PORTLAND, Maine » A boom that saw Maine fishermen harvest millions of pounds of sea urchins for the lucrative Japanese market depleted the spiny sea creatures, turning the ecosystem upside-down and creating an ideal habitat for an urchin predator that has flourished, according to a new scientific study.

The urchin bonanza of the 1990s triggered an ecological chain reaction that “flipped” the ecosystem from one with a stable amount of kelp and Jonah crabs to one with an overabundance of kelp and crabs — and a lack of urchins, the study said.

The urchin population might not recover unless fishery managers find ways to increase the number of fish that prey on Jonah crabs, whose strong numbers have been preventing the urchin population from rebounding, researchers said.

What has happened with urchins underscores the need for ecosystem-based ocean management, where regulators recognize that the rise or fall of one species can affect the rise or fall of another, said Robert Steneck, a professor at the University of Maine’s Darling Marine Center who led the study.

“This kind of ecological interaction was the impetus for President Obama’s initiative in 2010 to move the country toward ecosystem management,” Steneck said. “We have been ignoring strong interactions among species for decades. This is a great example of how it’s more complicated than just assuming that by reducing fishing mortality rates on a managed species, it’s going to recover.”

The paper, “Ecosystem Flips, Locks, and Feedbacks: The Lasting Effect of Fisheries on Maine’s Kelp Forest Ecosystem,” appears in the latest edition of the Bulletin of Marine Science, a peer-reviewed journal published by the Rosenstiel School of Marine and Atmospheric Science at the University of Miami.

The paper was written by a research team that included three University of Maine graduates who at one time studied under Steneck. Besides Steneck, co-authors were Douglas McNaught of the University of Maine at Machias; Amanda Leland of the Environmental Defense Fund in Washington, D.C.; and John Vavrinec of the Pacific Northwest National Laboratory in Sequim, Wash.

Sea urchins used to be a pest in Maine’s coastal waters, destroying kelp beds and clogging lobster traps.

But that changed in the late 1980s when processors developed markets in Japan for the urchin roe, or uni. With a gold rush mindset, thousands of fishermen harvested the globular spiny creatures from the ocean bottom by hand or in devices dragged behind their boats. Hundreds more people worked at processing plants along the Portland waterfront.

For three years straight, the harvest exceeded 30 million pounds, with a peak of 42 million pounds in 1993. The fishery was valued at more than $30 million, making it the state’s No. 2 fishery behind lobster.

But the catch fell sharply in ensuing years as the urchin population shrank. In 2012, the catch was 1.8 million pounds, the smallest harvest since 1987.

With fewer urchins around to graze seaweed, the kelp beds proliferated, providing an idyllic nursery habitat for Jonah crabs, the paper said. When the crabs grew to maturity, they in turn preyed on the urchins that remained.

In 2000 and 2001, Steneck led a team that transplanted more than 50,000 adult sea urchins in plots off Cape Elizabeth to see if the urchins could be brought back. In both years, roving bands of crabs migrated to the plots and wiped out the urchins.

Fishery regulations also have failed to help urchins recover. Despite the creation of fishing zones, limits on harvesters, size limits on urchins and fishing seasons, the urchin industry remains a skeleton of its former self.

Ian Emery, a lobsterman and urchin diver from Cutler in eastern Maine, said the growth in Jonah crabs is probably one of many factors affecting the urchin population. The urchin population varies from area to area, he said, and he sees the numbers ebb and flow on different beds from year to year.

Most people in the industry would be open to different regulations if it would help, he said.

“I think most people are wanting a new approach to management, but they don’t know exactly what that is,” he said.

Steneck said he thinks the oceans could be made more diverse by managing them on a local rather than a broad scale and placing more emphasis on the interactions among species.

“Ecosystem-based management is hard to get at,” Steneck said, “but if we ignore it, we do it at our own peril.”