New research shows that killer whales are inhaling bacteria, fungi and viruses once believed to be found only on land. Some of the pathogens are highly virulent. And some are even antibiotic-resistant.

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The scientists followed the killer whales by boat, trying to catch the precise moment the animals broke the surface.

Then, using a 25-foot pole strung with petri dishes, researchers leaned out and gathered samples of the moist exhaled air that shot like a geyser from each whale’s blowhole.

For four years a team of researchers gathered these orca breath samples from the waters of Washington and British Columbia. And by comparing them to surface waters and orca death records, the scientists stumbled upon a trend.

Killer whales — from Puget Sound’s endangered southern residents to the transient whales living hundreds of miles offshore — are inhaling bacteria, fungi and viruses once believed to be found only on land. Some of the pathogens are highly virulent. And some are even antibiotic-resistant.

The discovery comes as researchers also learn that respiratory ailments may be a leading cause of orca deaths, and that leads biologists to a new question:

Given that Puget Sound’s orcas are stressed and potentially more susceptible to illness, how much risk could exposure to new sources of infection pose?

“It’s pretty disturbing and opens a whole new can of worms,” said marine-mammal veterinarian Pete Schroeder. “We have an iconic species of animal that is in danger and whose ability to withstand a severe infection is in question. Now we know they can inhale antibiotic-resistant bacteria and it can live in their upper respiratory tract.”

The research is so new, it’s hard to draw firm conclusions.

“Just because you detect a particular pathogen, does that mean it will cause a problem? It may or may not,” said Brad Hanson, a marine-mammal biologist with the National Oceanic and Atmospheric Administration’s Northwest Fisheries Science Center in Seattle. “Are we detecting them because we’ve never looked before? We don’t know.”

But while none of the orcas sampled were sick, researchers said their findings suggest that contagions may be of greater concern for orcas than previously thought.

“It means we need to worry about disease outbreaks as a threat to the very survival of the population,” said David Bain, an orca expert and affiliate professor at the University of Washington. “We need to improve the barrier between our lives on land and whales’ lives at sea.”

Trouble with runoff

It’s no secret that a stew of microbes from land regularly invades Puget Sound. Bacteria and nutrients from humans and animals have for decades been funneled into estuaries and bays, causing oxygen problems in Hood Canal and resulting in shellfish-bed closures.

Chicken and cow waste has flowed from farms into rivers. Other nutrients from humans spread through leaky septic tanks or poor sewage treatment or from dumping by pleasure boats or cruise ships. Stormwater runoff over roads and parking lots washes in animal waste with other dangerous chemicals that rise through the food web and settle in the flesh and fat of marine mammals, including orcas.

But in the last decade a largely unheralded potential pollution source has started garnering new attention — the super-thin film that floats atop marine waters, called the sea-surface microlayer. This millimeter-thick sheen on the surface has long been known to carry fungi and bacteria, and those pathogens can easily become airborne.

So in the mid-2000s, after Puget Sound’s orcas were listed for protection under the Endangered Species Act, Schroeder and a group of whale scientists began wondering if the marine mammals could inhale contaminants when they break the surface.

It seemed like an important question. Whale respiration is particularly sensitive. With each breath, humans exchange up to 20 percent of the air in their lungs. Killer whales may exchange 70 percent at once. And whales don’t have a sinus network to extract harmful particles before they settle in the lungs.

Plus, marine biologists suspect Puget Sound’s southern residents already have weakened immune systems. Because they are at the top of the food chain, they’re loaded up with such toxic chemicals as DDT, and the long-lived banned solvent polychlorinated biphenyls (PCBs) found in fish. And the decline of Puget Sound chinook, their preferred food, means they have to work harder for each meal.

While that could make them more vulnerable to disease, scientists rarely know what kills a Puget Sound orca. Only two in the last 10 years have washed up dead in the U.S.

“When southern residents die, most of the time, they just disappear,” Hanson said. “We don’t have a good idea what happens to them.”

So Schroeder and several colleagues got access to a boat. They attached petri dishes to a shaft and followed whales as they traveled in pods. They gathered 23 breath samples from 14 whales, from Puget Sound to Vancouver Island. They also sampled the sea-surface microlayer.

Both the whale breath and the sea-surface samples contained bacteria that didn’t appear to belong there. Some bacteria did belong, but was antibiotic-resistant. There were strains of Salmonella and a rare bacteria known to cause pneumonia in humans. There was a pathogen responsible for gastroenteritis and gangrene, and a form of Staphylococcus resistant to penicillin. One pathogen normally found in marine waters was, surprisingly, resistant to six different antibiotics.

“In some of the bacteria we found some isolates were almost identical to what we recover in dairy cattle,” said Stephen Raverty, a veterinarian pathologist with B.C.’s Ministry of Agriculture.

Many of the bacteria were nonpathogenic, but a few appeared potentially dangerous.

“It’s not like there was a soup of terribly virulent bacteria out there. But there was enough to be concerned,” Schroeder said.

Why they die

As researchers tried to understand their findings, Raverty and others took on a new challenge — tracking why killer whales die. Of the 222 documented killer-whale strandings in the northeastern Pacific between 1944 and 2003, a thorough analysis had been done on 46 animals. Half of those died while sick with pneumonia.

Raverty and others also published a paper in 2010 about a killer whale that had washed up dead years earlier in California. It had been infected with a strain of Salmonella normally associated with birds, humans and livestock. It had never been seen before in a killer whale — and this particular animal was a transient that had spent most of its life far out to sea.

The researchers know their work just raises more questions, but few now dispute that the answers may matter.

“We’re beginning to see that understanding disease is going to be important — and a big challenge,” Hanson said.

Craig Welch: 206-464-2093 or On Twitter @craigawelch.