Chapter Summary


  • Archaeal membranes are composed of L-glycerol diether or tetraether lipids, with isoprenoid side chains that may include cross-links or pentacyclic rings.
  • Many archaea have no cell wall—only an S-layer. Some methanogens have cell walls of pseudomurein.
  • Glucose is catabolized by variants of the ED pathway. Other metabolic pathways found in archaea include methanogenesis and retinal-associated lightdriven ion pumps such as bacteriorhodopsin.
  • Central genetic functions of archaea resemble those of eukaryotes, as seen in the structure of DNA and RNA polymerases and of histone-like DNAbinding proteins.
  • Two major phyla or divisions of archaea are Crenarchaeota and Euryarchaeota. Crenarchaeota includes sulfur hyperthermophiles as well as mesophiles, while Euryarchaeota includes methanogens, halophiles, acidophiles, and thermophiles.
  • Metagenomics reveals uncultured organisms. We continue to discover deeply branching clades of archaea by designing new PCR primers, reverse-transcribing community rRNA, and sequencing metagenomes.


  • Crenarchaeol is a tetraether containing a sixmembered ring, found in varying amounts in all known species of the division Crenarchaeota.
  • Habitats for hyperthermophiles include hot springs and submarine hydrothermal vents. Vent organisms are barophiles as well as thermophiles.
  • Desulfurococcales includes diverse thermophiles. Most are anaerobes that use sulfur to oxidize hydrogen or organic molecules.
  • Pyrodictium species show unusual networked cells. Disk-shaped cells are interconnected by cytoplasmic bridges called cannulae.
  • Sulfolobus species are aerobic thermoacidophiles. Sulfolobus species oxidize sulfur to sulfuric acid or catabolize organic compounds.
  • Caldisphaerales and Thermoproteales include anaerobic hyperthermophilic acidophiles.


  • Oceans, soil, plant roots, and animals provide habitats for mesophilic and psychrophilic crenarchaeotes.
  • Psychrophiles in marine sediment play a key role in recycling methane hydrates produced by methanogens.
  • Ammonia-oxidizing crenarchaeotes contribute to global nitrogen cycling.


  • Methanogens gain energy through redox reactions that generate methane from CO2 and H2, formate, and acetate. They require association with bacterial species that generate the needed substrates.
  • Methanogens have rigid cell walls of diverse composition in different species, including pseudopeptidoglycan, protein, and sulfated polysaccharides.
  • Species of methanogens show a wide range of different shapes, including rods (single or filamentous), cocci (single or clumped), and spirals.
  • Methanogens inhabit anaerobic environments such as wetland soil, marine benthic sediment, and animal digestive organs.
  • Biochemical pathways of methanogenesis involve transfer of the increasingly reduced carbon to cofactors that are unique to methanogens.


  • Haloarchaea are extreme halophiles, growing in at least 1.5-M NaCl. They are isolated from salt lakes, solar salterns, underground salt micropockets, and salted foods.
  • Haloarchaea show diverse cell shapes, including slender rods (Halobacterium), cocci (Haloferax), and flat squares (Haloquadratum). The cell envelopes of most haloarchaea contain rigid cell walls of glycoprotein.
  • Molecular adaptations to high salt include DNA of high GC content and acidic proteins (proteins with a high number of negatively charged residues).
  • Retinal-based photoheterotrophy involves the proton pump bacteriorhodopsin or the chloride pump halorhodopsin. Both pumps contain retinal for light absorption.


  • Thermococcales includes hyperthermophiles and acidophiles. Most species use sulfur to oxidize complex organic substrates.
  • Pyrococcus and Thermococcus are the source of vent polymerases for polymerase chain reaction (PCR).
  • Tungsten is commonly used by enzymes of Thermococcales species.
  • Archaeoglobus species reduces sulfate. The methyl group of acetate is oxidized to CO2 by reverse methanogenesis.
  • Thermoplasmatales includes extreme acidophiles. Ferroplasma oxidizes iron pyrite ore (FeS2) in a process that generates concentrated sulfuric acid, causing acid mine drainage.
  • Nanoarchaeum equitans is a tiny obligate symbiont that grows attached to Ignicoccus hospitalis