Principles of Microbial Metabolism and Metabolic Ecology

Preface
Contents
1: Microbial Life on Earth, Metabolism, and Metabolic Diversity
	1.1 Introduction
	1.2 Principles and Patterns in Metabolic Ecology; the Julian Adams Experiment
	1.3 An Initial Metabolic View of the Julian Adams Experiment
	Further Reading
2: A Microbe´s Environment and Natural Selection
	2.1 Introduction
	2.2 Microbes and the Physics in Their Environment
		2.2.1 Maintaining Osmotic Pressure within a Prokaryotic Cell
		2.2.2 Diffusion into and Membrane Permeability of the Prokaryotic Cell
		2.2.3 Diffusion of O2
		2.2.4 Intracellular Compartmentalization via Proteins and the Constraint of Protein Space
		2.2.5 Facilitated Diffusion and Active Transport of Catabolic Substrates
	2.3 Microbes and the Chemistry of Their Environment
		2.3.1 Chemical Composition of the Prokaryotic Cell and Trace Element Requirements
		2.3.2 CO2 and pH
			2.3.2.1 Other Environmental Parameter Affecting Microbial Fitness
			2.3.2.2 Water Activity
	2.4 Environment-Specific Catabolic Fluxes
		2.4.1 Constant and Fluctuating Environments
		2.4.2 Unstructured and Structured Environments
		2.4.3 Microbial Biofilms
	2.5 Fitness
	2.6 Selection and Drift
		2.6.1 Evolutionary Selection
		2.6.2 Negative, or Purifying, Selection
		2.6.3 Ecological Selection
	2.7 Examples of Selection and Drift
		2.7.1 Selection in the Julian Adams Chemostat Experiment
		2.7.2 Selection During Isolation of Microbes in Pure Culture
	2.8 Other Selection Acting During Microbial Isolations
	Further Reading
3: Microbial Energetics
	3.1 Introduction
	3.2 Change in Gibbs Free Energy, (ΔG); in Brief
	3.3 Calculating ΔG of Metabolic Reactions
		3.3.1 From the Equilibrium Constant Keq
		3.3.2 From Kinetic Constants
		3.3.3 From the Free Energy Change of Formation
		3.3.4 From Redox Potentials
			An Intuitive Thinking About Reduction Potentials
			Electrical Energy Conversion
		3.3.5 Calculating ΔG at Temperatures Other Than 25 C
		3.3.6 Calculating ΔG of pH-Dependent Reactions at pH Other Than 7
		3.3.7 Calculating Redox Potentials of the 2H+/H2 Couple
		3.3.8 Accuracy vs Precision When Calculating ΔG Values and Redox Potentials
	3.4 ATP as Energy Carrier in all Living Cells
		3.4.1 ΔG of ATP Formation
		3.4.2 The Adenylate Energy Charge
			Light as Energy Resource
		3.4.3 nATP and Growth Yields YS and YATP
		3.4.4 Thermodynamic Efficiency of ATP Synthesis
	3.5 Different Thermodynamic Efficiencies and Their Ecophysiological Consequences
		3.5.1 Constant nATP in Anaerobic H2 Oxidizers Over a Wide Range of H2 Concentrations
		3.5.2 Different nATP in Glucose Oxidation to the Same End Products
		3.5.3 Different nATP of Glucose Fermentation to Different End Products
		3.5.4 Lowering nATP to Access Substrates at Low Concentrations
		3.5.5 Thermodynamic View of the Julian Adams Experiment
	Further Reading
4: Catabolism and Its Coupling to Anabolism
	4.1 Introduction
	4.2 Most Energy Metabolisms Are Redox Processes
	4.3 Classification of Microbial Metabolism
		Organotrophs Versus Heterotroph
	4.4 Major Catabolic Groups of Microbes
		4.4.1 Respiring Prokaryotes
		4.4.2 Fermenting Prokaryotes
		4.4.3 Chemolithoautotrophic Prokaryotes
		4.4.4 Phototrophic Prokaryotes
	4.5 Major Anabolic Metabolism
	4.6 Coupling of Catabolism and Anabolism
		4.6.1 Coupling Based on the Flux of ATP, Electrons, and Small Intermediates
		4.6.2 Coupling Based on the Amount of Energy Conserved in Catabolism
		4.6.3 Coupling Based on the Overall Metabolic State
