Head technician Rebecca Burrell shucks an oyster for analysis. (Courtesy of Smithsonian Environmental Research Center)

Every night, a deadly event shadows oysters in what was widely thought to be a safe haven in the Chesapeake Bay.

Low oxygen “dead zones” caused by nutrient pollution show up every night in shallow waters near the shores of creeks and rivers, according to a new study released Wednesday by the Smithsonian Environmental Research Center.

Research shows dead zones plaguing waters as low as 20 feet, but little is known about their presence at night near the water’s edge, and their impact on oysters.

Oysters fight to breathe, and that struggle compromises their immune systems long enough to make them vulnerable to the attack of a second nemesis, a disease called dermo.

This troubling finding could be one of the reasons behind why small-scale — but pricey — efforts by Virginia and Maryland to restock the bay’s decimated oyster population failed in years past, marine scientists said, and why today’s larger-scale efforts to seed huge reefs with tens of thousands of young oysters could require a closer watch.

Slides of oysters suffering different intensities of Dermo as the Perkinsus parasite multiplies, from healthy, left, to severely infected, right. (Courtesy of Smithsonian Environmental Research Center)

Unlike deep-water dead zones that can last for months, nightly oxygen depletions in the shallows last only a few minutes. They are caused by a cycle in which massive amounts of algae created by nutrient pollution release oxygen in photosynthesis during the day. But at night, plants and animals respire and take away too much oxygen, said the study’s lead author, Denise Breitburg, a marine ecologist at SERC.

“We usually think of shallow-water habitats as . . . refuges from deep-water dead zones,” she said. “But if low oxygen makes even these shallow waters inhospitable for fish and shellfish, the whole system may suffer.”

The younger oysters are more likely to struggle to breathe and fight off disease, the study found. Oysters 1 year in age and older also suffered in field observations and experiments, but better withstood the assault.

“How would you like it if we sucked the oxygen out of your bedroom for 15 minutes at night?” asked Mark Bryer, director of the Chesapeake Bay program for the nonprofit Nature Conservancy. “The shallow-water habitats, while they’re not without oxygen for a long period of time, are out of oxygen long enough to do damage.”

The study has drawn interest in Virginia and Maryland, where tens of millions of dollars are being spent to revive oyster populations that have fallen nearly 100 percent from their historic highs in the 1800s due to overfishing, pollution and disease.

In the 1958-1959 harvest season, 4 million bushels were fished out of the bay. But after dermo’s discovery in the 1940s, the harvest fell to a mere 17,500 bushels in the 1995-1996 fishing season. A second and more vicious disease, MSX, imported from Asia and discovered in the 1980s, helped to hasten their demise. The states celebrated a modest rebound to 900,000 bushels in 2013-2014.

Dermo is a native disease caused by a parasite that attacks the flesh. “Luckily . . . this particular parasite doesn’t kill oysters immediately. It takes a couple of years before the infection really harms it or kills it,” Breitburg said.

In the “Room of D.O.O.M.” (Dissolved Oxygen Oyster Mortality), oyster tanks mimic the day-night oxygen swings that oysters experience in shallow Bay waters. (Courtesy of Smithsonian Environmental Research Center)

The experiments for the study were conducted in a lab called the “Room of DOOM,” which stands for Dissolved Oxygen Oyster Mortality, and at more than 14 sites in the bay. Infection rates were as high as 100 percent, but none of the oysters died over the few months experiments were conducted — in three years, starting in 2008. The findings were published Wednesday in the journal PLOS ONE. Co-authors included scientists at the U.S. Geological Survey, the Virginia Institute of Marine Science and the Maryland Department of Natural Resources.

“Even though . . . they’re not dying, more of them are getting infected, and infection rates increased faster. It didn’t progress to mortality of the span of the experiment,” Breitburg said, but within two years it could. In the wild, spots with both low oxygen and higher salinity had a more deadly effect on oyster populations. And, Breitburg said, overfishing still is a much-bigger concern.

Oysters drive a weakened fishing industry, but they’re far more valuable to the bay than as money-generators. A 2013 study showed that oysters help filter pollution caused by human activity and improve water quality by eating microscopic plants called phytoplankton.

Phyto­plankton dine on nutrient waste that pours out of city sewers and from farms and animal feed operations located mostly on Maryland’s eastern shore. The organism is responsible for enormous algae blooms that lower the bay’s oxygen.

When oysters and other bivalves eat phytoplankton, they poop it into hidden areas on oyster reefs where microorganisms feed. They convert nitrogen pollution stored by phytoplankton into a gas that wafts into the atmosphere.

There’s a hopeful sign, Breitburg said. Evidence in the study suggests that large numbers of oysters working together to filter pollution and improve water quality can increase their chances of survival.

“If restoration is done at sufficiently large scales in shallow-water sites, where oysters can access and filter the entire water column, the oysters themselves may be able to transform habitats,” she said.

The oyster’s importance to fishing and water quality in the polluted bay are two reasons why Virginia and Maryland are spending nearly $100 million, with the aid of the U.S. Army Corps of Engineers, to revive their populations.

Virginia embarked on its largest state-funded oyster replenishment in history two years ago, building large reefs on the James, York, and Rappahannock rivers, as well as on the Chesapeake Bay — at Pocomoke and Tangier sounds. That effort added to large sanctuaries in public waters where watermen are restricted to harvesting oysters on a rotating basis about every two years.

Maryland has poured more than $50 million into its oyster recovery effort over the past 16 years, with varied success. The state forbids oyster harvesting on many of its reefs, protecting them with a fine of up to $25,000 and a sentence of 15 years in prison.

Unlike Virginia, where robust aquaculture is a major part of its harvest, Maryland oyster farming is still beginning to develop.