Microbial Ecology

Larry L. Barton studies the physiological activities of environmentally important microorganisms, focusing on energetics of bacterial inorganic metabolism and bacterial bioremediation. Larry has been the instructor of the course in General Microbiology for over 30 years. The author of five previous books, he was the founding editor and the initial editor-in chief of the international journal Anerobe, begun in 1995 and now published by Academic Press. Most recently, he published a college textbook on bacterial physiology. Diana E. Northup investigates the microorganisms that inhabit caves throughout the world. Her research was featured on the Nova episode, "Mysterious Life of Caves." Within the Department of Biology at UNM, she gives lectures, directs undergraduate students in research, supervises a postdoctoral fellow, and, currently, she is mentoring a doctoral student in microbial ecology of a cave in southern New Mexico.

• Preface xvii Glossary xix1 Microbial Ecology: Beginnings and the Road Forward 11.1 Central Themes 11.2 Introduction 21.2.1 Roots of Microbial Ecology 31.2.2 Current Perspectives 41.3 Timeline 51.4 Microfossils 71.5 Early Life 91.5.1 The Precellular World 91.5.2 The First Cell 101.5.3 Development of Cellular Biology 111.5.4 Evolution of Metabolic Pathways 121.6 Characteristics of Microbial Life 131.6.1 Structure and Evolution of Cell Shape 131.6.2 Metabolism and Use of Energy 161.6.3 Growth, Reproduction, and Development 171.6.4 Adaptations and Response to Stimuli 181.7 Classification and Taxonomy: The Species Concept 181.8 The Three Domains: Tree of Life 191.9 Relationship of Microbial Ecology to General Ecology 221.10 Changing Face of Microbial Ecology 231.10.1 Change in Focus 231.10.2 Diversity: From Culturing to Molecular Phylogeny 241.11 Summary 251.12 Delving Deeper: Critical Thinking Questions 262 Diversity of Microorganisms 292.1 Central Themes 292.2 The Ubiquity of Microorganisms 292.3 The Amazing Diversity of Morphologies 302.3.1 Comparison of the Three Domains 322.3.2 What’s in a Name: Prokaryotes 322.3.3 Winogradsky’s Experiments with Chemolithotrophs 322.4 Diversity of Bacterial Groups 332.4.1 Expansion of the Number of Bacterial Phyla 332.4.2 Bacterial Portrait Gallery: Processes and Players 352.5 Discovery of Archaea as a Separate Domain 382.6 Archaeal Diversity 392.6.1 Archaeal Portrait Gallery 392.7 Archaea–Bacteria Differences 452.8 Eukarya: A Changing Picture of Phylogenetic Diversity 462.9 Protist Diversity 462.9.1 Protist Gallery 492.10 Fungal Diversity 512.11 Algal Diversity 542.12 Viral Diversity 562.13 Summary 572.14 Delving Deeper: Critical Thinking Questions 583 Complexity and Simplicity of Cell Systems 613.1 Central Themes 613.2 Introduction 623.3 Cell Parameters 633.3.1 Life at the Lowest Level 643.3.2 Large Microorganisms 663.4 Cell Movement and Chemotaxis 683.5 Structures of Sporulation 713.6 Nutrient Reserves and Storage Materials 743.7 Cell–Cell Associations 753.7.1 Cell Attachment 763.7.2 Biofilms 783.7.3 Filamentous Growth 823.8 Cell Physiology and Metabolism 843.8.1 Sensory Response 843.8.2 Global Regulation 863.8.3 Internal Membranes in Bacteria 873.9 Energetics and Environment 883.9.1 Heterotrophs 883.9.2 