Environmental microorganisms exhibit marked and poorly understood genetic variation, even within the same nominal species, that cannot currently be resolved using metagenomics. A large-scale single-cell genomics study of planktonic bacteria and archaea that inhabit the surface ocean now broadens insights into the heterogeneity and genomic composition of this marine microbiome, which has essential roles in global biogeochemical processes but remains understudied owing to difficulties in cultivation.

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Using a randomized cell selection strategy, the team generated and sequenced an untargeted library of single amplified genomes (SAGs) of prokaryoplankton retrieved from 28 tropical and subtropical surface ocean water samples. This approach yielded 12,715 partial genomes (an estimated average of 38% of each cell’s genome) with no detectable contamination, a data set the authors termed Global Ocean Reference Genomes Tropics (GORG-Tropics).

Pairwise average nucleotide identity (ANI) measurements indicated that very few bacterial and archaeal cells in the ocean are sufficiently similar to each other to be called the same species using current species definitions. This large degree of genomic individuality provides a plausible explanation for the challenges in representing complex microbiomes in metagenomic assemblies. Taxonomic assignment based on complete or near-complete 16S rRNA gene sequences was possible for 5,536 SAGs. Identification of genes involved in energy and secondary metabolisms in this large, randomized set of genomes provided a bioprospecting roadmap for bioenergy, pharmaceutics and other applications.

Fragment recruitment, an alignment-based binning method whereby individual reads are aligned to homologous reference genomes, was used to determine the extent of global diversity represented in GORG-Tropics. This analysis showed that GORG-Tropics outperforms existing reference genome databases, as did a reference data set consisting of a subset of 6,236 genomes, which was obtained from a single, 0.4 ml seawater sample aliquot from the Sargasso Sea. The authors suggest that “a substantial fraction of the global coding potential of marine prokaryoplankton resides in each tiny parcel of ocean water, due to effective mixing on a global scale”.

cultivation-independent assessment of complex, natural microbial ecosystems

This study supports a growing body of work using single-cell genomic approaches for cultivation-independent assessment of complex, natural microbial ecosystems, broadens our perspective regarding the extent of genomic heterogeneity in natural microbiomes and offers new tools for improved interpretation of the numerous meta-omics studies of the marine microbiome. As microbial genetic variation can provide a selective advantage when conditions change, a detailed understanding of it might help predict how these communities respond to climate change.