Environmental Microbiology and Microbial Ecology

Larry L. Barton is Professor Emeritus, Department of Biology, University of New Mexico. He is author or co-editor of eight books on microbiology and is founding editor of the journal Anaerobe. Dr. Barton studies the physiological activities of microorganisms, focusing on energetics of anaerobic bacteria and bacterial inorganic metabolism.R.J.C. McLean is Regents’ Professor, Department of Biology, Texas State University. His research include biofilm growth and development as well as microbial mineral formation and nanobacteria.

• Preface xv1 Introduction to Microorganisms and Their Activities 11.1 Central Themes of Environmental Microbiology and Microbial Ecology 11.2 Are the Terms Prokaryotes or Eukaryotes Relevant? 11.2.1 Intracellular Membranes in Prokaryotes 21.2.2 Compartmentalized Heterotrophic Bacterial Cells 31.2.3 The Universal Tree of Life: Rooted or Unrooted 41.2.4 What About the Giant Viruses? 41.3 Major Approach to Study Microorganisms 51.3.1 Application of Genomics, Metagenomics, and Proteomics 61.3.2 Biochemical and Physiological Analysis 71.4 The Impact of Horizontal Gene Transfer Between Microorganisms 71.4.1 Genetic Islands 91.4.2 Risks from Genetically Modified Organisms 101.4.3 Microbial Viruses and Gene Transfer Agents 101.5 What Determines Which Microorganisms are Present? 121.5.1 Metabolism as a Basis of Selection 131.5.2 Is Persistence of Microorganisms Dependent Only on Spore Production? 141.6 Is the Size and Shape of a Prokaryotic Cell Important? 191.6.1 Nanobacteria 191.6.2 Ultramicroscopic Bacteria 211.6.3 Very Large Bacteria 211.6.4 Influence of Diffusion on Bacterial Cell Form 221.6.5 Features of a Specific Cell Form 221.6.5.1 Coccus Form 221.6.5.2 Rod Form 221.6.5.3 Curved Rod or Spirochete Form 231.6.5.4 Unusual Forms 231.7 Microbial Predation 231.7.1 Bacteria as Prey 231.7.2 Bacteria as Trackers and Predators 241.8 Summary 25Discussion Questions 25References 26Further Reading 312 Microbes in the Biosphere: Examination, Cultivation, and Communities 332.1 Overview and Focus 332.2 Microscopy to Study Environmental Microbes 332.2.1 Light Supported Microscopy 342.2.2 Fluorescence Microscopy 352.2.3 Scanning Confocal Laser Microscopy 372.2.4 High Resolution by Electron Microscopy 372.3 Internal Structures in Prokaryotes 412.3.1 Gas Vacuoles 412.3.2 Sulfur Globules 412.3.3 Polymeric Carbon Reserves 422.3.4 Polyphosphate Granules 432.3.5 Metallic Nanoparticles 432.4 Strategies for Culturing Microorganisms 442.4.1 Overview 442.4.2 Approaches for Isolation of Microorganisms 452.4.3 Establishing Microbial Communities 452.4.4 The iChip and Growing Uncultured Bacteria 462.5 Molecular Detection 492.5.1 Characterization of Microorganisms Using Genomics and Metagenomics 492.5.2 Physiological Analysis Using Metatranscriptomics and Metaproteomics 532.5.3 Lipid Biomarker Profiles 542.6 Examining Bacteria that Do Not Grow as Pure Cultures in the Laboratory 562.6.1 Host‐dependent Microorganisms 562.6.1.1 Bacteria as Obligate Pathogens 562.6.1.2 Bacteria as Endosymbionts 