1. Chapter 17
Archaea

2. I. Phylogeny and General Metabolism
17.1 Phylogenetic Overview of Archaea
17.2 Energy Conservation and Autotrophy in Archaea

3. 17.1 Phylogenetic Overview of Archaea
Archaea share many characteristics with both Bacteria and Eukarya
Archaea are split into two major groups
Crenarchaeota
Euryarchaeota

4. Detailed Phylogenetic Tree of the Archaea
Figure 17.1

5. 17.2 Energy Conservation and Autotrophy in Archaea
Chemoorganotrophy and chemolithotrophy
▪ With the exception of methanogenesis, bioenergetics and intermediary metabolism of Archaea are similar to those found in Bacteria
- Glucose metabolism
: EMP or slightly modified Entner-Doudoroff pathway
- Oxidation of acetate to CO2
: TCA cycle or some slight variations of TCA cycle
: Reverse route of acetyl-CoA pathway

6. : H2 as a common electron donor and energy source is well established
- Electron transport chains with a, b, and c-type cytochromes present in some Archaea
: use O2, S0, or some other electron acceptor (nitrate or fumarate)
: establish proton motive force
: ATP synthesis through membrane-bound ATPase
- Chemolithotrophy
: H2 as a common electron donor and energy source is well established

7. ▪ Autotrophy via several different pathways is widespread in Archaea
▪ acetyl-CoA pathway in methanogens and
most hyperthermophiles
▪ Reverse TCA cycle in some hyperthermophiles
▪ Calvin cycle in Methanococcus jannaschii and a Pyrococcus
species (both are hyperthermophiles)

8. II. Euryarchaeota 17.3 Extremely Halophilic Archaea
17.4 Methane-Producing Archaea: Methanogens
17.5 Thermoplasmatales
17.6 Thermococcales and Methanopyrus
17.7 Archaeoglobales
17.8 Nanoarchaeum and Aciduliprofundum

9. II. Euryarchaeota Euryarchaeota
Physiologically diverse group of Archaea
Many inhabit extreme environments
E.g., high temperature, high salt, high acid

10. 17.3 Extremely Halophilic Archaea
Haloarchaea
Extremely halophilic Archaea
Have a requirement for high salt concentrations
Typically require at least 1.5 M (~9%) NaCl for growth
Found in solar salt evaporation ponds, salt lakes, and artificial saline habitats (i.e., salted foods)

11. Hypersaline Habitats for Halophilic Archaea
Great Salt Lake, Utah
Figure 17.2a

12. Seawater Evaporating Ponds Near San Francisco Bay, California
Figure 17.2b

13. Pigmented Haloalkaliphiles Growing in pH 10 Soda Lake in Egypt
Figure 17.2c

14. SEM of Halophilic Bacteria
Figure 17.2d

15. 17.3 Extremely Halophilic Archaea
Extremely hypersaline environments are rare
Most found in hot, dry areas of world
Salt lakes can vary in ionic composition, selecting for different microbes
Great Salt Lake similar to concentrated seawater
Soda lakes are highly alkaline hypersaline environments

16. Ionic Composition of Some Highly Saline Environments

17. Haloarchaea Reproduce by binary fission
Do not form resting stages or spores
Most are nonmotile
Most are obligate aerobes
Possess adaptations to life in highly ionic environments

18. Some Genera of Extremely Halophilic Archaea

19. Some Genera of Extremely Halophilic Archaea

20. Micrographs of the Halophile Halobacterium salinarum
Dividing cell
Glycoprotein subunit structure
on the cell wall
Figure 17.3

21. Water balance in extreme halophiles
Halophiles need to maintain osmotic balance
This is usually achieved by accumulation or synthesis of organic compatible solutes
Halobacterium species instead pump large amounts of K+ into the cell from the environment
Intracellular K+ concentration exceeds extracellular Na+ concentration and positive water balance is maintained

22. Concentration of Ions in Cells of Halobacterium salinarum

23. Proteins of halophiles
Highly acidic
Contain fewer hydrophobic amino acids and lysine residues

24. Some haloarchaea are capable of light-driven synthesis of ATP
Bacteriorhodopsin
Cytoplasmic membrane proteins that can absorb light energy and pump protons across the membrane

