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Friday, September 24, 2021

Shedding light on the unseen world

When American scientist Carl Woese passed away Dec. 30, 2012 at the age of 84, he left behind an outsized legacy built on the study of the world’s smallest living things. In the past several years, this field has provided dramatic new insights into the pervasive influence of microorganisms on human health, global climate and the evolution of all life on earth.

By pioneering analytical methods that have since become commonplace at biological research centers such as UC Davis, Woese and his colleagues at the University of Illinois discovered in 1977 a hitherto unrecognized third domain of life — known as the Archaea — distinct from what had been the conventional two-fold division of the living world into bacteria (prokaryotes) and everything else (eukaryotes). Not only did the discovery spark an upheaval in the scientific community, but Woese’s methods also established for the first time a tree of life that fully incorporated microbes, which occupy virtually every branch on the tree.

“He just brought a lot of order to a lot of chaos in dealing with microbes,” said John Ingraham, an emeritus professor in UC Davis’ microbiology department and who is currently writing a book on the relationships among organisms in which Woese figures prominently.

The chaos stemmed largely from the challenges microorganisms present to traditional classification schemes: Many are virtually indistinguishable when viewed through the microscope, and they have left little in the way of a fossil record of evolutionary descent. Woese’s key insight was to look deep into the molecular makeup of organisms for an identifying marker. He found it in a type of gene shared by all organisms, which codes for a component of the cell called ribosomal RNA (rRNA).

Woese compared the slight variations in the composition of rRNA gene sequences of dozens of microorganisms in order to determine their evolutionary relationships, known as phylogeny. In the course of this painstaking work, Woese found that not everything that looks like bacteria is bacteria. A special kind of microbe known to produce methane, for example, turned out to belong to an entirely new class of organisms, later named the Archaea, which then took their place on a newly established universal tree of life built entirely from genetic information.

“What’s most astounding about Carl’s discovery is that it was done in a time when sequencing was really laborious and time consuming, and so this was really a labor of love that Carl did to put these organisms on a tree and [go] out on a limb to say there’s a new domain of life,” said UC Davis microbiologist Scott Dawson, who worked with Woese last year on a study of cellular evolution. “It took a lot of courage to do that.”

At first, scientists by and large ignored or disputed Woese’s controversial results, which were first published in the November 1977 issue of the Proceedings of the National Academies of Sciences. But as Woese and his collaborators continued and refined their studies, the new methods eventually became fundamental to the study of the microbial world.

Advances in rRNA sequencing have allowed researchers to begin compiling vast libraries of genetic information on microbes sampled from environments as diverse as the human gut, sulfurous ocean vents and the inside of clouds. Jonathan Eisen, a UC Davis microbiologist who studies microbial ecology and evolution, said Woese easily deserved the Nobel Prize in Medicine or Physiology given the profound application of his work for classifying pathogenic microbes by analyzing their phylogeny.

“What he did is transform classification of microbes into a very rigorous, useful tool where you could say something about the organism and it meant something,” Eisen said. “That single-handedly led to revolutions in understanding causative agents of hundreds to thousands of diseases.”

And then there’s that third domain of life. Follow-up studies to Woese’s 1977 paper have shown that the Archaea, which are often found in extreme environments such as boiling hydrothermal pools, are more closely related to the eukaryotes — which includes the plant and animal lineages — than bacteria. Dawson said that these implications of archaeal biology are still being absorbed by the scientific community.

“[Woese] opened up a whole world of biology we didn’t know about,” Dawson said. “Still now, a lot of people don’t understand the distinction or the implications of it. When you have something that really pokes at the foundation of what we think we know, it can take a generation to get the ideas solidified.”
More information on Woese’s life and work can be found on Eisen’s blog,
phylogenomics.blogspot.com/2012/12/rip-carl-woese-collecting-posts-notes.html.

OYANG TENG can be reached at science@theaggie.org.

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