A current limitation for biologically meaningful genomic analysis of single cells obtained by sorting from deep marine subsurface sediments
is the absence of a rapid, cost-‐effective molecular tool to help decide, which cells to advance for single cell genome sequencing. We
implemented and tested on subsurface sediments-‐derived single cells a unique nanoLiter qPCR tool that we have recently developed for
application to study population biology in complex environments. This nL-‐qPCR tool can interrogate simultaneously in up to several hundred
different qPCR reactions in nL samples the presence and abundance of candidate genes, and therefore provide a high level phylogenetic and
genomic overview of the genomic content of a cell. We showed that this information is key when screening hundreds of sorted single cells for
making decisions which amplified genomes to subject to sequencing. We developed and tested this new tool on the group of Chloroflexi, which
are present and sometimes dominant at numerous subsurface sites and used it to identify subpopulations for single cell genome sequencing.