Microbial Metabolism, Nutrition, Bioenergetics, and Growth

Microbial Metabolism and Nutrition

Metabolism: Catabolism and Anabolism

Metabolism encompasses all life-sustaining chemical transformations within cells. It is divided into two main processes:

• Catabolism: Energy-releasing reactions (exergonic) that break down molecules.

• Anabolism: Energy-requiring reactions (endergonic) that build cellular components.

Microbes display tremendous metabolic diversity, but all require liquid water, nutrients, free energy, and a source of electrons for biochemical reactions.

Microbial Nutrition: Macronutrients and Micronutrients

Microbial nutrition involves the acquisition of essential compounds for growth:

• Macronutrients: Required in large quantities (e.g., C, H, O, N, P, S, K, Mg, Na, Ca, Fe).

• Micronutrients: Needed in trace amounts (e.g., Mn, Zn, Co, Cu, Mo, Ni).

Cells are composed of various macromolecules and elements:

Macromolecule	Percent of dry weight
Protein	55
Lipid	9.1
Polysaccharide	5.0
Lipopolysaccharide	3.4
DNA	3.1
RNA	20.5

The elemental composition of an E. coli cell (dry weight) is dominated by carbon, oxygen, nitrogen, hydrogen, and phosphorus.

Macronutrients are typically acquired in specific forms from the environment:

Element	Usual form found in the environment
Carbon (C)	CO2, organic compounds
Hydrogen (H)	H2O, organic compounds
Oxygen (O)	H2O, O2, organic compounds
Nitrogen (N)	NH3, NO3-, N2, organic nitrogen compounds
Phosphorus (P)	PO43-
Sulfur (S)	H2S, SO42-, organic S compounds, metal sulfides
Potassium (K)	K+ in solution or as various K salts
Magnesium (Mg)	Mg2+ in solution or as Mg salts
Sodium (Na)	Na+ in solution or as NaCl or other Na salts
Calcium (Ca)	Ca2+ in solution or as CaSO4 or other Ca salts
Iron (Fe)	Fe2+ or Fe3+ in solution or as FeS, Fe(OH)3, or other Fe salts

Iron Acquisition by Siderophores

Iron is an essential micronutrient, often limiting in the environment. Microbes produce siderophores, specialized molecules with high affinity for iron, to facilitate its uptake.

• Phenolic siderophores: e.g., Enterobactin in E. coli

• Peptide siderophores: e.g., Aquachelin in marine microorganisms

• Hydroxamate siderophores: Recycled compounds for iron acquisition

• Some bacteria use "iron abstinence" and substitute manganese (Mn) instead

Carbon and Energy Acquisition in Microbes

Carbon Acquisition: Heterotrophy vs. Autotrophy

All life requires carbon, which is acquired in two main ways:

• Heterotrophy: Carbon from organic compounds

• Autotrophy: Carbon from CO2

Energy Production: Chemotrophy and Phototrophy

Microbes harness energy from various sources:

• Phototrophy: Energy from light

• Chemoorganotrophy: Energy from oxidation of organic chemicals

• Chemolithotrophy: Energy from oxidation of inorganic chemicals

Chemolithotrophy was pioneered by Sergei Winogradsky, who studied bacterial diversity and nutrient cycling.

Bioenergetics: Free Energy and Energy Conservation

Principles of Bioenergetics

Bioenergetics is the study of energy flow and conservation in biological systems. Key concepts include:

• Free energy (G): Energy available to do work, measured in kJ

• ΔG: Change in Gibbs free energy

• Exergonic reactions: ΔG negative, energy released

• Endergonic reactions: ΔG positive, energy required

Calculation of ΔG0' (standard conditions):

• $\Delta G^0' = G_f^0 [\text{products}] - G_f^0 [\text{reactants}]$

Actual free energy change in nature:

• $\Delta G = \Delta G^0' + RT \ln K$

• R = gas constant, T = temperature, K = equilibrium constant

Energy Storage and High-Energy Compounds

Cells conserve energy in high-energy phosphate bonds:

• ATP: Primary energy currency, low concentrations in cells

• Phosphoenolpyruvate, Acetyl phosphate, Acetyl CoA: Higher energy than ATP

• Energy is stored in polymers like glycogen, polyhydroxybutyrate (PHB), and elemental sulfur

Enzymes and Catalysis

Enzyme Function and Structure

Enzymes are biological catalysts that lower activation energy and increase reaction rates without altering the equilibrium or energetics of a reaction.

• Highly specific due to their 3D structure

• Active site: Region where substrate binds and reaction occurs

• Enzymes are not consumed in the reaction

Enzyme structure is primarily protein, sometimes aided by small non-protein molecules:

• Prosthetic groups: Tightly bound, permanent (e.g., cytochromes, heme)

• Coenzymes: Loosely bound, intermediate carriers (e.g., NAD+, NADH)

Protein Folding and Chaperones

Chaperones assist in proper protein folding, preventing aggregation and misfolding. ATP hydrolysis drives cycles of binding and release.

