Microbial Physiology
Unity and Diversity
ASM Books Series

Explore the fascinating world of microbes with this comprehensive, advanced undergraduate-level textbook

Microbial Physiology: Unity and Diversity takes readers on a captivating journey through the intricate and often underappreciated world of microbial physiology, emphasizing both the common features that unify microbes and the diversity that makes them unique.
In Part I: Unity, the book lays a strong foundation in the basics of microbial physiology. Delve into the three domains of life, get an intimate look at the metabolic pathways that fuel the microbial world, and take a deep dive into the cellular components that constitute a microbe. Further, explore the principles of cellular growth, bioenergetics, and the mechanics of respiration and fermentation. The Unity section concludes with a comprehensive discussion of regulation at posttranslational and gene levels, paving the way for a rich understanding of microbial function.
Part II: Diversity, takes the reader into the broad and versatile world of microbial metabolism, exploring the range of energy sources and metabolic pathways microbes employ. This section leads readers through topics such as autotrophy, phototrophy, chemotrophy, and microbial contributions to the carbon, sulfur, and nitrogen cycles. The complexity of microbial cell envelope structures, transport processes, and protein transport are explored, along with bacterial motility, chemotaxis, and the phenomenon of quorum sensing. The section concludes with an exploration of stress responses and the diverse lifestyles that bacteria can adopt.

Microbial Physiology: Unity and Diversity will engage readers with its accessible yet thorough treatment of this critical field of microbiology. Each chapter contains detailed illustrations that concisely explain complex topics and concludes with robust end-of-chapter questions that not only test understanding but also provide an opportunity for readers to dig deeper into the content. This book is a must-have for students studying microbiology, as well as researchers and professionals keen to brush up their knowledge or explore new facets of microbial physiology.

1. Microbial Phylogeny: The Three Domains of Life
The Three Branches of Life: Bacteria, Archaea, and Eukarya
The 16S/18S rRNA Gene as a Basis for Phylogenetic Comparisons
The Modern Molecular Phylogenetic Tree of Life
Phylogenetics and Earth History

2. Metabolic Unity: Generation of Biosynthetic Precursors
The Purpose of Central Metabolism
The 12 Essential Precursors
The Embden-Meyerhof-Parnas (EMP) Pathway (Glycolysis)
Structure and Energy Exchange of Key Coenzymes
Controlling the Direction of Carbon Flow during Glycolysis
The Pentose Phosphate Pathway (PPP)
The Entner-Doudoroff (ED) Pathway
The Transition Reaction: Carbon Flow into the Tricarboxylic Acid (TCA) Cycle
The Tricarboxylic Acid Cycle
Anaplerotic Reactions
The Branched or Incomplete Tricarboxylic Acid Pathway
The Glyoxylate Cycle
Reversing Carbon Flow from the Tricarboxylic Acid Cycle to the Embden-Meyerhof-Parnas Pathway

3. Cellular Components: What�s in a Cell
Estimating Molecular Concentrations
Physiologically Relevant Protein Concentrations
Measuring Enzyme Activity: Basic Principles of Enzyme Assays
Michaelis-Menten Kinetics
Studying the Proteome
The Physiological Role and Composition of Cellular RNA
The Physiological Role and Composition of Cellular DNA
Studying the Genome and the Transcriptome

4 Cellular Growth
Methods to Monitor Bacterial Growth
The Phases of Bacterial Growth in Batch Culture
Requirements for Microbial Growth
Diauxic Growth
Exponential Growth Kinetics
Chemostats
Characteristics of Stationary-Phase Cells
Proteins Important for Cell Shape and Cell Division
Chromosome Segregation

5. Bioenergetics and the Proton Motive Force
Cellular Mechanisms for ATP Synthesis
Chemiosmotic Theory
Chemiosmotic Theory
ATP Synthase
The Proton Motive Force (PMF)
Quantifying the Proton Motive Force
Cellular Proton Levels
Environmental Impacts on the Proton Motive Force
Experimentally Measuring the Proton Motive Force

6. Respiration and Fermentation
The Basic Components of an Electron Transport Chain
Electrode/Redox Potential (E0′)
Brief Review of the Electron Transport Chain in Mitochondria
Q Cycle of Mitochondria
Bacterial Electron Transport Chains
Q Loop of Bacteria
Electron Donors and Acceptors in Bacteria
Fermentation

7. Regulation: Posttranslational Control
Importance of Regulatory Processes
Allosteric Regulation of Enzymes
Allosteric Regulation of Branched Pathways
Covalent Modifications
Posttranslational Regulation in the Sugar Phosphotransferase System

8. Gene Regulation: Transcription Initiation and Posttranscriptional Control
Transcription Terminology
Bacterial Transcription Initiation and Elongation
Bacterial Transcription Termination
Regulatory cis- and trans-Acting Elements Impacting Transcription
Examples of Different Promoter Structures
Transcriptional Regulation of the lac Operon
Activation and Repression by the Global Regulator Cra
Attenuation
Posttranscriptional Regulation
Methods Used to Study Gene Regulation
Methods to Demonstrate Protein–DNA Interactions

