The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched approximately 10 years ago to systematically fill sequence space in the bacterial and archaeal phylogenetic tree of life. The results from this study had tremendous impact in terms of the reconstruction of phylogenetic histories, the discovery of new protein families, and the prediction of functions for known genes from other microorganisms. The GEBA-Microbial Dark Matter (MDM) project expanded on these efforts by accessing genomes from uncultivated, highly novel lineages using single-cell genomics. Here, the team aims to expand the dark matter reference catalog by specifically targeting taxonomic “blind spots” via novel approaches. We aim to select environments that were previously shown to be enriched in these and exploit (i) single-cell approaches by sequencing single-cell genomes that do not yield 16S rRNA amplification products from these environments and (ii) genomes extracted from metagenomes (GFMs) by leveraging coverage-based binning. The sampling sites we will target include deep subsurface, thermal springs, cold seeps, oil contaminated soils and marine sediments.
Proposer: Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences