Microbial Metabolism

Metabolism of Organic Carbon Molecules

Microbial metabolism involves the breakdown and synthesis of organic carbon molecules to generate energy and cellular building blocks. The main pathways include glycolysis, the transition reaction, and the tricarboxylic acid (TCA) cycle.

• Glycolysis: Converts glucose to pyruvate, generating ATP and NADH.

  • Reactant: Glucose

  • End products: 2 pyruvate, 2 ATP (net), 2 NADH

  • Importance: Provides energy and precursors for other pathways

• Transition Reaction: Links glycolysis to the TCA cycle.

  • Reactant: Pyruvate

  • End products: Acetyl-CoA, CO2, NADH

• Tricarboxylic Acid Cycle (TCA/Citric Acid Cycle): Completes oxidation of carbon, generating ATP, NADH, FADH2, and CO2.

• Net Balance: After one glucose molecule:

  • Glycolysis: 2 ATP, 2 NADH

  • Transition: 2 NADH, 2 CO2

  • TCA: 2 ATP (GTP), 6 NADH, 2 FADH2, 4 CO2

Citric Acid Cycle

The citric acid cycle is central to energy production and biosynthesis in cells.

• Important Enzymes: Citrate synthase, isocitrate dehydrogenase, succinate dehydrogenase

• Function: Oxidizes acetyl-CoA to CO2, produces NADH and FADH2 for electron transport chain

Glyoxylate Cycle

The glyoxylate cycle is a variation of the TCA cycle used by certain microorganisms to convert fatty acids into carbohydrates.

• Required by: Bacteria, fungi, plants (especially during growth on acetate or fatty acids)

• Importance: Bypasses decarboxylation steps, allowing net synthesis of carbohydrates from acetyl-CoA

Respiration and Electron Transport Chain (ETC)

Respiration involves the transfer of electrons from NADH and FADH2 to terminal electron acceptors via the ETC, generating a proton gradient for ATP synthesis.

• Redox Balance: Maintains cellular oxidation-reduction state

• Steps: Electron carriers (e.g., cytochromes, quinones) transfer electrons in one direction due to increasing reduction potential

• Result: Proton gradient across membrane, driving ATP synthesis

ATP Synthesis

ATP is synthesized by ATP synthase, which uses the proton motive force generated by the ETC.

• Connection: ETC creates proton gradient; ATP synthase converts this energy to ATP

• Structure: ATP synthase is a multi-subunit enzyme embedded in the membrane

Metabolic Diversity

Microorganisms exhibit diverse metabolic strategies, using different electron acceptors and phosphorylation mechanisms.

• Alternate Electron Acceptors: Nitrate, sulfate, iron, etc.

• Substrate-Level Phosphorylation: Used by fermentative microbes

• Oxidative Phosphorylation: Used by respiring microbes

Fermentation

Fermentation is an anaerobic process where organic molecules serve as both electron donors and acceptors.

• Need: Regenerates NAD+ in absence of external electron acceptors

• Difference from Respiration: No ETC, less ATP produced

• Importance: Food production (e.g., yogurt, bread), industrial applications

• Energetics: Lower ATP yield compared to respiration

Chemolithotrophy and Phototrophy

Chemolithotrophy and phototrophy are alternative energy-generating strategies used by microorganisms.

• Chemolithotrophy: Uses inorganic compounds (e.g., H2, NH3) as electron donors

• Phototrophy: Uses light energy to drive electron transport and ATP synthesis

• Benefit: Allows survival in diverse environments

Anabolism

Anabolic pathways build cellular macromolecules from simpler precursors.

• Calvin Cycle: Fixes CO2 into organic molecules; key enzymes include Rubisco

• Nitrogen Fixation: Converts N2 to NH3; nitrogenase enzyme is oxygen-sensitive

• Gluconeogenesis: Synthesizes glucose from non-carbohydrate precursors

• Pentose Phosphate Pathway: Generates NADPH and ribose-5-phosphate for biosynthesis

• Amino Acid and Nucleotide Synthesis: Pathways provide building blocks for proteins and nucleic acids

• Fatty Acid Synthesis: Acetyl-ACP is central; even-chain fatty acids from acetyl-CoA, odd-chain from propionyl-CoA

• Lipid Synthesis: Involves assembly of fatty acids and glycerol

Biogeochemical Cycles

Metabolic Guilds and Niches

Microbial communities are organized into metabolic guilds, each occupying a specific niche.

• Metabolic Guild: Group of organisms sharing similar metabolic functions

• Niche: The specific environmental conditions and resources utilized by a guild

Carbon and Nitrogen Cycles

Microorganisms drive the cycling of carbon and nitrogen through the environment.

• Carbon Cycle: Involves fixation, respiration, fermentation, methanogenesis

• Nitrogen Cycle: Includes nitrogen fixation, nitrification, denitrification, ammonification

• Connection: Steps in each cycle are interdependent; e.g., carbon cycling affects nitrogen transformations

Methanogenesis

Methanogenesis is the production of methane by archaea, important in anaerobic environments.

• Importance: Contributes to global warming as methane is a potent greenhouse gas

• Raw Materials: CO2, H2, acetate

• End Products: CH4 (methane), CO2

• Termite Guts: Methanogenic archaea and syntrophic bacteria collaborate to produce methane

Syntrophy

Syntrophy is a cooperative interaction where two or more microorganisms degrade a compound together.

• Role in Carbon Cycling: Enables breakdown of complex organic matter

• Connection with Methanogens: Syntrophic bacteria produce substrates (e.g., H2) for methanogens

Nitrogen Cycle Processes

The nitrogen cycle includes several key microbial processes.

