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.

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 113°C (235°F). In contrast, no known
eukaryote can survive over 60°C (140°F). Then there are also psychrophiles,
which like cold temperatures – there’s one in the Antarctic that grows best
at 4°C (39°F). 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.

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.

“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.”

What Next?

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.”