Lecture 3: Microbial Communities

Question 1

What are Windogradsky columns, and how are they created?

Answer 1

• Ecosystems created by mixing soil or sediment with water, adding carbon (e.g., cellulose) and nutrients
• Columns are then sealed and left for extended period
• RESULT: self-sustaining ecosystem within a confined space.

Question 2

What role do microbes play in Windogradsky columns, and how do they contribute to the longevity of these ecosystems?

Answer 2

Microbes fix carbon and recycle nutrients, allowing these ecosystems to thrive for many years

Question 3

How is carbon fixation achieved in Windogradsky columns, and what types of microbial layers can be present in these ecosystems?

Answer 3

• Carbon fixation achieved via cyanobacteria
• Columns can exhibit layers of both aerobes and anaerobes, showcasing a diverse microbial community with different metabolic preferences.

Question 4

Give examples of both positive and negative interactions in microbial communities

Answer 4

• Positive
  
  • Toxic product of one organism may be substrate for another
    
    • EXAMPLE: heterotrophs recycling nutrients n toxic waste of cyanobacteria
• Negative
  
  • Competition (species competes w another for substrates)
  • Inhibition (antibiotics produced by one species target another)

Question 5

How do microbes sense each other?

Answer 5

Quorum sensing

• Bacteria release autoinducers (compound that induces its own production) → allows them to sense population size
  
  • E.g. acyl-homoserine lactones
• Once autoinducer reaches a threshold, cells respond
• RESULT: cells change expression n function
  
  • E.g. biofilm forming → invasive

Question 6

Describe quorum sensing n virulence in S.aureus

Answer 6

• S.aureus is opportunistic (takes advantage of weakened immune systems or other factors to cause disease)
• Quorum sensing
  
  • Changes expression: adhesive colonizing commensal → invasive aggressive pathogen
• Age regulatory system
  
  • 2 component regulatory system based around an operon w 2 promoters
  • Constitutively expresses AgrA, B, C n D
    
    • AgrD — autoinducing peptide (AIP)
    • AgrB — transmembrane protein, secretes mature AIP
    • AgrC — AIP receptor, binds AIP then phosphorylates AgrA
    • AgrA — response protein, activates P3 producing RNA III
  • Low cell density (low bacteria), low AIP
    
    • AIP doesn’t bind to AgrC (AIP receptor)
    • No phosphorylation of AgrA, no P3 activation, no RNAIII production
  • Low threshold cell density [biofilm has matured], high AIP
    
    • AIP activates enough ArgC
    • ArgA phosphorylation
    • P3 activation
    • RNAIII production
  • RNA III acts as regulatory RNA
    
    • Represses adhesion → stops cell becoming biofilm
    • Induces elements that drive invasion → allows cell to invade cells
    • Carries hld (δ-haemolysin) → damages RBCs to release Fe2+ within Hb

Question 7

How does RNA III regulate α-hemolysin (hla) expression?

Answer 7

• Forms a 2° n 3° structure
• 14 hairpins bend n globular shape brings 3’ n 5’ end together
• Ends bind to hlaA RNA at Shine-Dalgarno (SD) region → translation

Question 8

What are biofilms?

Answer 8

Small clusters of cells, enclosed in a self-producer polymer matrix n attached to a surface

Question 9

Give 3 examples of implants where biofilms can form, the organisms most commonly associated, and the consequences

Answer 9

Implant | Organism | Consequence |
| — | — | — |
| Contact lenses | P. aeruginosa | Keratitis |
| Urinary catheter | E.coli, P. aeruginosa, P. mirabilis | Bacteriuria |
| Joint replacement | S. epidermis, S. aureus | Septicaemia, device failure |

Question 10

What are the 3 common characteristics of biofilms?

Answer 10

• Cells enclosed in polymer matrix of exopolysaccharides, proteins and nucleic acid
• Formation initiated by extracellular signals present in the environment
• Protection against the host immune response, desiccation and biocides (e.g. antibiotics or disinfectants)

Question 11

What are the 5 stages of biofilm formation?

Answer 11

1. Initial attachment – flagella, type I pili
2. Irreversible attachment – LPS, Type IV pili
3. Maturation I – mirocolonies, produce aliginate, repress flagella
4. Maturation II – Quorum sensing
5. Dispersion – release planktonic cells

Question 12

How might interactions of aerobes n anaerobes allow the biofilm to function like an ecosystem?

Answer 12

• Anaerobic environment in the middle of biofilm [anaerobes present]
• Aerobic environment outside [aerobes present]
• Aerobic fermentation on the outside produces organic acieds
  
  • Organic acid degraded into H2
  • H2 used by anaerobes in the enter

Question 13

What is σ22?

Answer 13

• Sigma factor
• Encoded by algT in the alginate synthesis operon
• Regulates (in Pseudomonas aeruginosa)
  
  • Expression of Type IV pili (tiny hairs that help it move in surfaces)
  • Induction of alginate production (EPS): alginate forms a protective layer → stick together and survive in harsh conditions
  • Repression of flagella expression [bacteria form colonies thus no longer need to swim using flagella]

Question 14

What is an example of how environmental signals can influence gene expression in bacteria?

Answer 14

• Vibrio parahaemolyticus switch between two flagella systems as it matures
• Bacteria encounter a surface → interferes with the rotation of their flagella → activation of a secondary flagella system
• Switch enables swarming motility (bacteria move along a surface in a coordinated manner)