The Secret Life of Viruses: How Microscopic Predators Could Save Coral Reefs

At 25 feet below the surface, just off the coast of Vieques, Puerto Rico, something strange was happening.

Suspended in the water, like an alien artifact from a future world, were two gleaming fiberglass and steel geodesic domes. On the outside, coral fragments—some no bigger than a matchbox—were attached to limestone tiles and facing upward toward the sun. This structure, known as a “Coral Ark,” is no ordinary restoration experiment. It’s part of a radical rethink of how we save coral reefs, not just by planting corals, but by changing the very microbial atmosphere in which they grow.

And at the heart of that transformation? Viruses—the very life forms we typically associate with pandemics and destruction.

In this underwater experiment, however, viruses aren’t killing. They’re saving.

The idea is as bold as it is counterintuitive: use marine viruses to improve coral survival. It’s a concept explored in a groundbreaking new study published in The ISME Journal in June 2025, led by Dr. Jason Baer (San Diego State University), with senior scientists including Dr. Aaron Hartmann, my delightful colleague at the Perry Institute for Marine Science. Their paper, “Viralization as a microbial approach for enhancing coral reef restoration,” dives deep into the role of viruses as ecosystem regulators—tiny predators of pathogenic bacteria that hurt corals and reefs overall may hold the key to reversing the decline of the ocean’s most fragile and vital ecosystems.

“We’ve spent years trying to plant corals on degraded reefs,” says Dr. Hartmann. “But if the water itself—the microbial conditions—are working against you, you’re just setting those corals up to fail.”

For 18 months, in a quiet bay in the northeastern Caribbean, the team ran this underwater experiment. What they found is changing how scientists think about restoration and who the true players in coral survival really are.

The Problem with Coral Restoration

Coral reefs are often called the rainforests of the sea—and for good reason. They shelter nearly 25% of all marine life, protect coastlines from storms, and feed millions of people. Yet despite their importance, reefs are vanishing at a staggering rate. Climate change, overfishing, sediment runoff, and nutrient pollution have left many coral reefs sickly, overgrown with algae, and nearly devoid of the vibrant marine life they once supported.

In response, scientists have ramped up coral restoration. Divers collect healthy coral fragments, grow them in nurseries, then “plant” them onto degraded reefs. It’s careful, manual work—part marine gardening, part triage. But there’s a problem.

In too many places, coral restoration simply doesn’t stick.

The corals are planted, they survive for a time—and then they die.

It’s a disheartening pattern. Despite millions of dollars and heroic conservation efforts, coral survival in degraded environments remains inconsistent and can be disappointingly low. And while visible threats like warming temperatures or overfishing get much of the attention, there’s an invisible player driving many of these failures: microbes.

Over the last decade, researchers have begun to understand that reefs don’t just suffer from environmental stress—they undergo a microbial shift. As corals die and algae take over, the surrounding seawater fills with dissolved organic carbon (DOC). This fuels an explosion of opportunistic and pathogenic bacteria, which consume oxygen, spread disease, and make the reef even less hospitable to coral.

This transformation is known as microbialization, a state where reef water becomes dominated by microbes that thrive in degraded conditions. Coral reefs caught in this feedback loop become microbial deserts, hostile to coral growth, and often impossible to rescue with planting alone.

So what if, instead of just focusing on the coral, we focused on the microbial community around it?

That’s the question the Coral Arks study in Puerto Rico sought to answer—and it led to a fairly promising breakthrough.

The Breakthrough Study

In November 2021, a team of marine scientists deployed two Coral Arks off the coast of Vieques, Puerto Rico. These spherical structures, suspended midwater about 8 meters below the surface, were designed to create an environment more like the open ocean: clear, well-oxygenated, and distant from the sediment and nutrient pollution often found near the seafloor.

Then, they brought in the coral.

