Part 3 of a 3-part series

In the summer of 1871, a young state official purchased 111 live Atlantic salmon from fishermen, loaded the fish into special boats and headed up the Penobscot River on an ambitious mission.

Charles Atkins didn’t have many tools at his disposal as he sought to save a species that had already become a powerful economic and recreational force in the state. All he had was an old mill near Orland, rudimentary equipment and a few ideas for keeping wild salmon alive in captivity.

But Atkins, the head of Maine’s fisheries department, would produce more than 70,000 eggs for rivers in Maine, Massachusetts and Connecticut at his Craig Brook hatchery that year.

More than 130 years later, a hatchery still operates at Craig Brook based upon many of Atkins’ pioneering goals and principles. But the techniques, and results, are likely beyond anything Atkins could ever have imagined.

Wild fish plucked from the waters as potential spawning “broodstock” undergo intensive health and genetic screening to avoid introducing diseases or non-native genes into the controlled environment. The salmon selected for breeding are then implanted with microchips that tell biologists the fish’s age, genetic profile, river of origin and spawning history. Computers crunch that data to determine the best pair to mate, based on each fish’s genetic history, in order to maximize the diversity of their offspring.

Each spring, between 2 million and 3 million salmon hatchlings are released into their ancestral rivers throughout Maine.

“We are not treating our fish as an agricultural commodity,” said Denise Buckley, a biologist and assistant manager at the Craig Brook National Fish Hatchery. “We are treating them as unique resources, and there is a huge amount of science behind it. We’re trying to ensure that we release the most genetically diverse, healthy fish as possible.”

Emphasis on genetic diversity is a fairly recent trend in Maine’s salmon restoration efforts, beginning in earnest about a decade ago. Prior endeavors all had the same noble goal – to protect a fish species in serious decline – but the tactics changed often.

For instance, scientists now believe that most Maine salmon rivers harbor unique populations genetically engineered by nature to thrive within that specific river. So a Penobscot salmon would be less fit to survive in the Machias River than a Machias salmon.

Yet for more than a century, eggs and young hatchlings from the Penobscot lineage were stocked in other Maine rivers. Likewise, when salmon populations in the Penobscot dwindled, the Machias and Narraguagus rivers became sources for eggs and broodstock.

More than 26 million Canadian eggs were used in Maine’s restoration program between about 1920 and 1987, according to egg utilization tallies compiled in the book “Maine Atlantic Salmon: A National Treasure” by former salmon biologist Ed Baum.

Researchers now know that salmon from Canadian waters such as the famed Miramichi River develop differently and may spawn at different points in their lives.

Salmon from the Pacific Northwest were even stocked in Maine rivers briefly, although none of the populations became permanently established.

Today, biologists at the U.S. Fish and Wildlife Service’s Craig Brook National Fish Hatchery run essentially six distinct hatcheries under one roof: One each for the Penobscot, Machias, East Machias, Dennys, Pleasant and Narraguagus rivers.

Each river’s stocks are isolated from the others to avoid contaminating the gene pool or spreading disease that could wipe out an entire year’s crop of young salmon.

“I think we are doing a pretty good job of maintaining genetically pure, clean salmon in our facility,” said Carl Burger, manager of the Maine Fisheries Program Complex, which includes the Craig Brook hatchery.

Atkins would likely have been most impressed, however, with biologists’ ability to glean a long list of detailed information about each broodstock fish’s history by literally waving a wand over the salmon’s spine.

Sitting in a conference room within the hatchery complex, Buckley held a small “tag” about a half-inch long in one hand and an electronic tag reader in the other. The tag, or “passive integrated transponder,” is implanted behind the dorsal fin of each of the hatchery’s 3,700 broodstock fish.

By waving the electronic reader over the salmon’s fin, biologists learn the tag number of the specific fish which, when entered into a computer, pulls up the fish’s age, river of origin and number of times it was spawned at the hatchery.

A special computer database can then cross-match that fish’s genetic profile with the hundreds of potential mates in that river’s broodstock to recommend the best combination. Fish in Craig Brook’s broodstock are collected in the wild when they are young, grown to sexual maturity at the hatchery and spawned at most twice before being re-released.”We know genetic diversity is healthy, so we want the smallest number of shared genes, and that’s what this software tells us,” Buckley said.

Baum, a 30-year veteran of Maine’s restoration efforts and the state’s former top salmon biologist, said working with salmon can be frustrating because of the challenge of observing and tracking the fish in the wild. But he said technology is helping.

“The research tools available to scientists are such a boon to the program,” said Baum, who retired in 2000. “We have learned so much about these salmon in recent years … but we still have a long way to go.”

Just outside of Ellsworth, at the Green Lake Fish Hatchery, also operated by the U.S. Fish and Wildlife Service, biologists speed up the growth cycle of salmon destined for the Penobscot by manipulating the water temperature and the fish’s food intake.

The result is 650,000 salmon smolts ready to make the transition from freshwater to saltwater in a little more than a year rather than the nearly two years it would take in the wild.

But the Green Lake program is costly – about $1 per smolt.

Several private organizations, such as the Downeast Salmon Federation, operate their own fry hatcheries to help with the restoration efforts. The federation, which focuses on Washington County rivers and education programs, released approximately 50,000 fry into Down East rivers last year.

A group in Aroostook County, meanwhile, is taking a decidedly lower-tech and less-expensive approach to restoration than the federal government.

Like the federal hatchery at Craig Brook, the hatchery owned and operated by Atlantic Salmon for Northern Maine raises only salmon fry because they do not require feeding. Newly hatched salmon live off the remains of their egg sacs for a few weeks – about the same time fry are typically stocked in Maine rivers.

Those fry will spend one to three years in the river before becoming smolts when they head to the ocean to begin their next life stage. By contrast, smolts raised at the federal hatcheries generally head for the ocean soon after being released in Maine rivers.

But just a quick tour of the group’s Ashland-area hatchery, which was built in the 1990s, is enough to realize that this nonprofit does things a bit differently than the feds.

Water from a nearby stream flows through a series of washable filters, identical to those used in paper mills, and into PVC piping like that found in any home improvement store. The water trickles down through large, fiberglass boxes holding up to 100,000 eggs, which are from St. John River broodstock supplied by Canadian fisheries officials.

As eggs hatch, the tiny fish swim to the top of the boxes and eventually into a giant tub that looks like a supersized Rubbermaid product. One employee and a bunch of volunteers oversee the whole operation on a “shoestring” budget because, until recently, the hatchery received no public money, according to member Jim Barresi.

Even the club’s impressive hatchery, which produced about 500,000 fry this year but has the capacity for more than 2 million, was financed with donations. The group also raised more than $200,000 to build a new fishway at Tinker Dam on the Aroostook River in New Brunswick just across the border from Fort Fairfield.

Barresi, a gregarious character well-known in Aroostook County business and political circles, exudes pride when he talks about the club’s fundraising successes over the years.

The club’s Dug Brook hatchery has yet to produce significant results, despite the number of fry that are stocked. Only a handful of adult salmon typically return to the Aroostook River annually, according to fish counts at Tinker Dam.

But Barresi remains convinced that the Aroostook can become Maine’s top Atlantic salmon river.

“All we have to do is be resolute and keep the thing going until the numbers are there,” Barresi said.