Part 2/20 – Core Microbial Physiology for Fermentation
To truly understand microbial fermentation, we must first understand the physiology of the microbes that make it possible. Microbial physiology is the study of how microorganisms grow, adapt, and transform substrates into energy and products. In the context of industrial fermentation, this knowledge becomes the foundation for optimizing growth conditions, maximizing yield, and engineering superior production strains. Whether you’re working with E. coli, S. cerevisiae, or more exotic chassis like C. glutamicum, the same physiological principles apply.
This lesson dives into the key phases of microbial growth, the elemental building blocks of metabolism, and the energy-generating pathways that underpin fermentation. We’ll also explore the strategic differences between facultative and obligate anaerobes, and how their lifestyles shape their usefulness in biotech.
📈 The Microbial Growth Curve
Microbial growth is not linear. In batch fermentation, cells follow a predictable path of population dynamics that can be divided into four key phases:
- Lag Phase
- Cells are metabolically active but not dividing.
- Time is spent synthesizing enzymes and adjusting to new conditions.
- Duration depends on the inoculum age, media composition, and environmental stress.
- Log (Exponential) Phase
- Cells divide at a constant rate, doubling each generation.
- Growth is at its maximum, assuming no nutrient limitation.
- This is the phase of highest metabolic activity and product formation (for growth-associated products).
- Stationary Phase
- Nutrients become limiting; waste accumulates.
- Growth rate slows and plateaus; some cells die while others persist.
- Secondary metabolite production often occurs here (e.g., antibiotics).
- Death Phase
- Viability declines as toxic byproducts accumulate.
- Useful in understanding longevity and bioburden dynamics in scale-up.
Knowing where your culture is on this curve is essential for timing sampling, inductions (in recombinant systems), and harvest.
⚛️ Nutrient Cycles: The Elements of Life
Microbes require a balanced diet to grow efficiently. Industrial media formulations must address the following elemental needs:
- Carbon (C): Backbone of all organic molecules; primary energy source.
- Sources: Glucose, glycerol, molasses, xylose
- Nitrogen (N): For amino acids, nucleotides, and cell wall components.
- Sources: Ammonium sulfate, urea, peptone, yeast extract
- Phosphorus (P): DNA, RNA, ATP, and membrane phospholipids.
- Sources: Phosphoric acid, potassium phosphate
- Sulfur (S): Amino acids (cysteine, methionine), vitamins (biotin, thiamine).
- Sources: Magnesium sulfate, sodium sulfate
Trace elements like magnesium, calcium, iron, zinc, and manganese also play catalytic and structural roles. Too much or too little of any one component can significantly affect fermentation outcomes.
🔋 Metabolic Pathways: From Sugar to Energy (and Product)
Microbes are efficient chemical engineers. At the core of fermentation is the conversion of glucose into energy and building blocks. Here’s a simplified breakdown of major pathways:
1. Glycolysis (Embden–Meyerhof–Parnas pathway)
- Converts glucose to pyruvate
- Produces 2 ATP and 2 NADH per glucose
2. Fermentation Pathways
Depending on the organism and environmental conditions, pyruvate can be converted into:
- Lactic acid (Lactobacillus, Streptococcus)
- Ethanol and CO₂ (S. cerevisiae)
- Acetic acid (Acetobacter)
- Propionic acid, butanol, or mixed acids (anaerobes)
These pathways regenerate NAD⁺, maintaining redox balance under anaerobic conditions.
3. TCA Cycle (Aerobic)
- Pyruvate enters mitochondria (in eukaryotes) or the cytoplasm (in prokaryotes)
- Full oxidation into CO₂
- Generates NADH and FADH₂ for oxidative phosphorylation
4. Electron Transport Chain (if aerobic)
- Located in membranes (inner mitochondrial in yeast, plasma in bacteria)
- ATP yield is highest here: up to 38 ATP per glucose in ideal conditions
📊 ATP Yield Comparison Table
| Pathway | Organism Type | ATP per Glucose |
|---|---|---|
| Glycolysis Only (Fermentation) | Anaerobes | ~2 |
| TCA + ETC (Respiration) | Aerobes | ~30–38 |
While respiration is more energy-efficient, fermentation is often faster and less regulated, allowing high rates of flux—even if it’s energetically wasteful.
🌬 Facultative vs. Obligate Anaerobes
Facultative Anaerobes
- Can grow in both aerobic and anaerobic conditions.
- Example: E. coli
- Useful for processes that transition between oxygen levels (e.g., start aerobic, then switch)
Obligate Anaerobes
- Oxygen is toxic; rely strictly on fermentation.
- Example: Clostridium spp.
- Often used for solvent fermentation (butanol, acetone)
Obligate Aerobes
- Require oxygen to survive; can’t ferment.
- Example: Pseudomonas
- Important in aerobic fermentation of enzymes
This classification determines not only reactor design but also media formulation, sparging strategy, and sensor choice.
🔬 Why Physiology Matters in Biotech
Understanding microbial physiology isn’t just academic—it directly impacts product yield, quality, and cost.
- Strain Engineering: To redirect carbon flux, you must first understand where it naturally flows.
- Induction Timing: For recombinant protein production, expression is often best during mid-log phase.
- Stress Response: Cells under nutrient limitation may activate unwanted proteases or stress pathways.
- Toxicity Management: Knowing metabolic bottlenecks helps prevent unwanted byproducts like acetate in E. coli.
Modern tools like flux balance analysis (FBA) and RNA-Seq allow us to model and optimize microbial physiology in silico before wet-lab work even begins.
🧪 Case Example: Lactic Acid Bacteria in Yogurt vs. Muscle
- In yogurt: Lactobacillus uses homolactic fermentation to convert lactose into lactic acid, lowering pH and coagulating milk proteins.
- In muscles: During intense exercise, human cells temporarily switch to lactic acid fermentation due to limited oxygen supply.
Same pathway, two species, different contexts—highlighting how universal and adaptable these systems are.
🧭 Coming Up Next:
Now that we’ve explored the internal world of microbes, it’s time to understand the energy economics of fermentation. In the next lesson, we’ll compare fermentation to respiration and dissect the trade-offs between speed, yield, and redox balance.
👉 Previous Page — Microbial Fermentation Course – Part 1
👉 Next page — Microbial Fermentation Course-Part 3