Over 400 coral fragments, representing eight different Caribbean species, were transplanted—half onto these floating Arks and half onto nearby seafloor reef sites using conventional restoration methods. For the next 18 months, the team tracked everything: coral survival, water chemistry, microbial abundance, viral activity, light, flow, and even the microbial genes involved in carbon metabolism.

The results were eye-opening:

• 47% of the corals survived on the Arks, compared to just 24% on the seafloor.
• New coral recruits—baby corals that naturally settled—were found only on the Arks.
• The Arks were colonized by healthy reef species like sponges and pink crustose coralline algae, known to support coral growth.
• Fish communities on the Arks included more predators and had higher biomass, a hallmark of functioning reef ecosystems.

But perhaps most remarkable were the microbial differences.

The water around the Arks was teeming with free-floating viruses. A good thing, it turns out. These viruses target dominant bacteria, keeping microbial populations in check. This led to higher virus-to-microbe ratios (VMR) on the Arks—an indicator of healthy microbial regulation. Indeed, VMR on the Arks were over 14 while the VMR at seafloor sites was below 10.

Meanwhile, microbial cell size and total biomass (both indicators of microbial overgrowth) were significantly lower on the Arks. That meant fewer oxygen-sapping, coral-stressing bacteria. The Arks also had more dissolved oxygen, especially at night, and experienced stronger water flow and better light conditions—vital for coral health.

The seafloor sites were classic examples of microbialized reefs: low oxygen, high microbial biomass, algae overgrowth, and poor coral survival. The Arks, by comparison, had been viralized—a term coined by the authors to describe a microbial state where viruses, not bacteria, dominate the ecological balance.

“In these beginning stages, Arks are being used as an underwater platform for studying coral reefs, testing new conservation and restoration strategies, and developing a deeper understanding of the conditions that a healthy coral reef needs to remain healthy,” notes lead author Jason Baer in a prior interview with Oceanographic.

By integrating microbial metrics into coral restoration, the study offers something rare in conservation: a path not only to stabilize reef restoration, but to amplify it by working with the ocean’s smallest predators.

Meet the Microscopic Heroes

Most of us think of viruses as harbingers of disease. The word conjures images of infection and collapse—not healing and harmony. But in the ocean, viruses play a very different role.

In every drop of seawater, there are millions of viruses. Most of them don’t infect humans or marine animals. Instead, they infect bacteria and other microorganisms, shaping entire ecosystems from the bottom up.

Scientists call this the Kill-the-Winner dynamic. When one microbial group becomes too dominant—say, a bloom of fast-growing, oxygen-hungry bacteria—viruses step in. They infect the overabundant bacteria, break them open through lysis, and redistribute nutrients back into the system. In doing so, viruses prevent microbial monopolies, promote diversity, and regulate energy flow through the food web.

On healthy coral reefs, this viral control helps maintain the microbial equilibrium that corals need to thrive. These ecosystems are said to be “viralized”—where high VMRs reflect active viral predation and a well-regulated microbial community.

But when reefs are stressed by pollution, algae overgrowth, or climate change, things shift. Algae release a sugary form of carbon (labile DOC) into the water, which fuels the rapid growth of bacteria. Viral predation can’t keep up. The viruses stop lysing bacteria and instead go dormant inside them—a state called lysogeny. As bacteria multiply unchecked, they consume oxygen and produce waste, pushing the reef into that microbialized state—hostile for corals and many reef organisms.

That’s why the Coral Arks’ higher VMRs were so significant. They signaled a return to microbial balance. Viruses were actively regulating the microbial population, reducing biomass, and helping stabilize oxygen levels, reestablishing the microbial checks and balances that support reef health.

Supporting Science from Around the World

What the Coral Arks revealed in the Caribbean isn’t happening in isolation. Around the world, scientists are uncovering the same invisible forces shaping the fate of coral reefs—and they’re pointing to a surprising truth: microbial and viral dynamics may be just as important as water temperature or ocean acidification in determining whether a reef lives or dies.

