Preface xv About the Authors xvii About the Companion Website xviii Part I: Unity 3 1 Microbial Phylogeny--The Three Domains of Life 5 Introduction 6 The Three Branches of Life: Bacteria, Archaea, and Eukarya 6 The 16S/18S rRNA Gene as a Basis for Phylogenetic Comparisons 7 The Modern Molecular Phylogenetic Tree of Life 12 Phylogenetics and Earth History 14 2 Metabolic Unity--Generation of Biosynthetic Precursors 21 Making Connections 22 The Purpose of Central Metabolism 22 The 12 Essential Precursors 23 The Embden-Meyerhof-Parnas (EMP) Pathway/Glycolysis 25 Structure and Energy Exchange of Key Coenzymes 28 Controlling the Direction of Carbon Flow during Glycolysis 29 The Pentose Phosphate Pathway (PPP) 31 The Entner-Doudoroff (ED) Pathway 33 The Transition Reaction: Carbon Flow into the Tricarboxylic Acid (TCA) Cycle 36 The Tricarboxylic Acid (TCA) Cycle 37 Anaplerotic Reactions 37 The Branched or Incomplete Tricarboxylic Acid (TCA) Pathway 41 The Glyoxylate Cycle 41 Reversing Carbon Flow from the Tricarboxylic Acid (TCA) Cycle to the Embden-Meyerhof-Parnas (EMP) Pathway 43 3 Cellular Components--What''s In a Cell 51 Making Connections 52 Estimating Molecular Concentrations 52 Physiologically Relevant Protein Concentrations 54 Measuring Enzyme Activity: Basic Principles of Enzyme Assays 55 Michaelis-Menten Kinetics 58 Studying the Proteome 59 The Physiological Role and Composition of Cellular RNA 61 The Physiological Role and Composition of Cellular DNA 63 Studying the Genome and the Transcriptome 64 4 Cellular Growth 73 Making Connections 74 Methods to Monitor Bacterial Growth 74 The Phases of Bacterial Growth in Batch Culture 78 Requirements for Microbial Growth 80 Diauxic Growth 80 Exponential Growth Kinetics 81 Chemostats 83 Characteristics of Stationary-Phase Cells 84 Proteins Important for Cell Shape and Cell Division 85 Chromosome Segregation 86 5 Bioenergetics and the Proton Motive Force 95 Making Connections 96 Cellular Mechanisms for ATP Synthesis 96 Chemiosmotic Theory 98 ATP Synthase 99 The Proton Motive Force (PMF) 99 Quantifying the Proton Motive Force 99 Cellular Proton Levels 100 Environmental Impacts on the Proton Motive Force (PMF) 100 Experimentally Measuring the Proton Motive Force (PMF) 101 6 Respiration and Fermentation 107 Making Connections 108 The Basic Components of an Electron Transport Chain (ETC) 108 Electrode/Reduction Potential ( E 0') 109 Brief Review of the Electron Transport Chain (ETC) in Mitochondria 110 Q Cycle of Mitochondria 113 Bacterial Electron Transport Chains (ETCs) 113 Q Loop of Bacteria 115 Electron Donors and Acceptors in Bacteria 115 Fermentation 117 7 Regulation--Posttranslational Control 127 Making Connections 128 Importance of Regulatory Processes 128 Allosteric Regulation of Enzymes 129 Allosteric Regulation of Branched Pathways 131 Covalent Modifications 134 Posttranslational Regulation in the Sugar Phosphotransferase System (PTS) 138 8 Gene Regulation--Transcription Initiation and Posttranscriptional Control 147 Making Connections 148 Transcription Terminology 148 Bacterial Transcription Initiation and Elongation 149 Bacterial Transcription Termination 151 Regulatory cis- and trans-Acting Elements Impacting Transcription 153 Examples of Different Promoter Structures 154 Transcriptional Regulation of the lac Operon 156 Activation and Repression by the Global Regulator Cra 158 Attenuation 158 Posttranscriptional Regulation 161 Methods Used to Study Gene Regulation 163 Methods to Demonstrate Protein-DNA Interactions 164 Interlude: From Unity to Diversity 177 Metabolic Diversity 178 Global Nutrient Cycles 179 Structural and Regulatory Diversity of Microbes 180 Part II: Diversity 183 9 Autotrophy 185 Making Connections 186 Autotrophy 186 Calvin Cycle 187 Reductive Tricarboxylic Acid (rTCA) Cycle 191 Reductive Acetyl-CoA Pathway 193 3-Hydroxypropionate (3HP) Bi-cycle 195 3-Hydroxypropionate-4-Hydroxybutyrate (3HP-4HB) and Dicarboxylate-4-Hydroxybutyrate (DC-4HB) Cycles 195 Why So Many CO2 Fixation Pathways? 