Equipment: Equipment: MRI: Track 2, Acquisition of a high-throughput workflow for environmental single cell genomics

About This Grant

A single cell is the most fundamental unit of biological organization. Identifying connections between its genomic blueprint and functional characteristics provides the ultimate resolution in microbiology. However, obtaining such information is challenging, which impedes foundational discoveries and biotechnological applications from the vast diversity of uncultivated microbial life on Earth. This project updates and enhances an analysis system for environmental single-cell genomics (eSCG), a method pioneered at Bigelow Laboratory for Ocean Sciences for sequencing individual uncultivated microbial cells and connecting their genetic information to physical traits. The updated system will reduce analytical costs and enable the development of new methodologies to analyze the genomes of cells shed by animals and plants, which hold the potential to inform the health of the studied populations and fundamentally change how species-based environmental research is conducted, enabling new forecasting tools. These new research opportunities will be showcased in symposia, workshops, courses, postdoctoral training programs, and undergraduate internships. The PIs have requested instrumentation that forms an integrated workflow for studies of environmental single-cell genomes and phenomes. The requested instrumentation will be integrated into an eSCG workflow instrument that meets the MRI requirement for “components that when combined serve as a single research instrument”. The new instrumentation comprises a state-of-the-art fluorescence-activated cell sorter, acoustic liquid handlers, a robotic plate reader, and plate sealers. It takes environmental samples as inputs and produces multiplexed single-cell sequencing libraries and cell phenotype measurements as outputs. This new system will be integrated into existing workflows for genomic and phenotypic profiling of microbial cells, leading to the development of new capabilities for characterizing extracellular nucleic acid-containing particles, such as viruses, and cells shed from eukaryotic organisms. The acquired instrumentation enables a comprehensive overhaul of the analytical workflow, introducing new capabilities, substantially reducing costs, and ensuring sustainable maintenance. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.