About This Project

Our goal is to adapt portable genome sequencing technology for high-pressure, underwater environments. Currently, deep-sea organisms are sequenced at near 1 atmosphere of pressure, a pressure many of them would never live in naturally. If successful, this technology will enable researchers to sequence deep-sea organisms in their natural environment and thereby gain valuable information about how organisms express their genes in response to their unique environments.

Ask the Scientists

What is the context of this research?

Scientists have been able to culture less than 1% of the bacteria species on Earth [1]. Many of the most interesting bacteria live at the bottom of the ocean in high-pressure environments with no oxygen and no light. We currently know nothing about these bacteria or how their genomes are expressed in the context of their environment, questions which can only be answered in situ using underwater biosensors. The first step is to understand the effects of pressure on nanopore sequencing technology: how does pressure create errors in mobile genome sequencing? We believe that developing underwater nanopore biosensors will open entirely new areas of research.

[1] Schloss and Handelsman. “Status of the microbial census.” Microbiol Mol Biol Rev (2004) vol. 68 (4): 686–91.

What is the significance of this project?

The aim of this project is to adapt portable genome sequencing technology for high-pressure deep-sea environments. If successful, it will dramatically expand our knowledge of deep-sea species, the functioning of deep-sea ecosystems, and ultimately the planet. Biosensors adapted for deep-sea use would allow researchers to study how deep-sea organisms express their genomes in their natural environment while reducing or eliminating the need for physical samples to be brought up from the deep. This modular, portable sensor technology can be integrated with existing exploration survey platforms (ROVs, UMS, terrestrial and marine NASA landers, etc.) and could be used to develop time-series data that would lead to the discovery of important new attributes of ocean environments.

What are the goals of the project?

The goals of this project are to perform proof-of-concept experiments showing how the nanopore flow cell can perform at varying pressure. First we will complete the construction of a pressure vesselwith a nanopore sensor. Our preliminary design has been approved by our collaborators at Scripps Institution of Oceanography, Oxford Nanopore Technologies, and Global Ocean Design. We will then sequence three types of DNA at varying pressure, including a metagenomic sample mixture, simulating the diversity of environmental DNA found in the ocean [2]. We have allowed time for iterative technology development in our workflow.

[2] Matthew A. Barnes, et al. “Environmental Conditions Influence eDNA Persistence in Aquatic Systems.” Environ. Sci. Technol. 2014 48 (3): 1819–1827.