According to Phys.org, researchers from Bigelow Laboratory for Ocean Sciences and Atrandi Biosciences have developed environmental microcompartment genomics, a new method that dramatically improves single-cell genetic sequencing. In their Nature Microbiology study, they processed over 2,000 particles from just 300 nanoliters of Gulf of Maine seawater, increasing throughput by an order of magnitude compared to traditional methods that handle only 384 particles per run. Lead author Alaina Weinheimer says this approach reduces costs without sacrificing quality while enabling comprehensive microbial community analysis. The method captured viruses of all sizes simultaneously, including the Naomiviridae family that other techniques would have missed entirely. This represents the first environmental application of microcompartment genomics, with early testing showing it also works on sediment and soil samples.
From tiny bubbles to big discoveries
Here’s how this actually works: they take a seawater sample and compartmentalize it into thousands of microscopic, semipermeable bubbles. Each bubble contains just a trillionth of a liter of water. When single cells or viral particles randomly end up in these compartments, researchers use reagents to amplify the DNA millions of times. Then they tag everything with unique barcodes before dissolving the bubbles and sequencing everything together. The barcodes act like return addresses, letting scientists reconstruct which sequences came from which original particle.
The real game-changer? No flow cytometry. Traditional single-cell sequencing uses flow cytometers that sort particles by size before sequencing. That means you’re only seeing what fits through the machine’s filters. But ocean viruses come in all shapes and sizes—many are too small for standard equipment. This method catches everything from large microbes down to free-floating DNA. Basically, you’re getting the whole picture instead of just the pieces that fit through the door.
The invisible becomes visible
So what did they actually discover with this new approach? The Naomiviridae family of viruses emerged as the most abundant in their dataset. These viruses have such unusual DNA structures that other methods would have filtered them out or missed them completely. Even more interesting—they found evidence suggesting these viruses infect the most abundant bacteria in the ocean. That’s like discovering your next-door neighbor has been throwing massive parties every night, but you never noticed because you were using the wrong tools to listen.
The quality improvements were striking too. Compared to widely used metagenomic methods, the microcompartment approach generated more complete genome sequences with higher quality. Traditional flow cytometry methods tended to pick up more large viruses, while this new technique captured the full size spectrum. It’s like switching from a fishing net with large holes to one that catches everything from whales to plankton.
Opening Pandora’s microbial box
Ramunas Stepanauskas, the study’s senior author, put it perfectly: “Nature’s microbial world remains full of mysteries.” We’re talking about the ocean here—where viruses outnumber every other microbe combined, yet we’ve barely scratched the surface of understanding them. Current methods have been like trying to study a city’s population by only counting people who fit through specific doorways. You’re missing everyone who’s too small, too large, or just shaped differently.
This isn’t just about seawater either. Early testing shows the method works on sediment and soil samples, which are notoriously difficult because it’s hard to differentiate biological particles from dirt and debris. The implications are huge for understanding everything from carbon cycling in the ocean to soil health on land. We’re basically getting a new pair of glasses for looking at the microbial world—and suddenly we can see details we never knew were there.
The researchers published their full methodology and findings in Nature Microbiology, making this approach available to other scientists. Given how much we still don’t know about ocean viruses—and how critical they are to global ecosystems—this could unlock discoveries we haven’t even thought to look for yet. The invisible majority of ocean life might finally get its moment in the spotlight.
