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The Three Domains of Life

Prokaryotes are primitive cells, without a nucleus or membrane bound organelles, has DNA located in a "nuclear area", but the DNA is not bound inside the nucleus as in Eukaryotes. Prokaryotes have ribosomes, although the ribosomes are slightly more primitive than Eukaryotic cells. Credit: OUC
by Leslie Mullen
for NASA Astrobiology Institute
Moffett Field - Nov 6, 2001
When scientists first started to classify life, everything was designated as either an animal or a plant. But as new forms of life were discovered and our knowledge of life on Earth grew, new categories, called "Kingdoms," were added. There eventually came to be five Kingdoms in all - Animalia, Plantae, Fungi, Protista, and Bacteria.

The five Kingdoms were generally grouped into two categories called Eukarya and Prokarya. Eukaryotes represent four of the five Kingdoms (animals, plants, fungi and protists). Eukaryotes are organisms whose cells have a nucleus -- a sort of sack that holds the cell's DNA. Animals, plants, protists and fungi are all eukaryotes because they all have a DNA-holding nuclear membrane within their cells.

The cells of prokaryotes, on the other hand, lack this nuclear membrane. Instead, the DNA is part of a protein-nucleic acid structure called the nucleoid. Bacteria are all prokaryotes.

However, new insight into molecular biology changed this view of life. A type of prokaryotic organism that had long been categorized as bacteria turned out to have DNA that is very different from bacterial DNA. This difference led microbiologist Carl Woese of the University of Illinois to propose reorganizing the Tree of Life into three separate Domains: Eukarya, Eubacteria (true bacteria), and Archaea.

Archaea look like bacteria - that's why they were classified as bacteria in the first place: the unicellular organisms have the same sort of rod, spiral, and marble-like shapes as bacteria. Archaea and bacteria also share certain genes, so they function similarly in some ways. But archaeans also share genes with eukaryotes, as well as having many genes that are completely unique.

Archaea are so named because they are believed to be the least evolved forms of life on Earth ('archae' meaning 'ancient'). The ability of some archaea to live in environmental conditions similar to the early Earth gives an indication of the ancient heritage of the domain.

The early Earth was hot, with a lot of extremely active volcanoes and an atmosphere composed mostly of nitrogen, methane, ammonia, carbon dioxide, and water. There was little if any oxygen in the atmosphere. Archaea and some bacteria evolved in these conditions, and are able to live in similar harsh conditions today. Many scientists now suspect that those two groups diverged from a common ancestor relatively soon after life began.

Millions of years after the development of archaea and bacteria, the ancestors of today's eukaryotes split off from the archaea. So although archaea physically resemble bacteria, they are actually more closely related to us!

If not for the DNA evidence, this would be hard to believe. The archaea that live in extreme environments can cope with conditions that would quickly kill eukaryotic organisms. Thermophiles, for instance, live at high temperatures - the present record is 113C (235F). In contrast, no known eukaryote can survive over 60C (140F). Then there are also psychrophiles, which like cold temperatures - there's one in the Antarctic that grows best at 4C (39F). As a group, these hard-living archaea are called "extremophiles."

There are other kinds of archaea extremophiles, such as acidophiles, which live at pH levels as low as 1 pH (that's about the same pH as battery acid). Alkaliphiles thrive at pH levels as high as that of oven cleaner. Halophiles, meanwhile, live in very salty environments. But there are also alkaliphilic, acidophilic, and halophilic eukaryotes. In addition, not all archaea are extremophiles. Many live in more ordinary temperatures and conditions.

In a eukaryote, the DNA is located in the nucleus of the cell. A DNA molecule is composed of two helically spiral strands, each composed of a linear chain of sugar and phosephate molecules. Credit: MIT
Many scientists think the thermophilic archaea - the heat-loving microbes living around deep-sea volcanic vents - may represent the earliest life on Earth. But NAI member Mitchell Sogin, a microbiologist with the Marine Biological Laboratory, says that instead of being the Earth's first life form, they could be the sole survivors of a catastrophe that occurred early in the Earth's history. This catastrophe could have killed off all other forms of life, including the universal ancestor from which both archaea and bacteria arose.

"Some have argued that the occurrence of thermophilic phenotypes in the deepest archaeal and bacterial lineages suggests that life had a hot origin," says Sogin. "However, there are other equally compelling arguments which suggest that this distribution of phenotypes on the tree of life reflects survival of heat-loving organisms during times of major environmental upheaval."

Such environmental upheavals include asteroid and comet bombardments, which we know happened frequently during the Earth's earliest years. Although our geologically active planet has erased much of the evidence of these cataclysmic events, the Moon bears witness to the amount of asteroid and comet activity that occurred in our neighborhood. Because the Moon is geologically inactive, its surface is still littered with scars from these early impacts.

Large impacts can create severe global environmental changes that wipe out life at the planet's surface. It is believed, for instance, that the dinosaurs fell victim to the environmental effects of a large asteroid impact. Among other effects, impacts throw a lot of dust and vaporized chemicals up into the atmosphere. This blocks sunlight, impairing photosynthesis and altering global temperatures.

But thermophilic archaeans are not dependent on the Sun for their energy. They harvest their energy from chemicals found at the vents in a process called chemosynthesis. These organisms are not greatly impacted by surface environmental changes. Perhaps the only organisms that were able to survive the large, frequent impacts of Earth's early years were the thermophilic organisms that lived around deep-sea volcanic vents.

