Minimalist Life

The newly discovered Nanoarchaeum equitans (tiny cells) attached to its host Ignicoccus spec. (big cells). Fluorescence light micrograph taken after DNA-specific staining. Bar 5 microns.
Credit: H. Huber, M. Hohn, R. Rachel & K.O. Stetter, Univ. Regensburg, Germany

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.

Co-culture of Ignicoccus spec. (green) and Nanoarchaeum equitans (red). ss rRNA sequence-specific fluorescence staining. Confocal laser micrograph. Bar 1 micron.
Credit: H. Huber, M. Hohn, R. Rachel & K.O. Stetter, Univ. Regensburg, Germany

"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)."

Cell of Ignicoccus spec. (big) with cells of Nanoarchaeum equitans (tiny) attached to its surface. Electron micrograph. Pt-contrasting. Bar 1 micron.
Credit: H. Huber, M. Hohn, R. Rachel & K.O. Stetter, Univ. Regensburg, Germany

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 Nanoarchaeum 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."

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