Ocean Enigma

This story originally appeared in the Winter 2025 edition of Transect.

Astronomers estimate that there are an unfathomable 200 billion trillion stars in the observable universe. But that number pales in comparison to the number of viruses found just in Earth’s oceans — by as much as 10 million times.

Viruses — tiny, organic, but not-quite-living genetic elements — are considered the most abundant biological entity on the planet. A single milliliter of water can hold as much as a million, or even a billion, individual viruses, each of which plays an essential role in the ecology and evolution of microbial life.

Despite their importance, though, viruses are still an enigma, and scientists are only beginning to understand the profound influence they have on the cycling of energy and nutrients around the ocean. Bigelow Laboratory researchers are helping drive that work forward, answering fundamental questions about viruses’ impact on the marine ecosystem and developing the cutting-edge tools needed to study them.

“Viruses are absolutely critical. They’re the lubricant of the oceanic engine because of their impacts on biogeochemistry, evolution, and physiology,” said Senior Research Scientist Joaquín Martínez Martínez. “You can swim in the ocean ‘viral soup’ without any danger to you. But the impact of viruses goes beyond illness, and it’s more global and more important than we ever thought.”

THE MINISCULE DRIVERS OF THE OCEAN ENGINE

Though microorganisms were discovered as early as the 1600s, it took another 200 years until viruses were uncovered. By employing a filter fine enough to remove bacteria, scientists realized there was something else, even smaller, in their samples making people sick. It wasn’t until the 1930s that scientists produced the first image of a virus.

“Initially humans only cared about what could cause disease, either to us or the plants and animals we depend on. We couldn’t imagine that there were viruses everywhere, much less floating around the ocean,” Martínez said. “When I began my Ph.D. in 2001, we were still at the point of just trying to understand basic things like how abundant marine viruses are and what they’re even capable of.”

It turns out they’re capable of quite a lot.

Every day, phages — viruses that infect bacteria and are the most common type — are estimated to kill upwards of 20 percent of the world’s bacteria. But the impact of viruses goes far beyond mortality.

In the process of infecting a host, viruses can leave behind bits of their own DNA and hijack pieces of their host’s DNA, taking on novel genes and pathways that allow them to infect and manipulate new hosts. In this way, viruses influence the evolution of marine life in real time. In some cases, viruses can also cause persistent infections where they integrate themselves so thoroughly into the host for an extended time that the host cell’s existence becomes centered largely on the virus’s needs. In those cases, traces of the virus can even persist in the next generation of the host cell, altering the evolutionary fate of that microbe.

“There’s probably a specific virus that can infect every kind of living organism,” said Postdoctoral Scientist Anne Booker. “That means how organisms simply live their lives and shape their environment is probably influenced at all times by viral activity.”

Viruses also help control the cycling of nutrients and energy in the ocean. Some infected algae, for example, have enhanced photosynthesis, increasing the amount of carbon dioxide they can pull out of the atmosphere. But other infected species appear to stop photosynthesizing entirely.

Meanwhile, viruses can also disrupt the flow of energy up the food chain. When a virus kills a microbe, the host cell bursts open. All the nutrients and organic matter within dissolve back into the surrounding water rather than moving up the chain to larger life forms, a process scientists call the “viral shunt.” There’s also evidence that some organisms feed directly on viruses — Martínez describes them as “little packages of nutrients” — which itself can alter the cycling of nutrients like carbon and nitrogen.

UNCOVERING THE HIDDEN WORLD OF VIRUSES

Bigelow Laboratory scientists are working to tease out these complicated processes and influences.

Research Scientist Julia Brown, for example, is doing essential research on viral communities in parts of the ocean where oxygen levels are unusually low. These oxygen minimum zones — some of which are naturally occurring and others a result of human activity — play an important role in global nutrient cycles and are expected to grow with warming temperatures.

Scientists have suggested that there are relatively fewer free-floating viruses in these areas compared to other parts of the ocean, hypothesizing that more viruses are locked up in persistent infections. Even so, they’re still influencing the behavior and life cycles of their microbial hosts. Brown is trying to understand what that relationship looks like and how it’s shaped by the lack of oxygen.

Brown and her collaborators at Woods Hole Oceanographic Institution have visited two different oxygen minimum zones in the Pacific, spending several weeks at each site, collecting some of the most complete data to date on the viral and microbial communities there.

