One of the major challenges in understanding microbial community function in natural environments is linking genome-level sequences to function and role in the ecosystem. Analysis of microbial genomes has led to the realization that a significant portion of genes in every microbial genome are of unknown function and also unique to that genome. This suggests that in complex natural communities, a significant pool of genes of unknown function is present. Examples are now emerging in which such genes are being discovered to be involved in familiar functions that had previously not been identified in that role. Therefore, it is likely that many of the genes of unknown function in complex environmental communities also carry out familiar functions. This leads to the concern that dominant functional populations may remain undiscovered in a specific ecosystem, essentially incognito, since the key metabolic modules involved in that function have yet to be identified.
The goal of this Single Cell Analysis project is to develop new technology for presorting functional populations and analyzing them at the single cell level for both phenotypic and genomic parameters. This approach will allow culture-independent enrichment of live cells involved in specific functions, analysis of a variety of phenotypic capabilities at the single cell level, then targeting of those cells that test positive for specific functions for further culture-dependent and sequencing analysis. In a relatively rapid and high throughput manner, this system would identify cells with functions of interest and carry out a set of phenotypic tests on those cells.