Redox Reactions and Electron Carriers

Oxidation-Reduction (Redox) Chemistry

Redox reactions involve electron transfer:

• Oxidation: Loss of electrons

• Reduction: Gain of electrons

• OILRIG: Oxidation Is Loss, Reduction Is Gain

Electron donors are oxidized; electron acceptors are reduced. Redox reactions drive energy generation in catabolism.

Reduction Potential and the Redox Tower

The tendency of a substance to be reduced or oxidized is measured by its reduction potential (E0'), in volts. The redox tower arranges couples by reduction potential:

• Most negative at the top: greatest tendency to donate electrons

• Most positive at the bottom: greatest tendency to accept electrons

• The greater the drop, the greater the energy release

Relationship between reduction potential and free energy:

• $\Delta G^0' = -nF\Delta E^0'$

• n = number of electrons transferred, F = Faraday constant (96.5 kJ/V)

Electron Carriers

Electron carriers mediate electron transfer in cells:

• Diffusible: NAD(H), NADP(H), FAD(H2)

• Fixed: Cytochromes, iron-sulfur proteins, quinones (membrane-associated)

Diffusible carriers transport electrons and protons; fixed carriers are part of electron transport chains and generate proton motive force (PMF).

Fermentation and Respiration

Fermentation vs. Respiration

Fermentation and respiration are two major catabolic pathways:

• Fermentation: Redox reactions occur without an exogenous terminal electron acceptor; ATP is generated by substrate-level phosphorylation.

• Respiration: Requires an exogenous electron acceptor (e.g., O2 for aerobic, nitrate for anaerobic); ATP is generated by oxidative phosphorylation via PMF.

Glycolysis and Fermentation Pathways

Glycolysis is the central pathway for glucose catabolism, leading to pyruvate. Fermentation pathways convert pyruvate to various products (e.g., lactic acid, ethanol) and recycle NADH.

Fermentative Diversity

Microbes can ferment a variety of sugars and polysaccharides, yielding diverse products such as alcohol, lactic acid, propionic acid, and mixed acids.

Respiration and Electron Transport Chains

Membrane-Associated Electron Carriers

Respiration involves electron transport chains (ETCs) in membranes, generating PMF:

• NADH dehydrogenase: Accepts electrons and protons

• Flavoproteins (FMN, FAD): Accept electrons and protons, transfer electrons only

• Cytochromes: Iron-containing proteins, transport electrons only

• Iron-sulfur proteins: Transport electrons only

• Quinones: Lipid-soluble, accept electrons and protons, donate electrons only

Proton Motive Force and ATP Synthesis

Electron transport chains create a proton gradient (PMF) across the membrane, which powers ATP synthase to produce ATP by oxidative phosphorylation.

Microbial Growth and Cell Division

Binary Fission and Cell Division Machinery

Microbial growth occurs via binary fission, requiring coordinated cell wall synthesis and division:

• Divisome: Protein complex centered on FtsZ, forms contractile ring at mid-cell

• MinCDE system: Oscillates to ensure FtsZ ring forms at mid-cell

• MreB: Actin-like protein, determines rod shape by recruiting cell wall synthesis proteins

Cell Wall Synthesis

Cell wall synthesis involves:

• Autolysins: Enzymes that create openings in the wall

• Bactoprenol: Lipid carrier transporting peptidoglycan precursors

• Transpeptidation: Crosslinking peptidoglycan layers (targeted by penicillin)

Bacterial Population Growth

Bacterial populations grow exponentially, with generation time depending on species and conditions. Growth phases in batch culture include lag, exponential, stationary, and death.

Measuring Microbial Growth

• Microscopic counts: Direct cell counting, cannot distinguish live/dead

• Viable plate counts: Colony-forming units (CFUs), requires serial dilution

• Turbidity: Optical density measurements using spectrophotometer

• Chemostat: Continuous culture system maintaining steady-state growth

Environmental Factors Affecting Microbial Growth

Temperature

• Microbes classified as psychrophiles, mesophiles, thermophiles, or hyperthermophiles

pH

• Acidophiles, alkaliphiles, neutrophiles

• Microbes maintain near-neutral cytoplasmic pH

Water Availability

• Measured as water activity (Aw), ranges from 0 to 1

• Halophiles (salt-loving), osmophiles (sugar-loving), xerophiles (dry-loving)

• Use compatible solutes to maintain osmotic balance

Oxygen Requirements

• Obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles, aerotolerant anaerobes

• Oxygen toxicity managed by enzymes: catalase, peroxidase, superoxide dismutase

Summary Table: Microbial Metabolic Diversity

Metabolic Type	Energy Source	Carbon Source	Example
Chemoorganotroph	Organic chemicals	Organic compounds	Escherichia coli
Chemolithotroph	Inorganic chemicals	CO2	Thiobacillus thiooxidans
Phototroph	Light	CO2 or organic compounds	Rhodobacter capsulatus

Key Equations

• $\Delta G^0' = G_f^0 [\text{products}] - G_f^0 [\text{reactants}]$

• $\Delta G = \Delta G^0' + RT \ln K$

• $\Delta G^0' = -nF\Delta E^0'$

Additional info:

Some details were inferred and expanded for completeness, such as the role of compatible solutes, the specifics of cell wall synthesis, and the summary table of metabolic diversity.