BANGOR DAILY NEWS PHOTO BY JOHN CLARKE RUSS The lighter-colored salmon eggs in this incubation tray of approximately 8,000 Penobscot strain salmon are dead. Biologists at the Craig Brook National Fish Hatchery in East Orland are concerned about a higher mortality rate for some of the eggs gathered from sea-run salmon. Buy Photo

EAST ORLAND, Maine — Biologists are scrambling to figure out what killed an estimated 800,000 Atlantic salmon eggs at the federal government’s Craig Brook National Fish Hatchery in recent months.

Officials say the massive die-off of eggs should not have an impact on the stocking of juvenile salmon smolts in the Penobscot River, a program that biologists often describe as the “life-support system” for Atlantic salmon in U.S. waters.

But those involved in Maine’s multimillion-dollar salmon restoration program said the event underscores the importance of a little-used contingency program that has been threatened by budget cuts in recent years.

“Because of our planning and because of our backup plan, we did avert a disaster,” said Paul Santavy, manager of the U.S. Fish and Wildlife Service’s Craig Brook National Fish Hatchery in East Orland.

The die-off comes on the heels of one of the best spawning runs of adult Atlantic salmon on the Penobscot in decades. More than 2,100 sea-run salmon returned to the Penobscot in 2008, and roughly 600 of those fish were taken to Craig Brook for use as broodstock in the hatchery program.

But biologists became seriously concerned in December when they began sorting the fertilized eggs. Rather than finding mostly translucent pink, pea-size eggs with the black eyes of the tiny salmon clearly visible, Craig Brook staff found masses of opaque, white eggs that already had died.

“We still don’t know what happened,” Santavy said Saturday while seated in his hatchery office. “We have a pretty wide-ranging investigation ... and internally, we have spent a significant amount of time looking at every single step” in the rearing process.

Santavy estimated that Craig Brook has lost 800,000 eggs from the Penobscot salmon, or about 35 percent of the hatchery’s anticipated production. Eggs produced at the hatchery for other Maine rivers, such as the Machias, do not appear to be affected by whatever is killing the Penobscot eggs.

Craig Brook ended up with about 1 million Penobscot eggs for the agency’s Green Lake Fish Hatchery in Ellsworth, which will raise the hatchlings more than a year until they are smolts — about 6 to 8 inches long. The vast majority of adult salmon that return to the Penobscot year after year can be traced to this smolt-stocking program.

The die-off wiped out more than half of the eggs that would have been used to produce “fry,” which are roughly inch-long salmon released throughout the Penobscot drainage.

Fry occupy an important ecological niche in rivers, even if the chances of their surviving to adulthood are infinitesimally small. Santavy pointed out that those few fry that do survive to adulthood likely will be stronger than their hatchery kin that began life in the wild as smolts.

The die-off has forced Craig Brook to turn to its “bank account” of eggs, which are produced from captive-reared adult salmon kept at the Green Lake hatchery. Craig Brook has dipped into this backup pool of eggs twice in recent years, but this year the hatchery plans to use nearly all of the eggs.

“Because of that ‘bank account,’ our high egg loss is going to be fairly invisible to the Penobscot program,” Santavy said.

Unfortunately, Craig Brook’s use of the backup eggs will be detrimental to a hatchery operated by one of Maine’s salmon clubs.

The Saco River Salmon Club typically receives most of those backup eggs and raises them to fry stage in the club’s extensive hatchery in Biddeford. The club’s volunteer membership then releases the hundreds of thousands of fry into the Saco and Big Ossipee rivers.

While the Fish and Wildlife Service offered to supply the Saco club with roughly 100,000 eggs gathered from other salmon hatcheries, the club’s leaders have opted to shut down the hatchery for the year.

Saco Club leaders could not be reached for comment Sunday.

Santavy said he and other staff with the federal agency are disappointed that the egg failures at Craig Brook have essentially shut down the Saco hatchery. But he said the die-off highlights the importance of the backup program, which has been threatened with closure several times by tight budgets.

Samples of dead eggs have been sent to numerous laboratories for study. Adding to the mystery, all of the batches of non-Penobscot fertilized salmon eggs that are raised at the hatchery had normal mortality rates.

Santavy said staff use the same techniques, the same types of equipment and processes, and the same water for all egg strains, regardless of the source river. Eggs and the resulting hatchlings from different Maine rivers are raised and incubated separately from one another in order to preserve the unique genetic pool of salmon from each river.

Patrick Keliher, who heads the Maine Department of Marine Resources’ Bureau of Sea-Run Fisheries and Habitat, said everyone involved in salmon restoration is upset about the losses. But because the smolt-stocking program was not affected, the egg die-off should not have a major impact, he said.

Like Santavy, Keliher said he is anxiously awaiting the results of the lab tests on the dead eggs.

“Our fingers are crossed that it is not a disease because that would have a big impact on the hatchery program,” Keliher said.