The PIs propose to acquire instrumentation that will form the basis for a new microbial single cell genomics facility at the institution. Single cell genomics represents a novel approach to study uncultured microorganisms and serves as a complement to metagenomics. The proposed instrumentation will enable research efforts investigating biogeochemistry and microbial interactions, microbial evolution and diversity, and biotechnology. The proposed instrumentation includes: nanoliter reagent dispenser, a thermal plate sealer, a PCR hood, an anaerobic chamber, a liquid handling workstation, a real-time PCR thermocycler, an ultracold freezer, and a bioinformatics computer cluster. The requested instrumentation would enable high throughput wetlab and computational DNA analyses and help reduce DNA contamination and overall per-sample costs, two of the most significant limitations for single cell genomics to date. The new facility will be operated in close collaboration with an existing aquatic cytometry facility using established user fees, scheduling and protocols. The lead PI will be responsible for the overall management of the purchase, installation, and operation of the instrumentation. A part-time technician will be employed for the wet lab instrumentation. The instrumentation will initially be located in different laboratories, but will be relocated to a dedicated workspace upon construction of new laboratory facilities at the institution projected for 2010.
Broader Impacts: In addition to establishing a shared-use facility to enable access to single cell genomics techniques, the PIs propose developing an annual course in single cell DNA analysis, as well as incorporating classes on single cell genomics into existing courses. The PIs will also encourage on-site visits by college and university faculty and students.
at Bigelow Laboratory for Ocean Sciences . To maximize the use and accessibility of these resources to the broad scientific community, we established the Bigelow Laboratory Single Cell Genomics Center (SCGC), the first core facility of this type (www.bigelow.org/scgc). DNA sequencing from individual cells is a novel approach in genetic research, which enables the analysis of hereditary information at the most basic biological level. In the case of prokaryotes and protists, each cell is a separate organism. Although invisible to the human eye without magnification, such unicellular microorganisms are the oldest, the most abundant, and the most diverse forms of life on our planet. They dominate many functions of the biosphere, including the productivity of the oceans; the health of large organisms such as humans; and the global cycles of carbon, nitrogen, and other elements. Microorganisms also harbor an enormous potential for novel natural product discovery and bioenergy production. However, over 99% of microbial species remain uncultured, making it impossible to study them using classical microbiology methods. Single cell genomics allows, for the first time, to study multiple genes or entire genomes of the uncultured microbial species from diverse natural environments. Since its establishment in November 2009, the SCGC has become a major engine of discovery in the areas of microbial ecology, evolution, and bioprospecting, supporting cutting-edge research projects at over 30 organizations around the globe, including the Department of Energy Joint Genome Institute, Harvard, Yale and Princeton Universities, and many others. Major discoveries to date include biochemical pathways for carbon fixation in dark ocean microorganisms, detailed trophic interactions of marine protists and identities of microorganisms harvesting sunlight. Over 200,000 individual cells have been analyzed by SCGC so far, providing access to previously inaccessible genetic material of uncultured microorganisms. The SCGC is essential for providing unique educational, professional development, and outreach opportunities at Bigelow Laboratory. Numerous students and postdoctoral associates received training or obtained data for their research projects from the SCGC. In September 2011, we hosted the second workshop on microbial single cell genomics (www.bigelow.org/scgc/workshop2010). The goal of the workshop was to gather the different groups that develop, use, or plan using microbial single cell genomics technology, exchange information, and thereby facilitate faster progress in this emerging field. A total of 73 individuals participanted in the workshop, including graduate students, postdoctoral researchers, principal investigators, and industry representatives from 15 countries. The workshop also included a bioinformatics tutorial to facilitate hands-on experience. SCGC research results have been disseminated through numerous professional seminars and conference presentations, as well as through Bigelow outreach activities to the general public, such as Café Scientifique series, the Bigelow Open House, and other venues.
