1. Bacteria and Archaea The Prokaryotic Domains

2. Prokaryotic Complexity Figure 4.5

3. Eukaryotic Complexity Figure 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 Morphologies Figure 27.13

6. Prokaryotic Morphologies Figure 27.1

7. photosynthetic bacteria Figure 27.7

8. photosynthetic archaea Figure 27.20

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

10. Energy/carbon Table 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. Morphology Figure 27.3 Streptococcus pyogenesStaphylococcus aureusNeisseria gonorrhoeae Diplococcus

16. bacterial gas vesicles Figure 27.4

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

18. axial filaments Figure 27.4

19. f l a g e l l a Figure 27.5

20. Prokaryotic Flagellum Figure 4.6

21. Gram’s Stain: Bacillus subtilis gram positive Figure 27.6

22. Gram’s Stain: E. coli gram negative Figure 27.6

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

24. Mycoplasma Figure 27.17

25. endospore - resting body Figure 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 parasite Figure 27.13

28. crown gall on geranium due to Agrobacterium tumefaciens Figure 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 Phylogeny Figure 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 groups Figure 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. Proteobacteria Figure 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 CO 2 & N 2 single or colonial - sheets, filaments, balls

46. Cyanobacteria fix CO 2 & N 2 Figure 27.11

47. Cyanobacteria are pond scum Figure 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 filaments Figure 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

51. Chlamydia Figure 27.13

52. Bacterial Phylogeny Molecular comparisons suggest several higher level groups –Firmicutes: a diverse (mostly) Gram positive group some produce endospores some are native flora –Staphylococcus

53. Gram + staphylococci Figure 27.15

54. Bacterial Phylogeny Molecular comparisons suggest several higher level groups –Firmicutes: a diverse (mostly) Gram positive group some produce endospores some are native flora some are filamentous (actinomycetes) –Mycobacterium tuberculosis –Streptomyces spp.

55. filamentous Actinomycete Figure 27.16

56. Bacterial Phylogeny Molecular comparisons suggest several higher level groups –Firmicutes: a diverse (mostly) Gram positive group some produce endospores some are native flora some are filamentous (actinomycetes) Mycoplasmas –small (~0.2 µm), no cell wall, low DNA

57. Mycoplasma Figure 27.17

58. unique membrane structure Figure 27.18

59. unique membrane structure See page 539

60. Archaean Phylogeny Most known archaea are extremophiles –many are not Archaea cell walls lack peptidoglycan Archaea possess unique cell membranes lipids Archaea share rRNA signature sequences >1/2 of Archaean genes are unlike genes known from Bacteria or Eukaryotes

61. Archaean Phylogeny Crenarchaeota –most live in hot, acidic habitats 70-75˚C; pH 2-3 –Sulfolobus pH = 0.9 –Ferroplasma pH = 0.0 –some maintain internal pH 7.0

62. a hot, acidic home Figure 27.19

63. Archaean Phylogeny Crenarchaeota –most live in hot, acidic habitats Euryarchaeota –Methanogens [CO 2 => CH 4 ] strict anaerobes in cow guts, rice paddies and hydrothermal vents all share rRNA similarities

64. Archaean Phylogeny Crenarchaeota –most live in hot, acidic habitats Euryarchaeota –Methanogens –extreme halophiles e.g. in the Dead Sea some use bacteriorhodopsin (retinal), not bacteriochlorophyll

65. Archaean Phylogeny Crenarchaeota –most live in hot, acidic habitats Euryarchaeota –Methanogens –extreme halophiles –Thermoplasma thermoacidophile, no cell wall genome size = Mycoplasmas (1.1 x 10 6 )