		4.6.4 Coupling Based on Proteome Allocation
	Further Reading
5: Microbial Kinetics
	5.1 Introduction
	5.2 Microbial Growth: In Brief
		5.2.1 Specific Growth Rate μ and Doubling Time td
		5.2.2 Dependence of μ on the Substrate Concentration: Rate and KS Specialists
		5.2.3 Fast and Slow-Growing Microbes
			Predicting Growth Rates from Genomic Data
		5.2.4 Dependence of Growth Yield on Growth Rate: The Costs of Maintenance
		5.2.5 Growth in Batch Culture
		5.2.6 Growth in a Chemostat
	5.3 Flux of Energy and Microbial Fitness
		5.3.1 Growth Rate and Thermodynamic Efficiency of ATP Synthesis: The Rate: Yield Trade-Offs
		5.3.2 Growth Rate and Length of the Catabolic Pathway
		5.3.3 Competition Favors Growth Rate Over Growth Yield
		5.3.4 Energy Flux-Driven Speciation
			5.3.4.1 Speciation in Constant, High Energy Flux Environments
			5.3.4.2 Speciation in Fluctuating Environments
	5.4 Enzyme Kinetics: In Brief
		5.4.1 Growth Rate and Thermodynamically-Based Kinetic Bottlenecks
		5.4.2 The Haldane Relationship
	5.5 A Kinetic View on the Julian Adam Experiment
		5.5.1 E. coli Glucose Metabolism and Strain Characteristics
		5.5.2 The Specific Chemostat Environment
		5.5.3 General Implications of the Julian Adams Experiment
	Further Reading
6: Mechanisms of Microbial Energy Conservation
	6.1 Introduction
	6.2 Electron Carriers
		6.2.1 One-Electron Carriers
			6.2.1.1 Ferredoxins
			6.2.1.2 Flavodoxins
			6.2.1.3 Cytochromes
		6.2.2 One- AND Two-Electron Carriers
			6.2.2.1 Flavins in Flavodoxin
			6.2.2.2 Methanophenazine
		6.2.3 Two-Electron Carriers
			6.2.3.1 NAD+ and NADP+
			6.2.3.2 Factor F420
	6.3 Energy Conservation by Substrate Level Phosphorylation (SLP)
		6.3.1 Substrate Level Phosphorylation via Organic Compounds
		6.3.2 Substrate Level Phosphorylation via Inorganic Compounds
		6.3.3 Arginine deiminase Pathway
	6.4 Energy Conservation via Ion Translocation-Coupled Phosphorylation
		6.4.1 Proton or Sodium Ion Translocation-Coupled Phosphorylation (TCP)
			Bioenergetics at Low Environmental pH
		6.4.2 Energy Conservation via FoF1 ATP Synthase
		6.4.3 The Triangular Relationship in TCP
		6.4.4 Mechanisms of Transducing Energy from Catabolic Pathway Reactions into an Electrochemical Gradient
			6.4.4.1 Linear Electron Transport in Chemotrophic Microbes
				6.4.4.1.1 Ferredoxin-Dependent Electron Transport Phosphorylation
				6.4.4.1.2 Quinone-Based Electron Transport Phosphorylation
				6.4.4.1.3 Plasticity in Energetic Coupling of Respiratory Processes
			6.4.4.2 Fumarate Respiration
			6.4.4.3 Photophosphorylation
				6.4.4.3.1 Chlorophyll-Based Photophosphorylation
				6.4.4.3.2 Bacteriorhodopsin
			6.4.4.4 TCP Coupled to Non-redox Reactions
				6.4.4.4.1 Decarboxylation of β-Keto Acids
				6.4.4.4.2 Methyltransferase in Methanogenic Archaea
				6.4.4.4.3 TCP Coupled to Metabolite Efflux
	6.5 Energy Interconversions
		6.5.1 Electron Bifurcation/Confurcation
			6.5.1.1 Flavin-Based Electron Bifurcation/Confurcation
				Quinone-Based Electron Bifurcation and Quinone-Dependent Reactions
				Quinones in Electron Transport vs Quinones in Electron Bifurcation
		6.5.2 Reverse Electron Transport
	Further Reading
7: Prototypic Reactions of Prokaryotic Carbon Catabolism
	7.1 Introduction
	7.2 Prototypic Oxidation/Reduction Reactions
		7.2.1 CH-OH Group Oxidations
			Lactate Dehydrogenase
		7.2.2 Hemiacetal Oxidation
			The Fate of Substrate Protons in Enzymatic Reactions
		7.2.3 Carbonyl Oxidation
		7.2.4 Acyl-CoA Oxidation
		7.2.5 Hydrogenases
	7.3 Prototypic C-C Cleavage Reactions