“The thing about viruses is that they’re kind of meaningless without the context of who they’re infecting,” Brown said. “You get a lot more insight into the role of viruses in the ecosystem with these kinds of projects where you can link viruses to their hosts.”

Martínez and Booker are also working to tease apart host-virus interactions in a new, complex environment: a harmful algae bloom. They’re examining the viruses that infect Karenia brevis, a species of algae that routinely produces large, dangerous, and economically disastrous “red tides” in the Gulf of Mexico.

“There’s been a lot of information on how temperature and nutrient runoff affect these blooms, but no one really knows much about the microbial community,” Booker said. “We’re trying to uncover this additional layer to the story of how these blooms work.”

As part of a multi-institutional team, the researchers are answering fundamental questions about which viruses are infecting Karenia and at what rate. But they are also working on a more applied question. If a virus can kill a Karenia cell, is it possible that a lot of viruses could kill enough Karenia to stop a harmful bloom?

The team recently took a sample of seawater from a Karenia bloom in the Gulf of Mexico and filtered out all of the larger organisms, leaving just viruses behind. They then added that seawater to a flask full of Karenia cells, taken from Bigelow Laboratory’s National Center for Marine Algae and Microbiota. Within a few weeks, many of the algae cells died.

Booker and Martínez are now mapping out all the DNA in the sample to characterize the kinds of viruses killing the Karenia cells. Meanwhile, collaborators at NYU Abu Dhabi are using a similar method to look at bacteria to understand how the algae, bacteria, and virus interact, and what impact that has on the fate of the harmful blooms.

The story, it turns out, is even more complicated than they imagined.

In the bloom seawater, they found at least six types of giant viruses, all of which appear to infect Karenia while competing with each other. They also identified several kinds of phages, some of which may indirectly harm the algae by infecting “good” bacteria the algae need and other phages that may protect the algae by killing off harmful, “algicidal” bacteria. And, on top of it all, the researchers found preliminary evidence of several smaller viruses in the sample that could be attacking the giant viruses.

Together these complex interactions appear to create an unexpected balance in the ecosystem that allows the bloom to linger.

The research will continue for another year. Booker says they’ve isolated several of the viruses in the sample and plan to sequence their individual DNA. They’re also continuing fieldwork in the Gulf of Mexico and lab experiments to unravel the mechanisms and consequences of these microbial interactions. The hope is to get enough data to improve the models that estimate how long a bloom will last. Even if they can’t use viruses to end blooms, having models that accurately account for viral activity will help managers better respond to and plan for them.

“Unfortunately, there is no simple answer,” Booker said. “There’s such a complex microbial web, and there are many complicating environmental factors, but if we keep asking the right questions, we may get solutions for the future.”

NEW TOOLS FOR VIRAL RESEARCH

What makes research projects like these difficult isn’t just the lack of prior knowledge to build off. It’s also just that viruses are extremely hard to study.

“Viruses are so diverse — probably more diverse that any other biological thing — and they encode so many genes that haven’t been identified,” Brown said. “They’re also just very small, so there are limited ways of seeing and detecting them.”

For example, on Brown’s recent oxygen minimum cruises, processing a single sample of seawater took upwards of 12 hours. Because viral genomes are so small, she had to collect a lot of water to get enough genetic material to detect viral DNA. She also had to filter and strain her samples repeatedly to concentrate them and remove any larger organisms. To produce each 300-milliliter sample for her research, she had to collect 300 times more raw seawater.

Viruses are also exceptionally “micro-diverse” meaning that no two individuals are the same. Each contains endless little mutations and hijacked bits of DNA, reflecting the particular infection history of that individual and all its evolutionary consequences.

Advanced technology adapted for virology over the last 20 to 30 years has created new possibilities but also new challenges.

Metagenomic sequencing, which has been applied to viruses since the early 2000s, for example, enables scientists to sequence all the DNA in a water sample and get some information on everything in it. But that approach biases results towards whatever organism has the most DNA, not what’s necessarily the most abundant or important. And because viruses have particularly small and diverse genomes, it can also be hard to assemble the different chunks of DNA. It’s like putting together multiple puzzles at once that all look similar — and are all missing pieces.

Single cell genomics, advanced by Bigelow Laboratory’s Single Cell Genomics Center for the last 15 years, has helped address some of those problems by enabling scientists to isolate and sequence virus genomes individually. That fixes the multiple puzzle issue, and the use of robots through much of the process minimizes the risks of contamination.

