Microbial Population Growth

Question 1

Why are prokaryotes so dominant?

Answer 1

They have a very fast growth rate (13 min doubling time) = evolve/adapt fast (eg. antimicrobial resistance)

Question 2

Describe the process of binary fission (going from one cell to two)

Answer 2

1. Chromosome replication begins
2. One copy of the origin (of replication) is now at each end of the cell
3. Replication finishes
4. Two daughter cells result

• Prokaryotes reproduce asexually by cell division through the process of binary fission
• Binary fission results in the formation of two cells that are genetically identical

Question 3

Describe the classic way of growing microbes: “closed” batch culture system

Answer 3

• Refers to a form of cell culturing
• Defined [limited amount] supply of nutrients is provided
• Once used [become limited] cells cannot proliferate
• Standard method of studying microorganisms in a culture
• Dictated by method not shape of flask

Question 4

Describe the phases of microbial growth (“feast and famine”)

Answer 4

• Lag Phase: length depends on history of inoculum, time required to get biosynthetic reactions running
• Exponential Phase (log phase): cells are active dividing and nothing is limiting for growth. Population is doubling in a constant time interval (under ideal conditions)
• Stationary Phase: cells stop growing and cryptic growth is observed.
  Cryptic growth is when organisms survive by consuming lysed cell constituents of other dead cells within the culture. This is not a static population but a dynamic population. There is an equilibrium between growing and dying cells.
• Death Phase: cell death. Equilibrium between growing cells and dying cells is skewed towards death.

Question 5

Are all cells created equal?

Answer 5

No growth actually means death rate and growth rate is in balance

Question 6

What do prokaryotes need to multiply?

Answer 6

1. Carbon source = building bocks for macromolecular synthesis
2. Energy source = energy (electrons) to drive anabolic and catabolic reactions in the cell
3. Reducing Power = carriers of energy/electrons (NAD+/NADP+)
   
   • Nicotinamide adenine dinucleotide (NAD)H = reduced form

Question 7

How do prokaryotic cells harvest energy?

Answer 7

Molecules = natural batteries

• Chemical energy stored in bonds
• Broken chemical bonds release energy that can be captured in new bonds (ATP)
• ATP = most common energy currency
• ATP bonds can be broken again later to release that energy
  - This reduction (-red) and oxidation (-ox) of couples compounds can be applied to many compounds and forms the basis for ‘redox reactions’

Question 8

Describe how simple transformations lead to big repercussions in prokaryotic cells

Answer 8

Breakdown:
- The cells take substrates and turns them into products (called catabolism: energy generation)

ATP is used for…

Buildup:
- The monomers (building blocks) are then used to create macromolecules and other cellular constituents (called anabolism: energy consumption)

Question 9

What are the limitations to pure cultures when studying communities?

Answer 9

Wild-type strain:
- Has all the essential genes
- Can grow by itself
- Can be isolated into pure culture

Auxotroph - an organism that is unable to synthesis one or more essential growth factors, and it will not grow unless factor is provided

• This means that autotrophs cannot be cultured unless we provide limiting factors
• 98% of all the microorganisms sequenced so far lack essential pathways or key genes for the synthesis of amino acids

Question 10

How do auxotrophs survive in nature?

Answer 10

Cross feeding: also called syntrophy, is when one species gains metabolic products of another species

• Cross feeding allows for survival of auxotrophs by harvesting resources generated by other organisms
• The interactions can benefit one, or both species
• Auxotrophy is common in nature and partially explains our inability to culture most microbes
• Cross feeding can be: Uni-directional or Bidirectional. The ‘food’ the auxotroph gains can be a byproduct of another organism or cooperative with the organism

Question 11

What is a microbiome and a microbiota?

Answer 11

Microbiome: The complete collection of microorganisms, and their genes, within a particular environment

Microbiota: Individual microbial species in a biome - bacteria, fungi, archaea and viruses

Question 12

Describe Culture dependent methods and their pros and cons

Answer 12

Culture dependent methods:
- Relies on culturing of microbes in the lab
- Uses pure cultures, or simple (reduced diversity) enrichments

Pros:
- Allows access to pheontype
- Can study one organism at a time
- Can manipulate conditions to see response of organism

Cons:
- Not all organisms can be cultured
- Too many species to grow them all
- Culturing required precise conditions to match microbial needs
- Does not match real world conditions

Question 13

Describe Culture independent methods and their pros and cons

Answer 13

Culture independent methods:
- Relies predominantly on nucleic acid-based methods. No culturing required.
- Uses sequencing or metabolic profiling to study all microbes in a sample

Pros:
- Allows access to genotype
- Can study many organisms at a time
- Shows communities as they are in nature
- Can target non-culturable organisms
- Provides access to unknown information/species

Cons:
- No pure culture, so no ability to manipulate
- Expensive and complex methods