Complex ecosystems need to be tackled using cultivation-independent methods and while both metagenomics and single-cell genomics are today’s most commonly used methodologies to gain genomic insights into complex environments, they represent two extremes with complementary strengths and limitations. Most importantly, neither approach is able to pair genomic data with phenotypic information about specific community members, which leaves the system-level analysis of complex microbial communities intractable even with terabase-scale sequencing efforts. What is needed are novel approaches that efficiently enrich or isolate, prior to sequencing, specific environmental cells that catalyze a function of interest or exhibit a wanted phenotype.
In an effort to develop such method, MIT, the University of Vienna and the DOE JGI are jointly working on the integration of single-cell isotope labeling with confocal Raman microspectroscopy and microfluidics for high-throughput sorting of labeled cells from environmental samples for subsequent FACS arraying and whole genome amplification. This work is being performed under JGI’s Emerging Technologies Opportunity Program umbrella.
PIs: Roman Stocker, MIT; Michael Wagner, University of Vienna; Tanja Woyke, JGI.