Much of human knowledge of the diversity of life has been based on what can be seen. Early attempts at classifying life considered just plants and animals, with fungi part of the plant kingdom. Once microscopes revealed microbial life, biologists could distinguish the bacteria and cyanobacteria, whose cells lack nuclei, from the more complex Protista, single-celled organisms that have nuclei and other organelles . However, lumping together all unicellular organisms lacking nuclei—the prokaryotes —as bacteria proved inaccurate too.
It took a different way of looking at life to recognize that a group of prokaryotes, the Archaea, actually represent a third major form of life, necessitating invention of a term to supercede kingdom, the domain. The three domains of life are the Bacteria, the Archaea, and the Eukarya. Evidence obtained so far indicates that the Bacteria and Archaea diverged from a common ancestor about 3.7 billion years ago, and somewhat later the Archaea diverged from the lineage that would become the Eukarya. Carl Woese, a microbiologist at the University of Illinois, identified the Archaea and proposed the three-domain system of classifying life in 1977.
Considering Different Characteristics
Traditionally, microbial classifications were based on superficial similarities, such as shape, habitat, or method of acquiring energy. This approach did not necessarily group organisms that are the most recently descended from shared ancestors. That is, traditional classification considered similarities, but not evolutionary relationships. For example, Thermus aquaticus and Thermoplasma volcanium both are thermophiles, thriving in hot springs, but the former is a bacterium, and the latter an archaeon. They are not closely related at all, but live in similar surroundings.
In the early 1970s, Woese and others began comparing nucleic acid sequences to discover the evolutionary relationships among microorganisms. Woese focused on ribosomal ribonucleic acid (rRNA) because these are very important molecules that are therefore unlikely to have changed much over evolutionary time. The more alike the rRNA sequences were between two microbes, the more recently they shared an ancestor. Because nucleic acid sequencing had not yet been invented, Woese used an indirect method to compare rRNA sequences. He cut rRNA molecules into pieces with enzymes , then visualized the pieces in size order using a technique called autoradiography.
Different patterns of rRNA pieces characterized the prokaryotes known at the time (bacteria), and the eukaryotes. At the suggestion of a colleague, Woese ventured beyond probing the rRNAs of common laboratory strains of bacteria and analyzed a microbe that a graduate student had collected from a nearby septic system. These microorganisms were methanogens; they produced methane (swamp gas) from hydrogen and carbon dioxide in the environment. Surprisingly, the rRNA pattern for the septic system microbe lacked some of the pieces that had been identified in more than forty types of bacteria, and had some mysterious spots of its own.
Woese found other methanogens that didn't fit the expected prokaryotic pattern or rRNA fragments. By 1977, he and his colleagues published a landmark paper that described ten species of methanogens that "appear to be only distantly related to typical bacteria" (Woese 1977, p. 5088). Even though further publications continued to make the case for two types of prokaryotes, the idea of domains in general, and of the newly distinguished archaea in particular, took a long time to gain acceptance. Confusion arose over the initial naming of the "new" organisms as "archaebacteria." They are not bacteria; they are archaea.
Since 1977, microbiologists have identified and described several more members of domain Archaea. An initial misnomer was that these microbes are only found in what scientists call extreme environments, such as hot springs and deep-sea hydrothermal vents. Continued research showed that this is not the case. Archaea have been found in rice paddies, soils, swamps, freshwater, and throughout the oceans.
As more microbiologists came to accept the idea that archaea are not bacteria, more distinctions emerged. Archaean transfer RNA (tRNA) molecules differ in sequence from their bacterial or eukaryotic counterparts. Archaean cell walls lack the peptidoglycans that are part of bacterial cell walls, yet archaean cell membranes include lipid molecules not seen in other types of organisms. Archaea make methane using different enzymes than do bacterial methanogens.
Archaeans are sensitive to different antibiotic drugs than are bacteria, indicating a basic difference in cell structure. However, archaea also share characteristics with members of the other two domains. They have some of the same surface molecules as bacteria and transport ions in much the same way. But archaea have proteins associated with their DNA that resemble the histone proteins of eukaryotes and synthesize proteins in a way similar to that of eukaryotes. Also like eukaryotes, archaean genomes have more genes interrupted with intron sequences, and more repeated sequences, than do bacterial genomes.
