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Mathematics and Computer Science Division

Metagenome Analysis of DOE Hanford Site

Enabling improved reconstruction of metabolic/physiological processes

A metagenome of the living microbial community present in low biomass subsurface sediments beneath a leaking high-level radioactive waste tank at the DOE Hanford Site was analyzed using advanced bioinformatics methods. Besides very high levels of radiation this microbial community was also subjected to high temperatures and desiccation, extremely high concentrations of chromium and nitrate, and alkaline conditions. The great majority of microbes in most natural environments will be represented in metagenome sequence by a limited number of genes which do not assemble, due to substantial community diversity and limited sequencing depth. Therefore, a critical need is more accurate and informative binning of genes into taxonomic groups, to enable improved reconstruction of the metabolic and physiological processes operating in the community. We have developed a new approach for binning metagenome sequences, and applied it to a low-biomass microbial community exposed for several decades to multiple extreme conditions. We have discovered that many of the proteins found in this metagenome show homology to those found in extremophilic microbes, indicating that the community has undergone systems-level changes.