		7.3.1 Aldol Cleavage/Condensation
		7.3.2 Ketol Cleavage
		7.3.3 Major Catabolic Pyruvate-Transforming Enzymes
		7.3.4 Comparison Between Aldol and Ketol Cleavage
		7.3.5 Radical Enzyme-Dependent Decarboxylations
	7.4 Auxiliary, Extension, and Funneling Reactions
		7.4.1 Mono- and Dioxygenases
		7.4.2 Fumarate Additions
		7.4.3 Benzoyl-CoA Reduction
		7.4.4 Carbon-Carbon Rearrangements
			Radical Reactions, Radical Enzymes, and O2-Sensitivity
		7.4.5 Addition/Elimination Reactions
		7.4.6 Hydroxy/Amino Eliminations
	Further Reading
8: Metabolic Modules, Pathways, and Nodes of Intermediates
	8.1 Introduction
	8.2 Metabolic Modules, Nodes, Pathways
		8.2.1 Frequently-Occurring Modules
			Substrates, Metabolites, and End Products
		8.2.2 Nodes
		8.2.3 Pathway Architecture
		8.2.4 Modules and Pathway Evolution
	8.3 Common Modules and Pathways in Organic Acid Oxidation/Degradation
		8.3.1 Activation of Organic Acids and the Acylate  Acyl-CoA Module
			Molecular Rate-Yield Trade-Off in Module Versions
		8.3.2 β-oxidation Module
		8.3.3 Succinate  Oxaloacetate Module
		8.3.4 Acyl-CoA Mutase Module
		8.3.5 Examples of β-Oxidation Modules in Different Pathways
			8.3.5.1 Aerobic n-Alkane Degradation
			8.3.5.2 Anaerobic n-Alkane Degradation
			8.3.5.3 Anaerobic Degradation of Alkyl-Substituted Benzenes
			8.3.5.4 Anaerobic Degradation of Benzoate
			8.3.5.5 Citric Acid Cycle
			8.3.5.6 Methylcitrate Cycle
			8.3.5.7 Anaplerotic Reactions
	8.4 Common Modules and Pathways of Carbohydrate Degradation
		8.4.1 The GAP  Pyruvate Module
		8.4.2 Aldolase and Phosphoketolase Reactions
		8.4.3 Examples of GAP  Pyruvate Modules and Aldolases/Ketolases in Different Pathways
			8.4.3.1 The Embden-Meyerhof (Glycolytic) Pathway
			8.4.3.2 Entner-Doudoroff Pathway
			8.4.3.3 Comparison Embden-Meyerhof and Entner-Doudoroff Pathway
			8.4.3.4 Phosphoketolase Pathway
			8.4.3.5 The (Oxidative) Pentose Phosphate Pathway
	8.5 Examples of Modules in Reductive Carbon Pathways
		8.5.1 Butyrate-Forming Fermentation
		8.5.2 Propionate-Forming Fermentation
		8.5.3 Citrate-Consuming Fermentations
		8.5.4 1,3-Propanediol-Forming Fermentation
		8.5.5 Wood-Ljungdahl Pathway
	Further Readings
9: Fermentative Metabolism
	9.1 Introduction to Fermentation
	9.2 Some Fundamentals of Fermentative vs. Respiratory Metabolism
		9.2.1 Predicting nATP (ATP Gain) from Thermodynamics and Mechanisms of ATP Synthesis
		9.2.2 Metabolic Options in Fermenting Microbes for Re-oxidation of NADH, Reduced Ferredoxin, and Reduced Menaquinone
		9.2.3 The Pyruvate: Acetyl-CoA Junction
		9.2.4 Ecophysiological Explanations of Fermentation Product Diversity
	9.3 Lactic Acid-Forming Fermentations
		9.3.1 Homofermentative Lactic Acid Bacteria
			9.3.1.1 Hexose Oxidation to Two Pyruvate via the Embden-Meyerhof Pathway
				Uptake of Carbohydrates
		9.3.2 Heterofermentative Lactic Acid Bacteria
			9.3.2.1 Pentose Fermentation by the Phosphoketolase Pathway
			9.3.2.2 Hexose Fermentation by the Phosphoketolase Pathway
		9.3.3 Rate-Yield Trade-Offs in Lactic Acid Bacteria
		9.3.4 Hexose Metabolism by Bifidobacterium
	9.4 Propionate-Forming Fermentations
		9.4.1 Propionate-Forming Fermentation via the Methylmalonyl-CoA Pathway
		9.4.2 Propionate-Forming Fermentation via the Acryloyl-CoA Pathway
			Other Anaerobic Pathways of Propionate Formation
	9.5 Clostridial Fermentations
		9.5.1 Fermentations of Carbohydrates by Ruminococcus albus, Clostridium pasteurianum, C. acetobutylicum and for Comparison by ...
