Pachiadaki, M. G. et al. Cell 179, 1623–1635 (2019).

Sequencing-based approaches have empowered us to decipher the largely unknown set of marine microorganisms and their roles in geochemical cycling and global ecosystems. However, the scarcity of reference genomes remains an obstacle for taxonomic and functional annotations. Pachiadaki et al. collected 28 water samples from the tropical and subtropical Atlantic and Pacific Oceans and used a single-cell genomics approach for surveying the complex microbiome in seawater samples. Unlike metagenomics analysis, single-cell genomics generates sequences of individual cells that do not make assumptions based on microbial abundances. The researchers generated untargeted libraries of single amplified genomes of prokaryoplankton, which recovered partial genomes of 12,715 sequenced cells. Surprisingly, in a single 0.4 mL seawater sample, they recovered a subpopulation of 6,236 genomes. They also offer a reference database, GORG-Tropics, for further prokaryoplankton taxonomy and function assignments.