Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes

Publication Summary

Nature Microbiology
November 5, 2025

Authors: Alaina R. Weinheimer, Julia M. Brown, Brian Thompson, Greta Leonaviciene, Vaidotas Kiseliovas, Simonas Jocys, Jacob Munson-McGee, Gregory Gavelis, Corianna Mascena, Linas Mazutis, Nicole J. Poulton, Rapolas Zilionis, and Ramunas Stepanauskas

Challenge addressed: While viruses are key members of ocean communities, scientists have struggled to characterize their full diversity. A metagenomic approach has allowed for some progress but it still delivers incomplete information. In this study, researchers from the Bigelow Laboratory’s Single Cell Genomics Center developed a novel method known as environmental micro-compartment genomics (EMCG) for a more comprehensive view of cell-free DNA in marine samples.

Major achievement: This new technique allowed scientists to obtain more complete genomic sequences of thousands of viruses and extracellular DNA from a small sample of seawater. Compared to metagenomic and other conventional methods, the approach generated richer datasets and uniquely revealed a previously undetected family of viruses whose genomes contain non-canonical DNA.

Role of SPCs: The team used Atrandi’s Semi-Permeable Capsules (SPCs) to divide the seawater sample into picoliter-sized compartments. Extracellular DNA was captured inside each capsule, while reagents could be added and removed as needed during the amplification process. This workflow yielded more than 2,000 single amplified genomes for downstream analysis.

Key quotes: “Our results suggest that viruses with non-canonical DNA may be abundant in certain ocean regions and play crucial roles in marine microbial ecology, yet remain undetected by standard metagenomics methods,” the team reports. “EMCG opens a new window into the biology of viruses with non-canonical DNA, which may be instrumental not only in microbial ecology but also in the expanding use of xenobiotic nucleotides in synthetic biology.”

Read full publication here: https://www.nature.com/articles/s41564-025-02167-5