Interlude: From Unity to Diversity
Metabolic Diversity
Global Nutrient Cycles
Structural and Regulatory Diversity of Microbes

10. Phototrophy
Phototrophy
Chlorophyll-Based Phototrophy
Cellular Structures Needed for Phototrophy: Light-Harvesting Complexes, Reaction Centers, and Unique Membrane Organizations
Oxygenic Photoautotrophy in the Phylum Cyanobacteria
Anaerobic Anoxygenic Phototrophy in the Phototrophic Purple Sulfur and Purple Nonsulfur Bacteria
Anaerobic Anoxygenic Phototrophy in the Phyla Chlorobi and Chloroflexi (Green Sulfur and Green Nonsulfur Bacteria, Respectively)
Anaerobic Anoxygenic Photoheterotrophy in the Firmicutes
Aerobic Anoxygenic Phototrophy
Retinal-Based Phototrophy

11. Chemotrophy in the Carbon and Sulfur Cycles
The Carbon Cycle
The Chemoorganotrophic Degradation of Polymers
The Chemoorganotrophic Degradation of Aromatic Acids
Chemoorganotrophy in Escherichia coli
Chemolithoautotrophy
Chemolithoautotrophy in Methanogens
Methylotrophy Enables Cycling of One-Carbon Compounds
One-Carbon Chemolithotrophy in Acetogens
The Sulfur Cycle
Chemoheterotrophy and Chemolithoautotrophy in the Sulfur Cycle: Sulfate Reducers
Chemolithoautotrophy in the Sulfur Cycle: Sulfur Oxidizers
The Anaerobic Food Web and Syntrophy

12. Microbial Contributions to the Nitrogen Cycle
Overview of the Nitrogen Cycle
Nitrogen Fixation
Biochemistry of Nitrogen Fixation
Regulation of Nitrogen Fixation
Symbiotic Plant-Microbe Interactions during Nitrogen Fixation
Assimilatory Nitrate Reduction
Ammonia Assimilation into Cellular Biomass
Nitrification: Ammonia Oxidation, Nitrite Oxidation, and Comammox
Anammox: Anaerobic Ammonia Oxidation
Denitrification

13. Structure and Function of the Cell Envelope
Fundamental Structure of the Cytoplasmic Membrane
Variation in Cytoplasmic Membranes
Transport across Cytoplasmic Membranes
Cell Wall Structures
Gram-Negative Outer Membrane
Periplasm
Additional Extracellular Layers

14. Transport and Localization of Proteins and Cell Envelope Macromolecules
Introduction to Cytoplasmic Membrane Protein Transport Systems
Secretory (Sec)-Dependent Protein Transport System
The Secrectory (Sec)-Dependent Protein Transport Process
Signal Recognition Particle (SRP)-Dependent Protein Transport Process
Twin-Arginine Translocation (Tat) Protein Transport Process
Integration of Cytoplasmic Membrane Proteins
Gram-Negative Bacterial Outer Membrane Protein Secretion Systems
Secretory (Sec)- and Twin-Arginine Translocation (Tat)-Dependent Protein Secretion Systems
Secretory (Sec)-Independent and Mixed-Mechanism Protein Secretion Systems
Importance of Disulfide Bonds
Transport and Localization of Other Cell Envelope Components

15. Bacterial Motility and Chemotaxis
Motility in Microorganisms
Bacterial Flagella and Swimming Motility
Regulation of Flagellar Synthesis in Escherichia coli
Mechanism of Swimming Motility
Archaeal Flagella
Bacterial Surface Motility
Chemotaxis
Conservation and Variation in Chemotaxis Systems among Bacteria and Archaea
Methods to Study Bacterial Motility and Taxis

16. Quorum Sensing
Fundamentals of Quorum Sensing
Quorum Sensing and Bioluminescence in the Vibrio fischeri-Squid Symbiosis
Basic Model of Quorum Sensing in Gram-Negative Proteobacteria
Basic Model of Quorum Sensing in Gram-Positive Bacteria
Interspecies Communication: the LuxS System
Regulatory Cascade Controlling Quorum Sensing in Vibrio cholerae
Quorum Quenching

17. Stress Responses
Oxidative Stress
Heat Shock Response
Sporulation

18. Lifestyles Involving Bacterial Differentiation
A Simple Model for Bacterial Cellular Differentiation: Caulobacter crescentus
Differentiation in Filamentous Cyanobacterial Species
Life Cycle of Filamentous Spore-Forming Streptomyces: An Example of Bacterial Multicellularity
Life Cycle of Myxobacteria: Predatory Spore-Forming Social Bacteria
Biofilms: The Typical State of Microorganisms in the Environment