197 10 Phototrophy 207 Making Connections 208 Phototrophy 208 Chlorophyll-Based Phototrophy 209 Cellular Structures Needed for Phototrophy: Light-Harvesting Complexes, Reaction Centers, and Unique Membrane Organizations 211 Oxygenic Photoautotrophy in the Cyanobacteria 215 Anaerobic Anoxygenic Phototrophy in the Phototrophic Purple Sulfur and Purple Nonsulfur Bacteria 218 Anaerobic Anoxygenic Phototrophy in the Chlorobi and Chloroflexi (Green Sulfur and Green Nonsulfur Bacteria, Respectively) 221 Anaerobic Anoxygenic Photoheterotrophy in the Firmicutes 224 Aerobic Anoxygenic Phototrophy 224 Retinal-Based Phototrophy 225 11 Chemotrophy in the Carbon and Sulfur Cycles 233 Making Connections 234 The Carbon Cycle 234 The Chemoorganotrophic Degradation of Polymers 236 The Chemoorganotrophic Degradation of Aromatic Acids 236 Chemoorganotrophy in Escherichia coli 241 Chemolithoautotrophy 246 Chemolithoautotrophy in Methanogens 248 Methylotrophy Enables Cycling of One-Carbon (C1) Compounds 251 One-Carbon (C1) Chemolithotrophy in Acetogens 253 The Sulfur Cycle 256 Chemoheterotrophy and Chemolithoautotrophy in the Sulfur Cycle: Sulfate Reducers 256 Chemolithoautotrophy in the Sulfur Cycle: Sulfur Oxidizers 259 The Anaerobic Food Web and Syntrophy 261 12 Microbial Contributions to the Nitrogen Cycle 275 Making Connections 276 Overview of the Nitrogen Cycle 276 Nitrogen Fixation 277 Biochemistry of Nitrogen Fixation 278 Regulation of Nitrogen Fixation 280 Symbiotic Plant-Microbe Interactions during Nitrogen Fixation 282 Assimilatory Nitrate Reduction 284 Ammonia Assimilation into Cellular Biomass 285 Nitrification: Ammonia Oxidation, Nitrite Oxidation, and Comammox 287 Anammox: Anaerobic Ammonia Oxidation 290 Denitrification 293 13 Structure and Function of the Cell Envelope 303 Making Connections 304 Fundamental Structure of the Cytoplasmic Membrane 304 Variation in Cytoplasmic Membranes 306 Transport across Cytoplasmic Membranes 306 Cell Wall Structures 311 Gram-Negative Outer Membrane 315 Periplasm 320 Additional Extracellular Layers 321 14 Transport and Localization of Proteins and Cell Envelope Macromolecules 333 Making Connections 334 Introduction to Cytoplasmic Membrane Protein Transport Systems 334 Secretory (Sec)-Dependent Protein Transport System 334 The Secretory (Sec)-Dependent Protein Transport Process 337 Signal Recognition Particle (SRP)-Dependent Protein Transport Process 338 Twin-Arginine Translocation (Tat) Protein Transport Process 339 Integration of Cytoplasmic Membrane Proteins 340 Gram-Negative Bacterial Outer Membrane Protein Secretion Systems 341 Secretory (Sec)- and Twin-Arginine Translocation (Tat)-Dependent Protein Secretion Systems 341 Secretory (Sec)-Independent and Mixed-Mechanism Protein Secretion Systems 343 Importance of Disulfide Bonds 347 Transport and Localization of Other Cell Envelope Components 348 15 Microbial Motility and Chemotaxis 363 Making Connections 364 Motility in Microorganisms 364 Bacterial Flagella and Swimming Motility 364 Regulation of Flagellar Synthesis in Escherichia coli 367 Mechanism of Swimming Motility 369 Archaeal Flagella 370 Bacterial Surface Motility 371 Chemotaxis 372 Conservation and Variation in Chemotaxis Systems among Bacteria and Archaea 380 Methods to Study Bacterial Motility and Chemotaxis 381 16 Quorum Sensing 389 Making Connections 390 Fundamentals of Quorum Sensing 390 Quorum Sensing and Bioluminescence in the Vibrio fischeri-Squid Symbiosis 391 Basic Model of Quorum Sensing in Gram-Negative Proteobacteria 395 Basic Model of Quorum Sensing in Gram-Positive Bacteria 398 Interspecies Communication: the LuxS System 400 Regulatory Cascade Controlling Quorum Sensing in Vibrio cholerae 400 Quorum Quenching 402 17 Stress Responses 415 Making Connections 416 Oxidative Stress 416 Heat Shock Response 419 Sporulation 420 18 Lifestyles Involving Bacterial Differentiation 441 Making Connections 442 A Simple Model for Bacterial Cellular Differentiation: Caulobacter crescentus 443 Differentiation in Filamentous Cyanobacterial Species 444 Life Cycle of Filamentous Spore-Forming Streptomyces: An Example of Bacterial Multicellularity 447 Life Cycle of Myxobacteria: Predatory Spore-Forming Social Bacteria 449 Biofilms: The Typical State of Microorganisms in the Environment 452 Index 467.