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3.1.2: Archaea

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    Learning Objectives
    • Describe why the Archaea have been difficult to place on the tree of life
    • Explain what it means to be an extremophile

    When these microscopic organisms were first separated from bacteria in 1977. When their ribosomal RNA was sequenced, it became obvious that they bore no close relationship to the bacteria and seemed to be more closely related to the eukaryotes. For a time they were referred to as archaebacteria, but to emphasize their distinctness, we now call them Archaea.

    Diversity of Archaea

    Though archaeans are involved in many important ecological processes and present across Earth's ecosystems, they are most known for being extremophiles, existing in conditions that prevent most organisms from functioning:

    • thermophiles live at high temperatures
    • hyperthermophiles live at really high temperatures (present record is 121°C!)
    • psychrophiles (also called cryophiles) like it cold (one in the Antarctic grows best at 4°C)
    • halophiles live in very saline environments (like the Dead Sea)
    • acidophiles live at low pH (as low as pH 1 and who die at pH 7!)
    • alkaliphiles thrive at a high pH.
    A variety of prokaryotic cell morphologies: some angular, some rod-shaped, some with many flagella, some growing filamentously
    Figure \(\PageIndex{1}\): Diversity of Archaea. Image by Maulucioni, CC BY-SA 4.0, via Wikimedia Commons.


    Methanogens are chemoautotrophs that use hydrogen as a source of electrons for reducing carbon dioxide to food. This process produces methane ("marsh gas", CH4) as a byproduct. These are found living in such anaerobic environments as:

    • the muck of swamps and marshes
    • the rumen of cattle (where they live on the hydrogen and CO2 produced by other microbes living along with them)
    • our colon (large intestine)
    • sewage sludge
    • the gut of termites

    Two methanogens that have had their complete genomes sequenced are Methanocaldococcus jannaschii and Methanothermobacter thermoautotrophicus.


    The first members of this group to be discovered like it really hot and so are called hyperthermophiles. One can grow at 121°C (the same temperature in the autoclaves used to sterilize culture media, surgical instruments, etc.). Many like it acidic as well as hot and live in acidic sulfur springs at a pH as low as 1 (the equivalent of dilute sulfuric acid). These use hydrogen as a source of electrons to reduce sulfur in order to get the energy they need to synthesize their food (from CO2).

    Aeropyrum pernix is one member of the group that has had its genome completely sequenced. Other members of this group seem to make up a large fraction of the plankton in cool, marine waters and the microbes in both soil and the ocean that convert ammonia into nitrites (nitrification).

    Evolutionary Position of the Archaea

    The Archaea have a curious mix of traits characteristic of bacteria as well as traits found in eukaryotes (discussed in Chapter 2.1). Table \(\PageIndex{1}\) summarizes some of them.

    Table \(\PageIndex{1}\): Traits that the Archaea have in common with Eukarya (left) and Bacteria (right).

    Eukaryotic Traits Bacterial Traits
    • DNA replication machinery
    • Histones
    • Nucleosome-like structures
    • Transcription machinery
      • RNA polymerase
      • TFIIB
      • TATA-binding protein (TBP)
    • Translation machinery
      • initiation factors
      • ribosomal proteins
      • elongation factors
      • poisoned by diphtheria toxin
    • Single, circular chromosome
    • Operons
    • No introns
    • Bacterial-type membrane transport channels
    • Many metabolic processes
      • energy production
      • nitrogen-fixation
      • polysaccharide synthesis

    Economic Importance of the Archaea

    Because they have enzymes that can function at high temperatures, considerable effort is being made to exploit the Archaea for commercial processes such as providing enzymes to be added to detergents (maintain their activity at high temperatures and pH) and an enzyme to covert corn starch into dextrins. Archaea may also be enlisted to aid in cleaning up contaminated sites, e.g., petroleum spills.

    There are no known pathogenic Archaea.


    Archaea are a group of prokaryotes that were distinguished from Bacteria in the late 1970s. These organisms often exist in extreme environments and have diverse metabolic processes, including anaerobes that produce methane. Archaea are difficult to place in the phylogenetic tree of life. Though they share many prokaryotic traits with Bacteria, they seem to be genetically closer to Eukarya, including the processes used to replicate DNA and synthesize proteins.


    Content authored and curated by Maria Morrow using the following sources:

    This page titled 3.1.2: Archaea is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Melissa Ha, Maria Morrow, & Kammy Algiers (ASCCC Open Educational Resources Initiative) .