RII Track-2 FEC: Single Cell Genome-to-Phenome: Integrating Genome and Phenome Analyses of Individual Microbial Cells in Complex Microbiomes

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Non-technical descriptionThe majority of biological diversity on Earth is found in microscopic, single-celled microbes, which are responsible for most of the cycling of carbon, nitrogen and other elements in the biosphere. However, less than 1% of microbes have been successfully isolated for detailed study in laboratory cultures, using traditional microbiology tools. Although newer ?meta-omics? research tools circumvent the need for laboratory cultivation by analyzing the molecular composition of entire microbial communities, these tools often blend information from highly diverse organisms, making it difficult to directly link the function of specific microbes (the ?phenome?) to their DNA code (the ?genome?). This project will tackle this technological weakness through a new combination of approaches that directly links functional and genomic properties of individual microbial cells. This new approach combines the project team?s ability to sequence the DNA of individual cells with the utilization of specific compounds that microbes incorporate in their cells in proportion to specific biological activities, such as respiration, growth, and uptake of nutrients. The researchers will validate this new approach in environments ranging from the Gulf of Maine to ocean crust and deep continental subsurface. This project will leverage genome research facilities at the Bigelow Laboratory Single Cell Genomics Center in Maine, expertise in the synthesis of fluorescent organic probes at the University of New Hampshire, continental geomicrobiology infrastructure at the Desert Research Institute in Nevada, and ongoing oceanographic research programs in Maine and New Hampshire. The project will contribute to the development of novel analytical capabilities for the national Research and Development (R&D) community, creation of new jobs, and training of skilled workforce in all three jurisdictions.Technical Description This award is for a multi-jurisdictional project that will capitalize on existing pilot results to achieve a breakthrough in microbial genome-to-phenome methodology at the most fundamental level of biological organization: the single cell. The overarching objective is to tie cell-specific genome data to expressed functions such that rates of environmental processes can be coupled to specific microbial lineages. The research team will: a) develop a new, integrated workflow for genome-to-phenome analyses of individual cells that takes advantage of fluorescent compounds to measure phenotypes; b) validate and utilize this workflow in studies of globally significant environments; c) share novel research tools with the research community through publications and core facility services; d) improve sustainable research infrastructure at collaborating EPSCoR jurisdictions; and e) create a multifaceted workforce development program to ensure expertise in these new research approaches. The project will establish and verify this workflow through three case studies that leverage the team?s expertise and access to environments of differing microbiome complexity: the coastal ocean, the deep dark ocean, and the marine and terrestrial subsurface. To further expand the societal impact and technological potential of the project, an added pilot study will focus on characterization of individual microbes responsible for degradation of an environmental contaminant (polyacrylamide/acrylamide). The overarching broader impact will be the development of a new tool: a pipeline for linking phenotype information to single microbial cells. This will have broad applicability across research communities and industrial applications and address a societal need to understand the critical function of microbes in the environment. The project will leverage the Bigelow Laboratory?s capabilities in single cell genomics and flow cytometry, New Hampshire?s expertise in the marine biogeochemistry of polymers and the synthesis of labeled organic molecules, and the Desert Research Institute?s (DRI) expertise and infrastructure in studying deep subsurface environments. New faculty members will be mentored, including a new senior staff member to be hired at Bigelow, and a new faculty member currently at the University of New Hampshire.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.