572.6.1.3 The Nanoarchaeum–Ignicoccus Relationship 582.6.2 Molecular Analysis of Uncultivable Bacteria 582.7 Microbial Community Structures 592.7.1 Primary Production and Microbial Communities 592.7.2 Biofilms 622.7.3 Role of Quorum Sensing 642.8 Summary 67Discussion Questions 68References 68Further Reading 753 Terrestrial Systems: Soil and Subsurface Environments 773.1 Overview and Focus 773.2 Soil: An Environment for Microorganisms 773.2.1 Soil Horizons 783.2.2 Soil Organic Matter (SOM) 783.3 Soil Microbiology 803.3.1 Soil Prokaryotes 803.3.2 Soil Fungi 823.3.3 Soil Crusts 833.3.4 Soil Invertebrates and Burrowing Animals 833.3.5 The Rhizosphere and Associated Bacteria 833.4 Understanding Soil Ecosystems 853.4.1 The Carbon : Nitrogen Ratio 853.4.2 The Fungi : Bacteria Ratio 853.4.3 SOM and Soil Food Webs 863.4.4 Influence of Agricultural Management on the Soil Microbe Community 893.4.5 Impact of Viruses on the Soil Microbiota 903.5 Subsurface Microbiology 903.5.1 Groundwater 903.5.2 Cave Water 923.5.3 Deep Subsurface Aquifers 923.5.3.1 Aquifer in a Coal‐bearing Basin 923.5.3.2 Deep Granitic Aquifer 933.5.3.3 Anaerobic, Alkaline Aquifer 943.5.3.4 Saline Hydrothermal Aquifer 943.6 Deep Subsurface Microbiology 953.6.1 Marine Sediment Microbiology 963.6.2 Deep Mines and Boreholes 973.6.3 Deep Subsea Floor 983.6.4 Deep Subsurface Storage Sites 983.6.4.1 Storage of Nuclear Fuel Waste 983.6.4.2 Underground Storage for H 2 and CH 4 1003.6.4.3 Underground Storage for CO 2 1013.6.4.4 Geothermal Energy Production 1023.6.5 Endolithic Microorganisms 1023.7 Life in Deep Subsurfaces 1033.7.1 Adjusting to a Subsurface Diet 1033.7.2 Energy Sources in the Deep Biosphere 1033.7.3 The Benefit of Living Together 1053.8 Geomicrobiology 1063.8.1 Rock and Mineral Weathering 1063.8.2 Mineral Transformations 1073.8.3 Microbial Metal Binding 1093.8.4 Microbiota of Subsurface Crystals 1093.9 Summary 110Discussion Questions 111References 111Further Reading 1164 Aquatic Surface Environments: Freshwater, Marine, and Wastewater 1174.1 Overview and Focus 1174.2 Water as Relevant to Microbial Growth 1174.2.1 Water Activity 1184.3 Marine Environments and Associated Microbiomes 1194.3.1 Marine Primary Productivity 1204.3.2 Marine Heterotrophs 1224.3.3 Bacterial Symbionts and Marine Hosts 1234.3.4 Microbial EPSs, Marine Snow, and Marine Gel Particles 1254.3.5 Brackish Water and Intertidal Zones 1274.3.6 Coral Reefs 1284.4 Freshwater Environments and Associated Microbiomes 1314.4.1 Lakes and Rivers 1324.4.2 Wetlands 1374.4.3 The Snow and Glacier Ice Ecosystems 1394.4.4 Microbiota of Cold and Hot Springs 1404.4.5 Microbial Mats 1424.5 Maintaining Populations in Low Nutrient Environments 1444.6 Aquaculture Wastewater 1484.7 Hormone Degradation in Fresh Water 1494.8 Human Activities and Influence on Microbial Ecology 1504.9 Drinking Water 1514.10 Municipal Water Treatment 1514.11 Wastewater Treatment Systems 1524.11.1 Septic Tanks 1524.11.2 Municipal Wastewater Treatment 1524.11.2.1 Primary Treatment 1534.11.2.2 Secondary Treatment 1534.12 Alternative Approaches for Wastewater