Shedding Light on the Dark: Single-Cell Genomics of Uncultivated Epsilonproteobacteria Inhabiting the Sub-Seafloor at Deep-Sea Hydrothermal Vents

Collaborators:
Ramunas Stepanauskas (Bigelow Laboratory for Ocean Sciences, ME)
Tanja Woyke (DOE Joint Genome Institute, CA)

The discovery of a subseafloor biosphere at deep-sea hydrothermal vents has far-reaching implications, ranging from speculations on the origins of life to the biogeochemistry of the oceans. Studies based on 16S rRNA have revealed a vast diversity of microorganisms potentially living in this habitat, with Epsilonproteobacteria being frequently identified as the dominant community members. However, a large fraction of the Epsilonproteobacteria identified at vents belongs to groups that have no cultured representative. In these cases only the 16S rRNA sequences are known, and thus the physiology and ecological role of these organisms remain elusive. Here we propose to sequence the genomes of at least 11 single-cells of uncultivated deep-sea hydrothermal vent Epsilonprotobacteria. By obtaining information on the physiology and metabolic potential of these uncultivated, yet numerically dominating microbes, this project will provide critical information to better constrain the potential importance of the subseafloor biosphere as a contributory factor to the overall productivity and functioning of deep-sea hydrothermal vents, and generate a rich repository for discovering novel metabolisms and functions. It will also provide an excellent opportunity for comparative genomics by being able to compare the 11 genomes obtained as part of this study with each other as well as with Epsilonproteobacteria from other environments. It will further set the stage for more in-depth post-genomic studies addressing functional aspects, aid in bringing these novel organisms into cultivation for targeted laboratory experiments, and thus provide a strong basis for future research by investigators working in a variety of fields.

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The work leading up to obtaining the single cell amplified genomes has been funded through NSF and internal WHOI funds. Sequencing will be carried out through a grant awarded by JGI.