Bacteria and Archaea

1. Bacteria and Archaea The Prokaryotic Domains

2. Prokaryotic ComplexityFigure 4.5

3. Eukaryotic ComplexityFigure 4.7

4. Prokaryotes • derived from ancient lineages • more biomass than all other life combined • “simple” cellular structure • no nuclear membrane • no membrane-bound organelles • no cytoskeleton • limited morphological variation

5. Prokaryotic MorphologiesFigure 27.13

6. Prokaryotic Morphologies Figure 27.1

7. photosynthetic bacteriaFigure 27.7

8. photosynthetic archaeaFigure 27.20

9. Prokaryotes • diverse metabolic “strategies” • photoautotrophy • chemoheterotrophy • most bacteria and archaea • chemoautotrophy • photoheterotrophy • energy from light • carbon from organic compounds

10. Energy/carbonTable 27.2

11. Prokaryotes • in nearly every habitat on Earth • terrestrial • aerobic/anaerobic • marine/freshwater • deep ocean rifts/deep in crust (>2 km) • antarctic ice pack • hot/acidic (>100˚C; pH = 2-3) • salty/alkaline (pH = 11.5) • etc.

12. Prokaryotes • a range of growth rates • generation times • 10 min • 1-3 hours • days - weeks • suspensions between growth periods • indefinite • years, decades, >century, millions?

13. Prokaryotes • Some defy taxonomic notions • get too big • possess internal membrane systems • exhibit “eukaryote-like” growth forms

14. Actinomycete Figure 27.16

15. MorphologyFigure 27.3 Diplococcus Neisseria gonorrhoeae Streptococcus pyogenes Staphylococcus aureus

16. bacterial gas vesiclesFigure 27.4

17. Prokaryotic Taxonomy • Historically • morphology • motility (+/-) • rolling/gliding • vertical positioning • flagella & axial filaments

18. axial filamentsFigure 27.4

19. flagellaFigure 27.5

20. Prokaryotic FlagellumFigure 4.6

21. Gram’s Stain: Bacillus subtilisgram positiveFigure 27.6

22. Gram’s Stain:E. coligram negativeFigure 27.6

23. Prokaryotic Taxonomy • Historically • morphology • motility • reactivity • Gram’s stain - peptidoglycan cell wall • metabolism • aerobic/anaerobic • resource utilization • products • inclusion bodies

24. MycoplasmaFigure 27.17

25. endospore - resting bodyFigure 27.14

26. Prokaryotic Taxonomy • Historically • distinctive features • size • very large or very small • stress response • endospore formation • life style • colonial/parasitic/pathogenic

27. Chlamydia: obligate intracellular parasiteFigure 27.13

28. crown gall on geraniumdue to Agrobacterium tumefaciensFigure 27.10

29. Prokaryotic Taxonomy • Pathogenic requirements • contact • entry • defense evasion • multiplication • damage • infectious transfer

30. Prokaryotic Taxonomy • Pathogen characteristics • Invasiveness • Toxigenicity • Corynebacterium diphtheriae vs. Bacillus anthracis • endotoxin vs. exotoxin • Salmonella vs. Clostridium tetani

31. Prokaryotic Taxonomy • Koch’s postulates • Always found in diseased individuals • Grown in pure culture from host inoculant • Cultured organisms causes disease • Newly infected host produces a pure culture identical to the infective culture

32. Prokaryotic Taxonomy • Historically • distinctive features • size • very large or very small • stress response • endospore formation • life style • parasitic/pathogenic • ecological niche

33. Methanogens & methane using Archaea • Methanogens release 80-90% of atmospheric methane, a greenhouse gas • Methane users intercept methane seeping from sub-oceanic deposits

34. Prokaryotic Taxonomy • Biofilm production • on solid surfaces • mixed colonies • polysaccharide matrix • resistant to treatments

35. Recent Prokaryotic Phylogeny • Based on rRNA • evolutionarily ancient • shared by all organisms • functionally constrained • changes slowly with time • encodes signature sequences • BUT - yields a different phylogeny than other sequences analyzed

36. Recent Prokaryotic Phylogeny • sources of phylogenetic confusion • Lateral gene transfer • among members of bacterial species • among members of different species • across domains… • phylogenetic analysis assumes cladogenic evolution • evolution may have been highly reticulate

37. Recent Prokaryotic Phylogeny • sources of phylogenetic confusion • Mutation • prokaryotes are haploid • “recessive” mutations are not masked • prokaryotes have very little non-coding DNA • many prokaryotes have very short generation times

38. Recent Prokaryotic Phylogeny • rRNA led to three domains • Archaea: more similar to Eukarya than to Bacteria • An ancient split between Bacteria and Archaea was followed by a more recent split between Archaea and Eukarya

39. The Three Domain PhylogenyFigure 27.2

40. Shared Features of the Three Domains • plasma membrane • ribosome structure • glycolysis • encode polypeptide sequences in DNA • replicate DNA semi-conservatively • transcribe, translate with same genetic code

41. Table 27.1

42. some major bacterial groupsFigure 27.8

43. Bacterial Phylogeny • Molecular comparisons suggest several higher level groups • Proteobacteria are highly diversified • gram negative • bacteriochlorophyll • source of mitochondria • N2-fixers, Rhizobium, Agrobacterium, E. coli, Yersinia, Vibrio, Salmonella, etc.

44. ProteobacteriaFigure 27.9

45. Bacterial Phylogeny • Molecular comparisons suggest several higher level groups • Proteobacteria are highly diversified • ancient Cyanobacteria produced oxygen and chloroplasts • “blue-green algae” • fix CO2 & N2 • single or colonial - sheets, filaments, balls

46. Cyanobacteria fix CO2 & N2Figure 27.11

47. Cyanobacteria are pond scumFigure 27.11

48. Bacterial Phylogeny • Molecular comparisons suggest several higher level groups • Proteobacteria are highly diversified • ancient Cyanobacteria produced oxygen and chloroplasts • Spirochetes have axial filaments • human parasites & pathogens • free living in water sediments

49. Spirochetes have axial filamentsFigure 27.12

50. Bacterial Phylogeny • Molecular comparisons suggest several higher level groups • Proteobacteria are highly diversified • ancient Cyanobacteria produced oxygen and chloroplasts • Spirochetes have axial filaments • Chlamydias have a complex life cycle • obligate intracellular parasites