The shift to less-nutritious species in the food web is widespread, but most pronounced in heavily populated South and Central Puget Sound.

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SKAGIT BAY, Skagit County — Correigh Greene hauled the dripping, black net over the stern of the RV Orca and dumped its meager contents into a blue plastic tub: Five fingerling surf smelt, one juvenile herring, a few nickel-sized jellyfish and a handful of assorted larvae.

Paltry catches aren’t unusual on cool, April days, explained Greene, a fisheries biologist at the National Oceanic and Atmospheric Administration (NOAA)’s Northwest Fisheries Science Center in Seattle.

“This is kind of a quiet time of year,” he said, scooping up the silvery fish to weigh and measure. “Things are just ramping up, biologically.”

Late last May, in this same spot near Deception Pass State Park, Greene and his crew hauled up a net so heavy they couldn’t winch it up on deck. But the contents didn’t speak well for the health of the ecosystem.

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Instead of the plump herring and smelt that used to be the dominant forage fish in Puget Sound, the net was bristling with 40,000 sticklebacks — bony, armored fish that seem to be on the upswing. In some parts of the Sound, the researchers’ nets are often crammed with jellyfish — another sign of a shift toward a less-productive environment.

Greene and several colleagues recently sorted through reams of data from similar shallow-trawl surveys dating back to the early 1970s. Their analysis is one of the first long-term looks at forage fish — the unglamorous, bait-sized species that sit in the middle of the food web and are vital to the diets of salmon, marine mammals, seabirds and other fish.

Over the past 40 years, the researchers found that the numbers of herring and smelt have plummeted, while less-nutritious species like sticklebacks, sand lance and jellyfish have proliferated. The shifts were documented throughout the Sound, but were most pronounced in heavily populated areas.

“What this says is that something happened in Puget Sound coincident with modern human activity that is probably not good, and we really need to get to the bottom of it,” said NOAA research biologist and co-author Casey Rice.

In Central and South Puget Sound, ringed by Seattle, Bremerton, Tacoma and other cities, the number of net hauls dominated by jellyfish increased more than sevenfold in places. At the same time, herring catches were 1 percent or less of what they were in the 1970s.

“When we look at the Sound from a boat or a ferry, it looks very beautiful,” Greene said. “But underwater it seems like things have changed quite a bit.”

Climate and commercial fishing were also implicated as factors in the changes, but were not found to be as dominant as the sheer numbers of people living nearby.

The study didn’t prove cause and effect, but it adds to growing concerns about development and its impacts.

“These results fit very well with other evidence that shows how human population is either directly or indirectly impacting fish,” said co-author Lauren Kuehne, an ecologist at the University of Washington.

Breakwaters, seawalls and docks destroy the eel grass beds and beaches where herring and smelt spawn. The structures can also act as jellyfish nurseries, giving larval stages hard surfaces to attach to. Urban runoff and other pollution can impair reproduction in forage fish, and recreational fishing can put a dent in population numbers.

But even in the relatively undeveloped Rosario and San Juan basins to the north, herring catches have fallen by more than 80 percent compared with 1970s levels — though surf smelt numbers actually increased over the same time period.

Long-ignored jellies

The decline of some Puget Sound herring stocks has already been well-documented, said Tim Essington, a University of Washington fisheries professor who was not involved in the project. But the new study is the first to look at jellyfish trends, and taps new sources of information on all forage-fish species.

“It’s a good demonstration of the value of rooting around in these old data sets,” Essington said.

Few early surveys focused on forage fish. So the researchers sought out records from studies of salmon or other species where crews had simply recorded everything their nets brought up. One collection of data was about to be thrown away when the team rescued it from the shredder.

Kuehne transferred data from hundreds of handwritten sheets and old dot-matrix printouts. The modern data came from NOAA surveys in 2003 and 2011. Greene’s Skagit Bay cruise in mid-April was part of ongoing surveys to continue monitoring the trends.

Historic jellyfish information was particularly hard to find, Greene said. About the only time researchers in the 1970s and ’80s took note of the gelatinous creatures was when they pulled up nets bulging with them.

From tiny ctenophores to giant lion’s mane jellies, Puget Sound is the native habitat of multiple species. Reports of large population explosions — called blooms or smacks — date back to the 1950s at least, Greene said. But the scientists were able to document significant upswings in South and Central Puget Sound. In some areas and at some times of year, more than nine out of every 10 recent trawl tows were dominated by jellyfish.

“People who have a history of being out on the water will say: ‘There sure are a lot more jellyfish than there used to be,’ ” Essington said. “This paper quantifies it.”

Climate didn’t appear to be a big factor driving the jellyfish boom, but population density did, Greene said.

Dead-end marine life

Whatever the reason, the rise of jellyfish isn’t good news, ecologically. Jellies compete with fish for plankton and other small prey, and may feed on salmon larvae as well. But few marine creatures relish jellyfish, which is why they are sometimes called biological dead ends.

As part of a program called Eyes Over Puget Sound, Washington Department of Ecology oceanographer Christopher Krembs flies regular surveys over the Sound. In recent years, he’s noticed larger and more frequent blooms.

“This fall and winter, the patches were just enormous,” Krembs said. “They were not just a few blocks long; some of them were 10 blocks long.”

Krembs and his crew landed their floatplane near a huge bloom of moon jellies in Budd Inlet near Olympia in October — when jellyfish usually start a seasonal decline. “It was so dense, you had the feeling you could just walk on them,” he said. As recently as last week, scattered blooms persisted in some spots.

Jellyfish blooms were less common in more sparsely populated parts of Puget Sound — underscoring distinctions between the basins. Those differences can help guide restoration efforts, the scientists say.

In the northern part of the Sound, it might make more sense to focus on protecting undisturbed areas, while in the south, the emphasis should be on restoring damaged habitat.

“In Puget Sound, we’re very fortunate to have a chance with things like wild salmon,” Rice said. “That story is over in Europe. It’s over in eastern North America.”