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Biological Sciences Division
Research Highlights

November 2012

New Bacteria Divisions Discovered

Potential roles in carbon cycling, bioremediation reported in Science

Brand New Genes Enlarge Image
PNNL staff contributed to research published in Science that expands what is known about bioremediating bacteria and could lead to improved methods to stimulate bacteria to uptake atmospheric carbon and to better apply microbes to remediate metal-contaminated environments.

Results: Proteomics experts at Pacific Northwest National Laboratory contributed to a study published in Science magazine centered on discovery of new bacteria and the metabolic roles, such as carbon cycling, of bacteria in the environment. The research contributes new insights into the physiology and diversity across several major branches of the tree of life.

A team from the University of California-Berkeley, Lawrence Berkeley National Laboratory, PNNL, and Oak Ridge National Laboratory sequenced nearly 150,000 genes from three microbial communities in samples from a subsurface aquifer at a uranium mill tailings site in Rifle, Colorado. Their purpose was to reconstruct genomes of organisms that may contribute to biogeochemical cycling in oxygen-free subsurface environments.

The researchers were able to assign these genes to, or reconstruct the genomes in part or in whole for, 87 different bacterial species. Impressively, 49 of the 87 genomes belong to species that had never before been genomically characterized. Some of these genomes were even found to merit a new phylogenetic classification—a whole new branch of bacteria in the family tree of life—named PER or Peregrine.

Why It Matters: All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of sedimentary carbon compounds. Until this study, only a few genes for these bacteria had been identified. Now, thanks to this work, there are tens of complete or nearly complete genomes. Using proteomics, the scientists were able to confirm the activity of these bacteria in complex subsurface environmental samples.

Methods: The scientists collected groundwater samples from an acetate-amended aquifer at the site. Acetate, similar to diluted vinegar, had been added to the aquifer to stimulate metal-reducing bacteria that can remove uranium from groundwater.

PNNL scientists Dr. Mary Lipton and Dr. Michael Wilkins carried out the proteomic analyses of the samples, using capabilities at EMSL, a national user facility located at PNNL. The studies provided valuable data about the metabolic activity of the bacteria in their native complex subsurface environment, showing that they may play roles in carbon cycling, sulfur cycling, and hydrogen production.

What's Next? The team's groundbreaking results could lead to improved methods to stimulate bacteria to uptake atmospheric carbon, thus reducing greenhouse gases, and to better apply microbes to remediate toxic metal-contaminated environments. 

Acknowledgments:

Sponsors: The work was funded by the U.S. Department of Energy Office of Biological and Environmental Research's Subsurface Biogeochemical Research Program.

User Facility: EMSL

Research Team: Michael Wilkins and Mary Lipton, PNNL; Kelly Wrighton, Jillian Banfield, Itai Sharon, Brian Thomas, and Chris Miller, UC Berkeley; Cindy Castelle, Ken Williams, and Phil Long, LBNL; and Nathan VerBerkmoes and Robert Hettich, ORNL.

Reference: Wrighton KC, BC Thomas, I Sharon, CS Miller, C Castelle, NC VerBerkmoes, MJ Wilkins, RL Hettich, MS Lipton, KH Williams, PE Long, and JF Banfield. 2012. "Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla." Science 337(6102):1661-1665. DOI:10.1126/science.1224041.

Also see the UC Berkeley news release.


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