MSU team discovers organism in Yellowstone hot spring potentially linked to earliest life on Earth

An organism that lives in a smelly cauldron in Yellowstone National Park has yielded new information about how its ancient relatives might have survived without oxygen.

Montana State University scientists said in their recent paper in the journal Nature Microbiology that the unusual microorganism has the genes necessary for two types of metabolism. One produces methane while the other uses different forms of sulfur to produce sulfide. Neither involves oxygen.

"That's a big deal. This is the first microbial population to be described that has both of these abilities. We show that methane oxidation may be coupled with the reduction of sulfite, which represents a previously unreported metabolism for life," said lead author Luke McKay, an assistant research professor in the Department of Land Resources and Environmental Sciences in the College of Agriculture and MSU's Center for Biofilm Engineering.

Principal investigator Bill Inskeep, a professor in MSU's Thermal Biology Institute and Department of Land Resources and Environmental Sciences, said the results have implications for the evolution of those traits through the Archaea, one of the three domains of life, along with Eukarya and Bacteria. Archaea describes single-celled organisms that lack a nucleus and which often have complex metabolisms. They have been found living in some of the most extreme environments on Earth.

The newly described organism, called Methanodesulfokores washburnensis, is believed to be a modern relative of an obscure group of microorganisms that lived around the time life began on Earth. That group, known as the Korarchaeota, might have been a very early branch in the tree of life. It is a subgroup of Archaea, one of the three domains of life. The other domains are Bacteria and Eukarya, the latter of which includes humans and animals.

Inskeep and former doctoral student Zackary Jay, another coauthor on the paper, extracted DNA from the sediments of Washburn Hot Springs in 2012. The specific pool lies near the base of Mount Washburn and measures about 25-by-100 feet across. It averages 149 to 158 degrees Fahrenheit and contains high concentrations of methane, hydrogen, carbon dioxide, sulfide and sulfate.

"It's an ominous looking pool,” Inskeep said. “I wouldn't want to fall in."
On the other hand, McKay said, "This is an important environment with relevance to early life."

The Washburn Hot Springs, named after early Yellowstone explorer Henry D. Washburn, contain an interesting mixture of chemical ingredients that make the site extreme, Inskeep said. That, in fact, may explain why scientists didn't discover the Methanodesulfokores earlier somewhere else in the world.

"Washburn is extremely unique on the planet," McKay said. "The geochemistry of the spring makes it like a window into ancient environments on Earth. That's exciting because it provides a glimpse of the conditions that early microorganisms may have experienced after the origin of life, 4 billion years ago."

McKay came to MSU in 2015 with a particular interest in research that might relate to the origin of life. He acquired a postdoctoral fellowship through the NASA Astrobiology Institute. Besides studying the extremophiles of Yellowstone, he has studied microorganisms that live in extreme environments all over the world, including Antarctica and the hydrothermally active Guaymas Basin in the Gulf of California. More recently, McKay was one of nine scientists featured in the science documentary, "The Most Unknown,” which is available on Netflix.

He said he is especially interested in carbon and energy sources in microorganisms that might be important in early life.

To come to the conclusions that led to the Nature Microbiology paper and a related paper in the same issue, McKay worked with scientists from MSU, the University of Chicago, Indiana University and the Marine Biological Laboratory in Woods Hole, Massachusetts. His MSU collaborators, in addition to Inskeep and Jay, were Mensur Dlakić, an associate professor in the Department of Microbiology and Immunology; Matthew Fields, director of the Center for Biofilm Engineering and a professor in the Thermal Biology Institute and the Department of Microbiology and Immunology; and Korinne Klingelsmith, an undergraduate student majoring in biochemistry and microbiology.

Dlakić used the largest super computer in Montana — the research computing cluster at MSU called Hyalite — to analyze the newly described microorganism and find its position in the tree of life, Inskeep said.

"That kind of analysis helped us say that the genes for methane metabolism in this newly described organism might have been important in early members of the Archaea," McKay said.

Besides publishing their paper in Nature Microbiology, Inskeep and McKay are coauthors of a second manuscript in the same journal. That paper was written by Guillaume Borrel and Simonetta Gribaldo from the Pasteur Institute in France. In it, the scientists elaborate on the diversity and distribution of methane metabolism in the Archaea. They also introduce several new lineages that contain genes for methane metabolism. Some of the microbial sequence data used in that study is from the same sample taken from Washburn Hot Springs and was sequenced by the Department of Energy-Joint Genome Institute in Walnut Creek, California.  

"Collectively, these findings have big implications for the evolution of methane and sulfur metabolisms and their potential importance in early life," McKay said.