Single cell genomics identifies frozen bacteria


Incoming postdoctoral researcher Stephanie A. Carr and Dr. Beth Orcutt used single cell genomics to identify an Atribacteria (uncultivated bacteria that live without oxygen) cell from frozen Antarctic deep subsurface sediment. Reported in Frontiers in Microbiology, this demonstrates the huge potential for single cell techniques to be used to help unlock a massive amount of genomic information stored in previously collected frozen sediment cores.

The sampled sediment was collected from the Adélie Basin, Antarctica, from 97.4 meters below sea floor during Expedition 318 of the Integrated Ocean Drilling Program. Originally, the sediment sample was frozen for DNA analyses, which is less than ideal for single cell sorting techniques.

Given the amount of existing frozen sediments that have been collected for biological studies throughout the history of ocean drilling programs, the successful isolation of an Atribacteria cell from frozen sediment demonstrates how single cell techniques can potentially unlock genomic information from a huge reservoir of already collected, frozen sediments.

This finding was also the first report of a single cell Atribacteria genome from marine sediment and highlights the potential role of Atribacteria in carbon cycling in the deep biosphere. In non-marine Atribacteria, a partial single cell genome suggests that Atribacteria use carbon to grow and produce waste products such as acetate, ethanol, and carbon dioxide. These products may support methane-producing bacteria and help explain the frequent occurrence of Atribacteria in anoxic methane-rich sediments.

Kevin W. Mandernack of Indiana University and Purdue University Indianapolis and John R. Spears of Colorado School of Mines were also co-authors of the report. Funding for this work was provided by C-DEBI (Center for Dark Energy Biosphere Investigations), which is funded by the National Science Foundation.

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