ArchaeaArticle Contents: Archaean Characteristics   Archaean Classification 

Also known as: archaebacteriaFrom: Encyclopedia of Life Science.

According to the five-kingdom classification scheme proposed byRobert Whittaker, the kingdom Monera comprised all prokaryoticorganisms. In 1977 Carl Woese from the University of Illinois at Urbana-Champaign performed an extensive molecular analysis of several types of prokaryotic organisms and obtained surprising results. Comparison of the sequences for the 16S ribosomal ribonucleic acid (RNA) genes showed that some of the prokaryotes differed tremendously from others, enough so that they warranted their ownsuperkingdom on the tree of life. He proposed the formation of three domains of living organisms: Eukaryota, which contains the protists, fungi, plants, and animals; Bacteria, or Eubacteria, which includes the more familiar prokaryotic organisms; and Archaea, which includes the most recently recognized forms of prokaryotic life.

Comparison of Archaea, Bacteria, and Eukarya

  Archaea Bacteria Eukaryanuclear envelope absent absent presentmembrane-bound organelles

absent absent present

cell wall composed of proteinaceous subunits (in most), in some made of pseudomurein

made of peptidoglycan

if present, composed of a variety of substances such as cellulose or chitin

lipids in the cell membrane

branched carbon chains made of isoprene derivatives, ether-linked

straight chain fatty acids, ester-linked

straight chain fatty acids, ester-linked, contain sterols

initiator tRNA methionine N-formyl-methionine

methionine

introns absent present in some genes

present

sensitive to the antibiotics streptomycin, kanamycin, and chloramphenicol

no yes (for most) no

DNA bound by histones

yes no yes

chromosome single, circular single, circular linear, number varies

microtubule cytoskeleton

no no yes

ribosomes 70S 70S 80Splasmid DNA present present rareribosomes sensitive to diphtheria toxin

yes no yes

polycistronic mRNA present present absent

The domain Archaea is named for the Greek word meaning "ancient," because archaea live in conditions similar to those on Earth 3.5 billion years ago. Most of the planet was covered in water that contained harsh chemicals and often reached boiling temperatures. Microbiologists do not yet know nearly as much about archaea, which have only been recognized for a few decades, as they do about bacteria. Archaea often live in extreme environmental conditions; such organisms are called extremophiles, and their unusual growth requirements make it more difficult to study them in the laboratory. Not all archaea are extremophiles, and not all extremophiles arearchaea. Thermophiles are extremophiles that live at very high temperatures, and psychrophiles live in extreme cold. Acidophiles and alkalinophiles live in acidic or basic environments. The halophiles ("salt lovers") live in very salty environments. Another major group ofarchaea are the methanogens, which produce methane gas (CH4) as a by-product of their metabolism.

Archaean CharacteristicsArchaea are unicellular, prokaryotic organisms that have a variety of shapes, such as rods, cocci, and other unusual forms including triangles. Members of this domain share similarities with both bacteria and eukaryotic organisms. As prokaryotes, archaea lack internal compartmentalization. The single chromosome that makes up their genome is not bound by a nuclear envelope. Like bacteria, archaeacan be gram-negative or gram-positive, but the composition of theircell

walls differs. Bacterial cell walls consist of peptidoglycan, made of chains of alternating subunits of N-acetylglucosamine and N-acetylmuramic acid and linked together by short peptide bridges. Gram-negative archaea have a proteinaceous layer associated with their cell membranes. In some gram-positive archaea, the thick cell wall consists of pseudomurein, which contains N-acetylalosaminuronic acid in place of N-acetylmuramic acid in addition to different types of amino acids. Other archaea contain different complex polysaccharides. Because of this, antibiotics that are harmful to bacteria, such as penicillin, and chemicals, such as lysozyme, that target peptidoglycan are ineffective against archaea.

The membrane lipids of archaea are also distinctive. The lipids contain branched isoprenes rather than fatty acids, and the lipids are linked to glycerol through ether bonds rather than ester bonds as in bacteria and eukaryotic organisms. Sometimes the branched portions cyclize, providing more rigidity to the membrane.

Archaea contain a single, circular chromosome, but the sequence of the archaean genome is genotypically distinct from that of bacteria and eukaryotes. Histonelike proteins bind the chromosomes of archaeain a manner similar to the way they bind to eukaryotic chromosomes. As bacteria do, archaea have polycistronic genes that contain nointrons, or intervening sequences between coding regions ofmessenger RNA (mRNA). The initiator transfer RNA (tRNA) is methionine, as in eukaryotic organisms. Their ribosomes are 70S, as in bacteria, but the ribosomes' shape differs and they are insensitive to antibiotics that inhibit bacterial ribosomes. Also, the RNA polymerasesare more similar to eukaryotic RNA polymerases than to bacterial RNA polymerases.Archaea exhibit a variety of means for obtaining their energy and nutrients. Scientists have identified both aerobic and anaerobic species, and autotrophs and heterotrophs. Hydrogen gas (H2), carbon dioxide (CO2), or sulfur provides energy for some archaea, and some are photosynthetic. Their metabolisms vary greatly among the different groups of archaea.Archaean ClassificationSequence similarities of 16S rRNA genes group the archaeans into four main clades: Euryarchaeotes, Crenarchaeotes, Korarchaeotes, and Nanoarchaeotes. The Euryarchaeota include the methane producers and the halophiles (salt lovers). Some extreme thermophiles are also in Euryarchaeota, but most thermophiles belong to Crenarchaeota. Methanogens, one type of Euryarchaeota, oxidize hydrogen gas (H2) for energy and are the most common of the Archaea. Molecular oxygen (O2) is toxic to methanogens; instead they use an inorganic substance such as CO2 as the oxidizing agent, in the process reducing it to

