Chapter 9 – Microbial Nutrition, Ecology & Growth

Essential Nutrients and Cellular Composition

• Macronutrients (needed in bulk)

  • The usual CHONPS core: C, H, O, N, P, S.

  • Form the six major biomolecule classes: proteins, RNA, DNA, carbohydrates, lipids, miscellaneous small molecules.

• Micronutrients / Trace elements

  • Required only in small quantities.

  • Function mainly as enzyme cofactors that drive or stabilize catalytic reactions (e.g.
    Fe, Mn, Zn, Cu, Co, Mo).

Nutritional Classifications ("-trophs")

• Autotrophs ("self-feeders")

  • Convert inorganic CO₂ (or occasionally other simple molecules) into organic carbon; nutritionally independent of other living things.

• Heterotrophs

  • Rely on pre-formed organic molecules; extremely diverse food sources.

• Energy sources cross-cut the above

  • Phototrophs – harvest sunlight via photosynthesis.

  • Chemotrophs – oxidize chemicals. Two common sub-sets:

  • Chemoorganic: organic e⁻ donors.

  • Chemoautotrophs (lithotrophs): inorganic e⁻ donors (H₂, S, Fe²⁺, NH₃, etc.)

• Representative by-product patterns

  • Photosynthesis → O_2 released (major planetary O₂ source comes from microbes, not trees).

  • Certain chemoautotrophs generate CO2, N2 or methane (CH₄)—explains intestinal gas & swamp gas.

Oxygen Relationships & Respiratory Types

• Aerobic respiration (requires O₂)

  • Core equation: C6H{12}O6 + 6O2 \rightarrow 6CO2 + 6H2O + \text{ATP}.

• Oxygen toxicity & protective enzymes

  • Reactive Oxygen Species (ROS): O2^- (superoxide), H2O_2 (peroxide), \cdot OH.

  • Crucial detox enzymes: superoxide dismutase & catalase.

  • Example: 2H2O2 \xrightarrow{\text{catalase}} 2H2O + O2 \uparrow — bubbling you see when peroxide meets skin-dwelling Staphylococcus.

• Terminology

  • Obligate aerobes – must have O₂; possess full ROS-detox toolkit.

  • Facultative anaerobes – prefer O₂ (grow better with it) but can switch to anaerobic modes (fermentation). Name looks contradictory: they are essentially "facultative aerobes".

  • Obligate (strict) anaerobes – lack ROS-detox enzymes; O₂ is lethal.

  • Aerotolerant anaerobes – never use O₂ but can survive limited exposure.

  • Microaerophiles (mentioned implicitly) – need O₂ but at lower-than-atmospheric levels.

• Clinical / lab notes

  • Hyperbaric O₂ therapy kills anaerobes (Clostridium).

  • Anaerobic growth jar: sealed container + O₂-absorbing chemical packet (single-use, costly, often imported from Japan).

  • Reducing stab tubes or thioglycollate broth reveal gas production & depth-dependent growth patterns.

Physical Transport Processes Across Cell Membranes

• Passive mechanisms (no ATP)

  • Simple diffusion – high → low concentration gradient.

  • Facilitated diffusion – still gradient-driven but needs a specific carrier/channel; saturates when binding sites filled; multiple substrates may compete for the same carrier.

• Osmosis – water movement across semipermeable membrane; effectively low-solute → high-solute until equilibrium (isotonic, hypotonic, hypertonic concepts reviewed in prior term).

• Active transport (energy-dependent)

  • Moves substances against gradient; requires pumps.

  • Key examples: Na⁺/K⁺ pump, proton pumps that stabilize pH.

Environmental Factors Influencing Microbial Growth

Temperature Ranges

• Enzymes & nucleic acids denature above maximum → basis of heat stroke lethality.

pH

• Acidophiles – thrive at low pH; involved in pickled foods; some are probiotic.

• Alkalinophiles – prefer alkaline soils & lakes.

Salinity & Pressure

• Halophiles – require/highly tolerate salt.

• Barophiles – adapt to high hydrostatic pressure (deep-sea trenches) and, at the opposite extreme, very high altitudes (low pressure) for certain variants.

Radiation & Moisture

• UV radiation disinfects; many microbes are UV-sensitive.

• Some phototrophs possess pigments shielding them from harmful wavelengths.

• Adequate water activity (Aw) is essential; drying inhibits most vegetative cells.

Symbiotic & Ecological Associations

• Symbiosis (general) – close coexistence of two organisms.

• Mutualism – both benefit ("win–win").

• Commensalism – one benefits, the other neutral.

• Parasitism – one benefits at the expense of the host (damage / disease / death).

• Synergism – cooperative interaction benefits participants but not obligatory for survival.

• Antagonism / competition (discussed briefly): organisms inhibit or out-compete others (e.g., antibiotic secretion).

Biofilms & Quorum Sensing

• Biofilm – structured, multi-species community encased in extracellular matrix; affords protection and resource sharing.

• Quorum sensing – population-density monitoring via chemical signals; regulates gene expression for growth, virulence, and biofilm maturation.

Microbial Growth Kinetics

• Generation (doubling) time – interval required for a population to double; many bacteria = 15–20 min under optimum conditions.

• Mathematical expression

  • Nf = Ni \times 2^n

  • n = \dfrac{t}{g}, where $t$ = elapsed time, $g$ = generation time.

  • Example: 100 cells; g = 15 min; t = 2 h → n = \frac{120\text{ min}}{15\text{ min}} = 8 → N_f = 100 \times 2^8 = 25\,600 cells.

Standard Bacterial Growth Curve (Batch Culture)

1. Lag phase – adjustment; no net population increase yet; metabolism ramps up.

2. Exponential / log phase – maximal, constant doubling; nutrients & space abundant.

3. Stationary phase – nutrient depletion & waste buildup balance births & deaths; cells enter survival mode.

4. Death (decline) phase – limiting factors intensify; deaths exceed reproduction; exponential die-off.

• Practical implications: antibiotics often target log-phase cells; stationary-phase physiology linked to persistence in chronic infections.

Laboratory & Clinical Connections

• Catalase test (H₂O₂ bubbling) identifies Staphylococcus vs Streptococcus species.

• Amoxicillin–clavulanate (Augmentin)

  • Clavulanic acid inhibits β-lactamase enzymes (defensive mechanism in bacteria), allowing amoxicillin activity.

• Food safety

  • Pasteurization kills mesophiles but thermoduric microbes may survive → spoilage.

  • Pickling relies on low pH & salt to block most spoilage agents while fostering acidophiles/probiotics.

• Dean’s vs President’s list (lecture anecdote)

  • ≥3.5 GPA = Dean’s List; ≥3.75 GPA = President’s List (non-microbial but mentioned).

"Learning changes everything" – Chapter 9 wrap-up covers: nutrient types, trophic strategies, transport processes, environmental tolerances, symbiotic relationships, biofilms/quorum sensing, and the full bacterial growth cycle—from lag to death.