Maine laboratory study: Strange microbe from deep in the Earth hasn't evolved in millions of years

An exotic microbe, Candidatus Desulforudis audaxviator (CDA), found very deep in the Earth on three continents has developed almost identically in each location, with minimal evolution over millions of years. 

CDA was first discovered about 2 miles down in South African gold mines in 2008. More recently it was found in deep boreholes in Death Valley, California, and western Siberia.

The evolutionary standstill and the independent but identical development of the microbes are intriguing. Other microbes evolve rapidly in response to their environment, and it's assumed that the same organism will adapt differently to different physical conditions. 

A study by a research group at Bigelow Laboratory for Ocean Sciences in Maine analyzed isolated CDA samples and found more than 99.2% agreement in the genomes of the 126 microbes they examined. Their research appears in the microbial ecology journal ISME on April 6.

Ramunas Stepanauskas, senior research scientist at Bigelow Laboratory and a co-author of the work, told Current Science Daily that the CDA findings surprised the research team, adding. "The apparent halt of evolution in Desulforudis is highly unexpected."

"Many well-characterized microbes evolve very fast, he said. "It takes only a few years for human pathogens to evolve resistance against a new antibiotic. With the ongoing COVID-19 pandemic, we all know how quickly viruses can evolve into new variants."

Evolutionary standstill, or stasis, is not the usual evolutionary route of organisms. 

"Of the two key drivers of evolution--genetic variation and natural selection--the deep subsurface bacterium Desulforudis audaxviator appears to have ceased the former and escaped the latter," Stepanauskas said.

He characterized the CDA as "living fossils," potentially going back 175 million years, to the time of the breakup of the supercontinent Pangea.

What might contribute to the halt of CDA evolution? 

"Our working hypothesis is that these microorganisms have unusually accurate DNA replication and/or repair mechanisms," Stepanauskas said.

In a news release on the research paper, Stepanauskas said about potential uses that might be made of CDA's properties, “There's a high demand for DNA polymerases that don't make many mistakes. Such enzymes may be useful for DNA sequencing, diagnostic tests and gene therapy.”

A strange bacterium

Stepanauskas characterized CDA as really strange. 

"Desulforudis live so deep that no organic matter or other nutrients ever reach them from the surface," he said. "They live off of chemical reactions, for which the ultimate source of energy is very slow nuclear fission in rocks. These microbes are completely independent of the energy of the sun and the rest of the global biota. One can imagine similar environments deep underground on Mars and other planets."

The fact the DNA of the CDA from different continents had not evolved differently was unexpected, Stepanauskas said.

"To our great surprise, their DNA was essentially identical on all three continents," he said. "This got us scratching our heads. All the data at our disposal tell us that these microbes are found only in deep, continental subsurface. They are never detected in the ocean or soils. In fact oxygen is toxic to them.

"There is no obvious way for them to travel and intermix around the globe. As crazy as it sounds, the best explanation we have is that these microbes originate from the same source and have remained virtually unchanged since they became separated by plate tectonics a very long time ago."

Broader implications

"Deep subsurface microorganisms," the paper reports, "are estimated to constitute about 10% of our planet's total biomass and are found to contain a large fraction of yet uncharacterized biological diversity, the so-called 'microbial dark matter.'"  

The researchers conclude, "It may be expected that CDA is not the only living microbial fossil in this vast environment, potentially offering unique sources of information about the history of life."

As for the future, Stepanauskas told Current Science Daily, "We hope to secure funds for further research of deep subsurface, which harbors some of the most unusual and least understood microbiomes on the planet."

Stepanauskas called the study "a highly collaborative endeavor'' and praised the contributions of co-authors Eric Becraft, a former researcher at Northern Illinois University, Tullis Onstott, Esta van Heerden and Kotryna Kauneckaite-Griguole.