The research was conducted by the Bigelow Laboratory for Ocean Sciences and Atrandi Biosciences, using Gulf of Maine surface seawater, and the findings were published in Nature Microbiology around November 2025.

The method yielded more complete and higher-quality viral genomes than some existing metagenomic approaches and captured viruses across the size spectrum, including Naomiviridae, an unusual DNA viral family.

Unlike flow cytometry-based methods, this approach is size-agnostic and detects a broader range of viral sizes, revealing genomes that might be missed by other techniques.

A new environmental microcompartment genomics approach dramatically increases throughput for single-particle genomics, enabling sequencing of thousands of individual particles from tiny seawater samples at reduced cost and with improved data quality.

In a Nature Microbiology study, researchers demonstrated the method by sequencing genomes from over 2,000 particles in roughly 300 nanoliters of Gulf of Maine seawater, illustrating substantial gains in speed, scale, and data quality.

The Gulf of Maine sample yielded genomes from more than 2,000 particles within 300 nanoliters, highlighting about an order of magnitude boost in throughput and enhanced data quality for environmental single-particle genomics.

Beyond seawater, the approach could apply to sediments and soils, offering broad environmental utility for investigating complex microbial and viral communities.

Overall, environmental microcompartment genomics provides a rapid, scalable, and cost-effective platform for environmental viromics and microbiome studies, expanding the toolkit for exploring viral diversity in natural environments.

The Nature Microbiology study showcases the first environmental application of this approach using Gulf of Maine surface seawater, demonstrating clear advantages over traditional single-cell genomics and metagenomics.

Compared with traditional flow-cytometry-based single-cell genomics, the method is size-agnostic, allowing sequencing of particles of all sizes, including large microbes, tiny viruses, and free-floating DNA.

Funding for the work came from the National Science Foundation, Simons Foundation, and the Research Council of Lithuania, with collaborators at Vilnius University and Atrandi Biosciences alongside Bigelow Laboratory researchers.

The authors see potential to extend the method to sediment and soil samples, expanding its use for studying environmental microbial communities and ocean viromes, especially elusive or hard-to-culture viruses.

The approach produced more complete viral genomes and uncovered families like Naomiviridae that may infect abundant ocean bacteria, highlighting its potential to reveal previously hidden viral diversity.

By enabling access to marine viral diversity and their hosts, the method addresses a major gap in understanding the ocean's microbial ecosystem, particularly the abundant but poorly characterized viral component.

The technique uses thousands of tiny semipermeable microcompartments to isolate single particles in a minuscule water volume, enabling in-compartment DNA amplification, barcoding, pooling, and sequencing to reconstruct complete genomes without pre-sorting.

In essence, thousands of tiny semipermeable bubbles compartmentalize samples for random single-cell or single-particle isolation, DNA amplification, barcoding, and sequencing to assemble genomes without flow cytometry.