EAST BOOTHBAY, ME – A consortium of scientists, led by Bigelow Laboratory’s Ramunas Stepanauskas, has received a major award of services from the U. S. Department of Energy (DOE) Joint Genome Institute to perform single cell whole genome sequencing of over 300 deep subsurface microbes that have lived in isolation for millions of years.

The project, titled “Enigmatic life underneath us: genomic analysis of deep subsurface microorganisms,” is a multi-year collaboration between scientists at Bigelow Laboratory, Princeton University, New Mexico Institute of Mining and Technology, Desert Research Institute, Technical Research Center of Finland, University of Delaware, and Western Washington University.

“Although still in its infancy, research on deep subsurface microorganisms suggests that they constitute a major fraction of the living biomass on our planet and play significant roles in the global cycles of carbon and other elements,” Stepanauskas said. “Our project takes advantage of the cutting-edge research tools at previously unimaginable scales to decode the mysteries of this vast, yet virtually unexplored environment right underneath us, potentially challenging many of our perceptions about life on Earth.”

Researchers in South Africa collecting rock samples for DNA analysis of microbes living deep below ground. Photo Credit: TC Onstott

Bigelow Laboratory’s Single Cell Genomics Center employed its novel technology to extract and amplify DNA from individual, uncultured microbial cells that appear to thrive in miles-deep subsurface environments, which until recently were though to be devoid of life. Field study sites include the world’sdeepest gold mines in South Africa; deep marine sediment and oceanic crust samples, and boreholes in Finland and Nevada. Initial characterization of microbes from this disparate mix of geographic locations suggests shared evolutionary histories over geological time scales.

“Subsurface microorganisms inhabit stable, energy-poor environments,” said Dr. TC Onstott, professor of geosciences at Princeton University and a key collaborator on this project. “These habitats constitute a kind of ‘microbial Galapagos,’ providing natural, long-term genetic records that can give us important perspectives on evolution, as well as unique information about the ecology and biogeochemical impact of deep surface microbial communities.”

The DOE sequencing project builds upon an earlier, multi-institutional grant from the Alfred P. Sloan Foundation to study “deep life,” which included funding for field sample collection and single cell DNA preparation and identification.

“We’re delighted to hear about the DOE award,” said Dr. Robert Hazen, director of the Sloan Foundation’s Deep Carbon Observatory. “This large-scale genomics effort will help us to achieve a transformational understanding of Earth’s deep carbon, an area where the Observatory’s interests intersect and benefit the mission of the DOE.”

The project will investigate the biochemical and evolutionary mechanisms by which microorganisms on the planet’s surface adapted to deep subsurface environments. This knowledge will help scientists to develop new avenues of carbon sequestration and alternative energy production for human benefit.

Bigelow Laboratory for Ocean Sciences is an internationally known, independent, non-profit center for global ocean research, ocean science education, and technology transfer. A recognized leader in Maine's emerging innovation economy, the Laboratory’s research ranges from microbial oceanography to the large-scale biogeochemical processes that drive ocean ecosystems and global environmental conditions.