Microbial Ecology

Microbial Ecology Foundations - Eco Essentials

• Microbial Ecology: Study of microbes, their interactions with each other & their environment.
• Ecosystem: Biotic community & its abiotic (non-living) environment.
• Habitat: Physical location where a microbial population lives.
• Niche: Functional role of a microbe within its habitat.
• Microbial Community: Assemblage of different microbial populations interacting in a given environment.
• Population: Group of individual microbial cells of the same species.
• Biodiversity:
  • Alpha ($\alpha$): Species richness within a single habitat/sample.
  • Beta ($\beta$): Difference in species composition between habitats.
  • Gamma ($\gamma$): Total species diversity in a landscape (across habitats).
• Major Microbial Habitats:
  • Soil (e.g., Rhizosphere)
  • Aquatic (Freshwater, Marine - Photic/Aphotic zones)
  • Atmospheric
  • Host-associated (e.g., Gut, Skin)

⭐ The vast majority of microbial life remains uncultured (the great plate count anomaly).

Microbial Interactions - Mingling & Mayhem

• Symbiosis: Close, long-term interaction between species. 📌 MCP: Mutualism, Commensalism, Parasitism.
  • Mutualism (+/+): Both benefit. E.g., Lichens (algae/fungi), mycorrhizae, gut flora.
  • Commensalism (+/0): One benefits, other unaffected. E.g., Skin flora (S. epidermidis).
  • Parasitism (+/-): One (parasite) benefits, other (host) harmed. E.g., Pathogens (Plasmodium).
• Antagonism: One organism negatively impacts another.
  • Competition (-/- or -/0): For limited resources. E.g., E. coli strains.
  • Amensalism (Antibiosis) (0/-): One produces substance (antibiotic) harmful to another, itself unaffected. E.g., Penicillium.
  • Predation (+/-): Predator engulfs/attacks prey. E.g., Bdellovibrio.
• Neutralism (0/0): Coexistence with no effect on each other; rare.

⭐ Syntrophy is a special case of mutualism where two or more microbes cooperate to degrade a substance that neither can alone.

Biogeochemical Cycles - Elemental Envoys

Microbes are crucial for global nutrient recycling, transforming elements.

• Nitrogen Cycle: Essential for proteins & nucleic acids.

  • 📌 Mnemonic: 'No NAP': Nitrification (Nitrosomonas, Nitrobacter), N-fixation (Azotobacter, Rhizobium), Ammonification, Denitrification (Pseudomonas).

  ⭐ Denitrification (e.g., by Pseudomonas) is an anaerobic process that converts $NO_3^-$ to $N_2$ gas, returning it to the atmosphere.

• Carbon Cycle: Backbone of organic molecules.

  • $CO_2$ Fixation: By photoautotrophs (e.g., Cyanobacteria) & chemoautotrophs.
  • Methanogenesis (Anaerobic Archaea, e.g., Methanobacterium): Organic C or $CO_2 \rightarrow CH_4$. E.g., $CO_2 + 4H_2 \rightarrow CH_4 + 2H_2O$.
  • Methane Oxidation (Methanotrophs, e.g., Methylococcus): $CH_4 + 2O_2 \rightarrow CO_2 + 2H_2O$.

• Sulfur Cycle: For key amino acids.

  • Oxidation of $H_2S$: $H_2S \rightarrow S^0 \rightarrow SO_4^{2-}$ (e.g., Thiobacillus).
  • Sulfate Reduction (Anaerobic): $SO_4^{2-} \rightarrow H_2S$ (e.g., Desulfovibrio).

• Phosphorus Cycle: For nucleic acids, ATP.

  • Solubilization of inorganic $PO_4^{3-}$ (e.g., Pseudomonas, Bacillus).
  • Mineralization of organic P to $PO_4^{3-}$.

Microbial Communities & Biofilms - Slime Scene

• Biofilm: Structured community of microorganisms encased in self-produced Extracellular Polymeric Substances (EPS), adherent to a surface.

• Formation Stages 📌 Mnemonic: All Cats Meow Deliciously (Attachment, Colonization, Maturation, Dispersal).

• Key Features:

  • EPS: Polysaccharides, proteins, DNA, lipids; provides structure & protection.
  • ↑ Resistance: To antibiotics, disinfectants, host defenses.

  ⭐ Bacteria within biofilms can be up to 1000 times more resistant to antibiotics than their planktonic counterparts.

• Quorum Sensing (QS): Cell-to-cell communication using autoinducers (e.g., AHLs, AIPs); regulates biofilm formation, virulence.

• Significance: Dental plaque, catheter infections (e.g., Staphylococcus epidermidis), cystic fibrosis (Pseudomonas aeruginosa), biofouling, bioremediation.

High‑Yield Points - ⚡ Biggest Takeaways

• Niche is functional role; Habitat is the physical address.
• Biofilms: Microbial communities in Extracellular Polymeric Substances (EPS), confer ↑ drug resistance & persistence.
• Quorum sensing: Cell-density dependent coordination of bacterial gene expression.
• Microbes are key in biogeochemical cycles (N, C, S, P); e.g., nitrogen fixation, nitrification.
• Symbiosis (mutualism, commensalism, parasitism) is crucial; e.g., gut microbiota aiding digestion.
• Indicator organisms (e.g., E. coli, coliforms) signal fecal contamination in water.
• Bioremediation: Using microbes to degrade environmental pollutants like oil spills or pesticides.