“With metagenomics, it can be hard to assemble a complete genome because of the huge diversity of viruses,” said Senior Research Scientist Ramunas Stepanauskas, director of SCGC. “That’s why the approach of sequencing individual viral particles is so powerful because we don’t have to rely on so many assumptions to stitch together the bits of DNA.”

But even single cell genomics has its limits. A scientist needs to know what kinds of viruses they’re targeting and have tools for isolating those individuals. The first step of SCGC’s workflow, for example, is to use flow cytometry to sort the sample into individual particles, but because of their miniscule size, viruses often get lost in the process.

“The tools are improving all the time, but we need to adapt them to apply to viruses, and there’s no one tool that works for all different types of viruses in all different environments,” Martínez said. “You need a suite of complementary tools to look at the same thing from different angles.”

These challenges are inspiring Bigelow Laboratory scientists to develop new tools.

Brown and Stepanauskas, with Postdoctoral Fellow Alaina Weinheimer, have been working to design a method — called Environment Microcompartment Genomics — that can give scientists the same, fine-grained detail they can get from single cell genomics approaches but at a much larger scale.

“This new approach allows us to work with pretty much any size of virus, and we can process a much larger number of them without significantly increasing cost,” Stepanauskas said. “We’d have to fill a whole wing of our laboratory with equipment to increase the capacity of our current techniques to the same level.”

In the new method, an infinitesimally small amount of seawater, containing a single cell or particle, is stored in a tiny capsule. The DNA in each individual capsule is given a unique barcode so every segment that is sequenced can be traced back to the individual it came from. Because the approach skips the initial flow cytometry step, scientists aren’t able to get additional information about each particle, like its size. The benefit, though, is that they can process many more — and much smaller — viruses than ever before. It will also make it easier to detect viruses from sediment or soil without them getting missed or confused for other particles.

With the capsule method, Brown said they’ve gotten some of the highest quality viral genome sequences she’s seen recovered from an environmental sample. Stepanauskas added that the diversity of viruses they’re seeing so far is “mind boggling.” The team hopes to publish their first results in the coming months.

“We need these kinds of technologies to start understanding how viruses evolve,” Stepanauskas said. “That’s important for the ocean, but eventually it’s also going to inform everything from medicine to the agricultural field.”

For better or worse, all the scientists point out, it’s not hard to make the case for why viral research matters post-Covid.

“I used to say microbes rule the world, but it seems more and more that viruses dictate most of what’s going on, and we had no idea until relatively recently,” Booker said. “Anytime you can answer one small question about viral interactions, it really moves the whole field forward.”

Photo Captions

Photo 1: A microscopy image at 600 times magnification, shows plankton (the bright green dots) alongside more numerous and smaller marine viruses (the faint, smaller green dots) in a water sample from West Boothbay Harbor (Credit: Julia Brown).

Photo 2: JJ Custer, a University of New England student and participant in the Bigelow Laboratory Sea Change Semester program, combines seawater enriched with viruses and a culture of Karenia brevis to study the impacts of viruses on harmful algal blooms (Credit: Leah Campbell).

Photo 3: Microscopy images show several different kinds of marine viruses (Credit, top to bottom: E. Ghigo, J. Kartenbeck, P. Lien, L. Pelkmans, C. Capo, J.L. Mege, and D. Raoult; Graham Beards; M.B. Sullivan, M.L. Coleman, P. Weigele, F. Rohwer, and S.W. Chisholm).

Photo 4: Research Scientist Julia Brown examines data while aboard a cruise studying viral and microbial communities in an oxygen minimum zone in the Pacific Ocean (Credit: Julia Huggins).

Photo 5: A bloom of the harmful algae Karenia brevis is visible off the coast of Sarasota, Florida, in August 2018 (Credit: Vince Lovko).

Photo 6: Robotic equipment processes samples at the Single Cell Genomics Center, which sorts and analyzes the genetic information of individual cells and viruses (Credit: Rachel Kaplan).

Photo 7: Senior Research Scientist Joaquín Martínez Martínez examines viral samples in the lab (Credit: Rachel Kaplan).

Photo 8: A choanoflagellate is a microscopic organism that Bigelow Laboratory scientists have shown can consume viruses directly as food (Credit: Mark Dayel).