Algae-Fungi Mutualism -- 6.3.1 Distribution and Organization -- 6.3.2 Natural Products of Lichens -- 6.4 Mutualisms with Cyanobacteria as Intracellular or Epiphytic Organisms -- 6.4.1 Bryophytes -- 6.4.2 Mosses -- 6.4.3 Azolla -- 6.4.4 Gunnera -- 6.4.5 Cycads -- 6.4.6 Geosiphon -- 6.4.7 Diatoms -- 6.5 Rhizobia-Legume Symbiosis -- 6.5.1 Bacterial Species Involved -- 6.5.2 Rhizospheric Rhizobia -- 6.5.3 The Root Nodulation Process -- 6.5.4 Nodules on Plant Stems.

6.6 Frankia and the Non-legume Nitrogen-fixing Nodule -- 6.7 Mycorrhizae -- 6.7.1 Arbuscular Mycorrhizae (AM) -- 6.7.2 Ectomycorrhiza (EcM) -- 6.8 Patterns of Regulation for Plant-Microbe Mutualism -- 6.9 Bacterial-Fungal Interactions -- 6.9.1 Direct Effects -- 6.9.2 Plant Growth-promoting Bacteria -- 6.9.3 Systemic Induction of Plant Immunity -- 6.10 Endophytic Microorganisms -- 6.11 Microbiology of the Phyllosphere -- 6.12 Summary -- Discussion Questions -- References -- Further Reading -- Chapter 7 Mutualism: Microorganisms and Animals -- 7.1 Overview and Focus -- 7.2 Building a Microbial Community - The Role of the Host -- 7.2.1 Microbiology and Innate Immunity -- 7.2.2 Microbiology and Adaptive Immunity -- 7.3 Host Models to Study Parasite Relationships -- 7.3.1 Germ-free Animals -- 7.3.2 Caenorhabditis elegans -- 7.3.3 Drosophila melanogaster -- 7.3.4 Galleria mellonella -- 7.4 Digestive Tract Environment -- 7.4.1 Omnivores -- 7.4.2 Carnivores -- 7.4.3 Herbivores -- 7.4.3.1 Bacteria and Archaea -- 7.4.3.2 Anaerobic Protozoa -- 7.4.3.3 Anaerobic Fungi -- 7.4.3.4 Probiotics and Methane Mitigation Strategies -- 7.5 The Human Microbiome -- 7.5.1 Skin -- 7.5.2 Oral Microorganisms -- 7.5.3 Intestinal Microbiome -- 7.5.3.1 Establishment of Intestinal Flora -- 7.5.3.2 The Healthy Gut -- 7.5.3.3 Influence of the Intestine on Human Health -- 7.5.3.4 Obesity, Diabetes, and Health Issues -- 7.5.3.5 Probiotics -- 7.6 Gut Microbiota across the Animal World -- 7.6.1 Systems of Maternal Transmission -- 7.6.2 Microbiota of Ruminates and Hindgut Fermenters -- 7.6.3 Gut Microbiota of Bears -- 7.6.4 Microbiota of Birds -- 7.6.5 Intestinal Bacteria of Fish -- 7.7 Insect-Fungus Symbiosis -- 7.7.1 Scale Insects and Septobasidium -- 7.7.2 Attine Ant-Fungus Symbiosis -- 7.7.3 Woodwasp-Fungus Symbiosis -- 7.7.4 Ambrosia Beetles-Fungus -- 7.7.5 Termite-Fungus.

Intro -- Title Page -- Copyright Page -- Contents -- Preface -- Chapter 1 Introduction to Microorganisms and Their Activities -- 1.1 Central Themes of Environmental Microbiology and Microbial Ecology -- 1.2 Are the Terms Prokaryotes or Eukaryotes Relevant? -- 1.2.1 Intracellular Membranes in Prokaryotes -- 1.2.2 Compartmentalized Heterotrophic Bacterial Cells -- 1.2.3 The Universal Tree of Life: Rooted or Unrooted -- 1.2.4 What About the Giant Viruses? -- 1.3 Major Approach to Study Microorganisms -- 1.3.1 Application of Genomics, Metagenomics, and Proteomics -- 1.3.2 Biochemical and Physiological Analysis -- 1.4 The Impact of Horizontal Gene Transfer Between Microorganisms -- 1.4.1 Genetic Islands -- 1.4.2 Risks from Genetically Modified Organisms -- 1.4.3 Microbial Viruses and Gene Transfer Agents -- 1.5 What Determines Which Microorganisms are Present? -- 1.5.1 Metabolism as a Basis of Selection -- 1.5.2 Is Persistence of Microorganisms Dependent Only on Spore Production? -- 1.6 Is the Size and Shape of a Prokaryotic Cell Important? -- 1.6.1 Nanobacteria -- 1.6.2 Ultramicroscopic Bacteria -- 1.6.3 Very Large Bacteria -- 1.6.4 Influence of Diffusion on Bacterial Cell Form -- 1.6.5 Features of a Specific Cell Form -- 1.6.5.1 Coccus Form -- 1.6.5.2 Rod Form -- 1.6.5.3 Curved Rod or Spirochete Form -- 1.6.5.4 Unusual Forms -- 1.7 Microbial Predation -- 1.7.1 Bacteria as Prey -- 1.7.2 Bacteria as Trackers and Predators -- 1.8 Summary -- Discussion Questions -- References -- Further Reading -- Suggested Video -- Chapter 2 Microbes in the Biosphere: Examination, Cultivation, and Communities -- 2.1 Overview and Focus -- 2.2 Microscopy to Study Environmental Microbes -- 2.2.1 Light Supported Microscopy -- 2.2.2 Fluorescence Microscopy -- 2.2.3 Scanning Confocal Laser Microscopy -- 2.2.4 High Resolution by Electron Microscopy.

An authoritative overview of the ecological activities of microbes in the biosphere. Environmental Microbiology and Microbial Ecology presents a broad overview of microbial activity and microbes' interactions with their environments and communities. Adopting an integrative approach, this text covers both conventional ecological issues as well as cross-disciplinary investigations that combine facets of microbiology, ecology, environmental science and engineering, molecular biology, and biochemistry. Focusing primarily on single-cell forms of prokaryotes - and cellular forms of algae, fungi, and protozoans - this book enables readers to gain insight into the fundamental methodologies for the characterization of microorganisms in the biosphere. The authors draw from decades of experience to examine the environmental processes mediated by microorganisms and explore the interactions between microorganisms and higher life forms. Highly relevant to modern readers, this book examines topics including the ecology of microorganisms in engineered environments, microbial phylogeny and interactions, microbial processes in relation to environmental pollution, and many more. --Amazon.com