Extinct microbes sought from the Lost World

Gogarten dino

     The scientists in Sir Arthur Conan Doyle’s 1912 novel, The Lost World nearly lost their lives discovering long-extinct animals on a remote South American plateau. A similar adventure being undertaken by Prof. Peter Gogarten should not be so dangerous, but is nonetheless just as exciting. Gogarten was recently awarded a $337,287 NASA grant to find extinct families of microorganisms that contributed genes to the ancestors of living microbes. His findings could lead to the discovery of living descendants of those donor microbes, echoing the discovery in Doyle’s story.

     Instead of slashing through jungles, Gogarten will compare the sequences of genes of modern microbes to find evidence of lost microbial lineages. He will use these sequence comparisons to construct evolutionary trees, diagrams like family trees of all living things. These trees can look like a Tree of Life depicting new species arising in lineages to form new branches, but trees can be deceiving. "We look at that tree and we think that this is the Tree of Life,” Gogarten said. “But it is only the organisms that have the lucky ancestors that have living descendants … most lineages went extinct."

Original illustration from The Lost World

     Those extinct organisms may still have contributed to successful lineages by transferring some genes to them by a process called horizontal gene transfer. Organisms normally transmit their traits to descendants vertically through their offspring, but bacteria and archaea also transmit genes to other species, sometimes to species distantly related to the gene donor. Gogarten plans to find the sources of horizontally transferred genes that appear to have come from extinct lineages.

     To do so, he and his team will compare gene trees to a tree thought to be most like the “true” Tree of Life. The gene trees will be made by comparing sequences of the same gene found in many microbes. If the test gene was passed on only by vertical transmission, then its tree would have identical branching patterns to the Tree of Life. If it has a branch unlike that of the Tree of Life, then horizontal transfer of that gene to the organisms on that branch would be indicated.

     If he finds several horizontally inherited genes seem to have come from a branching point on the “true” tree, he will have found evidence of an extinct lineage as the source of those genes. The functions of those genes will give clues to the nature of that extinct gene donor. “The hope is we can learn what these organisms were doing because of what kind of enzymes they were using,” Gogarten explained.

     Once he discovers genes that were inherited from extinct lineages, he can hunt for living descendants of supposedly extinct lineages. Scientists have been collecting DNA from waters and soils around the world for many years to sequence the genes in microbes living there and putting those sequences in databases. If Gogarten finds his genes in those databases, then he may have discovered a place where these “extinct” organisms still live.

     Gogarten’s work takes us to the edge of our knowledge of the microbial world. Like the bacteriologist Tarp Henry, from Doyle’s novel who remarked, "I'm a bacteriologist, … I'm a frontiersman from the extreme edge of the Knowable…," Gogarten, too, is a molecular frontiersman in his searches through lost microbial worlds.