CMMB 543 Study Guide

Studying microbial systems to learn basic things about Biology
Advantages
Disadvantages
1. Quick generation time
2. Ease of experimental design, replication
3. Highly developed molecular techniques available
4. MANY practical spinoffs
5. Far more diversity in microorganisms
1. Direct observation difficult due to size and other problems.
2. Difficulty of extrapolating lab results to nature
3. Tracking individual organisms difficult
4. Vast majority of microorganisms still labeled “unculturable”

Progress in studying microbial systems:
Metagenomics
Study of metagenomes: genetic material recovered directly from environmental samples
Studying diversity and metabolic pathways in an organisms’ natural environment. Use this to get an idea of the diversity by extracting their DNA and sequencing it all
> 4000 bacterial genomes sequenced
New labeling systems available (GFP etc)
New microscopy (SCLM etc) Stable isotope feeding experiments
New approaches to culturing

Genetics + Ecology = Evolution

R vs K Selection

R selection
Density-Independent selection
Growth is continuous  population rarely attains the carrying capacity of the environment or niche
Selection Favours: increased growth rate / high reproductive rate reduced body size reduced interspecific competitive ability

K selection
Density-Dependent selection
Population rarely undergoes prolonged periods of growth  population is usually at its carrying capacity / saturation density
Selection Favours: reduced growth rate increased body size greater efficiency in competition and enhanced use of resources
 Which best describes microbes? R selection
 Always a trade-off when you select organisms under one type of regime
Inversely relate parental investment and the quantity and quality of offspring

Designing experiments to impose R and K type selection on populations

R selection
Use a batch culture also known as a serial culture (the liquid culture in the test tubes). Use this because they have an abundant amount of nutrients, just make sure that you transfer the culture to a new fresh tube everyday so the bacteria will continue in the exponential phase of growth, therefore always being selected to grow as fast as possible.
(you could also use a chemostat which is a continuous culture system)

K selection
K selection you could use continuous culture device or a batch culture but with this you would be tryig to keep them in stationary phase as long as possible, you could use a continuous culture device like a chemostat, but only use a small amount of substrate therefore the cells are competing for the nutrients.

What consequences does bringing them into the lab have for our view of microbial growth in nature?
 Does not represent the true strains that are present in nature.... Gives us a false idea
Luckinbill (Science 202:1201-1203; 1978)
(First work on R and K selection)

Rock/Paper/Scissors
Colicin (bacteriocin - narrow spectrum antibiotic)
WT: S
 Colicin producing strains (C) outcompete non-producers/sensitive strains (S)
 Colicin resistant strains (R) outcompete colicin producers
 Non-producers/sensitive strains(S) outcompete colicin resistant mutants (R)
C beats R
S beats R
R beats C
Dynamic equilibrium, all three strains can coexist stably
 To run an experiment must have all three, if only have two then one would be annihilated

Emumeration and Cultivation of Microorganisms
Counting/Enumeration – HOW?
1) Viable counts (plating, CFU)
You are assuming that everything is growing from one individual cell. Then you count. This one will be an underestimate
2) Direct counts (but are they bacteria, and are they alive?)
Take a liter of water and use a grid to just count all that is in there. You will most likely get a higher number than what you got from your viable counts. Problem: is everything you are counting bacteria?.This one will be an