The cycling of plant nutrients, such as carbon, nitrogen, and sulfur, requires the activity of microorganisms that convert these elements to forms readily available to plants. These microorganisms, which are generally found in both soil and water, include both prokaryotic organisms of the domain Bacteria and the domain of prokaryotes called Archaea, which play significant roles in nutrient cycling.
Along with Eukarya, to which protists, fungi, plants, and animals belong, the Archaea formone of the three domains of life. The Archaea are related to both Bacteria and Eukarya and, in some respects, appear to bemore closely related to Eukarya.
Biochemical and genetic studies, including information obtained from whole genome sequencing, suggest that Archaea may be closely related to an ancestor that gave rise to both Bacteria and Eukarya. Thus, Archaea may provide some insight into the processes that resulted in the evolution of higher life-forms, including plants and animals.
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A Third Domain
For more than fifty years, biologists categorized living organisms into two groups based on their cellular organization and complexity: prokaryotes (originally all classified in kingdom Monera), the single-celled organisms whose chromosomes are not compartmentalized inside a nucleus (which include the domainBacteria), and eukaryotes, consisting of all other organisms, whose cells contain a nucleus. In the late 1970’s studies on a unique group of microorganisms led investigators to question the accepted classification of prokaryotes.
Originally called Archaebacteria by molecular biologist Carl Woese and his colleagues in 1977, these microorganisms were isolated from environments characterized by extremes in heat, acidity, pressure, or salinity, and many were found to be able to utilize sulfur and molecular hydrogen as part of their growth process.
Like all prokaryotes, Archaea do not have a nucleus. However, in their biochemistry and the structure and composition of their molecular machinery, they are as different from bacteria as they are from eukaryotes.
Woese and his colleagues analyzed and compared specific molecules of ribonucleic acid (RNA) present within the ribosome in all organisms, called ribosomal RNA (rRNA). Their findings suggested that all extant life is composed of three distinct groups of organisms: the eukaryotes, or domain Eukarya, which includes plants and animals, and two different prokaryotes, domains Bacteria and Archaea.
In 1990 Woese and others recommended the replacement of the simple prokaryote/ eukaryote view of life with a new tripartite scheme based on three domains: the Bacteria, Archaea, and Eukarya. Since 1990 the three-domain classification has been the subject of considerable debate, and as a consequence, both old and new terminology are used in scientific and popular literature.
Characteristics
Generally, the size and shape of Archaea are similar to those of Bacteria. They are single-celled microscopic organisms that, in some cases, are motile (capable of self-movement) and may be found in chains or clusters.
Archaea multiply in the same manner as bacteria: via binary fission, budding, or fragmentation. Like Bacteria, archaeal chromosomes are circular, indicating the absence of breaks or discontinuities, and many genes are organized in the same fashion as those found in Bacteria.
On the other hand, the specific chemical composition of Archaea plasma membranes and cell walls is unique to the Archaea and is quite different from the composition of these structures typically found in either Bacteria or Eukarya. In fact, the distinctive ether-linked isoprenoid lipids that compose the external membranes of Archaea are a hallmark of these microorganisms.
Another unique characteristic of Archaea is the composition of the molecular genetic machinery, which is amosaic of the components found in Bacteria and Eukarya. For example, the ribosomes (which are responsible for protein synthesis) of Archaea resemble the ribosomes of Bacteria in shape and composition and are distinct from the ribosomes of Eukarya.
On the other hand, the enzyme utilized by Archaea in the production of RNA, namely RNA polymerase, is quite different from the enzyme found in Bacteria. In Bacteria, RNA polymerase molecules are composed of four major proteins, while in the Archaea, RNA polymerase molecules consist of more than ten proteins and are surprisingly similar to the enzyme found in Eukarya.
In fact, archaeal RNA polymerase is so similar to the eukaryotic enzyme that combining certain proteins from both archaeal and eukaryotic sources results in a functional enzyme, a manipulation that is not possible with any bacterial RNA polymerases.
Among species of the Archaea, there is a variety of metabolic processes that differ greatly from the better-known metabolic routes of Bacteria and Eukarya. Many of the archaeal pathways used to convert food sources to energy and building blocks for growth involve enzymes having biological activities not found in any other biological systems.
In some cases, the enzymes require the involvement of rare metals, such as tungsten. While a requirement for metals in the activity of many bacterial and eukaryotic enzymes is ubiquitous, the use of tungsten appears to be unique to Archaea.
Diversity
A fascinating feature of Archaea is that they are found in niches that support the growth of few other organisms. These include highly reduced (oxygen-free) environments or very high-temperature environments found near hot springs or undersea hydrothermal vents as well as sites that are sulfur-rich and highly acidic.
Archaea are also found in highly saline marine environments and hypersaline lakes where the salinity is as much as ten times that in seawater. Based on the comparison of ribosomal RNA sequences as well as physiological and metabolic characteristics, the Archaea have been divided into three subdomains: Euryarchaeota, Crenarchaeota, and Korarchaeota.
