Illuminating Microbial Dark Matter via Single-Cell Genomics
Our view of microbial genomic diversity is severely skewed with the majority of all sequenced bacterial and archaeal genomes belonging to only four bacterial phyla. This bias results in part from our inability to cultivate most microbes, a necessary step for traditional whole genome sequencing. Through cultivation-independent approaches such as single-cell genomics, one can now explore the genetic diversity and metabolic potential of uncultivated environmental microorganisms. We successfully amplified several hundred single cells from free-living and symbiotic populations without cultured representatives, known as microbial dark matter. The single-cell genomes allowed us to explore their intra- and inter-phylum-level relationships, to decipher encoded pathways, and to discover novel metabolic features and re-coding events. The single- cell reference genomes also facilitate the interpretation of metagenomic data sets and substantially improve phylogenetic anchoring of metagenomic reads. While there is still much ground to cover, single-cell-genomics has proven to be a valuable tool to improve our understanding of microbial evolution on earth.