25. Model for the Mechanism of Bacteriorhodopsin
Figure 17.4

26. Other rhodopsins can be present in Archaea
Halorhodpsin
Light-driven pump that pumps Cl- into cell as an anion for K+
Sensory rhodopsins
Control phototaxis

27. 17.4 Methane-Producing Archaea: Methanogens
Microbes that produce CH4
Found in many diverse environments
Taxonomy based on phenotypic and phylogenetic features
Process of methanogensis first demonstrated over 200 years ago by Alessandro Volta

28. The Volta Experiment
Figure 17.5

29. Habitats of Methanogens

30. Micrographs of Cells of Methanogenic Archaea
Methanobrevibacter
ruminantium
Figure 17.6a

31. Micrographs of Cells of Methanogenic Archaea
Methanobrevibacter
arboriphilus
Figure 17.6b

32. Micrographs of Cells of Methanogenic Archaea
Methanospirillum hungatei
Figure 17.6c

33. Micrographs of Cells of Methanogenic Archaea
Methanosarcina barkeri
Figure 17.6d

34. Characteristics of Some Methanogenic Archaea

35. Characteristics of Some Methanogenic Archaea

36. Diversity of Methanogens
Demonstrate diversity of cell wall chemistries
Pseudomurein (e.g., Methanobacterium, Methanobrevibacter)
Methanochondroitin (e.g., Methanosarcina)
- (N-acetylgalactosamine + glucuronic acid)n
Protein or glycoprotein (e.g., Methanocaldococcus)
S-layers (e.g., Methanospirillium)

37. Micrographs of Thin Sections of Methanogenic Archaea
Methanobrevibacter ruminantium
Methanosarcina barkeri
Figure 17.7a

38. Hyperthermophilic and Thermophilic Methanogens
Methanocaldococcus jannaschii
Figure 17.8a

39. Substrates for Methanogens
Obligate anaerobes
11 substrates, divided into 3 classes, can be converted to CH4 by pure cultures of methanogens
Other compounds (e.g., glucose) can be converted to methane, but only in cooperative reactions between methanogens and other anaerobic bacteria
(syntrophic metabolism)

40. Substrates Converted to Methane by Methanogens

41. 17.5 Thermoplasmatales
Methanocaldococcus jannaschii as a model methanogen
Contains 1.66 mB circular genome with about 1,700 genes
Genes for central metabolic pathways and cell division
- Similar to those in Bacteria
Genes encoding transcription and translation
- More closely resemble those of Eukarya
Over 50% of genes
- Have no counter parts in known genes from Bacteria and Eukarya

42. Thermoplasmatales Taxonomic order within the Euryarchaeota
Contains 3 genera
Thermoplasma
Ferroplasma
Picrophilus
Thermophilic and/or extremely acidophilic
Thermoplasma and Ferroplasma lack cell walls

43. Thermoplasma Chemoorganotrophs
Facultative aerobes via sulfur respiration
Thermophilic
Acidophilic

44. Thermoplasma Species
Thermoplasma acidophilum
Figure 17.9a

45. Thermoplasma Species Thermoplasma volcanium Isolated from Hot Springs
Figure 17.9b

46. A Self-Heating Coal Refuse Pile, Habitat of Thermoplasma
Self-heats from microbial metabolism.
Figure 17.10

47. Thermoplasma (cont’d)
Evolved unique cytoplasmic membrane structure to maintain positive osmotic pressure and tolerate high temperatures and low pHs
Membrane contains lipopolysaccharide-like material (lipoglycan) consisting of tetraether lipid monolayer membrane with mannose and glucose
Membrane also contains glycoproteins but not sterols

48. Structure of the Tetraether Lipoglycan of T. acidophilum
Figure 17.11

49. Ferroplasma Chemolithotrophic Acidophilic
Oxidizes Fe2+ to Fe3+, uses CO2 as carbon source
Grows in mine tailings containing pyrite (FeS)
- Generates acid (acid mine drainage)

50. Picrophilus Extreme acidophiles Have an S-layer
Grow optimally at pH 0.7
Have an S-layer
Model microbe for extreme acid tolerance

51. 17.6 Thermococcales and Methanopyrus
Three phylogenetically related genera of hyperthermophilic Euryarchaeota
Thermococcus
Pyrococcus
Methanopyrus
Comprise a branch near root of archaeal tree

52. Detailed Phylogenetic Tree of the Archaea
Figure 17.1

53. Thermococcales
Distinct order that contains Thermococcus and Pyrococcus
Thermococcus: organics + So, 55-95oC
Pyrococcus: organics + So, opt. 100oC, oC
** In the absence of So, form H2
Indigenous to anoxic thermal waters
Highly motile

54. Spherical Hyperthermophilic Archaea
Shadowed cells of
Thermococcus celer
Figure 17.12a

55. Dividing cell of
Pyrococcus furiosus
Figure 17.12b

56. Methanopyrus Methanogenic (CO2 + H2)
Isolated from hot sediments near submarine hydrothermal vents and from walls of “black smoker”
Opt. temp. 100oC, max. temp. 110oC (the most thermophilic of all known methangens)
Contains unique membrane lipids: unsaturated form
Contains 2,3-diphosphoglycerate in the cytoplasm (> 1 M)
Functions as thermostabilizing agent

57. Methanopyrus Electron Micrograph of a cell of Methanopyrus Kandleri
Figure 17.13a

58. Methanopyrus
Structure of novel lipid of M. kandleri
Figure 17.13b

59. 17.7 Archaeoglobales Archaeoglobales Hyperthermophilic
Couple oxidation of H2, lactate, pyruvate, glucose, or complex organic compounds to the reduction of SO42- to H2S
Archaeoglobus
Opt. temp. 83oC
Produce methane, but lacks genes for methyl-CoM reductase
Ferroglobus
Opt. temp. 85oC
Fe2+ + NO3- → Fe3+ + NO2- + NO

60. Archaeoglobales
TEM of Archaeoglobus fulgidus
Figure 17.14a

61. Freeze-etched Electron Micrograph of Ferroglobus placidus
Figure 17.14b

62. 17.8 Nanoarchaeum and Aciduliprofundum
Nanorchaeum equitans
One of the smallest cellular organisms (~0.4 µm)
Obligate symbiont of the crenarchaeote Ignicoccus
Contains one of the smallest genomes known
(0.49 mbp)
Lacks genes for all but core molecular processes
Depends upon host for most of its cellular needs

63. Nanoarchaeum Ignicoccus Nanoarchaeum Fluorescence micrograph
of cells of Nanoarchaeum
Ignicoccus
Nanoarchaeum
Figure 17.15a

64. TEM of a thin section of a cell of Nanoarchaeum
Figure 17.15b

65. Aciduliprofundum Thermophilic: 55-75oC
Acidophile: pH , lives in sulfide deposits in hydrothermal vents
Oragnics + So or Fe3+

66. III. Crenarchaeota
Habitats and Energy Metabolism of Crenarchaeota
Hyperthermophiles from Terrestrial Volcanic Habitats
Hyperthermophiles from Submarine Volcanic Habitats
Nonthermophilic Crenarchaeota

67. 17.9 Habitats and Energy Metabolism of Crenarchaeota
Inhabit temperature extremes
Most cultured representatives are hyperthermophiles
Other representatives found in extreme cold environments

68. Habitats of Crenarchaeota

69. Habitats of Hyperthermophilic Archaea
A typical Solfatara in
Yellowstone National Park
Figure 17.16a

70. Sulfur-rich hot spring
Figure 17.16b

71. A typical boiling spring of neutral pH
in Yellowstone Park; Imperial Geyser
Figure 17.16c

72. An acidic iron-rich
geothermal spring
Figure 17.16d

73. Hyperthermophilic Crenarchaeota
Most are obligate anaerobes
Chemoorganotrophs or chemolithotrophs with diverse electron donors and acceptors

74. Energy-Yielding Reactions of Hyperthermophilic Archaea

75. Properties of Some Hyperthermophilic Crenarchaeota

77. 17.10 Hyperthermophiles from Terrestrial Volcanos
Sulfolobales
An order containing the genera Sulfolobus and Acidianus
Sulfolobus
Grows in sulfur-rich acidic hot springs
Aerobic chemolithotrophs that oxidize reduced sulfur or iron
Acidianus
Also lives in acidic sulfur hot springs
Able to grow using elemental sulfur both aerobically and anaerobically (as an electron donor and electron acceptor, respectively)