Chemolithotrophs 913.9.3 Photophosphorylation 943.9.4 Bacteriorhodopsin Reaction 943.10 Bioelectrochemical Activities 973.11 Summary 993.12 Delving Deeper: Critical Thinking Questions 1004 The Microbial Habitat: An Ecological Perspective 1034.1 Central Themes 1034.2 Habitats: An Overview 1044.2.1 The Niche 1054.3 Aquatic Habitats 1054.3.1 Freshwater 1074.3.2 Marine Habitats 1104.4 Soil Habitats 1114.4.1 Microbial Food Webs in the Soil Habitat 1124.5 Rock and Subsurface Habitats 1174.5.1 Rock Varnish 1174.5.2 Cave Habitats 1194.5.3 Groundwater 1204.5.4 Deep Subsurface 1204.6 Atmospheric Habitats 1214.6.1 Atmospheric Microbial Diversity: African Dust 1214.6.2 Mysteries Remain 1224.7 Population Ecology Across Habitats 1244.7.1 Population Growth and Dynamics 1244.7.2 Horizontal Gene Transfer 1254.7.3 Biogeograpy versus Everything is Everywhere; the Environment Selects 1264.8 Summary 1284.9 Delving Deeper: Critical Thinking Questions 1295 The How of Microbial Ecology Studies 1315.1 Central Themes 1315.2 Introduction 1325.3 Sampling and Sample Storage 1345.4 Microscopy 1355.4.1 Gram Stains 1355.4.2 Direct Count Procedures 1355.4.3 Determining Actively Respiring Cells 1365.4.4 Fluorescent in situ Hybridization (FISH) 1375.4.5 Electron Microscopy 1395.5 Cultivation of Microorganisms 1395.5.1 Microbial Respiration 1445.5.2 Microbial Biomass 1445.5.3 Measuring Carbon Substrate Utilization 1455.6 Molecular Phylogenetics 1465.7 Culturing Versus Molecular Techniques: Comparisons from Soil Studies 1485.8 Community Fingerprinting Methods 1495.8.1 Denaturing Gradient Gel Electrophoresis 1495.9 Metagenomics: A New Tool for Answering Community Ecology Questions 1495.10 Environmental Proteomics 1505.11 Stable-Isotope Studies 1525.11.1 Using Stable Isotopes: Movile Cave Food Web Case Study 1535.12 Summary 1545.13 Delving Deeper: Critical Thinking Questions 1556 Microbe–Microbe Interactions 1596.1 Central Themes 1596.2 Introduction 1606.3 Classification of Microbial Interactions 1616.3.1 Neutralism 1626.3.2 Commensalism 1626.3.3 Competition 1626.3.4 Parasitism 1636.3.5 Predation 1646.3.6 Antagonism (Amensalism) 1646.3.7 Syntrophism 1676.4 Symbiotic Associations 1686.4.1 Diatoms 1686.4.2 Lichen 1696.4.3 Hatena 1716.4.4 Symbiosis between Bacteria and Protozoa 1736.5 Fungus–Bacterium Symbiosis 1746.6 Prokaryote–Prokaryote Interactions 1746.6.1 Two-Member Mutualism 1746.6.2 Examples of Parasites and Predators 1746.7 Establishing a Symbiosis: The Nostoc–Geosiphon Association 1766.8 Sexual Interactions 1766.9 Summary 1786.10 Delving Deeper: Critical Thinking Questions 1807 Interactions Between Microorganisms and Plants 1837.1 Central Themes 1837.2 Introduction 1847.3 Symbiotic Associations with Cyanobacteria 1867.4 Interactions in the Rhizosphere 1877.5 Mycorrhizae 1897.5.1 Ectomycorrhizae 1907.5.2 Endomycorrhizae 1937.5.3 Other Mycorrhizal Associations 1937.6 Nitrogen-Fixing Bacteria and Higher Plants 1957.6.1 Root Associations 1957.6.2 Stem Associations 2027.7 Bacteria Supporting Plant Growth 2027.7.1 Production of Hormones 2027.7.2 Growth-Promoting Rhizobacteria 2027.7.3 Cactus Symbiosis 2047.8 Leaf Surfaces and Microorganisms 2057.9 Detrimental Activities of Microorganisms on Plants 2067.9.1 Fungal Parasites 2067.9.2 