The Euryarchaeota includes members of the methanogenic (methane-producing) and halophilic (salt-requiring) Archaea as well as many that grow at very high temperature, the thermophilic and extremely thermophilic, or hyperthermophilic, Archaea.
Representatives of hyperthermophilic Archaea are found in the Crenarchaeota, which also includes cold-dwelling Archaea that have been isolated in association with certain marine sponges. The Korarchaeota also includes hyperthermophilic Archaea, although these were not isolated or characterized as of 2001, but whose presence in hot spring and deep-sea samples has been identified by molecular biological techniques.
Methanogenic Archaea
Methane-producing Archaea are found in strictly anaerobic environments. They have no tolerance for oxygen: Trace amounts are inhibitory for growth, and too much is lethal. These Archaea obtain energy for growth by a process called methanogenesis, which results in the conversion of carbon dioxide to methane gas.
Methane production requires several enzymes that use coenzymes unique to methanogenic Archaea. The production of methane is of great importance to carbon cycling inmany anaerobic environments, and microorganisms that produce this gas have been known for centuries.
In 1776 the scientist Alessandro Volta demonstrated that air generated from sediments rich in decaying vegetation, such as those present in bogs, streams, and lakes, could be ignited. It is now known that methanogenic Archaea are responsible for generating this "marsh gas".
Because methanogens require an oxygen-free environment for growth, they are found onlywhere carbon dioxide and hydrogen are available and oxygen has been excluded. Thus, methanogens thrive in stagnant water, natural wetlands, paddy fields, and in the rumen of cattle and other ruminants as well as in the intestinal tracts of animals and the hindguts of cellulose-digesting insects, such as termites.
Methanogens are also found in hot springs and the deep ocean and are major components of the anaerobic process in waste treatment facilities. It has been estimated that production of methane by themethanogenicArchaeamay account for almost 90 percent of the total methane released into the atmosphere each year.
In addition to playing a role in carbon cycling, several methanogenic Archaea are also involved in nitrogen cycling, as they are able to convert molecular nitrogen into organic nitrogen via nitrogen fixation, a process that is shared by only a few prokaryotes.
Thermophilic Archaea
These Archaea have been isolated from hot sulfur springs, sulfur-laden mud at the base of volcanoes, and near very hot deep-sea hydrothermal vents where super heated water is emitted at very high temperatures under pressure.
Species that can use oxygen, as well as those that have no tolerance for oxygen, are known. Many of the anaerobic representatives obtain energy for growth by the metabolism of elemental sulfur.
In addition, many are found in environments that are extremely acidic, including those that are members of Thermoplasmatales. This group is noted for its ability to growat a pHof 2.0 and below(on a scale where pH 7.0 is neutral), which is equivalent to the acid in car batteries.
Arepresentative is Thermoplasma, which does not possess a cell wall but has a chemically unique structure composed of a lipid-polysaccharide (tetraether lipid with mannose and glucose units) that is distinctly different from the unusual ether-linked lipids found in the membrane components of typical Archaea.
Halophilic Archaea
The salt-dependent halophilic Archaea require extremely high concentrations of salt for survival, and some grow readily in saturated brine, where the salt concentration reaches 32 percent (in seawater it is approximately 3.5 percent) and where very alkaline conditions are not uncommon. Halophilic Archaea are found in salty habitats along ocean borders and inland waters such as the Dead Sea and the Great Salt Lake.
The reddish-purple color observed in salt evaporation ponds is due to production of red- and orange-colored carotenoids and other pigments associated with the massive growth of halophilic Archaea.
Some halophilic Archaea are capable of harvesting light to provide energy for growth by a mechanism that does not involve chlorophyll pigments. Light harvesting by these halophilicArchaea is done by a membrane-bound protein called bacteriorhodopsin that is equivalent to the mammalian eye pigment rhodopsin in both function and structure.
Bacteriorhodopsin contains retinal, a purple carotenoid like molecule used for light trapping. Interestingly, retinal is produced via a pathway that contains many of the same enzymes used for the production of lycopene by tomatoes during ripening.
Window to the Past
The extreme conditions in which Archaea are found suggests that these organisms have adapted to environments thought to exist during early life on earth, three billion to four billion years ago. Thus, the Archaea might be considered as a window into the past, and they may shed light on the processes involved in evolution as well as their relationships with Bacteria and Eukarya.
In order to survive in their unique environments, Archaea possess molecules that withstand heat or cold, acids, salt, and in some cases, pressure—characteristics that are tailor-made for specific applications inmolecular biology and biotechnology.
Uses
A number of important applications have been developed as a consequence of studying the Archaea. These include the identification of heat stable enzymes for analyses used in genetic fingerprinting and cancer detection (certain polymerase chain reaction enzymes), the use of halophilic pigments for holographic applications, optical signal processing and photoelectric devices, and methanogenesis as an alternative fuel source.
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