Genome studies confirm that the archaea mix characteristics of the other two domains of life, and much more. A team from The Institute of Genomic Research (TIGR), which included Carl Woese, published the first genome sequence of an archaeon in 1996. The researchers collected samples of Methanococcus jannaschii from a "white smoker" chimney 2,600 meters (over 8,500 feet) deep in the Pacific Ocean, an environment that lacks oxygen and has extremely high temperature (near 85 degrees Celsius [185 degrees Fahrenheit]) and pressure (exceeding 200 atmospheres). Of M. jannaschii 's 1,738 protein-encoding genes, more than half are unknown in other organisms. Analysis of its genes revealed that its metabolism , cell surface, and ion transport mechanisms resemble those of bacteria, yet its DNA replication and protein synthesis mechanisms are more like those of eukaryotes.
Two years later, TIGR sequenced a second archaeon, Archaeoglobus fulgidus. Now researchers could compare archaea. Although A. fulgidus resembles M. jannaschii in DNA replication, protein synthesis, and biosynthetic pathways, it differs markedly in how it senses the environment, moves substances into and out of cells, and regulates metabolism. One quarter of A. fulgidus' genes encode proteins that are uncharacterized, but two-thirds of them are also found in M. jannaschii. Half of A. fulgidus' proteins are known in other organisms. However, one-quarter of its genes are not known, even in M. jannaschii. A. fulgidus is a thermophilic anaerobe like J. jannaschii, but also leads a very different lifestyle in that it metabolizes sulfur. In 1999, TIGR introduced the genome sequence of another archaeon, Aeropyrum pernix K1. It differs from the other two in that it lives in the presence of oxygen, but it also has many unique genes.
Compared to other types of organisms, biologists know very little about the archaea. However, the diversity seen among the few known types indicate that not only are the members of this third domain of life quite distinctive from members of the others, but they also differ from each other.
see also Bacterial Cell; Cell Wall; Eubacteria; Extreme Communities; Kingdom; RNA; Taxonomy, History of
Bult, C. J., et al. "Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii." Science 273 (1996): 1058–1073.
The Institute for Genomic Research. <http://www.tigr.org>.
Lewis, Ricki. "Going Out On a Limb for the Tree of Life." In Discovery: Windows on the Life Sciences. Malden, MA: Blackwell Science, 2001.
Woese, Carl R., and George E. Fox. "Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms." Proceedings of the National Academy of Sciences 74 (1977): 5088–5090.
Members of the Archaea comprise one of the three principal domains of living organisms in the universal phylogenetic tree of life. The other two principal domains are the Bacteria and the Eukarya. The phylogenetic tree is a theoretical representation of all living things, constructed on the basis of comparative ribosomal RNA sequencing and reflecting evolutionary relationships rather than structural similarities.
Characteristics of Archaea
Many scientists hypothesize that the Archaea are the closest modern relatives of Earth's first living cells. Called "universal ancestors," these are the cells from which all other life is believed to have evolved. This hypothesis is based on two types of evidence. Genetic analyses indicate that the Archaea domain branches off of the phylogenetic tree at a point that is closest to the tree's root. Furthermore, it has been observed that many of the Archaea prefer to live in extremes of temperature, salt concentration, and pH—environmental conditions thought to be similar to those found on Earth over 3.5 billion years ago, when life first originated.
The Archaea share certain characteristics with Bacteria, others with Eukarya, and have some characteristics that are unique. For example, cells of the Archaea are structurally more similar to Bacteria, live predominantly as single cells, and have cell walls, although the walls do not contain the complex material called peptidoglycan that is a signature molecule of the Bacteria. While some Eukarya have cell walls, it is not a universal characteristic of that domain, and the Eukarya walls are composed of chitin or cellulose, neither of which occurs in cell walls of Archaea or Bacteria. Like the Bacteria, the Archaea lack a membrane-enclosed nucleus and their DNA exists in a circular form. On the other hand, their DNA is associated with histones, a characteristic of Eukarya, and their cell machinery (such as proteinsynthesizing enzymes and RNA polymerases) more closely resembles that found in the Eukarya. The lipids that comprise their membranes are unique, resembling neither the Bacteria nor the Eukarya.
