ARCHAEA AND THE TREE OF LIFE

Before 1977 and Dr. Carl Woese, the domain Archaea didn’t exist. It was with the advent of the phylogenetic tree concept that microbiology was overturned and a new “three’domain” taxonomic system established. Rather than identify and classify species by appearances or habits (as Carolus Linnaeus did in 1735), Woese’s team from the University of Illinois at Urbana-Champaign used a completely different and new system that became revolutionary in biology.

Beginning in the twentieth century, data began to conflict with Linnaean taxonomy. The proposal given by Linnaeus, a Swedish botanist, stated that all organisms of Earth fit into two categories–plants or animals. Bacteria directly contradicted this theory of limited taxonomic categorization.

In 1969, R.H. Whittaker claimed that a system of five kingdoms–Monera, Protista, Plantae, Fungi, and Animalia–best classified all of the organisms in nature. He based his “five-kingdom system” on observations gained by other biologists on organisms.

Under Whittaker’s system, archaea would be classified under Monera. However, Woese and his team of researchers proposed a new system, based not on morphology, but on phylogeny. In order to determine where a species belonged in the tree of life, Woese used a molecule found in every organism: small sub-unit rRNA or simply, SSU RNA.

Biologists were shocked by Woese’s results. Instead of a main division between plants and animals or eukaryotes and prokaryotes, Woese found that three major groups, what he eventually called “domains,” existed–Bacteria, Archaea, and Eukarya.

More than twenty kingdoms exist under the domains in the tree of life, far more than the five original kingdoms suggested by Whittaker in 1969. In fact, Woese’s team found that archaea were more related to eukarya (plants, animals, fungi, etc.) than to bacteria. This accounted for the renaming of “Archaebacteria,” the original name given by Woese, to “Archaea.”

Woese—s phylogenetic tree of life failed to gain full acceptance until the late 1980s. Other microbiologists were unprepared for these discoveries. The journal Science named Woese “Microbiology’s Scarred Revolutionary” after sharp criticisms from the likes of Ernst Mayr and Salvador Luria. Eventually, however, Archaea began to be truly accepted as a new domain.

Another concept by Johann Peter Gogarten, based largely on the tree of life, was the proposed “net of life.” In the 1990s, when microbiologists began a massive project to sequence the genomes of bacteria and archaea, they found many instances of “lateral transfer,” where instead of genes being inherited, they were “swapped” among distantly related organisms.

Archaea saw an unprecedented amount of study since Woese’s revolutionary discovery, particularly because of their intriguing ability to live in extreme habitats. Such “thermophiles” are often found in Yellowstone National Park, living in geysers with temperatures frequently rising up to 100 degrees Celsius (212 degrees Fahrenheit).

Furthermore, some species of archaea existed over 3.7 billion years ago, when life was just beginning to form. This unchanged nature gives paleobiologists much more incentive to study archaea to investigate life on this planet prior to the existences of dinosaurs and trilobites.

The consensus of biology in geysers during the 1960s claimed that monerans, at the time including both archaea and bacteria, could not survive in temperatures above 73 degrees Celsius (131 degrees Fahrenheit). All deoxyribonucleic acid (DNA) and required proteins would die when subjected to such heat. Archaea, as do other thermophiles, use enzymes that are able to function at very high temperatures.

Some archaea are found at the bottom of the ocean floor, 2100 meters deep, in formations called “black smokers.” Because sunlight is nonexistent, organisms cannot utilize photosynthesis to provide sustenance. Instead, archaea use a process called “chemosynthesis,” a process of converting heat, methane, and sulfur, which are provided by the black smokers, into energy.

Archaea are not limited to high temperatures, however. Psychrophiles, organisms that are able to survive at temperatures of 15 degrees Celsius or lower, are often found in glaciers and seawater. Nutrients are found in cracks through glaciers or ice and often in seawater or even soil. Psychrophiles release characteristic enzymes that leave crystalline traces on ice.

Furthermore, methanogenic archaea are found in the digestive tracts of humans, termites, and ruminants. Unlike some forms of bacteria, none of the archaea, as yet, are known to cause disease in any organism. In fact, acidophiles, which live at a very acidic pH of 1, can die in distilled water, which has a pH of 7. Some acidophiles can even survive at pH 𔂾.06.

But what of archaean structure? Archaea, which are unicellular, range from 0.1μm to more than 15μm and do not have a nucleus. In order to tell the difference between bacteria and archaea, one must look into the structure of the cell.

Although archaea usually have bacterial structures (coccus and bacillus), several species of archaea are known to be quadrilateral or triangular. Many archaea also have flagella, hairlike appendages used for mobility, attached to the outer cell membrane. However, as the domain Archaea is the least understood, microbiologists have discovered a motile archaeon that does not use any conventional means of transportation; scientists are unsure how the recently sequenced Methanosarcina acetivorans moves.

Many archaea also have a very rigid outer wall, made up of different sugars and amino acids than those in bacteria. Cell membranes of archaea also have differing lipid structures and chemical links from bacteria. This characteristic allows archaea to repel drugs that kill bacteria by interfering with their protein production.

The domain Archaea is divided into three kingdoms: Euryarchaeota, consisting of methane-producing archaea, otherwise known as “methanogens,” and halophiles, which live in highly saline conditions; Crenarchaeota, consisting of archaea that live in very high temperatures and acidic conditions; and Korarchaeota, a very recently discovered kingdom which has yet to be fully identified.

Euryarchaeota is predominantly made up of three groups: methanogens, halogens, and thermoacidophiles. Microbiologists have found methanogens in very anaerobic environments, such as the muck of swamps and wetlands, rumen of cattle, sewage sludge, and the organs of termites. Because they have a limited amount of oxygen, methanogens are required to use hydrogen electrons to reduce carbon dioxide so that it can survive, giving off methane as a byproduct.

Prior to the discovery of euryarchaeota living in the organs of eukaryotes, it was thought that animals were responsible for the methane in our atmosphere. However, it is now known that the euryarchaeota are fully responsible for producing the methane found in our air. Most methanogens are capable of converting at least ten unique substrates into methane, including carbon monoxide and hydrogen gas, formate, methanol, and acetate.

On the other hand, Crenarchaeota consists of hyperthermophiles and acidophiles, although other members of this kingdom are supposedly plankton that live in relatively cool marine water. Hyperthermophiles live in often unbearably hot temperatures (usually more than 100 degrees Celsius) more extreme than those of thermophiles.

A number of biotechnological companies and entrepreneurs have discovered that crenarchaeal enzymes are extremely resilient to acid and heat, a trait that could be utilized for research purposes and industry. One such company is Diversa Corporation, which is working to improve ethanol production using crenarchaeal enzymes.

However, humans have affected the environment in the use of ammonia-based fertilizers, which are derived from nitrogen in the atmosphere. Ammonia is an electron donor (a chemical entity that donates electrons to another compound) by archaea located in the soil underneath the corn and wheat that are using the fertilizer. Nitrate, a byproduct of archaea and bacteria, quickly runs off into nearby water and subsequently into aquatic ecosystems. Cyanobacteria and algae flourish in nitrate, resulting in an increase of population. Consequently, archaean decomposers quickly grow after algae and cyanobacteria die in the water. These archaean decomposers use up all of the available oxygen in the water and produce “dead zones,” or “anaerobic zones,” such as the one found at the mouth of the Mississippi River in the Gulf of Mexico.