Treatment 1544.13 Coliforms and Other Indicator Organisms 1554.14 Viruses in Aquatic Environments: Diversity and Activity 1564.15 Summary 158Discussion Questions 159References 159Further Reading 1665 Life in Extreme Environments 1675.1 Overview 1675.2 Sampling in Extreme Environments 1685.3 Extreme Temperature Environments 1735.3.1 Psychrophiles 1745.3.2 Thermophiles 1765.3.2.1 Alpine Environment – Yellowstone National Park 1765.3.2.2 Hydrothermal Vent Communities 1795.3.2.3 The Guaymas Basin 1805.4 Xerophiles 1805.5 Piezophiles 1825.6 Acidophiles 1835.7 Alkaliphiles 1875.8 Halophiles and Chaophiles 1895.9 Radioresistant Microorganisms 1945.10 Membrane Adaptations to Extreme Conditions 1955.10.1 Low Temperatures 1955.10.2 High Temperatures 1965.10.3 pH Extremes: Low and High 1965.11 Astrobiology 1975.12 Nutrient Limited Environments 1985.13 Volcanic Surfaces 2005.14 Summary 202Discussion Questions 202References 202Further Reading 2096 Mutualism: Microorganisms and Terrestrial Plants 2116.1 Overview and Focus 2116.2 Cyanobacteria and the Chloroplast Ancestor 2116.3 Lichens: Cyanobacteria/Algae–Fungi Mutualism 2176.3.1 Distribution and Organization 2176.3.2 Natural Products of Lichens 2196.4 Mutualisms with Cyanobacteria as Intracellular or Epiphytic Organisms 2206.4.1 Bryophytes 2206.4.2 Mosses 2216.4.3 Azolla 2216.4.4 Gunnera 2226.4.5 Cycads 2226.4.6 Geosiphon 2226.4.7 Diatoms 2246.5 Rhizobia–Legume Symbiosis 2246.5.1 Bacterial Species Involved 2246.5.2 Rhizospheric Rhizobia 2256.5.3 The Root Nodulation Process 2266.5.4 Nodules on Plant Stems 2306.6 Frankia and the Non‐legume Nitrogen‐fixing Nodule 2316.7 Mycorrhizae 2336.7.1 Arbuscular Mycorrhizae (AM) 2356.7.2 Ectomycorrhiza (EcM) 2366.8 Patterns of Regulation for Plant–Microbe Mutualism 2376.9 Bacterial‐Fungal Interactions 2386.9.1 Direct Effects 2386.9.2 Plant Growth‐promoting Bacteria 2396.9.3 Systemic Induction of Plant Immunity 2396.10 Endophytic Microorganisms 2406.11 Microbiology of the Phyllosphere 2416.12 Summary 242Discussion Questions 243References 243Further Reading 2477 Mutualism: Microorganisms and Animals 2497.1 Overview and Focus 2497.2 Building a Microbial Community – The Role of the Host 2497.2.1 Microbiology and Innate Immunity 2497.2.2 Microbiology and Adaptive Immunity 2507.3 Host Models to Study Parasite Relationships 2517.3.1 Germ‐free Animals 2517.3.2 Caenorhabditis elegans 2517.3.3 Drosophila melanogaster 2527.3.4 Galleria mellonella 2527.4 Digestive Tract Environment 2527.4.1 Omnivores 2537.4.2 Carnivores 2547.4.3 Herbivores 2557.4.3.1 Bacteria and Archaea 2577.4.3.2 Anaerobic Protozoa 2577.4.3.3 Anaerobic Fungi 2587.4.3.4 Probiotics and Methane Mitigation Strategies 2607.5 The Human Microbiome 2607.5.1 Skin 2607.5.2 Oral Microorganisms 2617.5.3 Intestinal Microbiome 2637.5.3.1 Establishment of Intestinal Flora 2637.5.3.2 The Healthy Gut 2647.5.3.3 Influence of the Intestine on Human Health 2657.5.3.4 Obesity, Diabetes, and Health Issues 2667.5.3.5 Probiotics 2697.6 Gut Microbiota across the Animal World 2697.6.1 Systems of Maternal Transmission 2707.6.2 