Archaea: The Third Domain of Life

The biodiversity of the Earth never ceases to astonish. One example that has radically changed the face of biology is the discovery of a group of organisms called archaea (pronounced “ar-kee-ah”). It was thought that all creatures on Earth were divided into two main evolutionary categories, but this changed in the 1990s with the discovery of archaea. Today, all known organisms belong to one of three groups, or domains: eukaryotes (which include animals like us, plants, fungi, and some single-celled organisms), bacteria, and archaea.

Despite its status as one of the three domains that make up all life on the planet, public awareness of archaea is low. This is probably because of their recent addition to the tree of life, but also because they are so alien compared to our idea of “life.” Archaea look like bacteria but are more closely related to eukaryotes. These small, single-celled organisms thrive in the most extreme environments on Earth, such as sulfuric hot springs near volcanoes or deep-ocean hydrothermal vents that reach 236 degrees Fahrenheit under colossal pressure. In these inhospitable conditions, archaea survive and eat some bizarre substances that barely qualify as food, from iron and sulfur to toxic compounds.

These astounding adaptations are undoubtedly related to their evolutionary age. Having been around nearly four billion years, they’ve had plenty of time to adapt and evolve. So how was the existence of archaea so long overlooked? A large part was because they live in places where no life was thought to exist, eating inedible chemicals, happily living as they have been for billions of years.

As usual in science, their discovery was due to researchers utilizing new technologies and open-mindedness. Until the 1960s, organisms were mostly grouped based on appearance, but this changed with the emergence of genetic studies, where researchers compared DNA sequences. In the 1970s, Carl Woese, a biophysicist and molecular biologist at the University of Illinois at Urbana-Champaign, was analyzing DNA signatures used to tell which of the two domains (eukaryote or prokaryote, which includes bacteria) an organism belonged to. After Woese had established this characterization system, a collaborator brought him a new, unusual critter.

It produced methane (natural gas). Methanogens are single-celled organisms that create methane. Archaea are the only methanogens on Earth, although nobody knew this when Woese got his hands on the first sample. The methanogen Woese analyzed (Methanobacterium thermoautotrophicum) was taken from the municipal waste-treatment facility in Champaign, Illinois; a perfumed heaven for M. thermoautotrophicum. Woese set to work analyzing its DNA signature, only to find that these creatures didn’t cleanly fit into either domain; they had some DNA belonging to the eukaryotes, some to the prokaryotes, and lacked some from both. Like all good scientists, Woese continued to look at several other methanogens throughout 1976, only to find they all shared these unique patterns.

Woese first reported the discovery of archaea in 1977. His findings were met with much general skepticism; many scientists thought that the broad groups of life had already been discovered, and there wasn’t room for a third group. But Woese persevered with his archaea research. Over time other archaea were discovered in other extreme environments. Norman Pace, at the University of Colorado at Boulder, is the second leading pioneer in the archaea field. He perfected methods of going into the field and collecting specimens for genetic analysis. It was long thought archaea only survived in harsh conditions, but recent discoveries place them in more mild environments as well.

As gene sequencing technology improved throughout the 1990s, for the first time Woese’s group sequenced the entire genome of an archaea, Methanococcus jannaschii, in 1996. M. jannaschii, which lives in hydrothermal vents on the ocean floor under extremely high pressures, was declared a representative of the third domain. Although this helped solidify archaea’s claim, by this time most researchers had accepted that archaea, indeed, made up a third domain of life. As the DNA unraveled, archaea’s key role in Earth’s history was becoming better understood.

Archaea are extremely ancient organisms (their name in Greek is literally “ancient things”). Archaea have inhabited Earth for nearly 4 billion of its 4.6 billion years in existence, making them possibly the oldest living life form. Early Earth is thought to have had little oxygen, but abundant carbon dioxide. The first bacteria and archaea probably did not require oxygen, but consumed carbon dioxide. They thrived for two billion years, covering the ocean floors and forming strong, collective mats. However, around 2.4 billion years ago global oxygen levels increased; the organisms may have released oxygen from the Earth’s crust, or created it as a by-product, but either way they poisoned themselves with the oxygen, forcing them to quickly adapt or die out.

