lecture 9: bacterial diversity reading assignments in text: lengeler et al. 1999 text:pages 674-676...

Lecture 9: Bacterial Diversity

Reading assignments in Text: Lengeler et al. 1999

Text: pages 674-676 Bacterial diversitypages 700-704 Phylogenetic treespages 704-716 Early life/ evolutionpages 723-728 Food in the real worldpages 746-750 Biofilmspages 754-761 Cooperation and methanogenspages 763-774 Bugs in waterpages 775-778 Bugs in sedimentspages 779-784 Bugs in soilpages 784-792 Bugs in extreme environmentspages 879-882 Bugs in food productspages 907-908 Bio-treatment

Lecture 8Text: pages 586-601 Sporulation

pages 627 Secondary metabolism

Lecture Overview

Bacterial populations (lab conditions)

Metabolism

GROWTH

Bacteria as single cells (“cell cycles”)

DifferentiationSymbiosis

Sporulation

Bacterial Environments and Diversity

Spreading sea-floor

Alvin

Smoker/hot vent~15x106 yr cycle “tube worms” + ecosystem

Deep-sea symbiosis between lithotrophs and eukaryotes

H2S O2 ATP/NADPH CO2 fixn = food

Epulopiscium fishelsonii (the big one)

250 microns

“Molecular” 16S rRNA phylogenic analysis

Value?

c

d

a

b

“Wt” reference

“mutation”

A sequencing example:

Any organism, even non-culturable

a

b

cd

1

23

Analysis

Un-rooted “tree”

The 16S rRNA “Tree of Life”

3 Kingdoms1 2

3

E. fishelsonii ~ B. subtilis

Multi-cellularnarrow diversity

People ~ Yeast

Mitochondria ~ Bacteria

Chloroplasts ~ Cyanobacteria

Many diverse non-culturable

Root maybe a Thermo-phile

Archaea versus Bacteria (are they really different?)

Biosynthesis, amino acids, etc.

Yes No

XCell division

X

Membranes X(unique)

Polymerization DNA X(eukayotic)

RNA X(eukayotic)

Translation X(eukayotic)

Chemistry / Cofactors (unique) X

Signaling, Chemotaxis X

Photosynthesis X(unique)

Operons, small circular chromosomes X

Human pathogens? ?(None known)

Bacterial numbers and distributions

(from Whitman et al. 1998 PNAS 95:6578.)

Total = 4-6 x 1030 cells

Water 12 x 1028 cells

Sediments 355 x 1028 cellsBiofilms

Soil 26 x 1028 cells

Deep earth 25-250 x 1028 cells

Air ~5 x 1019 cells

People 6 x 109 4 x 1023 colon

Cows 1 x 109 29 x 1023 rumenTermites 2 x 1017 7 x 1023 gut

Animals Bacteria

Symbiosis

Growth / Turnover in Days (not DT)

Water shallow 16

Water deep 300

Phototrophs 1.5

Sediments 500,000

Soil 900

Animals ~1

adhesion threads

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

Actinobacillus actinomycetemcomitans (stained with crystal violet)Biofilm colony on polystyrene petri dishReleases cells to form new colonies

Biofilm spread

4 mm

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.

Natural bacterial distributions

Sauerkraut

Cabbage 40

NaCl 1Cover 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 ?