78. Acidophilic Hyperthermophilic Archaea, the Sulfolobales
Sulfolobus acidocaldarius
Figure 17.17a

79. Acidianus infernus
Figure 17.17b

80. Thermoproteales
An order containing the key genera Thermoproteus, Thermofilum, and Pyrobaculum
Inhabit neutral or slightly acidic hot springs or hydrothermal vents

81. Rod-Shaped Hyperthermophiles, the Thermoproteales
Thermoproteus neutrophilus
Figure 17.18a

82. Thermofilum librum
Figure 17.18b

83. Pyrobaculum aerophilum
Figure 17.18c

84. 17.11 Hyperthermophiles from Submarine Volcanos
Shallow-water thermal springs and deep-sea hydrothermal vents harbor the most thermophilic of all known Archaea
Pyrodictium and Pyrolobus
Desulfurococcus and Ignicoccus
Staphylothermus

85. Desulfurococcales with Temperature Optima > 100°C
Pyrodictium occultum
Thin-section electron
micrograph of P. occultum
Figure 17.19a

86. Thin section of a cell of Pyrolobus fumarii
Figure 17.19c

87. Negative stain of a cell of strain 121,
the most heat-loving of all known
Figure 17.19d

88. Desulfurococcales with Temperature Optima Below Boiling
Thin section of a cell of
Desulfurococcus saccharovorans
Figure 17.20a

89. Thin section of a cell of Ignicoccus islandicus
Extremely large periplasm
Thin section of a cell of
Ignicoccus islandicus
Figure 17.20b

90. The Hyperthermophile Staphylothermus marinus
Figure 17.21

91. 17.12 Nonthermophilic Crenarchaeota
Nonthermophilic Crenarchaeota have been identified in cool or cold marine waters and terrestrial environments by culture-independent studies
Abundant in deep ocean waters
Appear to be capable of nitrification

92. Cold-Dwelling Crenarchaeota
DAPI (diamidino-2-phenylindole) stained
Photo of the Antarctic peninsula
Flouresence photomicrograph of
seawater treated with FISH probe
Figure 17.22

93. IV. Evolution and Life at High Temperatures
An Upper Temperature Limit for Microbial Life
Adaptations to Life at High Temperature
Hyperthermophilic Archaea, H2, and Microbial Evolution

94. 17.13 An Upper Temperature Limit for Microbial Life
What are the upper temperature limits for life?
Laboratory experiments with biomolecules suggest
140–150°C

95. Thermophilic and Hyperthermophilic Prokaryotes
Figure 17.23

96. 17.14 Adaptations to Life at High Temperature
Stability of Monomers
Protective effect of high concentration of cytoplasmic solutes
Use of more heat-stable molecules
e.g., use of nonheme iron proteins instead of proteins that use NAD and NADH

97. Protein Folding and Thermostability
Amino acid composition similar to that of nonthermostable proteins
Structural features improve thermostability
Highly hydrophobic cores
Increased ionic interactions on protein surfaces

98. Chaperonins Class of proteins that refold partially denatured proteins
Thermosome
A major chaperonin protein complex in Pyrodictium

99. DNA Stability High intracellular solute levels stabilize DNA
Reverse DNA gyrase
Introduces positive supercoils into DNA, which stabilizes DNA
Found only in hyperthermophiles
High intracellular levels of polyamines (e.g., putrescine, spermidine) stabilize DNA and RNA
DNA-binding proteins (archaeal histones) compact DNA into nucleosome-like structures

100. Archael Histones and Nucleosomes
Figure 17.25

101. SSU rRNA Stability Lipid Stability Higher GC content
Possess dibiphytanyl tetraether type lipids; form a lipid monolayer membrane structure

102. 17.15 Hyperthermophilic Archaea, H2, and Evolution
Hyperthermophiles may be the closest descendants of ancient microbes
Hyperthermophilic Archaea and Bacteria are found on the deepest, shortest branches of the phylogenetic tree
The oxidation of H2 is common to many hyperthermophiles and may have been the first energy-yielding metabolism

103. Upper Temperature Limits for Energy Metabolism
Figure 17.26