• Nitrogen Fixation: N2 to NH3; favored in anaerobic conditions

• Nitrification: NH3 to NO2 and NO3; aerobic

• Denitrification: NO3 to N2; occurs in low-oxygen environments, important for removing excess nitrate

Microorganisms and Global Warming

Microbes influence global warming through greenhouse gas production and decomposition.

• Permafrost Melting: Microbial activity increases, releasing CO2 and CH4

• Experiment: Objective: Assess microbial response to permafrost thaw; Methods: Controlled thawing, gas measurements; Key Findings: Increased greenhouse gas emissions

Microbial Growth and Its Control

Types of Media

Different media are used to cultivate and study microorganisms.

• Defined Media: Exact chemical composition known

• Complex Media: Contains undefined components (e.g., yeast extract)

• Selective Media: Favors growth of specific microbes

• Differential Media: Distinguishes between organisms based on biochemical reactions

Bacterial Growth Curve

Bacterial populations grow in distinct phases.

• Lag Phase: Adaptation, no cell division

• Log (Exponential) Phase: Rapid cell division

• Stationary Phase: Nutrient depletion, growth rate equals death rate

• Death Phase: Cell death exceeds growth

Generation Time Calculations

Generation time is the time required for a population to double.

• Formula:

• Practice: Use these formulas to solve problems on cell numbers and growth rates

Counting Number of Cells

Several techniques are used to estimate microbial cell numbers.

• Microscopic Cell Count: Direct observation; advantages: quick, disadvantages: cannot distinguish live/dead cells

• Viable Cell Count: Plate counts; advantages: counts live cells, disadvantages: time-consuming

• Turbidity Measurements: Optical density; advantages: rapid, disadvantages: indirect, requires calibration

• Instruments: Microscope, spectrophotometer, colony counter

Continuous Culture

Continuous culture maintains microbial populations in exponential phase.

• Importance: Allows study of growth under steady-state conditions

• Applications: Industrial fermentation, physiological studies

Environmental Effects on Microbial Growth

Microbes adapt to various environmental conditions.

• Psychrophile: Grows at low temperatures; adaptations: flexible enzymes, unsaturated membrane lipids

• Mesophile: Grows at moderate temperatures

• Thermophile: Grows at high temperatures; adaptations: stable proteins, saturated membrane lipids

• Hyperthermophile: Grows at very high temperatures

Controlling Microbial Growth

Various methods are used to control microbial populations.

• D Value: Time required to reduce population by 90%

• Thermal Death Time: Time to kill all cells at a given temperature

• Sterilization: Complete elimination of all microbes; process: autoclaving

• Pasteurization: Reduces microbial load; process: heat treatment

• Difference: Sterilization kills all, pasteurization reduces pathogens

• Radiation: Ionizing (deep penetration) vs. UV (surface sterilization)

• Filtration: Removes microbes from liquids

• Antimicrobial Agents: Chemicals that inhibit or kill microbes

Assaying Antimicrobial Activity

Antimicrobial activity is measured in liquid and solid cultures.

• MIC (Minimum Inhibitory Concentration): Lowest concentration preventing growth in liquid culture

• Zone of Inhibition: Area around antimicrobial agent in solid culture where growth is prevented

Molecular Information Flow

DNA Replication, Transcription, Translation

Genetic information flows from DNA to RNA to protein via three key processes.

• DNA Replication: Semi-conservative; enzymes: DNA polymerase, helicase, primase

• Transcription: DNA to RNA; enzyme: RNA polymerase

• Translation: RNA to protein; enzymes: ribosome, tRNA synthetase

• Differences: DNA is double-stranded, stable; RNA is single-stranded, less stable

• Degeneracy: Multiple codons code for same amino acid

• Central Dogma: DNA → RNA → Protein

Microbial Regulatory Systems

Constitutive vs. Regulated Expression

Gene expression can be constant or regulated in response to environmental signals.

• Constitutive Expression: Genes always expressed (e.g., housekeeping genes)

• Regulated Expression: Genes expressed only under certain conditions (e.g., lac operon)

Levels of Regulation

Gene regulation occurs at multiple levels, with transcriptional control being primary in bacteria.

• Transcriptional Regulation: Most common in bacteria

• Other Levels: Translational, post-translational

Operons

Operons are clusters of genes regulated together, allowing coordinated expression.

• Structure: Promoter, operator, structural genes

• Function: Efficient regulation of related genes

Activators and Repressors

Regulatory proteins control gene expression by binding DNA.

• Activators: Enhance transcription; example: catabolite activator protein (CAP)

• Repressors: Inhibit transcription; example: lac repressor

• Conditions: Activation or repression depends on presence of inducers or corepressors

Sensing and Signal Transduction

Bacteria sense environmental signals via two-component systems.

• Components: Sensor kinase, response regulator

• Example: Regulation of chemotaxis; attractant causes phosphorylation cascade, altering flagellar rotation

Quorum Sensing

Quorum sensing enables bacteria to coordinate behavior based on population density.

• Definition: Cell-to-cell communication via signaling molecules

• Importance: Controls virulence, biofilm formation

• Example: Vibrio fischeri uses quorum sensing to regulate bioluminescence

• Pathway: Signal molecule (autoinducer) produced, detected, activates gene expression

Global Control Systems

Global regulatory systems coordinate multiple genes and pathways.

• Catabolite Repression: Prevents expression of genes for alternative carbon sources when preferred source is available

• Example: lac operon; growth curve shows diauxic growth, with sequential use of glucose and lactose

• Sequence of Events: Glucose depletion triggers cAMP increase, CAP activation, lac operon expression