Microbiota of Ruminates and Hindgut Fermenters 2707.6.3 Gut Microbiota of Bears 2757.6.4 Microbiota of Birds 2757.6.5 Intestinal Bacteria of Fish 2787.7 Insect–Fungus Symbiosis 2797.7.1 Scale Insects and Septobasidium 2797.7.2 Attine Ant–Fungus Symbiosis 2797.7.3 Woodwasp–Fungus Symbiosis 2807.7.4 Ambrosia Beetles–Fungus 2817.7.5 Termite–Fungus 2817.8 Mutualisms Involving Insects and Bacteria 2827.8.1 Aphids–Buchnera and Endosymbionts 2827.8.2 Wolbachia–Insects 2837.8.3 Mealybug–Bacteria 2837.8.4 Termite Gut–Bacteria 2847.9 Mutualisms Involving Invertebrates 2857.9.1 Microbiome of Marine Worms 2857.9.2 Squid (Euprymna)–Vibrio fischeri Symbiosis 2867.9.3 Medicinal Leech–Aeromonas sp. and Rikenella‐like Bacteria 2877.9.4 Nematode–Bacteria 2887.10 Summary 288Discussion Questions 289References 290Further Reading 2958 Microbes Driving the Nutrient Cycles 2978.1 Overview and Focus 2978.2 Nutrient Cycles and What Drives Them 2978.3 The Aerobic Environment 2998.3.1 The “Great Oxidation Event” 2998.3.2 Oxygen Cycle 3008.3.3 Hydrogen Peroxide and ROS 3038.4 Carbon – A Renewable Resource 3048.4.1 Carbon Dioxide Fixation and Carbonate Reduction 3058.4.2 Methanogenesis, Methanotrophy, and Methylotrophy 3068.4.3 Mineralization of Carbon Compounds 3088.4.4 Production and Utilization of CO 3118.4.5 Production and Utilization of Hydrogen Cyanide 3128.5 Nitrogen for Biosynthesis and Energy 3128.5.1 Nitrification 3148.5.2 Denitrification 3148.5.3 Nitrate Reduction 3158.5.4 Nitrite Reductase 3168.5.5 Metabolism of NO and N 2 O 3168.5.6 Production of NO by NOS 3178.5.7 Respiratory Ammonification 3178.5.8 Anammox Reaction 3188.5.9 Assimilation of Nitrogen 3188.5.10 Dinitrogen Fixation 3188.6 Sulfur Cycling 3198.6.1 Oxidation of Hydrogen Sulfide 3208.6.2 Oxidation of Elemental Sulfur 3218.6.3 Dissimilative S 0 Reduction 3218.6.4 Dissimilative Sulfate Reduction 3228.6.5 Assimilatory Sulfate Reduction 3228.6.6 Production of H 2 S and Dimethyl Sulfide 3228.6.6.1 Hydrogen Sulfide 3228.6.6.2 Dimethyl Sulfide 3238.7 Cycling of Trace Elements 3248.7.1 Iron 3248.7.2 Manganese 3268.8 Phosphorus Cycling 3288.9 Selenium Cycling 3308.10 Cycling Toxic Elements 3318.10.1 Mercury 3318.10.2 Arsenic 3328.11 Summary 335Discussion Questions 335References 336Further Reading 3409 Bioremediation Using Microorganisms 3419.1 Overview and Focus 3419.2 Microbial Bioremediation: Strategies and Applications 3419.2.1 Biostimulation 3439.2.2 Bioaugmentation 3449.2.2.1 Indigenous Bacteria 3449.2.2.2 Genetically Modified Organisms 3449.2.3 Intrinsic Bioremediation 3459.2.4 Microbial Consortium 3459.2.5 Co‐metabolism 3469.3 Organic Compounds and Xenobiotics Degraded 3479.3.1 Pesticides 3479.3.2 Chlorinated Organic Compounds 3489.3.2.1 Chloroethylenes 3499.3.2.2 Chloromethanes 3509.3.2.3 Polychlorinated Biphenyl Compounds 3519.3.3 Population Dynamics in Degradation of Hydrocarbons 3529.3.3.1 Oil Spills 3529.3.3.2 Fuel Hydrocarbons 3539.3.3.3 Polyaromatic Hydrocarbons 3559.3.3.4 Azo Dyes 3579.3.4 Explosives 3579.3.4.1 Trinitrotoluene 3579.3.4.2 RDX and HMX 3599.3.4.3 Perchlorate 3599.3.5 Bioremediation