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BROCKTON, Mass. — Two major environmental groups are split on whether commuter trains should cross Hockomock Swamp in Easton and Raynham — home of a 5-inch salamander and other tiny creatures that some say could derail the project, the Brockton Enterprise reports.

The Sierra Club has given “conditional” support to a $669 million rail extension between Stoughton and Fall River-New Bedford, saying traffic congestion is more destructive to the environment than would be the train.

“You have to look at the alternatives. And the alternative is highway expansion,” said James McCaffery, the Sierra Club’s Massachusetts director.

However, the Massachusetts Audubon Society said the project may not be worth the cost to the environment, though policy specialist Heidi Roddis said a proposed $50 million trestle to raise the tracks above much of the swamp “intrigues” her.

“We have been generally supportive of commuter rail … but we have concerns with this project,” said Roddis.

Debate continues to rage over the MBTA’s proposed Stoughton rail extension as opponents and supporters wait to find out if the state’s environmental chief will issue a permit for the project.

Many officials and residents of Easton, Raynham and Stoughton say the train would harm the environment and pose safety hazards.

City leaders in New Bedford and Fall River say the rail line is needed to connect their cities with Boston, spur economic development and ease traffic congestion on routes 24 and 140 and Interstate 495.

State Secretary of Environmental Affairs Robert Durand is expected to make his decision on the permit in late July or early August. A public-comment period ends on July 8. If Durand gives the project a green light, other state and federal permits will also be needed.

The MBTA filed its final environmental impact report in May with proposed ways to soften the rail line’s impact on environmentally sensitive Hockomock Swamp.

The rail line would extend from existing tracks that connect Stoughton with Boston. It would run through Easton, Raynham and part of Taunton, fork in the Berkley area and head on two lines to Fall River and New Bedford.

The proposed trestle would start at Foundry Street in Easton and end at the Raynham-Taunton Greyhound Park crossing. The structure would be made of concrete beams supported by piles spaced 30 feet apart.

The trestle would span the swamp for a 2.25-mile stretch, stand three feet above existing ground level and be 20 feet wide, the MBTA report indicates.

Roddis, of the Audubon Society, said the trestle might have the benefit of reuniting segmented parts of the swamp. Large, uninterrupted habitats are important for some species, and are becoming rare. Currently, the existing rail bed divides the swamp into two unequal areas.

The Sierra Club’s McCaffery said the existing rail bed is a problem because it attracts all-terrain vehicle riders and no one is responsible for maintaining it. Making the rail line active would help stop ATV activity and bring back a “responsible party to maintain culverts,” he said.

The MBTA is proposing to build culverts along the rail line’s path through the swamp to help preserve wildlife habitats. The agency is proposing $5 million in non-infrastructure, mitigation measures to ease the rail line’s environmental impact. Some local officials say the decision over the rail line could come down to the fate of a salamander.

While at least 13 endangered and rare species live in the swamp, such as the Eastern box turtle and the Mystic Valley amphipod, the 5-inch-long blue-spotted salamander has garnered the most attention. Protecting that species prompted the MBTA to propose the $50 million trestle.

The current dilemma dates back to an unknown 19th-century railway engineer who decided to route the train’s path through the Hockomock Swamp.

In that environmentally deaf era, cost and convenience dictated routes, with little thought given to the environmental consequences. This was the same era that saw the destruction of thousands of acres of wetlands to provide land needed by a growing Boston. And without that land, Boston could never have become a major city.

Now, Boston-bound commuters clog every available route to get to that hub, creating the impetus for MBTA’s expansion of commuter rail throughout eastern Massachusetts. The MBTA has already restored commuter-rail lines between Boston and Middleboro-Lakeville and Plymouth-Kingston, and plans to start building the Greenbush line down the shoreline to Scituate-Cohasset.

The Stoughton rail extension is the next big project. But 21st-century rail planners have to consider the welfare of endangered species and preserve their surviving habitats.

So the 16,950-acre Hockomock Swamp has become the focus of attention. The proposed rail expansion would run through two miles of the swamp, which is a state-designated Area of Critical Environmental Concern. Assistant Town Administrator Martha White, who is leading Easton’s fight against the rail plan, says the swamp is the linchpin of the fight.

The town still questions an earlier MBTA analysis that concluded the Stoughton line is the only viable route for the Fall River-New Bedford commuter rail, she said.

The town believes the MBTA manipulated its study data to exclude an Attleboro alternative in order to please Taunton, she said. Taunton officials prefer the Stoughton extension because there would be fewer rail crossings in their city than an Attleboro line.

However, Doug Prizzi, spokesman for the Executive Office of Environmental Affairs, has said Durand accepted the MBTA’s analysis and is very unlikely to ask the agency to go back and look at the rejected alternatives.

So now, White said, the swamp – and its creatures – will likely make or break the project. “And it’s the reason why we want to kill the project. We’re not using the swamp to achieve another objective,” she said. Easton residents worked hard to get the Hockomock designated an Area of Critical Environmental Concern long before there was any railroad proposal, she said.

The noise and quality-of-life issues always come up when a rail line is proposed and are not enough to stop one, White said.

But with the Stoughton rail extension, the law is on the town’s – and the salamanders’ side, White said. Kyla Bennett of Easton, New England director of the Public Employees for Environmental Responsibility, said that if it is necessary now to choose between the Hockomock environment and Fall River and New Bedford’s interests, the environment must prevail.

“We have been erring on the side of development for 300 years. That had to reach a critical point,” she said.

“Biodiversity is an important concept. We don’t know what we have lost,” she said.

The Sierra Club has parted company with other environmental groups because it considers the big picture, McCaffery said.

“We recognize that it’s not without controversy,” he said. “You don’t put a rail line through an Area of Critical Environmental Concern without considering the consequences.”

But southeastern Massachusetts is the fastest growing area in the state, and expanding the highways is far more destructive than a rail line, he said. The Sierra Club is making its support conditional because it is not convinced the MBTA has done all it could do to mitigate the impact, he added.

Even if the MBTA can show the rail’s benefits outweigh the cost, it still needs to protect the environment, Roddis said.

White said the project cannot be accomplished in a way that will meet the requirements of environmental-protection laws.

“If they adhere to the law, it can’t be permitted,” she said. “The laws were not created to hurt Fall River and New Bedford.”