Minimalist Life: Clues to Early Earth Life

By Stephen Hart

The life surrounding hydrothermal vents came as a surprise when two
scientists got the first close-up look at a vent community in 1977.
And it wasn’t long before biologists began wondering whether such
environments might closely resemble the hotbed of earth’s earliest
life.

The idea that some microbes could love temperatures that killed
others fired the imagination of Karl Stetter, a microbiologist at the
University of Regensburg in Germany. “I did a lot of bug hunting
during the last 22 or 23 years since I became interested in hot stuff
among the microbes,” he says.

Stetter’s latest hot-vent discovery came from the Kolbiensey Ridge,
just north of Iceland–the ironic land of ice and volcanoes–which he
calls “one of my major hunting grounds.” Stetter collected samples
of hot rocks about 120 meters deep, using the Jago research
submarine.

The two-part find began with a new species of the archaean
Igniococcus (fire ball), which Stetter and crew grew in the
laboratory. But a close look at the Igniococcus cells revealed
something completely new: tiny, spherical cells stuck to the surface
of many Igniococcus cells. These spheres measured merely 400
nanometers, around a quarter of the diameter of Igniococcus.
Electron microscopy revealed internal features of the small spheres,
indicating that they were indeed cells. Stetter and colleagues from
the University of Regensburg and the Max Planck Institute, in
Heidelberg, published the findings in May 2002 in the journal Nature.

“We are able to separate them now, the tiny guys, from the big ones,
and we are studying their biochemical properties and their enzyme
activities and of course their genes and also their habits of life,”
Stetter says.

One of the first steps in studying the new organism was attempting to
grow it separately from Igniococcus. That failed. While some of the
small cells appear to float free in a mixture of the two organisms,
Stetter’s “tiny guys” would not grow without their bigger hosts. The
hosts, however, got along fine without their riders.

Next, Stetter wanted to know where these cells fit on the tree of
life. The team turned to the gold standard of molecular taxonomy,
the ribosomal RNA (rRNA) genes. But so-called universal probes,
capable of detecting rRNA genes of all previously known organisms,
didn’t detect DNA from the new organism. “So these so-called
universal probes, which work the same with humans, with animals, with
plants, with all eukaryotes and with bacteria and archaea, they did
not work in this organism,” Stetter says.

Turning to another method of detecting DNA, the researchers found two
rRNA genes, both archaeal in nature, in the mixture of the two
organisms, but only one when the host was grown alone. The rRNA
genes of the tiny organism didn’t resemble those of any known
organism. The authors conclude “Therefore, the tiny cocci represent
a new archaeal phylum. On the basis of its extremely small cell
size, we name it ‘Nanoarchaeota’ (the dwarf archaea) and the
corresponding species ‘Nanoarchaeum equitans’ (riding the fire
sphere).”

Microbiologists have previously established three phyla of archaea,
the Crenarchaeota, the Euryarchaeota and the Korarchaeota, known only
from environmental DNA samples. Finding a new species is one thing.
Claiming that it represents a new and distinct fourth phylum of
Archaea is quite another.

Carl Woese, the father of the rRNA tree of life, and certainly one of
the world’s foremost experts on archaea, does not see the claim as
too much of a reach. “They’re pretty good experimentalists, so if
they say that, I would accept it,” he says. But he’s anxious to see
the complete genome published. “They also have a genome sequence
which they haven’t published, unfortunately. It’s being done by a
company of which Stetter is a partner.”

The for-profit company, called Diversa, has completed the
Nanoarchaeum equitans genome, Stetter says. “They sequenced the DNA
and at present we are writing up a paper together. So it will
definitely be published and the results look very exciting.”

What’s next?

Since May, Stetter has found relatives of Nanoarchaeum in several
locations around the world. All of these belong in the newly created
phylum, Stetter says. But their rRNA differs from that of
Nanoarchaeum equitans enough to place them in different families,
hinting at a large, widespread group of previously overlooked
organisms.

“For example, nanoarcheotes are also in Yellowstone National Park,”
he says, “and we found them in Kamchatka, even, in eastern Siberia.
And I bet my last hat that they are also in many other places around
the world and nobody has ever detected them so far.”

Because the paper describing the genome remains in preparation,
Stetter won’t say exactly what the sequence reveals or what use
Diversa might make of it. “This is a very unusual organism and
therefore it looks promising,” he says. “On the other hand, it’s a
really tiny guy, and so one could learn more about the essentials
which are necessary for a living organism. I don’t know for what
kinds of things it could be used in the future, but such a tiny
organism, maybe even artificial life.”

Speaking of artificial life, Craig Venter and his colleague Hamilton
Smith have announced an initiative to build a genome from scratch.
Might Venter be interested in Nanoarchaeum? “I think so, yeah, he
could be very interested,” Stetter says, laughing. “This is the
smallest genome of a complete organism known so far.”

The genome, Stetter says, turns out to be slightly smaller than 0.5
megabases, about a tenth of the size of the E. coli genome, and even
smaller than the former small-genome record holder, the bacterium
Mycoplasma genitalium. Woese says “It’s as small as you can go as
far as I know, in terms of self-replicating organisms.” No
comparable archaean is known, he continues. “This is sort of
something that’s unique.”

Nanoarchaeum sits, Stetter says, very deep in the tree of life, an
indication that members of the phylum may resemble the earliest cells
and the earliest common ancestor of all life on earth. “We have
speculated a bit, you know, in the [May ’02] Nature paper. But it’s
not speculation any more. So it’s a really very deep branch and how
deep we will show in our [upcoming] paper,” he says.

But even the phylum Nanoarchaeota may not be the last word, Stetter
says.

“I think that this is just the tip of a really hot, completely
unknown iceberg, that there may be other lineages around which are
similarly deeply branching.”

Additional information on this article is available at
http://www.astrobio.net/news/article332.html.