One of the first scientists to articulate the power of marine viruses was Dr. Curtis Suttle. In a landmark 2005 Nature paper, he estimated that viruses kill up to 20% of the ocean’s microbial biomass every day. Destructive, yes—but also essential. Without that turnover, nutrients wouldn’t cycle, oxygen would drop, and ecosystems would stagnate.

In coral reef research, similar findings have emerged again and again. A 2020 study by Anny Cárdenas and colleagues found that reefs with healthy coral cover tend to have high VMRs and diverse viral communities, while degraded reefs exhibit the opposite: low viral activity, high microbial biomass, and increased disease. Meanwhile, work by Haas et al. (2016) showed that algae-dominated reefs emit large amounts of easily consumed organic carbon, which fuels bacterial blooms and triggers rapid oxygen depletion—creating hypoxic “dead zones” around coral fragments.

These findings reinforce a sobering idea: the decline of reefs isn’t just a matter of heat or overfishing. It’s a shift in invisible chemistry and biology, driven by changes in microbial relationships.

What’s exciting is that we now know how to measure these changes—using metrics like VMR, microbial biomass, gene expression—and even intervene. The Coral Arks experiment didn’t just document a viralized environment. It created one. And it did so by design, suggesting that reef restoration can be reimagined at the microbial scale.

Hope from the Microbial World

For years, coral restoration has focused on structure—building artificial reefs, propagating and transplanting coral fragments, reinforcing damaged skeletons. But structure alone isn’t enough. As the Coral Arks have shown, what really matters is the quality of the environment, especially the microscopic one.

Fortunately, a new wave of research is embracing this microbial perspective. From floating nurseries to microbial probiotics, scientists are now designing interventions that target not just the where of restoration, but the how—by shaping the microbial and viral communities that corals depend on.

Among the most promising tools:

• Elevated reef frameworks (e.g., Reef Stars): provide structure above microbially stressed seafloors, avoiding sediment and DOC buildup that fosters microbialization.
• Coral probiotics: including work led by the Perry Institute for Marine Science in Colombia, aiming to stabilize the coral microbiome with beneficial strains to improve resistance to bleaching and disease.
• Phage therapy: targeted use of viruses to eliminate harmful bacterial pathogens like Vibrio coralliilyticus, with encouraging lab results (e.g., a 2018 study showing therapeutic potential of a jumbo phage).
• Real-time microbial monitoring: genomic tools to track VMR, DOC, and microbial gene expression as early-warning systems.

In this new microbial toolkit, viruses aren’t a problem to be solved but part of the solution. As seen in the Coral Arks, fostering viral activity can re-balance microbial communities, boost coral survival, and potentially tip a degraded system back toward recovery.

A New Restoration Mindset

We tend to look at coral reefs and see color, structure, life—or the absence of it. But what the Coral Arks remind us is that much of a reef’s fate is shaped by what we don’t see: invisible microbial dramas unfolding in the seawater around every polyp and sponge.

As this paper demonstrates, by shifting our focus from physical transplantation to microbial transformation, it invites us to view reef recovery not as a matter of planting coral, but of engineering the right conditions for coral to flourish on its own.

Perhaps it’s a call to think smaller (ironic, we know!)—to look beyond fish and coral and even algae—and instead consider the fluid, unseen networks that govern reef health. Viruses, often dismissed as threats, emerge here as regulators and recyclers. Such tiny lifeforms, long overlooked, may even become the gatekeepers of coral survival.

The lesson is clear: restoring reefs means restoring balance—not just in the food web, but in the microscopic exchanges that keep the whole system alive.

If we can harness that balance, we may not just recover what was lost, we may help coral reefs adapt to the future conditions they’ll face.

About the Perry Institute for Marine Science

The Perry Institute for Marine Science (PIMS) is a nonprofit organization working across The Bahamas and the Caribbean to protect and restore ocean life through science, innovation, and community action. Our programs advance reef restoration, sustainable fisheries, and climate resilience—including the Reef Rescue Network, the largest coral restoration initiative in the Caribbean. Support our work or learn more about the Reef Rescue Network.

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