1. Lecture 9: Bacterial Diversity
Reading assignments in Text: Lengeler et al. 1999
Text: pages Bacterial diversity
pages Phylogenetic trees
pages Early life/ evolution
pages Food in the real world
pages Biofilms
pages Cooperation and methanogens
pages Bugs in water
pages Bugs in sediments
pages Bugs in soil
pages Bugs in extreme environments
pages Bugs in food products
pages Bio-treatment
Lecture 8
Text: pages Sporulation
pages 627 Secondary metabolism

2. Differentiation Lecture Overview Symbiosis Sporulation
Metabolism
GROWTH
Bacterial populations (lab conditions)
Bacteria as single cells (“cell cycles”)
Differentiation
Symbiosis
Sporulation
Bacterial Environments and Diversity

3. Deep-sea symbiosis between lithotrophs and eukaryotes
Alvin
“tube worms” + ecosystem
Spreading sea-floor
Smoker/hot vent
~15x106 yr cycle
H2S O ATP/NADPH CO2 fixn = food

5. Epulopiscium fishelsonii (the big one)
250 microns

6. “Molecular” 16S rRNA phylogenic analysis
Value?
Any organism, even non-culturable a b
“Wt” reference
“mutation”
A sequencing example: a b c d 1 2 3
Analysis
Un-rooted “tree” c d

8. The 16S rRNA “Tree of Life”
3 Kingdoms 1 2 3
Mitochondria ~ Bacteria
E. fishelsonii ~ B. subtilis
Many diverse non-culturable
Chloroplasts ~ Cyanobacteria
Root maybe a Thermo-phile
People ~ Yeast
Multi-cellular
narrow diversity

10. Archaea versus Bacteria (are they really different?)
Yes No X
Cell division
Biosynthesis, amino acids, etc. X X
Signaling, Chemotaxis
Polymerization
DNA X
(eukayotic)
RNA X
(eukayotic)
Translation X
(eukayotic)
Operons, small circular chromosomes X
Chemistry / Cofactors
(unique) X
Photosynthesis X
(unique)
Membranes X
(unique)
Human pathogens? ?
(None known)

12. Bacterial numbers and distributions
(from Whitman et al PNAS 95:6578.)
Animals Bacteria
Symbiosis
Total = 4-6 x 1030 cells
Water 12 x 1028 cells
Sediments 355 x 1028 cells
Biofilms
Soil x 1028 cells
People 6 x x 1023 colon
Cows 1 x x 1023 rumen
Deep earth x 1028 cells
Termites 2 x x 1023 gut
Air ~5 x 1019 cells
Growth / Turnover in Days (not DT)
Water shallow 16
Sediments 500,000
Water deep 300
Soil
Phototrophs
Animals ~1

14. Deinococcus geothermalis
adhesion threads
Deinococcus geothermalis
This pink-pigmented bacterium often forms biofilms. This electron micrograph shows cells attached on polished stainless steel in sterilized paper machine water at 45C.

15. Actinobacillus actinomycetemcomitans (stained with crystal violet)
Biofilm spread
4 mm
Actinobacillus actinomycetemcomitans
(stained with crystal violet)
Biofilm colony on polystyrene petri dish
Releases cells to form new colonies

16. Natural bacterial distributions
Imprint of a clover leaf on a methanol mineral salts plate incubated at 30C for 2 days to allow outgrowth of the pink-pigmented Methylobacterium strains.

18. Sauerkraut Cabbage 40 NaCl 1 ~ weeks ? So what ?
Cover with water, cold w/o air
~ weeks
1 NaCl, lysis, microbes digest polysaccharides proteins
2 Complex fermentation period
3 Leuconostoc mesenteroides take over
Heterolactic fermentation:
mannitol, acetic acid, ethanol, CO2, etc.
pH~5.5
4 Acidophiles, e.g. Lactobacillus sps. take over
Homolactic fermentation
~ 0.15 M lactate
? So what ?