Certain members of the Archaea are able to produce methane gas, another unique characteristic. Methane is one of the most important greenhouse gases. An Italian scientist named Alessandro Volta first discovered it as a type of "combustible air" over two hundred years ago. He trapped gas from marsh sediments and showed that it was flammable long before we knew that it was produced by members of the Archaea that lived in salt marsh sediment. Other important habitats for Archaea with this unique ability include the digestive tracts of animals and sewage sludge digesters.
Thriving in Environmental Extremes
The ability of many members of the Archaea to thrive in environmental conditions that we would find extreme is perhaps one of their most fascinating characteristics. There are genus like Halobacterium, which inhabit extremely salty environments, such as the Great Salt Lake in Utah and the Dead Sea in Israel. The salt concentration in these lakes is at least ten times that of seawater. Still other lakes, like Lake Magadi in Kenya, are not only extremely salty, but are also extremely alkaline, with pH values as high as 10 or 12. Archaea can be found even here, and their names reflect their habitat: Natronobacterium, Natronosomonas, and Natronococcus ("natro" means "salt"). The reddish-purple color sometimes seen in seawater-evaporating ponds, where solar salt is prepared, is the result of the growth of red-pigmented Archaea.
Extremes of temperature offer no challenge to certain members of the Archaea. A number of species, in fact, require temperatures over 80 °C in order to grow. Some live quite happily in the superheated outflow of geothermal power plants. Others thrive in the conditions of extreme acidity and temperature found in sulfur-rich, acidic hot springs like those in Yellowstone National Park, in the United States.
Archaea also populate the areas surrounding deep-sea vents, underwater volcanoes that form when the earth's crust opens along the ocean floor's spreading centers. The deep-sea vents have the hottest temperatures at which any living organism has been found. As of 2001, the current record for heat tolerance belonged to Pyrolobus fumarii, which can grow in water at a maximum temperature of 113 °C, well above boiling. At the opposite extreme, Archaea are among the few organisms found in the frigid waters of the Antarctic.
Value to Industry and Research
As a consequence of their ability to thrive in extreme conditions, the Archaea have become increasingly valuable. For example, the DNA polymerase of Thermus aquaticus, an Archaea found in the Yellowstone hot springs, is a heat tolerant enzyme that is crucially important in modern molecular biology laboratories, because of its use in the polymerase chain reaction. Archaea have also become important for commercial purposes. Their enzymes, sometimes called extremozymes, have made their way into laundry detergent, for example, where they digest proteins and lipids in hot water or cold, and in extremely alkaline conditions, thus helping to remove life's little messes.
see also Cell, Eukaryotic; Eubacteria; Polymerase Chain Reaction; Ribosome.
Cynthia A. Needham
Madigan, Michael T., John M. Martinko, and Jack Parker. Brock Biology of Microorganisms, 9th ed., Upper Saddle River, NJ: Prentice Hall, 2000.
Campbell, Neil A. Biology, 4th ed. Menlo Park, CA: Benjamin Cummings, 1996.
Madigan, Michael T., and Barry Marrs. "Extremophiles." Scientific American (April, 1997): 82-87.
The high-salt density of the Dead Sea makes it difficult for humans to swim in its waters. Human bodies are much more buoyant in the Dead Sea waters than in fresh water. It is possible to lay back in the water—floating as if on an air mattress.
At first glance, members of domain Archaea look very much like Bacteria in morphology , but biochemical and evolutionary studies have shown that they are a unique branch of life, separate from Bacteria (Eubacteria) and Eukaryotes. This was first recognized by comparing the sequences of their ribosomal deoxyribonucleic acid (DNA) and their type of cell wall to those of other organisms. Although Archaea also have a prokaryotic cell organization, other differences set them apart from Bacteria. While most Archaea have cell walls, they do not contain murein as in Bacteria, but are made of a number of different molecules, including proteins. The lipids found in their cell membranes are also different from those found in Bacteria and eukaryotes . Archaea can be motile by rotating flagella , but the proteins that make up the flagella are different from those found in Bacteria. Archaea have a number of traits that make them more similar to eukaryotes than to Bacteria. For example, in Archaea ribonucleic acid (RNA) polymerases and other proteins involved in making RNA from DNA are more similar to those in eukaryotes than those in Bacteria. Because of these and other similarities to eukaryotes, Archaea are thought to be the ancestors of the nuclear and cytoplasmic portions of eukaryotes.
