Bringing Molecular and Genomic Data to the Uncultivable Masses

The microbial world represents the greatest fraction of the world’s biodiversity, but most of this diversity remains unexplored because less than 1% of these organisms are readily cultivated by known means. Historically, this imposed severe limitations on our ability to ask even the most fundamental questions about most microbial life, but in the last decade advances in molecular methods to study uncultivable microorganisms have led to radical revisions to our understanding of microbial diversity. The first stage of this transformation was the use of environmental surveys to examine molecular diversity of a given gene from a certain environment. This led to the realization that microbial diversity had been greatly underestimated, and that many major microbial lineages and biological processes had been wholly overlooked. But how do we attach biological significance to these ‘environmental’ lineages? Metagenomics seek to do so by connecting molecular sequences from the environment to one another, but another approach is to use culture-independent methods applied to single-cells physically isolated from the environment. Gene sequences from isolated cells have been used to identify a number of ‘environmental’ lineages, in several cases showing them to have been identified and described many years ago, but never analysed at the molecular level. In the same way, single cells from environmental samples can be barcoded and compared with the known diversity of cultured species. These methods have moved from being exceptional to being routine in the space of a few years, but the real revolution in our understanding of microbial diversity will take place when the same shift takes place with single-cell whole genome and transcriptome sequencing: acquiring whole-genome data from physically isolated cells allows us to reconstruct the biological activities of whole environments without sacrificing important subtleties such as how functions are partitioned between cells and how lineages share genetic information by horizontal gene transfer.