Archaea

Abstract

Analysis of the nucleotide sequences of ribosomal ribonucleic acid (RNA) led in the 1970s to the recognition of the existence of three domains of life, named Eukarya (Eukaryotes), Bacteria (Eubacteria) and Archaea (Archaebacteria). This classification replaced the earlier accepted Eukaryotes–Prokaryotes dichotomy. Archaea resemble Bacteria in cell size and cell structure but possess many distinguishing features, including lack of peptidoglycan in their cell wall, presence of unique membrane lipids not found in the other domains of life and other unique biochemical and genetic properties. Most cultivated Archaea were recovered from extreme environments characterised by high salt concentrations, high temperatures and/or very high or very low pH. Some nonextremophilic aerobic ammonia‐oxidising chemoautotrophs are abundant in the marine environment and in soils. The strictly anaerobic methanogenic prokaryotes also belong to the archaeal domain. Cultivation‐independent studies have shown the existence of many more archaeal lineages for which no cultivated representatives have yet been obtained.

Key Concepts

  • The Archaea form a second lineage of prokaryotes, evolutionarily distant from the Bacteria.
  • Most Archaea are classified within the phyla Crenarchaeota and Euryarchaeota; a few cultivated nonextremophilic Archaea are classified in the phylum Thaumarchaeota.
  • Cultivation‐independent approaches have led to proposals for many more archaeal phyla whose representatives are still awaiting to be isolated.
  • Archaea resemble Bacteria in cell size, morphology and ultrastructure but differ from the Bacteria in many biochemical, physiological and genetic features.
  • The cell membrane lipids of the Archaea are based on branched (isoprenoid) hydrophobic carbon chains linked to glycerol by ether bonds.
  • Peptidoglycan, the characteristic cell‐wall constituent of the Bacteria, does not occur in the Archaea.
  • Obligately anaerobic methanogenic Archaea are responsible for the formation of nearly all biogenic methane.
  • Most cultivated Archaea are extremophiles that live at high temperatures, sometimes combined with low pH, or at high salt concentrations, sometimes combined with high pH.
  • Archaea contribute to the autotrophic oxidation of ammonia to nitrite in different ecosystems.
  • Thanks to their unique biochemical features, the Archaea have considerable potential for biotechnological applications.

Keywords: Archaea (Archaebacteria); Euryarchaeota; Crenarchaeota; Korarchaeota; Nanoarchaeota; Thaumarchaeota; methanogens; halophiles; thermophiles; thermoacidophiles

Figure 1. Phylogenetic 16S rRNA tree of Archaea. C1, Pyrodictium (Desulfurococcales, Pyrodictiaceae, Crenarchaeota); C2, Thermoproteus (Thermoproteales, Thermoproteaceae, Crenarchaeota); E1, Thermococcus (Thermococcales, Thermococcaceae, Euryarchaeota); E2, Methanococcus (Methanococcales, Methanococcaceae, Euryarchaeota); E3, Methanobacterium (Methanobacteriales, Methanobacteriaceae, Euryarchaeota); E4, Methanosarcina (Methanosarcinales, Methanosarcinaceae, Euryarchaeota); E5, the class Halobacteria of extremely halophilic Euryarchaeota (Halobacteriales). For more detailed trees that include nonextremophilic Archaea and environmental sequences from cold marine and terrestrial environments, see Figures 3, 4 and 5 in Forterre and Figure 1 in Euryarchaeota. Adapted from Woese et al. .
Figure 2. Electron micrographs of diverse morphological forms of Archaea (platinum shadowing: a, b, d, e, f, h, i, j, h, l, m and n; thin sections: c and g). (a) Methanobrevibacter smithii (short rod; bar, 1 μm); (b) Methanobacterium uliginosum (rod; bar, 1 μm); (c) Methanosphaera stadtmanae (coccus; bar, 1 μm); (d) Methanoplanus limicola (irregular flat cells; bar, 1 μm); (e) Methanospirillum hungatei (spirilli; bar, 4 μm); (f) Halobacterium salinarum (rod; bar, 1 μm); (g) Halococcus morrhuae (coccus; bar, 0.5 μm); (h) Thermoplasma acidophilum (irregular rod‐shaped cell; bar, 0.5 μm); (i) Methanolobus vulcani (cocci in packets; bar, 1 μm); (j) Pyrococcus furiosus (coccus with archaella; bar, 0.5 μm); (k) Haloferax mediterranei (irregular to rectangular flat cells; bar, 0.5 μm); (l) Thermofilum sp. (long filament; bar, 1 μm); (m) Pyrodictium occultum (irregular cocci with tubules; bar, 1 μm); (n) Thermoproteus tenax (branching rods; bar, 2 μm).
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Further Reading

Albers S‐V, Forterre P, Prangishvili D, et al. (2013) The legacy of Carl Woese and Wolfram Zillig: from phylogeny to landmark discoveries. Nature Reviews Microbiology 11: 713–719.

Cavicchioli R (ed.) (2007) Archaea: Molecular and Cellular Biology. American Society for Microbiology Press: Washington, DC.

Eme L and Doolittle WF (2015) Archaea. Current Biology 25: R851–R855.

Friend T (2007) The Third Domain: The Untold Story of Archaea and the Future of Biotechnology. Joseph Henry Press: Washington, DC.

Garrett RA and Klenk H‐P (eds) (2007) Archaea: Evolution, Physiology, and Molecular Biology. Wiley‐Blackwell: Hoboken, NJ.

Howland JL (2000) The Surprising Archaea: Discovering Another Domain of Life. Oxford University Press: New York.

Katō SY (2011) Archaea: Structure, Habitats and Ecological Significance. Nova Biomedical Publications: New York.

Oren A and Papke RT (eds) (2010) Molecular Phylogeny of Microorganisms. Caister Academic Press: Norfolk, UK.

Robb FT, Place AR, Sowers KR, et al. (eds) (1995) Archaea. A Laboratory Manual. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.

Whitman WB (ed.) (2015) Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc. in Association with Bergey's Manual Trust.

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Oren, Aharon(May 2020) Archaea. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000443.pub3]