Genomics of environmental microcompartments reveals novel viruses and other genetic elements in the ocean

Viruses and other extracellular genetic elements constitute a major fraction of marine DNA and play important roles in plankton ecology and evolution, but their composition remains challenging to decipher. Here, we report a novel technology that involves compartmentalization of natural samples into picolitre-sized semipermeable capsules (SPCs) and subsequent amplification, barcoding and sequencing of DNA from individual SPCs. Our workflow enabled quantitative de novo assemblies of thousands of single-amplified genomes (SAGs) from the SPCs of a single experiment, capturing a broad range of both cellular and extracellular entities. The technology was successfully applied on surface and deep ocean water samples and on marine sediments. Over 2,000 SPC SAG genomes were sequenced from a 250nL sample of surface seawater. The obtained 11:1 virus-to-cell ratio, the predominance of Caudoviricetes, and the taxonomy of cellular SAG assemblies were in good agreement with the current knowledge of marine plankton composition. Genomes of a substantial fraction of viral SAGs were similar to the dUTP-containing Naomiviridae and lacked matches in a metagenome from the same sample, indicating their use of non-canonical DNA (e.g. not A, T, C and G). The reported Environment Micro-Compartment Genomics (EMCG) technology offers transformative opportunities for unbiased and cost-effective studies of individual viruses and other genetic elements in nature.

Presentation Preference: Oral

Primary Presenter: Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences (rstepanauskas@bigelow.org)

Authors:

Alaina Weinheimer, Bigelow Laboratory for Ocean Sciences  (aweinheimer@bigelow.org)

Brian Thompson, Bigelow Laboratory for Ocean Sciences  (bthompson@bigelow.org)

Gregory Gavelis, Bigelow Laboratory for Ocean Sciences  (ggavelis@bigelow.org)

Greta Leonaviciene, Vilnius University  (greta.stonyte@bti.vu.lt)

Vaidotas Kiseliovas, Atrandi Biosciences  (vaidotas.kiseliovas@atrandi.com)

Simonas Jocys, Atrandi Biosciences  (simonas.jocys@atrandi.com)

Corianna Mascena, Bigelow Laboratory for Ocean Sciences  (cmascena@bigelow.org)

Linas Mazutis, Vilnius University  (linas.mazutis@bti.vu.lt)

Nicole Poulton, Bigelow Laboratory for Ocean Sciences  (npoulton@bigelow.org)

Julia Brown, Bigelow Laboratory for Ocean Sciences  (julia@bigelow.org)

Rapolas Zilionis, Atrandi Biosciences  (rapolas.zilionis@atrandi.com)