Lecture 9: Bacterial Diversity Reading assignments in Text: Lengeler et al. 1999 Text: pages 674-676 Bacterial diversity pages 700-704 Phylogenetic trees pages 704-716 Early life/ evolution pages 723-728 Food in the real world pages 746-750 Biofilms pages 754-761 Cooperation and methanogens pages 763-774 Bugs in water pages 775-778 Bugs in sediments pages 779-784 Bugs in soil pages 784-792 Bugs in extreme environments pages 879-882 Bugs in food products pages 907-908 Bio-treatment Lecture 8 Text: pages 586-601 Sporulation pages 627 Secondary metabolism

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

Deep-sea symbiosis between lithotrophs and eukaryotes Alvin “tube worms” + ecosystem Spreading sea-floor Smoker/hot vent ~15x106 yr cycle H2S O2 ATP/NADPH CO2 fixn = food

Epulopiscium fishelsonii (the big one) 250 microns

“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

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

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)

Bacterial numbers and distributions (from Whitman et al. 1998 PNAS 95:6578.) Animals Bacteria Symbiosis Total = 4-6 x 1030 cells Water 12 x 1028 cells Sediments 355 x 1028 cells Biofilms Soil 26 x 1028 cells People 6 x 109 4 x 1023 colon Cows 1 x 109 29 x 1023 rumen Deep earth 25-250 x 1028 cells Termites 2 x 1017 7 x 1023 gut Air ~5 x 1019 cells Growth / Turnover in Days (not DT) Water shallow 16 Sediments 500,000 Water deep 300 Soil 900 Phototrophs 1.5 Animals ~1

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.

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

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.

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 ?