The Archaea:
In the 1970s while analyzing ribosomal RNA sequences of different types of bacteria, Carl Woese
discovered that the methanogens ("bacteria" that produce methane gas) had a very unique pattern of A,
U, C, and G. A pattern that he had not seen in any other bacteria. Since methanogens are killed by
oxygen (anaerobic), they were not so easy to work with or grow in culture, but Woese's colleague was
growing them down the hall. Woese began collecting other "bacteria" that were known to have unique
metabolisms and whose cell walls and membranes differed chemically from "normal" bacteria. As he
examined the rRNA sequences of other "bacteria" from extreme environments, he realized that many of
these organisms were fundamentally different. So different, in fact, that he finally published a peerreviewed paper announcing his discovery of a "third" type of cell. He called them Archaeabacteria
initially, and because they tended to be anaerobic (like the early earth) he figured they were
descendents of the earliest cells… thus "archaea" or ancient.
The NYTImes picked up on his scientific paper and put him on the front page with a headline
"Scientist discovers new form of Life." The NYTimes article - written for general audiences - did not
go into the details of the science behind the claim, and as a result, many scientists were immediately
skeptical and Woese became the target of intense criticism from the scientific community.
He stood his ground, and found kindred spirits in Germany where his work was not only accepted, but
greatly admired. German scientists had been working with many of the same organisms and noting the
significant uniqueness of their cell walls, cell membranes, and metabolic pathways. But Woese was
the only scientist sequencing nucleic acids at the time. When the German scientists (Kandler, Zillig,
Stetter, and others) realized the correlation between their work and that of Woese, the Archaea began to
gain broader acceptance. In 1990, Woese and George Fox published a paper proposing a new highest
taxonomic level… above the Kingdom. Some scientists had already proposed TWO
SUPERKINGDOMS - Prokaryota and Eukaryota. The work of Woese and colleagues showed very
clearly (to anyone capable of analyzing their data) that the Archaea were metabolically more closely
related to Eukaryotes than either was to Bacteria. So Woese and Fox proposed THREE LINEAGES
OF LIFE - BACTERIA, ARCHAEA, AND EUKARYA. And it was Woese who proposed the term
DOMAIN. Once again, the scientific community was critical, but as scientists set about trying to
disprove Woese's contention, they slowly but surely came to the realization that he was right and had
been all along.
Scientists can be dogmatic and prone to paradigm paralysis. Some of what you might call the "Old
Guard" simply ignored the data and refused to abandon the Prokaryote/Eukaryote dichotomy. There
was great debate in scientific circles and while some scientists still hold firm to the
Prokaryote/Eukaryote division of life, most (especially the young ones) are prepared to abandon
"Prokaryote" altogether. Today the THREE DOMAINS OF LIFE are widely accepted. It took decades,
but Woese has finally been vindicated.
Woese is obsessed with the evolution of the earliest life, the origin of the genetic code and the
transitional forms whose existence would have necessarily predated the "cell" with its complete
functionality. (These predicted transitional forms have never been found, and likely never will be.) He
is also very much concerned with the role of bacteria and archaea in the earth's ecosystems.
Woese's colleague and collaborator, Norman Pace, developed a technique in the late 80s/early 90s for
"isolating" bacteria and archaea that could not be grown in culture (previously a necessity for studying
microbes). The technique that Pace developed has allowed scientists to identify organisms previously
unknown to scientists. In the past decade, the number of "environmental isolates" has grown to far
exceed the number of microbes known to exist before, and their numbers are growing day by day.
Only about 6,000 "species" of bacteria are classified and identified, but scientists estimate the number
of "species" to be in excess of 10 million!
For some, the Pace technique was/is seen as a way to make money through bioprospecting, and indeed,
some entrepreneurial types have become fabulously wealthy. The field of environmental microbiology
is now capable of examining genes responsible for vital processes in biogeochemical cycles. What we
know now is that the microbes are keeping the planet "alive." The planet does not need animals, but
Earth could not exist as we know it without the microbes. The growing field of "bioremediation"
borrows the genetic/molecular capacity of microbes to clean up the toxic mess we humans seem so
inclined to make.
What we've learned since you were born (mid 1990s): The Archaea are not restricted to extreme
environments, AND bacteria have also adapted to extreme environments. Before this discovery, it was
thought that the EXTREMEOPHILES were the Archaea, and the microbes in less hostile environments
(heat, acid, salt, etc..) were bacteria. Now we know that both Bacteria and Archaea can exist in both
extreme environments and in common environments like water and soil. While some bacteria are
photosynthetic (cyanobacteria), some are chemosynthetic. Most are heterotrophic. The same can be
said of the Archaea, though the photosynthetic Archaea tranform light energy in a fundamentally
different manner than the photosynthesis you learned. As for the chemoautotrophs, both bacteria and
archaea have been found exploiting just about any substance that has energy within its chemical bonds,
including, for example, iron. Think about it… iron "eating" microbes. That's what's gobbling up the
Titanic right now. At the current rate of decay, when you are my age, there will be nothing left of the
Titanic but iron ore (and that stash of diamonds).
Terms of interest/trivia:
Extremophile - Any organism that lives in an environment that is considered to be hostile to us and the
microbes in contact with us.
Thermophile - Heat lover. We've found microbes living at 121 degrees C.
Acidophile - Acid lover. Microbes living in acid environments with pH <1.
Halophile - Salt lover. High salt concentration is lethal to most bacteria.

NASA has supported research into extremophiles because the conditions on other planets are
within the range of environments known to exist on other planets (in our solar system) and
some of their moons.
It is a great time to be a microbiologist. Medical, environmental, industrial, evolutionary. This century
will be for biology what the 20th century was for physics. There is so much to learn, and only now do
we have the tools we need.
* There are no known human pathogens among the Archaea.