Bacterial Pathogens 2077.9.3 Rhizosphere Activities and Plant Diseases 2097.10 Fungi Promoting Increased Heat Tolerance in Plants 2117.11 Biocontrol of Pests and Pathogens 2117.12 Summary 2147.13 Delving Deeper: Critical Thinking Questions 2148 Interactions Between Microorganisms and Animals 2178.1 Central Themes 2178.2 Introduction 2188.3 Primary and Secondary Symbionts 2228.4 Microbe–Animal Interactions: Parasitism 2238.4.1 Parasitism Introduction 2238.4.2 Nematode Parasitism of Insects 2238.4.3 Effects of Multiple Parasitic Infections on Virulence 2248.4.4 A Widespread Endosymbiosis: Wolbachia —Parasitism or Mutualism? 2248.5 Microbe–Animal Interactions: Mutualism 2258.5.1 Gut Animal–Microbe Mutualistic Interactions 2258.5.2 Case Study: Unique Bacterial–Polychaete Endosymbiosis 2278.5.3 Case Study: Beetles Cultivating Fungal Gardens 2288.5.4 Mealybug Mutualisms 2298.5.5 Luminescent Bacteria in Fish and Squid:Turning on the Lights 2308.6 Lessons from the Deep: Evolutionary and Ecosystem Insights from Deep-Sea Vents Symbioses 2308.7 Microbial–Vertebrate Interactions 2338.7.1 Bacteria and Birds 2358.7.2 Microorganisms and Humans 2368.8 Grazing and Predation by Animals 2368.9 Summary 2398.10 Delving Deeper: Critical Thinking Questions 2399 Living Together: Microbial Communities 2439.1 Central Themes 2439.2 Introduction 2449.2.1 Dominant Issues and Questions in Microbial Community Ecology 2459.3 Metagenomics: A New Tool for Answering Community Ecology Questions 2469.4 Biomats and Biofilms 2479.4.1 Changes in Community Structure during Biofilm Succession 2499.5 Formation of Organized Communities: Quorum Sensing 2499.6 Colonization and Recolonization by Microorganisms 2519.6.1 Case Study: Colonization of the Sterile Newborn Gut 2529.6.2 Case Study: Undesirable Colonization—Factors in Disease 2539.6.3 Case Study: Recolonization and Early Succession in Intertidal Sediments 2539.7 Dispersal, Succession, and Stability 2539.7.1 Case Study: Dispersal and Succession in the Oceans—Whale Falls as Dispersal Agents between Vents 2549.7.2 Competition as a Structuring Force in Succession 2549.7.3 Stability in Microcosm Studies 2559.8 Species Diversity 2569.8.1 Diversity Indices 2579.8.2 Connections between Metazoans and Microorganisms: Co-ocurrence Patterns 2589.8.3 Disturbance and Diversity 2589.9 Food Webs 2599.9.1 Structure of Microbial Food Webs 2609.9.2 Keystone Species Effects on Food Webs and Diversity 2619.10 Primary Production and Energy Flow 2619.10.1 Cycling of Nutrients 2619.11 Microbial Community Examples 2629.11.1 Plankton in Marine Ecosystems 2639.11.2 Hot Springs 2649.11.3 Wine and Cheese 2669.12 Summary 2699.13 Delving Deeper: Critical Thinking Questions 27010 Microbial Processes Contributing to Biogeochemical Cycles 27310.1 Central Themes 27310.2 Introduction 27410.3 Energy Flow 27610.4 Oxygen and Carbon Cycling 27810.5 Nitrogen Cycling 28110.5.1 Nitrogen Fixation 28210.5.2 Nitrogen Assimilation 28310.5.3 Nitrification 28310.5.4 Denitrification 28410.6 Sulfur Cycling 28410.6.1 Organic Sulfur Metabolism 28510.6.2 Inorganic Sulfur Metabolism 28510.7 Phosphorus Cycling 28610.8 Iron Cycling 28710.8.1 Siderophores 28810.8.2 Ferritin and Magnetosomes 28910.9 Cycling of Manganese and Selenium 