methane gas (CH4), which they release into the environment. In addition to CO2, methanogenic species convert other substances, such as formate, methanol, acetate, carbon monoxide, and methylamine, into methane. Methanogens inhabit marshes, producing swamp gas; live as endosymbionts of cattle and termites; or reside in the human gut. Sewage treatment facilities utilize methanogens to help decompose organic matter in wastewater, and some industrial plants harvest the gas given off to utilize as a source of energy. At least 17 methanogenic archaean genera and 93 species have been identified.The extreme halophiles, which grow in very salty conditions, also belong to Euryarchaeota. Organisms that live in environments that have a higher concentration of solutes than inside the cell must have special adaptations that prevent the cell from dehydrating. Natural tendencies cause the water to diffuse from inside the cell to the outside, but the loss of too much water causes cell death. Some halophiles overcome this obstacle by transporting other solutes, such as potassium, into the cell to balance the osmolarity with the external environment and prevent excessive water loss. Extreme halophiles require a high percentage of salt, a minimum of 9 percent but on average 12–23 percent (for comparison, normal seawater contains 0.9 percent salt). One type of halophile is photosynthetic. The purple pigment bacteriorhodopsin, found in its cell membranes, harvests light energy from the Sun and uses it to generate adenosine triphosphate (ATP). Scientists have identified 20 species of extreme halophiles so far.The Crenarchaeota includes most of the organisms that live in extreme temperatures, both hot and cold, and the organisms that can tolerate extreme acidity. Most bacteria and eukaryotic organisms are mesophiles, meaning their optimal growth temperature ranges from 68°F to 113°F (20°C–45°C). Bacteria that live in symbiotic relationships with humans or that are pathogenic to humans must be mesophiles, since normal body temperature, 98.6°F (37°C) falls within this range. Thermophiles thrive at a range of 104°F–176°F (40°C–80°C). Extreme thermophiles (hyperthermophiles) prefer temperatures even higher, with an optimum around 212°F (100°C), the temperature at which water boils at standard pressure. Thermophiles and hyperthermophiles have special enzymes and molecules that preventdenaturation at such high temperatures. Thomas D. Brock at the University of Wisconsin at Madison first discovered thermophiles in 1966 in hot springs at Yellowstone National Park. Since then, scientists have discovered microbes that can withstand surprising conditions. In 2003 Derek Lovley and Kazem Kashefi of the University of Massachusetts at Amherst identified a spherical, flagellatedarchaean species that can thrive at 250°F (121°C), the current record held by a living organism, and, interestingly, the temperature at which autoclave ovens sterilize the equipment and media used in most

microbiological research. They discovered these archaea, named Strain 121, near some black smokers 200 miles from Puget Sound and one and one-half miles deep in the Pacific Ocean. Strain 121 respires using iron as the final electron acceptor, forming magnetite in the process. This microbe "breathes" iron, in comparison to aerobic organisms, which "breathe" oxygen. At the other end of the spectrum, psychrophiles can grow at temperatures as low as 32°F (0°C), but they grow best between 68°F and 86°F (20°C–30°C). These organisms can spoil food quickly, even when it is kept in a refrigerator. Some have been found living in an Antarctic lake of ice. Not very much is known about the psychrophiles.

Most organisms grow best at a neutral pH, around 7.0. Acidophiles, also in Crenarchaeota, have the rare quality of growing best in acidic conditions, and alkalinophiles grow best in basic conditions. Molecules inside the cell, such as the DNA, cannot withstand a pH of this level; thus the cells have mechanisms for maintaining a neutral internal pH despite the harsh external conditions that the cell surface molecules must tolerate.

Korarchaeota is a relatively new clade, first recognized in 1996 when an organism living in a hot spring in Yellowstone National Park was found to be very different from the Euryarchaeota or the Crenarchaeota. Korarchaeota includes members that are more distantly related to the other archaea. Scientists believe that the korarchaeote species more closely resemble the ancient ancestral life-form common to prokaryotes and eukaryotes than the other archaea. The newest clade, Nanoarchaeota, discovered in 2002, contains organisms that are tiny, even by prokaryotic standards. Approximately 1.57 × 10-5 inch (0.4 µm) in diameter, nanoarchaeote genomes only contain 500,000 base pairs, smaller than any other known organism.