Subsurface Sediment Yields Novel Organism - DOE Joint Genome Institute

Metagenomic analysis emphasizes the “extraordinary microbial novelty” of poorly-explored subsurface ecosystems

The Science

Through metagenomics, researchers reconstructed a dominant organism and member of a new phylum-level lineage from an aquifer sediment in Colorado.

The Impact

Analysis of the complete microbial genome led to a detailed metabolic model with evidence for multiple new enzymes and pathways. The findings serve to emphasize the unexplored diversity of subsurface microbes, considered by the researchers to be the “dark matter of the carbon and other biogeochemical cycles.”

Summary

The 1,450-mile long Colorado River flows from the southwestern United States to northwestern Mexico.

Despite the efforts made to learn more about the microbial diversity in, on and around the planet in the past decade, the microbes located below the Earth’s surface remain difficult to characterize, in part due to their locations. However, these microbes are known to play significant roles in biogeochemical cycles. To help fill in the gaps of knowledge about these microbes, a team of researchers led by DOE JGI collaborator Jillian Banfield of UC Berkeley and Lawrence Berkeley National Laboratory sequenced samples from a contaminated aquifer at the Rifle Integrated Field Research Challenge site adjacent to the Colorado River in western Colorado. The two microbial communities found in the samples were studied as part of a 2012 DOE JGI Community Sequencing Program project.

As reported in the study published August 27, 2013 in Nature Communications, analyses of the datasets indicated that the subsurface microbial communities consisted of many bacteria and archaea from classes and orders that had not been previously recognized or sampled. Additionally, the researchers were able to completely reconstruct the genome of a dominant organism called RBG-1 in a microbial community, one previously unknown and which turned out to be a member of a new phylum lineage.

“We document extraordinary microbial novelty and the importance of previously unknown lineages in sediment biogeochemical transformations,” the researchers reported. “Many bacteria and archaea in these communities are novel at the phylum level or belong to phyla lacking a sequenced representative.”

Contact

Jillian Banfield
UC Berkeley/LBNL
jbanfield@berkeley.edu

Funding

DOE Office of Science, Office of Biological and Environmental Research
Integrated Field Research Challenge
Subsurface Biogeochemical Research Program

Publications

Castelle CJ et al. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013 Aug 27. doi: doi:10.1038/ncomms3120.