Researchers team up to solve a ‘50-year old murder mystery’: What’s killing sharks in the San Francisco Bay?

Spirits were low in McCovey Cove as the San Francisco Giants played a discouraging game against the Kansas City Royals. The visitors were on track to win, holding on to an 8-1 lead for several innings.

The atmosphere was buoyed, however, when a cameraman spotted an unlikely supporter in the cove: a leopard shark swimming along the surface of the water. Giants player Jeff Samardzija’s nickname is “Shark,” and fans seemed to interpret the animal as a good omen.

The shark was quickly projected onto the ballpark’s big screen, and announcers took the opportunity to crack jokes about its odd behavior between plays.

Josh Porter, a biologist who works with the East Bay Park District in Alameda, remembers watching the game on television and seeing the leopard shark.

“He was swimming erratically in the water, and it was really fun, happy-go-lucky commentary,” Porter recalled. “I looked out at the screen and was like: Actually, what’s happening is that shark is one of the victims of this outbreak.”

Porter knew the shark wasn’t celebrating — it was dying.

For roughly 50 years, something had been killing leopard sharks and other species in San Francisco Bay. Recent outbreaks in 2006 and 2011 had killed hundreds, possibly thousands, of fish. But the spring of 2017 was one of the worst seasons on record.

Porter estimates that more than 1,000 leopard sharks were killed, in addition to hundreds of bat rays and several other sea creatures, including: brown sharks, smooth hound sharks, seven gill sharks, shovel-nose guitar fish, thornback rays and other bony fish species.

The animals were all exhibiting the same strange behavior. Porter described it as “erratic or almost confused swimming” with their heads above the water, “almost like you could picture a dolphin sticking his head out of the water.” That confused swimming pattern led many sharks to become beached or stranded in shallow water — which, coupled with their odd behavior — gave scientists their first clue in terms of where to look for the killer: inside the sharks’ brains.

The leopard sharks that had beached themselves, or had washed up on shore later, all showed signs of brain inflammation similar to Meningitis in humans. They were suffering from infections, in a massive die-off scientists refer to as an “epizootic event.”

In other words, these weren’t isolated incidents. This was an epidemic.

*During the height of this year’s stranding event, Bay Area residents were invited to contribute their own observations to this record of stranded leopard sharks and bat rays.

Source: iNaturalist

Early signs

Sean Van Sommeran heads up the Pelagic Shark Research Foundation, a nonprofit research organization based in Capitola. He was one of the first researchers to get involved with the leopard sharks, back in the early 1990s.

“We actually established a strandings unit,” said Van Sommeran, who explained the earliest reports came to him from the Marine Mammal Center in Sausalito. “They would get a call about a stranded shark or fish. [And they’d say], ‘Call Sean. He’s crazy. He’ll come get it.’”

Van Sommeran said that it became a routine. Most years, he would receive a handful of reports about stranded or dead leopard sharks. “A dozen would be a big season,” he said. But all of that changed in the early 2000s.

“We had these chronic, repeated reports of big abundances of dead critters, sharks and fish, washing up,” said Van Sommeran.

The Pelagic Shark Research Foundation (PSRF) is a small organization, with roughly half-a-dozen volunteers and student researchers. Van Sommeran said that in the spring and summer, when these strandings reached their zenith, his team was often overwhelmed.

Then, in 2016, the California Department of Fish and Wildlife got involved. Mark Okihiro is a researcher who works for the state; he’s California’s senior fish pathologist. And the leopard sharks had caught his attention.

Okihiro, who was not permitted by Fish and Wildlife to comment on this article, expanded upon Van Sommeran’s efforts to collect shark specimens — coordinating between public land organizations like East Bay Parks, researchers at PSRF, and pathologists at the University of California San Francisco.

Under the microscope

On a recent tour of the East Bay Park District’s aquarium, Josh Porter gestured to a corner of his office. It’s a warehouse-like space, with a single desk and several rows of shelving units. One unit is filled with various glass jars — each containing a different marine animal specimen.

“This is what we sent all the dead sharks in,” said Porter, pointing to an Igloo-brand cooler labelled with duct tape. It reads: California Department of Fish and Wildlife.

