Science Daily — Thirty years ago this month, researchers at the University of Illinois published a discovery that challenged basic assumptions about the broadest classifications of life. Their discovery – which was based on an analysis of ribosomal RNA, an ancient molecule essential to the replication of all cells – opened up a new field of study, and established a first draft of the evolutionary “tree of life.”

Microbiologist Carl Woese led the team that identified the archaea as a unique domain of life, distinct from bacteria and other organisms. Prior to this finding, generations of evolutionary biologists and microbiologists believed that the microbes now called archaea were simply another taxon among bacteria. (Credit: Photo by Don Hamerman)

To mark the anniversary of this discovery, the university is holding a symposium Nov. 3-4  with a public lecture at the Spurlock Museum on the evening of Nov. 2. “Hidden Before Our Eyes: 30 Years of Molecular Phylogeny, Archaea and Evolution” will detail the exacting work that led to the discovery of a “third domain” of life, the microbes now known as the archaea. The event will revisit the program of research that led to the discovery, explore its impact on the study of evolution, and describe the way in which genetic analysis continues to revolutionize biology, in particular microbial ecology.

In 1977, microbiology professor Carl Woese led the team that identified the archaea as a unique domain of life, distinct from bacteria and other organisms. Prior to this finding, generations of evolutionary biologists and microbiologists believed that the microbes now called archaea were simply another taxon among bacteria. They had divided all living organisms into two broad superkingdoms, or domains: the “prokaryotes,” which included both the true bacteria and archaea; and “eukaryotes,” including all animals, plants, fungi and protists (a diverse group that includes protozoans, algae, slime molds and other organisms). Some prominent biologists still hold to this classification scheme.

Woese had set out to map the evolutionary history of life by comparing RNA sequences of a molecular sequence common to all living cells: the ribosome, which manufactures a cell’s proteins.

Each group of organisms contains sets of genetic sequences in their ribosomal RNA that are distinctive. These genetic “signatures” differentiate the groups. Woese’s analysis of a variety of organisms’ genetic signatures told a story that was different from the conventional wisdom, however.

This surprising discovery came when the researchers looked at the ribosomal RNA (rRNA) of a group of methane-generating microbes that had been classified as bacteria. Illinois microbiology professor Ralph Wolfe, an expert on these “methanogens,” was a member of Woese’s team, along with postdoctoral researcher George Fox, graduate student William Balch and lab technician Linda Magrum.

“Of all the numerous suggestions we had gotten for organisms to study, the one I solicited from my colleague, Ralph Wolfe, turned out to be the most important,” Woese wrote in an account of the discovery. “Ralph was in the process of working out the biochemistry of methanogenesis, which made it natural for him to suggest we characterize the methanogens.”

Wolfe was one of only a handful of researchers studying methanogens in the mid-1970s. These organisms were notoriously difficult to grow in culture because they could survive only in an oxygen-free atmosphere that was rich in hydrogen and carbon dioxide. Balch, a graduate student in Wolfe’s lab, had found a way to create a sealed and pressurized atmosphere inside a test tube that would support these organisms, however. Using this technique, a methanogen now called M. bryantii, was grown in sufficient quantities for study.

Woese had already found a collection of rRNA sequences that were specific to bacteria, and another set of sequences unique to plants, animals and other eukarya. When he sequenced the ribosomal RNA of Wolfe’s methanogen, however, he found that it was strikingly different from that of eukarya and bacteria. Although it shared some universal sequences with the other organisms, it also carried its own unique set of sequences that did not fit with either group. It was “neither fish nor fowl,” Woese said.

The scientists were astonished, and quickly turned their attention to other methanogens. The genetic pattern held: The rRNA signatures of the methanogens were distinct from those of eukaryotes and bacteria. Woese concluded that the methanogens were not bacteria.

Wolfe recalled, “When Carl said they weren’t bacteria, I said: ‘Of course they are bacteria! They look like bacteria! They have this prokaryotic morphology and cell structure.’ ”

But when Wolfe saw how the sequence data fell into discrete groups, with all the methanogens in a category of their own, “I became a believer,” he said.

Their findings were published in the Proceedings of the National Academy of Sciences in October 1977.  The paper’s three-sentence abstract stated simply that “the methanogens constitute a distinct phylogenetic group… only distantly related to bacteria.”

A second PNAS paper, published the following month by Woese and Fox, outlined the evidence that there were three – rather than two – superkingdoms, or domains, of life.

“There was general amazement and feeling that something great had been discovered among the physical scientists,” Woese said.

Many microbiologists and other life scientists were unwilling to accept the new classification scheme, however. They continued to see the archaea as a highly differentiated offshoot of the bacterial line.

In 2003, Woese won the $500,000 Crafoord Prize in Biosciences for his discovery of this “third domain of life.” The prize, given by the Royal Swedish Academy of Sciences, marks accomplishments in scientific fields not covered by the Nobel Prizes in sciences, which the academy also selects.

Controversy over the work continued, however. Some scientists described the 1977 announcement of a third domain as an achievement comparable to that of the discovery of a new continent. Others discounted the idea as a “fantastic” hypothesis based on a limited and unreliable pool of data. To this day, many textbooks, dictionaries and other science reference materials include the “classical” and the Woese classification schemes.

Now 79, Woese continues his work as a member of the “Biocomplexity” theme at the Institute for Genomic Biology. He works with collaborators in physics, chemistry, geology and microbiology in a continuing exploration of the genomic complexity of biological systems. He worries about what he sees as a general lack of interest in evolution among microbiologists and other life scientists. And he hopes that a new generation of scientists will make full use of the genomic tools that he believes could revolutionize the study of the origins and evolution of life.

Wolfe, 86, an emeritus professor of microbiology, continues his interest in the physiology and biochemistry of the methanoarchaea.

Note: This story has been adapted from material provided by University of Illinois at Urbana-Champaign.

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