1. Prokaryotic Diversity: The Archaea
CHAPTER 13
Prokaryotic Diversity: The Archaea

2. PART I Phylogeny and General Metabolism   Phylogenetic Overview of the Archaea

3. Archaea form four major phyla, the Euryarchaeota, the Crenarchaeota, the Korarchaeota, and the Nanoarchaeota.

4. Figure 13.1 shows a phylogenetic tree of Archaea.

6. Energy Conservation and Autotrophy in Archaea
With the exception of methanogenesis, bioenergetics and intermediary metabolism in species of Archaea are much the same as those in various species of Bacteria.

7. Several Archaea are chemoorganotrophic and thus use organic compounds as energy sources for growth. Chemolithotrophy is also well established in the Archaea, with H2 being a common electron donor.

8. The capacity for autotrophy is widespread in the Archaea and occurs by several different pathways. In methanogens, and presumably in most chemolithotrophic hyperthermophiles, CO2 is incorporated via the acetyl-CoA pathway or some modification thereof.

9. Phylum Euryarchaeota Extremely Halophilic Archaea

10. Extremely halophilic Archaea require large amounts of NaCl for growth
Extremely halophilic Archaea require large amounts of NaCl for growth. These organisms accumulate high levels of KCl in their cytoplasm as a compatible solute.

11. These salts affect cell wall stability and enzyme activity
These salts affect cell wall stability and enzyme activity. The light-mediated proton pump bacteriorhodopsin helps extreme halophiles make ATP (Figure 13.4).

12. Model for the mechanism of bacteriorhodopsin activity
Light near 570 nm converts the protonated retinal bacteriorhodopsin from the trans form (RetT) to the cis form (RetC), along with translocation of a proton to the outer surface of the membrane, thus establishing a proton motive force. ATPase activity is driven by proton motive force.
Chlorophyll pigments also synthesize ATP, a light driven process

13. Table 13.1 gives the ionic composition of some highly saline environments.

15. Table 13.2 lists the currently recognized species of extremely halophilic Archaea.

17. Methane-Producing Archaea: Methanogens
A large number of Euryarchaeota produce methane (CH4) as an integral part of their energy metabolism. Such organisms are called methanogens. Methanogenic Archaea are strictly anaerobic prokaryotes.

18. Habitats of methanogenic Archaea are listed in Table 13.4.

20. Table 13.5 gives characteristics of some methanogenic Archaea.

23. Substrates converted to methane by various methanogenic Archaea are listed in Table Acetotrophic substrates are those that consume acetate.

25. Thermoplasmatales: Thermoplasma, Ferroplasma, and Picrophilus

26. Thermoplasma, Ferroplasma, and Picrophilus are extremely acidophilic thermophiles that form their own phylogenetic family of Archaea inhabiting coal refuse piles and highly acidic solfataras.

27. Cells of Thermoplasma and Ferroplasma lack cell walls and thus resemble the mycoplasmas in this regard.

28. To survive the osmotic stresses of life without a cell wall and to withstand the dual environmental extremes of low pH and high temperature, Thermoplasma has evolved a unique cell membrane structure (Figure 13.11).

29. Structure of the tetraether lipoglycan of Thermoplasms acidophilum – monolayer of lipid rather than bilayer membrane

30. Hyperthermophilic Euryarchaeota: Thermococcales and Methanopyrus

31. A few euryarchaeotes thrive in thermal environments, and some are hyperthermophiles. All organisms in this group have growth temperature optima above 80°C.
Thermococcus is a spherical hyperthermophilic euryarchaeote indigenous to anoxic thermal waters in various locations throughout the world.

32. Methanopyrus is a rod-shaped hyperthermophilic methanogen isolated from sediments near submarine hydrothermal vents and from the walls of "black smoker" hydrothermal vent chimneys.

33. Methanopyrus is unusual because it contains membrane lipids found in no other known organism.
In the lipids of Archaea, the glycerol side chains contain phytanyl rather than fatty acids bonded in ether linkage to the glycerol.

34. In Methanopyrus, this ether-linked lipid is an unsaturated form of the otherwise saturated dibiphytanyl tetraethers found in other hyperthermophilic Archaea (Figure 13.13).

35. Methanopyrus produces CH4 from CO2 and H2
Unsaturated phytanyl, Geranylgeraniol produced by Methanopyrus for cell membranes

36. Hyperthermophilic Euryarchaeota: The Archaeoglobales

37. Archaeoglobus was isolated from hot marine sediments near hydrothermal vents. In its metabolism, Archaeoglobus couples the oxidation of H2, lactate, pyruvate, glucose, or complex organic compounds to the reduction of sulfate to sulfide.

