Lecture 28

Question 1

Why are prokaryotes so dominant?

Answer 1

Fast growth rate (13 min doubling time) = evolve/adapt fast
- linear relationship between the size of an organism and how fast they replicate (core)

• they are very old so have adapted to many environments thus colonising most habits with their extreme ecological and metabolic activity (not core slide)

Question 2

How does the process of binary fission work?

Answer 2

• from one cell to two

1. Chromosome (single and circular) replication begins - copying the genome
2. One copy of the origin is now at each end of the cell and call begins to divide
3. Replication finishes
4. Two daughter cells result

Question 3

How do prokaryotes reproduce?

Answer 3

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 4

Composition of microbial cells

Answer 4

• not much different than eukaryotic cells in their cellular requirements
• microbes need the same building blocks as us, just different amounts
• if we supply them with all required materials they can reproduce

Question 5

Classic way of growing microbes: closed batch culture system

Answer 5

• 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 culture
• dictated by method not shape of flask

Question 6

Microbial growth: “feast and famine” - 4 stages of microbial growth cycle in the lab

Answer 6

Lag phase = length depends on history of the inoculum time, time is required to get biosynthetic reactions running

Exponential phase (log phase) = cells are actively dividing and nothing is limiting for growth - populating is doubling in a constant time interval (under ideal conditions).

Stationary phase = cells stop growing (run out of nutrients) and cryptic growth is observed (amount of cells growing = amount of cells dying) - they can also make nasty end products that inhibit growth

Death phase = cell death, equilibrium between growing cells and dying is skewed towards death (very small amount survive sometimes)

Question 7

‘Closed’ batch culture system

Answer 7

• easy lab model, but biased towards fast growing organisms like pathogens

Question 8

What is cryptic growth

Answer 8

• When organisms survive by consuming lyses cell constituents of dead cells within the culture
• this is not a static population but a dynamic population. There is an equilibrium between growing and dying cells

Question 9

Are all cells created equal?

Answer 9

• some cells behave differently
• batch culture assays measure the average behaviour of cells
• no growth means death rate and growth rate in balance

Question 10

What do prokaryotes need to multiply

Answer 10

Microorganisms need three things to grow:

1. Carbon Source:
   - building blocks for macromolecular synthesis (microbes harvest carbs from autotrophs as sources of carbon/energy)
2. Energy Source:
   - energy (electrons) to drive anabolic and catabolic reactions in the cell (transform light energy into carbs, NADPH and ATP)
3. Reducing Power
   - carriers of energy/electrons (NAD+/NADP+)
   - nicotinamide adenine dinucleotide (NAD)H = reduced form

All reactions are coupled together just like in plant, mammalian and bacteria cells

Question 11

How do prokaryotes harvest energy?

Answer 11

Molecules = natures 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 and oxidation of coupled compounds can be applied to many compounds and forms the basis of ‘redox reactions’

(- bacteria form pyruvic acid, ATP and NADH from splitting glucose (how the energy get harvested) (from lecture talking))

Question 12

Simple transformation —-> big repercussions

Answer 12

• subsatrates turned into monomers
• some carbon (monomers - building blocks) from the conversion of substrates to produces are taken and used for anabolism (energy consumption) to make other macromolecules and other cellular constituents
• the energy from anabolism comes from catabolism - the energy released when the substrates are broken down

Question 13

Tropic (nourishment) groups in microbiology. (NOT CORE SLIDE)

Answer 13

• can characterise bacteria depending on the nourishment that they get
• only two ways they can generate energy:
  
  • light
  • chemical compounds
• only two carbon sources
  
  • carbon dioxide (auto) - self built
  • organic compounds (hetero) - feeding on others

Chemoheterotrops
Chemoautotrops
Photoheterotrophs
Photoautotrophs

Question 14

Limitations to pure cultures when studying communities - WILD TYPE STRAIN

(- bacteria either needs to be either given the nutrients required
- or it needs to be able to synthesise its own nutrients you dont need to add )

Answer 14

WILD TYPE
- has all the essential genes
- can grow by itself
- can be isolated into pure culture
- EG Leucine biosynthesis
- able to synthesise required nutrients (amino acids)

Question 15

Limitations to pure cultures when studying communities: AXOTROPH

Answer 15

• lacks or is defective in one or more essential genes
• cannot grow unless missing factor is supplied
• EG: LEUCINE

Question 16

Limitations to pure cultures when studying communities

Answer 16

• auxotrophs cannot be cultured unless we provide limiting factors
• 98% of all the microorganisms sequences so far lack essential pathways or key genes for the synthesis of amino acids

Question 17

Auxotroph =

Answer 17

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

Question 18

Cross feeding =

Answer 18

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

Question 19

What is cross feeding?

Answer 19

• cross feeding allows for survival of auxotrophs by harvesting resources generated by other organisms
• the interactions can benefit one, or both of the partners
• auxotrophy is common in nature and partially explains our inability to culture most microbes

Question 20

What is a microbiome?

Answer 20

• the complete collection of microorganisms, and their genes, within a particular environment

Question 21

What is a microbiata?

Answer 21

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

Question 22

Culture dependent methods

Answer 22

• relies on culturing of microbes in the lab - need to know how to grow it
• uses pure cultures, or simple (reduced diversity) enrichments

Question 23

Pros of culture dependent methods

Answer 23

• allows access to phenotype
• can study one organism at a time
• can manipulate conditions to see response of organism

Question 24

Cons of culture dependent organisms

Answer 24

• not all organisms can be cultured
• too many species to grow them all
• culturing require precise conditions to match microbes needs
• doesn’t match real world conditions

Question 25

Culture independent methods

Answer 25

- relies predominantly on nucleus acid based methods, nu culturing required. - uses sequencing or metabolic profiling to study all microbes in a sample

Question 26

Pros of culture independent methods

Answer 26

- allows access to genotype - can study many organisms at a time - shows communities as they are in nature - can target non-culturally organisms - provides access to unknown information/species

Question 27

Cons of culture indipendent methods

Answer 27

- no pure culture, so no ability to manipulate - expensive and complex methods

Question 28

Traditional microbiology was driven by pathology (NOT CORE)

Answer 28

- tens of thousand and of microbes cultures and characterised - mostly identified pathogens or fast growing organisms - ignores complex interactions and fact the most organisms live in communities

Question 29

The ________ microbial world is far greater then the _______ world

Answer 29

The uncultured microbial world is far greater then the cultured world (We have a good pricture of the microbial world through phylogenetic signatures, metagenomics)