			Butyrate in the Human Gut
		9.5.2 Ethanol-Acetate Fermentation of Clostridium kluyveri
		9.5.3 Proteolytic Clostridial Fermentations
			9.5.3.1 Stickland Fermentations
				Glycine Reductase
			9.5.3.2 Alanine Fermentation via the Acryloyl-CoA Pathway
			9.5.3.3 Glutamate Fermentations
				9.5.3.3.1 Glutamate Fermentation via Hydroxyglutarate in Acidaminococcus fermentans and Clostridium symbiosum
				9.5.3.3.2 Glutamate Fermentation via Methylaspartate in Clostridium tetanomorphum
			9.5.3.4 Metabolism of Clostridium difficile
	9.6 Metabolism of Syntrophs Involved in Interspecies H2 or Formate Transfer
		9.6.1 Syntrophic Oxidation of Ethanol to Acetate and H2
		9.6.2 Syntrophic Oxidation of Lactate to Acetate, CO2, and H2
		9.6.3 Syntrophic Oxidation of Butyrate to Acetate and H2
		9.6.4 Syntrophic Oxidation of Propionate to Acetate, CO2, and H2
		9.6.5 Syntrophic Acetate Oxidation to H2 and CO2
		9.6.6 Syntrophic Oxidation of Hexadecane to Acetate and H2
		9.6.7 Syntrophic Methane Oxidation to CO2 and H2
	9.7 Metabolism of Syntrophs Involved in Direct Interspecies Electron Transfer
	Further Reading
10: Prototypic Reactions, Modules, and Pathways of C1 catabolism
	10.1 Introduction to C1 Transformations
	10.2 C1 Modules
		10.2.1 Formyl  Methyl Module
			H4F versus H4MPT
		10.2.2 CO2  Formyl Conversions
			Why is CO2  formyl conversion in hydrogenotrophic methanogens independent of ATP while acetogens spend 1 ATP for this conversi...
		10.2.3 Prototypic Reactions in Methyl Conversions
			10.2.3.1 Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase
			10.2.3.2 Methyl-H4MPT: Coenzyme M Methyltransferase
			10.2.3.3 Methyl-Coenzyme M Reductase
			10.2.3.4 Heterodisulfide Reductase
				10.2.3.4.1 Cytoplasmic Electron-Bifurcating Heterodisulfide Reductase
				10.2.3.4.2 Membrane-Associated Methanophenazine-Dependent Heterodisulfide Reductase
					HdrABC Genes in Genomes
	10.3 CO2-Reducing Microbes Involving the Reductive Wood-Ljungdahl Pathway
		10.3.1 Energetics and Reversibility of the Wood-Ljungdahl Pathway
			Acetogens and Syngas Fermentation
		10.3.2 Metabolism of Acetogenic Microbes
			10.3.2.1 Acetobacterium woodii
			10.3.2.2 Moorella thermoacetica
			10.3.2.3 Clostridium autoethanogenum
			10.3.2.4 Metabolic Flexibility of Microbes with the Wood-Ljungdahl Pathway
	10.4 CO2-Reducing Microbes Involving the Methanogenesis Pathway
		10.4.1 Energetics and Reversibility of the Methanogenesis Pathway
		10.4.2 Metabolism of Methanogenic Archaea
			10.4.2.1 Methanothermobacter and Methanococcus Species
			10.4.2.2 Methanosarcina and Methanosaeta Species
			10.4.2.3 Methanosphera stadtmanae
	10.5 Anaerobic Methanotrophs
	10.6 The Aerobic Methanotrophic Pathway
	Further Readings
Appendix
Index