29010.10 Cycling of Hydrogen 29310.11 Transformation of Mercury 29410.12 Closed Systems 29510.13 Summary 29610.14 Delving Deeper: Critical Thinking Questions 29711 Microbes at Work In Nature: Biomineralization and Microbial Weathering 29911.1 Central Themes 29911.2 Introduction 30011.2.1 Passive versus Active Biomineralization 30211.3 Cell Characteristics and Metal Binding 30311.3.1 Passive Metal Adsorption 30311.3.2 Active Metal Adsorption 30311.4 Energy Flow: Shuffling Electrons; Redox Reactions 30411.5 Dissolution Versus Precipitation 30511.6 Formation of Ores and Minerals 30611.6.1 Biomining 30711.6.2 Recovery of Petroleum 30711.6.3 Sulfuric Acid–Driven Speleologenesis 31011.7 Microbial Participation in Silicification 31211.7.1 Silica Formation in Diatoms, Radiolarians, and Sponges 31211.7.2 Geyserites 31311.8 Biomineralization of Ferromanganese Deposits 31411.8.1 Magnetite Formation 31411.8.2 Rock Varnish 31511.9 Microbial Carbonate Microbialites 31711.10 Stromatolites 31911.10.1 Thrombolites 32011.10.2 Travertines and Tufas 32111.10.3 Coccolithophores and Foraminifera: Biologically Controlled Mineralization 32311.11 Summary 32411.12 Delving Deeper: Critical Thinking Questions 32412 Decomposition of Natural Compounds 32712.1 Central Themes 32712.2 Introduction 32812.3 Decomposition of Wood 32912.4 Digestion of Plant Cell Wall Structures 33112.4.1 Protopectinase and Pectinase Activities 33312.4.2 Microbial Decomposition of Lignin 33312.4.3 Degradation of Hemicelllose 33412.4.4 Enzymatic Degradation of Cellulose 33512.5 Starch Hydrolysis 33612.6 Inulin Hydrolysis 33612.7 Decomposition of Diverse Biopolymers Including Animal Fibrous Proteins 33712.7.1 Chitin Digestion 33712.7.2 Decomposition of Keratin 33712.7.3 Fibroin Decomposition 33812.7.4 Collagen Breakdown 33912.8 Ecology of Fermented Foods 34112.9 Ecology of Bioenergy Production 34312.9.1 Alcohol Production 34512.9.2 H2 Production 34612.9.3 Methane Production 34712.9.4 Biodiesel Production by Algae 34812.10 Waste Treatment Systems 34912.11 Composting of Plant Organic Matter 35012.12 Impact of Microbial Degradation on Humans 35212.13 Summary 35412.14 Delving Deeper: Critical Thinking Questions 35513 Microbes at Work: Bioremediation 35913.1 Central Themes 35913.2 Introduction 36013.3 Bioremediation as a Technology 36113.4 Genetic Engineering 36213.5 Design and Implementation of Bioremediation 36213.5.1 Bioreactors 36213.5.2 Biofarming 36313.5.3 Permeable Reactive Barriers 36313.5.4 Optimizing Bioremediation 36313.6 Bioremediation of Organic Compounds 36513.7 Degradation of Hydrocarbons 36513.7.1 Oil Spills 36613.7.2 Methane Utilization 36613.7.3 Fuel Hydrocarbons 36813.7.4 Polyaromatic Hydrocarbons 37213.8 Degradation of Xenobiotics 37313.8.1 Detoxification of Chlorinated Organic Compounds 37513.8.2 Herbicides and Pesticides 37613.8.3 Biodegradation of Explosives 37713.8.4 Decomposition of Textile Dyes 37813.9 Bioremediation with Inorganic Pollutants 38013.9.1 Microbe–Toxic Metal Interactions 38113.9.2 Detoxification of Selenium 38413.9.3 Reactions with Arsenic 38513.9.4 Bioremediation of Perchlorate Sites 38713.9.5 Bioremediation of Nitrate Pollution 38713.10 Summary 38913.11 Delving Deeper: Critical Thinking Questions 390index 395