and Detoxification of Metal(loid)s 3599.3.5.1 Dissimilatory Metal(loid) Reduction 3609.3.5.2 Methylation Reactions 3619.4 Design of Systems for Bioremediation 3629.4.1 In Situ vs Ex Situ 3629.4.2 Bioreactors 3639.4.3 Biofarming 3639.4.4 Permeable Reactive Barriers 3639.4.5 Groundwater and Lagoon Treatment 3639.4.6 Bioventing 3649.5 Summary 364Discussion Questions 364References 365Further Reading 37010 Biocorrosion and Geomicrobiology 37110.1 Overview and Focus 37110.2 Microbially Influenced Corrosion (MIC) of Ferrous Metals 37110.2.1 Current Theories of Biocorrosion 37110.2.1.1 Emic 37310.2.1.2 Cmic 37410.2.1.3 Iron Sulfide Crusts 37410.2.1.4 Biofilms and Extracellular Matrix 37410.2.2 Biocorrosion of Nonferrous Materials 37510.2.3 Control of Biocorrosion 37610.3 Bioalteration of Rocks, Monuments, and Other Surfaces 37610.3.1 Biofilms on Rocks and Buildings 37610.3.2 Biodegradation of Art Objects 37710.3.2.1 Marble Statues in Italy 37710.3.2.2 Paintings in the Lascaux Cave in France 37710.3.2.3 Mogao Grottoes in China 37810.3.2.4 Damage to Frescoes 37810.3.3 Biotechnology for Restoration of Artworks and Historic Stones 37810.4 Biodeterioration of Concrete 38010.5 Mineral Interaction and Biomineralization 38210.5.1 Iron Hydroxides 38210.5.2 Magnetic Mineral Crystals 38310.5.3 Manganese Oxides 38310.5.4 Carbonates 38410.5.5 Phosphates 38410.5.6 Sulfates 38510.5.7 Sulfides 38510.5.8 Clays 38510.5.9 Uranium Precipitate and Crystals 38610.5.10 Gold Grains 38610.6 Interactions with Transition and Rare Earth Elements 38710.6.1 Transition Elements 38710.6.2 Rare Earth Elements 38810.7 Toxic Elements 38910.7.1 Mercury 38910.7.2 Chromium 38910.7.3 Arsenic 39010.7.4 Selenium 39010.8 Metallic and Metalloid Nanoparticles of Microbial Origin 39110.9 Summary 393Discussion Questions 393References 394Further Reading 39811 Microbial Communities and Metabolic Networks 39911.1 Overview and Focus 39911.2 Examples of Succession of Populations 39911.2.1 Development of Coral Black Band Disease 40011.2.2 Population Succession in Production of Dairy Products 40011.2.3 Population Dynamics in Fermentation of Non‐dairy Foods 40111.2.3.1 Kimchi 40111.2.3.2 Coffee 40111.2.3.3 Cocoa 40211.2.3.4 Chinese Soy Sauce 40211.2.4 Composting Plant Material 40311.3 Impact of Climate Change on Microorganisms 40311.3.1 Marine Environment 40311.3.2 Soil Environment 40411.4 Syntrophy and Co‐metabolism 40611.5 Ecosystem Created by Hydraulic Fracturing in Shale 40811.6 Extracellular Electron Transport 40811.6.1 Membrane‐bound Proteins 40911.6.2 Electron Shuttling 40911.6.3 Nanowires 41011.6.4 Extracellular Electron Movement in Biofilms 41011.7 Cross‐talk: Interkingdom Signaling 41011.7.1 Microbial Endocrinology 41111.7.2 Cross‐signaling in Nonhuman Systems 41211.8 Evolving Systems of Interest 41211.8.1 Polyploidy in Bacteria 41211.8.2 Impact of Viruses and CRISPR‐cas Systems 41411.8.3 Impact of Outer Membrane Vesicles 41611.8.4 Atmospheric Microbiology 42011.8.5 Long‐distance Electron Transfer 42311.9 Summary 424Discussion Questions 425References 425Further Reading 433Index 435