The Third Domain: The Untold Story of Archaea and the Future of Biotechnology by Tim Friend. Joseph Henry Press, $27.95, 296 pages.

The News & Observer

July 22, 2007

Little big microbe


By PHILLIP MANNING

Until recently, the tree of life had two main branches, and all organisms grew from one or the other. The branches are called domains — the most fundamental grouping in biology, more basic than the familiar kingdoms of plant, animal, fungi, bacteria and protista. In one domain were all organisms with cells that did not have a nucleus. The other domain contained organisms whose cells did have a nucleus. Bacteria were the sole members of the no-nucleus domain; all other organisms — from humans to dandelions — were in the nucleated-cell domain. This division of life was straightforward and almost universally accepted. But, according to one man, it was wrong.
The story starts with cow manure or, more accurately, with a microbe in cow manure that produces methane (or natural gas). Like bacteria, those microbes were single-celled organisms without nuclei, but they contained DNA sequences never seen in bacteria. Carl Woese, a molecular biologist at the University of Illinois, was studying bacteria when he became interested in the strange methane-producing microbes.
Historically, relationships between species were based primarily on appearance. You and I look more like chimpanzees than we look like worms. Therefore, humans and chimps must be more closely related than either species is to a worm. Woese was trying to establish the relationships between species of bacteria. But bacteria are single-celled organisms, many of which look pretty much alike. So, he took a different approach. Rather than rely on appearance, Woese did detailed genetic analyses of bacteria species to establish which were close kin. He had been studying bacterial DNA for years, and he knew there was something quite different about the microbe found in cow patties.
He searched for other oddball microbes, especially those from harsh environments. These microbes are called extremophiles — organisms that thrive in very hot or cold or extremely salty or yucky environments. The ability of microbes to survive almost anywhere led one scientist to offer an explanation for their ubiquity: “Everything is everywhere. Nature selects.”
Woese analyzed the DNA of several extremophiles. “They didn’t look like anything [bacteria] we had ever seen,” Woese told author Tim Friend. He became convinced that these microbes were not bacteria but members of a new domain of life. He called them archaea.
Woese published his data and conclusions in 1977. The popular press picked up on it immediately, with headlines such as “Scientists study third form of life.” But most scientists either ignored the paper or derided it. Woese “was called a crank and a crackpot, out of his league ....” writes Friend. But he persevered with his research. And by the 1990s, further studies led one prominent scientist to conclude that “two-thirds of the [archaean] genes do not look like anything we’ve ever seen in biology before.” Then, in 1996, the editors of the prestigious journal Science organized a press conference and announced that the archaea represented a new domain of life. In a 2003 speech, Woese, older and somewhat bitter about his treatment by his colleagues, began his talk with “The Archaea were unexpected to begin with, and having arrived, they were unwelcome.”
In “The Third Domain,” Friend tells Woese’s story well and with empathy. But it takes up less than half the book. And what’s left does not add much to the story of the archaea. Instead, the author recounts his trips with scientists to Germany, Costa Rica, Yellowstone, and the wreck of the Titanic.
Each of these episodes is interesting and relates in some way to the microbial world, but no unifying theme holds them together. Furthermore, by making himself central to the action, Friend too often involves the reader in the details of his own life. This can lead to tedious housekeeping passages, such as “I arrived at the Hotel Bougainvillea in San Jose in the late afternoon and finished reading the background materials while waiting for the Diversa team to arrive. At 10:30 p.m. the phone in my room rang.”
Despite these flaws, Friend takes the reader to some interesting places and describes some truly weird microbes. For example, while exploring the Titanic in a submersible, he introduces us to the “rusticle.” The name is a portmanteau, a combination of “rust” and “icicle.” And it fits perfectly. Rusticles are the reddish, finger-like protuberances that grow on the steel of sunken ships. Although rusticles appear to be ordinary rust, they are not. Only about a third of a rusticle is iron or iron oxides. The rest is an extraordinarily complex community of bacterial and archaean microbes feeding on iron and other elements present in steel.
The Titanic is loaded with rusticles. One investigator, the microbiologist Russ Cullimore, summed up what was happening to the Titanic in almost poetic language: ”As deep ocean microbes convert the Titanic’s mass to their own, it becomes possible to say that something is indeed coming to life on the Titanic.” Cullimore is right. Even though the great ship lies in dark, icy waters 12,600 feet below the surface of the sea, its steel is nourishing an incredible array of microbes. Life is, indeed, everywhere, and it feeds on whatever is handy.
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