The ancestor of eukaryotes most likely branched off from archaea around 2 billion years ago, although multi-cellular organisms did not appear until around 1 billion years ago. Archaea were thus key players for most of our planet’s history, altering the atmosphere, biology, and geology around them, all the while surviving in unique environmental niches.

Archaea today have a wide variety of unique metabolisms that allow them to live in the most inhospitable places on Earth. Archaea can eat iron, sulfur, carbon dioxide, hydrogen, ammonia, uranium, and all sorts of toxic compounds, and from this consumption they can produce methane, hydrogen sulfide gas, iron, or sulfur. They have the amazing ability to turn inorganic material into organic matter, like turning metal to meat. Their unique metabolisms allow them to live in oxygen-free habitats, boiling sulfuric acid pools near volcanoes, sulfur hot springs, glacial ice, methane seeps, rock four miles into the Earth, desert sands, acid mines, oil leaks, polluted waters, and toxic waste dumps. And while it hasn’t been shown that they are responsible for any diseases, they also call the insides of animals home; they’re in our gums, living with infectious bacteria, and in the guts of animals, producing methane.

Truly, archaea inhabit incredible niches around the globe. Many fascinating members of the phylum Crenarchaeota have been described: Pyrolobus fumarii, which holds the record for the highest temperature an organism can live at, grows best around 236 degrees Fahrenheit in deep ocean hydrothermal vents; while the genus Sulfolobus lives in very hot (170 degrees Fahrenheit) and very acidic (pH 2 to 3) volcanic springs. However, other archaea of the Crenarchaeota phylum inhabit “normal” soil, fresh waters, and moderate temperatures; they may be found in most environments.

Another branch of archaea (the phylum Euryachaeota) contains the methanogens, which live in environments with very little oxygen, including marshes, sewage, and the guts of cattle and termites. Other members of this phylum include the halophiles, salt-lovers which thrive in places such as the Great Salt Lake and the Dead Sea, but would die in normal drinking water; and Ferroglobus placidus, which can consume iron, hydrogen gas, or sulfide, all at 185 degrees Fahrenheit.

Archaea has attracted attention from several quarters. It is adaptations such as unique, rigid membranes that allow archaea to withstand a much greater range of temperatures than bacteria and eukaryotes can. These heat-stable changes have caught the attention of businesspeople; they can be used to process food at high temperatures. Methanogens have also attracted attention due to their novel metabolism. The production of methane by methanogens in animal guts contributes to greenhouse gas emissions; it is essential to understand archaea when studying global warming. Because only archaea are methanogens, some scholars, such as John Perona at the University of California at Santa Barbara (UCSB), study archaea to better understand the enzyme reactions that go on in methanogenesis.

Researchers still have much to learn about archaea, such as their sheer range of diversity, and where they can live (if there’s anywhere they can’t!). David Valentine at UCSB studies archaea in extreme environments, such as the Salton Sea, California’s largest lake. The Salton Sea has high levels of salt, and a range of sulfur and oxygen levels; Valentine’s group found that archaea reside in all the gradients present, and were less affected by the changes than bacteria. Because of their amazing durability, some archaea researchers hypothesize that these astonishing critters could be flying around on comets or on other planets, such as in Mars soils, awaiting our discovery.

For more on the amazing domain of the archaea, see Tim Friend’s The Third Domain, Roger A. Garrett and Hans-Peter Klenk’s Archaea: Evolution, Physiology, and Molecular Biology, Wikipedia’s “Archaea,” Wikipedia’s “Carl Woese,” the lab Web site of Prof. Norman Pace, the lab Web site of Prof. David Valentine, or the lab Web site of Prof. John Perona.

Biology Bytes author Teisha Rowland is a science writer, blogger at All Things Stem Cell, and graduate student in molecular, cellular, and developmental biology at UCSB, where she studies stem cells. Send any ideas for future columns to her at science@independent.com.