A Low-Power, Low-Cost Microbial Genetic Analyzer For Discovery and Monitoring of Ocean Microbes

Arizona State University, Scottsdale AZ

Investigators

Abstract

In this project, a team of engineers and biologists will work together to develop an Ocean Microbial Surveyor (OMS); a miniature, autonomous genetic analyzer that can quantitatively analyze DNA and RNA of the microbial biomass sampled from an aquatic environment such as the ocean. Current technologies are typically expensive, cumbersome, complex, and power-hungry, limiting the number of users as well as the number of systems that can be deployed for scientific measurements. The OMS developed in this project will leverage technology from the biomedical research field to enable new capabilities for ocean monitoring, to make these new technologies easily accessible to oceanographers, and to increase the number of systems that can be deployed for scientific discovery. The OMS will be inexpensive, low power, small and autonomous to enable large networks of OMS systems to be used and to provide new measurement capabilities. Marine microbes account for more than 90% of the ocean biomass, but they are among the most under-studied life forms because of their often-inaccessible habitats. It is important to be able to measure microbes in their natural environment over time and space (spatiotemporal) scales to understand the effects of climate change and other environmental factors on microbial abundance, distribution, function, and production. The long-term goal is to integrate the OMS into other ocean testing platforms and ultimately as a broad network of industry-refined, multi-target microbial analyzers dispersed throughout the globe, in the hands of diverse scientific investigators. The broader impacts of this project are to build science, technology, engineering, and mathematics (STEM) talent, innovate for the future, improve society, and engage a wide audience in the technology and science. STEM talent will be increased by providing excellent training opportunities for two postdoctoral fellows and numerous undergraduate students in a multidisciplinary research environment. The innovative technology developed in this project will inspire diverse generations of scientists and engineers to explore the oceans and enable access to new data from the genetic instruments that may lead to new discoveries. Monitoring marine microbial activities may help society understand critical issues such as how climate change and other environmental stresses impact the primary production from marine microbes. The new genetic sensors will be displayed and operated in the Biosphere 2 Ocean habitat, near Tucson, Arizona, to provide outreach to groups of school children and adults enabling them to observe science-driven technology development and ocean microbial monitoring experiments. The OMS to be developed in this project is based on the integration of loop-mediated isothermal DNA and RNA amplification (LAMP) with microfluidics to produce a small footprint, low energy consumption analytical module that can be used on various platforms such as buoys, autonomous underwater vehicles (AUVs), and robotic floats. LAMP is a fast, selective, sensitive isothermal reaction that requires only "one-pot" and produces large quantities of amplification product, enabling simple optical colorimetric detection. The completed OMS prototype, incorporating the LAMP capability, will be able to perform 50 assays per deployment with a user-specified sampling interval. Each assay will measure a user-designed pair of DNA and RNA targets in triplicate. A prototype OMS will be developed that integrates all hardware systems into a single microfluidic chip. The project plan includes development of the hardware subsystems including chassis design, power circuitry, pump and valve automation, illumination and imaging systems, and thermal control design. A microfluidic chip for microbial lysis and nucleic acids extraction (on-chip extraction) will be developed on the benchtop and then integrated into a single microfluidic device with an "on-chip quantification" unit for measurement of DNA and RNA from captured microbes. LAMP reagents will be lyophilized with a company partner, and a chip will be developed to dispense and lyophilize reagents. The target cost of the OMS unit will be less than 1/10th that of existing instruments, supporting experiments requiring multi-node sampling of microbial abundance and/or function.