38. Ferroglobus is related to Archaeoglobus but is not a sulfate-reducing bacterium. Instead, Ferroglobus is an iron-oxidizing chemolithotrophic autotroph, conserving energy from the oxidation of Fe2+ to Fe3+ coupled to the reduction of NO3– to NO2– plus NO (see Table 13.8).

40. PART III Phylum Crenarchaeota  Habitats and Energy Metabolism of Crenarchaeotes

41. Table 13. 7 summarizes the habitats of Crenarchaeota
Table 13.7 summarizes the habitats of Crenarchaeota. They include very hot and very cold environments.

43. Most hyperthermophilic Archaea have been isolated from geothermally heated soils or waters containing elemental sulfur and sulfides.
Hyperthermophilic Crenarchaeota inhabit the hottest habitats currently known to support life.

44. Cold-dwelling crenarchaeotes have been identified from community sampling of ribosomal RNA genes from many nonthermal environments.

45. Crenarchaeotes have been found in marine waters worldwide and thrive even in frigid waters and sea ice.

46. Hyperthermophiles from Terrestrial Volcanic Habitats: Sulfolobales and Thermoproteales

47. Two phylogenetically related organisms isolated from these environments include Sulfolobus and Acidianus. These genera form the heart of an order called the Sulfolobales (Table 13.9).

49. Key genera within the Thermoproteales are Thermoproteus, Thermofilum, and Pyrobaculum.

50. Hyperthermophiles from Submarine Volcanic Habitats: Desulfurococcales

51. Submarine volcanic habitats are homes to the most thermophilic of all known Archaea. These habitats include both shallow-water thermal springs and deep-sea hydrothermal vents.

52. Pyrodictium and Pyrolobus are examples of prokaryotes whose growth temperature optimum lies above 100ºC. The optimum for Pyrodictium is 105ºC and for Pyrolobus is 106ºC.

53. Cells of Pyrodictium are irregularly disc-shaped and grow in culture in a mycelium-like layer attached to crystals of elemental sulfur.

54. Other notable members of the Desulfurococcales include Desulfurococcus and Ignicoccus.

55. Like Pyrodictium, Desulfurococcus is a strictly anaerobic S0-reducing bacterium, but it differs from Pyrodictium in that it is much less thermophilic, growing optimally at about 85°C. Ignicoccus grows optimally at 90ºC, and its metabolism is H2/S0 based.

56. Phylum Nanoarchaeota Nanoarchaeum

57. Nanoarchaeum is a small, parasitic, early-branching member of the Archaea. Its genome is the smallest of all known organisms. Nanoarchaeum lacks genes for all but core molecular processes and thus depends on its host, Ignicoccus, for most of its cellular needs.

58. Evolution and Life at High Temperatures Heat Stability of Biomolecules

59. Although hyperthermophiles live at very high temperatures, in some cases above the boiling point of water, there are temperature limits beyond which no living organism can survive. This limit is likely 140ºC to 150°C (Figure 13.25).

61. Protein and DNA stability in hyperthermophiles is critical to surviving high temperature. Because most proteins denature at high temperatures, much research has been done to identify the properties of thermostable proteins.

62. The solution to protein thermostability turns on the folding of the molecule. Temperature is also a factor, and unique solutions have evolved in hyperthermophiles to keep their DNA intact.

63. Hyperthermophilic prokaryotes typically produce special classes of chaperonins that function only at the highest growth temperatures.
In cells of Pyrodictium, for example, the major chaperonin is a protein complex called the thermosome.

64. This complex (thermosome) functions to keep the cell's other proteins properly folded and functional at high temperature and can help cells survive even above their maximal growth temperature.

65. All hyperthermophiles produce a DNA topoisomerase called reverse DNA gyrase.
Reverse gyrase introduces positive supercoils into DNA (in contrast to the negative supercoils introduced by DNA gyrase, found in all nonhyperthermophilic prokaryotes).

66. Hyperthermophilic Archaea, H2, and Microbial Evolution

67. Why do so many Archaea seem to inhabit extreme environments?
Extreme environments of various types existed on early Earth just as they do today, and it is within such environments that life may first have flourished.

68. At the time that cellular life evolved nearly 4 billion years ago, it is almost certain that Earth was far hotter than it is today and probably suitable only for hyperthermophiles.

69. If life originated on a hot planet Earth, as most evolutionary scenarios predict, then hyperthermophilic Archaea and Bacteria are likely the closest living relatives to early life forms that remain today.
Therefore the biology of these hyperthermophiles is not only interesting but may offer us a window into the past.

70. Hydrogen catabolism may have been the first energy-yielding metabolism of cells.