"Certainly the discovery of the archaea pointed out microbial diversity - particularly in extreme environments - that was previously unrecognized," says Sogin. "As to what this data has to say about the origins of life, I am of the opinion that we still do not know where the root lies within the three kingdom tree."

Woese is currently working to unearth that root. But he says the search for the universal ancestor is a far more subtle and complex problem than most people realize.

"The problem is not merely a case of identifying some original cell or cell line that gave rise to it all," says Woese. "The universal ancestor may not be a single lineage at all."

Instead, says Woese, lateral gene transfer - a process where genes are shared between microorganisms - may have been so prevalent that life did not evolve from one individual lineage.

"At the universal ancestor stage, horizontal gene transfer may have been so dominant that the ancestor may in effect have been a community of cell lineages that evolved as a whole. We will be able to trace all life back to an ancestor, but that state will not be some particular cell lineage."

The transfer of bacterial genes seems to have been a vital part of the evolution of archaeans and eukaryotes. In fact, it is believed that such a transfer was responsible for the development of the first eukaryotic cell. As oxygen accumulated in the atmosphere through the photosynthesis of blue green algae, life on Earth needed to quickly adapt. When a cell consumed aerobic (oxygen-using) bacteria, it was able to survive in the newly oxygenated world. Today, the aerobic bacteria have evolved to become mitochondria, which helps the cell turn food into energy.

Modern-day archaea and eukarya seem to rely on such bacterial intervention in their metabolisms. This points to the possibility that bacterial genes may have replaced other genes in the two lineages over time, erasing some features of the last common ancestor. But Woese says there are certain molecular similarities among all three domains that still may point to a universal ancestor.

"Although there are differences in the information-processing systems, there are many universal features in translation and core similarities in transcription that link all three domains," says Woese. "But this is a very complex and hard to understand area. These early interactions were almost certainly between entities the like of which no longer exist. They were primitive entities that were on their way of becoming one of the three modern cell types, but were definitely not modern cells. Their interactions were peculiar to that particular era in evolution, before the modern cell types arose."

Perhaps the universal ancestor is not to be found on Earth. Because life on Earth seems to have appeared very soon after the planet became habitable, many scientists think that life could have arrived from outer space, via the asteroids and comets that bombarded the Earth in its earliest years.

In addition, because some Martian rocks that have arrived on our planet seem to contain fossilized microbes, some have speculated that life on Earth might originally have come from Martian meteorites. However, Woese believes that if we find evidence for life on Mars, it will either be unrelated to Earth-based life, or be the result of contamination of Mars by rocks from Earth.

Sogin also doesn't think that the first microbes were brought to Earth by a Martian asteroid or comet. However, he does believe that microbial life may be a common feature of the Galaxy.

Eukaryotes probably emerged from prokaryotic ancestry about 1.6 - 2.1 billion years ago. The evolutionary diversification of eukaryotes has involved invention of organelles, and their modification. Credit: UCLA
"Life at extreme environments as represented principally by the archaea forces us to consider the possibility of living organisms on other solar system bodies under conditions that we would not have deemed possible just ten or fifteen years ago," says Sogin. "For example, we can imagine life under the ice on Europa and even the possibility of subsurface life on Mars. Certainly microbial life is far more robust and can survive and even thrive under conditions that are likely to be found elsewhere in the solar system and certainly in the galaxy."

Woese, on the other hand, hasn't yet made up his mind about the occurrence of life elsewhere.

"Life in Universe - rare or unique? I walk both sides of that street," says Woese. "One day I can say that given the 100 billion stars in our galaxy and the 100 billion or more galaxies, there have to be some planets that formed and evolved in ways very, very like the Earth has, and so would contain microbial life at least. There are other days when I say that the anthropic principal, which makes this universe a special one out of an uncountably large number of universes, may not apply only to that aspect of nature we define in the realm of physics, but may extend to chemistry and biology. In that case life on Earth could be entirely unique."

Whether or not Earth-like life is common or unique, Sogin says it will be a long time before we can answer that question with any certainty.

"I think that life occurs elsewhere in the universe," says Sogin. "However, I am not sure we will ever be able to obtain conclusive evidence of life elsewhere given today's technology, or even tomorrow's technology."

The development of the Three Domains concept has, in Woese's opinion, dramatically altered the way scientists view life on Earth. He says the concept has highlighted the shared traits - as well as the differences - among all three groups.

"Most biologists still speak of prokaryotes versus eukaryotes, but now they discuss their similarities, says Woese. "In the old days, they focused mainly if not solely on their differences. I often analogize the conceptual climate before and after the discovery of the archaeas to changing from monocular to binocular vision."

By finding out what he can about the similarities among all three domains, Woese says he is "studying the two interrelated fundamental biological problems of the nature of the universal ancestor and the evolutionary dynamic of horizontal gene transfer."

Sogin, meanwhile, is exploring the evolution of biological complexity in microbial ecosystems.

"Life is very old - appearing on Earth at least 3.5 billion years ago and possibly 3.9 or 4 billion years ago," says Sogin. "It was microbial and continued in that mode for the first 70 to 90 percent of Earth's history. Complex multicellularity in the form of differentiated tissue is a relatively recent event. Throughout time the microbes ruled and continue to govern all biological processes on this planet."

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