“We literally have to cut the head off of the animal, put that in a bag, put some ice packs on it, and ship an ice chest overnight to San Diego,” he said. “My end is, uh, a little less scientific.”

For a more “scientific” research setting, one might look to the DiRisi Pathology Lab at UC San Francisco. Hanna Retallack is a graduate student at the university, and she studies infectious disease. She explained that her involvement with the project actually began with another notable shark species: a Great White.

Retallack had been looking into a separate and unrelated incident involving a shark that had washed up in southern California, when she connected with Okihiro in spring of 2017. She said he clued her into the “much bigger thing going on in San Francisco” with the leopard sharks.

“We didn’t know what we would find, and it was happening right next door. The animals were washing up on the beach right next to us,” said Retallack.

She took vials of the sharks’ spinal fluid — collected from the heads that Porter had been sending to San Diego — and began to look for anomalies in the DNA. By comparing healthy leopard shark DNA and RNA sequences with samples from the diseased specimens, the pathologists at UCSF were able to identify organisms in the animals’ brains that didn’t belong.

At last, researchers had a culprit.

Closing in on a killer

Miamiensus Avidus is a tiny protozoan pathogen — and the primary suspect in researchers hunt for the leopard shark killer. In addition to genetic evidence uncovered by the UCSF pathologists, Miamiensus Avidus has also been identified in tissue samples of the dead sharks’ brains.

But that doesn’t mean the mystery has been easy to solve.

There were a number of false leads. Previously, researchers thought the animals might be contracting a fungal or bacterial infection. One challenge, according to Porter, was that most of the sharks had been dead for a while before researchers could collect tissue samples. And it was hard to separate infections that might have affected the living shark, from products of the dead animal’s decomposition.

Despite setbacks and slow progress, however, Okihiro called the pathogen’s identification a big step forward for the investigation in a written statement issued this fall.

But not everyone is so relieved. Van Sommeran points out that, while we now know the name of the pathogen, we aren’t much closer to stopping future outbreaks. He would like to see more energy focused on environmental factors than on the microscopic invader.

“They’re finding necrotizing protozoans and fungal inclusions. It’s all basic water quality artifacts. That’s all that is,” said Van Sommeran. He believes that Miamiensus Avidus, and the leopard shark die-off, fit into a larger narrative about water quality and habitat preservation in the bay.

“The whole stranding die-off is an artifact of former tidal marine estuaries becoming these deathtraps to wildlife that historically and naturally had always gone in there,” he explained.

In recent decades, scientists have begun to notice outbreak patterns. For example, Okihiro summarized in a statement this summer: Die-offs are typically worse in the spring, when leopard sharks come into the shallow waters to breed. And the worst seasons on record — 2006, 2011 and 2017 — have all been preceded by especially wet winters, when a lot of rain water runoff was pouring into the bay.

This, researchers hypothesized, resulted in lower salinity water and a higher volume of contaminants from the Bay Area’s human population — both of which could weaken the sharks’ immune systems, and make them more susceptible to pathogens like Miamiensus Avidus in the water. (It’s worth noting that no one knows whether the protozoa occurs naturally in the bay, or if it was introduced to the marine environment.) Additionally, the spring spawning brought sharks together in higher numbers, likely increasing the chance of the disease passing from one animal to another.

Van Sommeran doesn’t buy into the idea that “too much fresh water” is killing the sharks, however. He introduced another possible factor: destroyed and altered habitat.

San Mateo, Alameda, Berkeley, sections of Oakland, Richmond and San Francisco — they’re all built on what used to be tidal estuaries, according to Van Sommeran. Estuaries are the shallow, marshy areas where leopard sharks gather to spawn. And some of them, like Lake Merritt in Oakland, have been altered dramatically as the urban landscape changes.

But the sharks don’t know that, he added: “They didn’t get the memo that the tidal estuarian lagoon is now a storm water basin, and those tidal creeks and canals are culverts.”

And with diminishing habitat, Van Sommeran worries that deadly infections among the leopard sharks will only continue. He doesn’t want to see the sharks disappear for good.

“They’re a signature species for California. Like the poppy, the grizzly bear,” he said. “They’re a historic symbol.”