BANGOR (AP) – A federal judge has approved the second phase of a study looking at mercury pollution in the Penobscot River.

One issue is whether it would be better to remove toxic mercury downstream from the former HoltraChem factory in Orrington or let the Penobscot River flush the pollution naturally.

Earlier this year, Senior U.S. District Judge Gene Carter agreed with a team of researchers who said mercury pollution in the lower Penobscot posed a threat to the health of wildlife and humans.

From the 1960s until it closed in 2000, the HoltraChem factory used mercury to produce chemicals for paper mills and other industries.

The study is being paid for by Mallinckrodt Inc., the sole surviving former corporate owner of the chlor-alkali factory.

Mallinckrodt spokeswoman JoAnna Schooler said Monday that the company remains committed to a “thorough assessment of all pertinent data related to the HoltraChem site … and the Penobscot River.”

Schooler said the company continues to work with state environmental officials and already has spent nearly $40 million on the cleanup.

“Consistent with being a good neighbor in this community, Mallinckrodt takes its responsibility toward the cleanup of this site very seriously and remains committed to a diligent and thoughtful approach to completing the environmental remediation of the former manufacturing site,” Schooler said.

The Maine People’s Alliance and the Natural Resources Defense Council won a legal victory against the company in 2002.

“The recent court approval means we can now look forward to the next phase of the downriver study and to ensuring Mallinckrodt continues to be held accountable for threatening our health and environment,” Adam Goode, a community organizer with the Maine People’s Alliance, said in a statement.