Archaea include many organisms that live in extreme environments or that have unique metabolisms. These include methanogenic (methane-making) Archaea, halophilic (salt-loving) Archaea, extremely thermophilic (heat-loving) sulfur metabolizers, and thermoacidophiles, which live in acidic high-temperature environments.
Methanogens are killed in the presence of oxygen and live in anoxic places, such as the muds of rice fields and the guts of animals, particularly insects and cows. They produce methane, or natural gas, which is used by humans as a source of energy.
Halophiles can only live in places with very high salt concentrations, much saltier than the open oceans. They contain a pigment similar to one found in human eyes, bacteriorhodopsin, which allows them to use light energy to make adenosine triphosphate (ATP ). Carotenoid pigments, which help shield the cells from damaging ultraviolet (UV) light, make the cells appear orange-red. High-salt aquatic areas containing many halophilic Archaea can be seen from a distance because of this red color.
Thermoacidophiles are a group of Archaea that can live in very acidic environments at elevated temperatures. They are found in hot springs such as those in Yellowstone National Park, volcanoes, burning coal piles, or at undersea hydrothermal vents. Many of them use sulfur compounds for their metabolism. Some are hyperthermophiles, organisms that live at the highest temperatures known (between 80° and 113°C). They are even found living in boiling water.
Because Archaea inhabit extreme environments that were probably prevalent on the early Earth, some believe that they are an old group of organisms (hence their name) that may hold clues to the origin of life. However, extreme thermophiles have also been found among the Bacteria, and Archaea have been shown to be abundant in more moderate environments as well. Environmental studies using DNA survey techniques (PCR) show that low-temperature Archaea make up a significant portion of the prokaryotic biomass in terrestrial and planktonic marine environments. From these types of environmental PCR studies, which can tell us what kind of organisms are present in the environment without relying on traditional methods of culturing, we know that both Archaea and Bacteria are abundant in the biosphere, and that the majority of these organisms and their ecological role have yet to be described and understood.
see also Eubacteria; Evolution of Plants.
J. Peter Gogarten
Needham, Cynthia, Mahlon Hoagland, Kenneth McPherson, and Bert Dodson. Intimate Strangers: Unseen Life on Earth. Washington, DC: ASM Press, 2000.
Woese, C. R. "Bacterial Evolution." Microbiological Reviews 51 (1987): 221-71.
Genes that code for vital cellular functions are highly conserved through evolutionary time, and because even these genes experience random changes over time, the comparison of such genes allows the relatedness of different organisms to be assessed. American microbiologist Carl Woese and his colleagues obtained sequences of the genes coding for RNA in the subunit of the ribosome from different organisms to argue that life on Earth is comprised of three primary groups, or domains. These domains are the Eukarya (which include humans), Bacteria , and Archaea.
While Archae are microorganisms , they are no more related to bacteria than to eukaryotes . They share some traits with bacteria, such as having a single, circular molecule of DNA , the presence of more mobile pieces of genetic material called plasmids , similar enzymes for producing copies of DNA. However, their method of protein production and organization of their genetic material bears more similarity to eukaryotic cells.
The three domains are thought to have diverged from one another from an extinct or as yet undiscovered ancestral line. The archae and eukarya may have branched off from a common ancestral line more recently than the divergence of these two groups from bacteria. However, this view remains controversial and provisional.
The domain Archae includes a relatively small number of microoganisms. They inhabit environments which are too harsh for other microbes. Such environments include hot, molten vents at the bottom of the ocean, the highly salt water of the Great Salt Lake and the Dead Sea, and in the hot sulfurous springs of Yellowstone National Park. Very recently, it has been shown that two specific archael groups, pelagic euryarchaeota and pelagic crenarchaeota are one of the ocean's dominant cell types. Their dominance suggests that they have a fundamentally important function in that ecosystem.
See also Bacterial kingdoms; Evolution and evolutionary mechanisms; Evolutionary origin of bacteria and viruses