Few federal agencies are expected to undergo as radical a transformation under President-elect Barack Obama as the Environmental Protection Agency and the Interior Department, which have been at the epicenter of many of the Bush administration's most intense scientific and environmental controversies.

    The agencies have different mandates - the EPA holds sway over air and water pollution, while Interior administers the nation's vast federal land holdings as well as the Endangered Species Act - but both deal with some of the country's most pressing environmental concerns, such as climate change. And over the past eight years, many career employees and rank-and-file scientists have clashed with Bush appointees over a number of those of issues, including whether the federal government should allow California to regulate tailpipe emissions from automobiles and how best to prevent imperiled species from disappearing altogether.

    In June 2007, Obama told reporters in Reno, Nev., that he would not hesitate to reverse many of the environmental policies Bush has enacted by executive order.

    "I think the slow chipping away against clean air and clean water has been deeply disturbing," Obama added. "Much of it hasn't gone through Congress. It was done by fiat. That is something that can be changed by an administration, in part by reinvigorating the EPA, which has been demoralized."

    Global warming policies are expected to mark one of the sharpest breaks between the Obama and the Bush administrations.

    EPA Administrator Stephen L. Johnson overruled his career advisers in deciding to deny California authority to control tailpipe emissions and rejecting their conclusion that global warming poses a threat to public welfare, and Obama is likely to reverse both of those policies shortly after taking office. This month, the president-elect told delegates to the Governors' Global Climate Summit that he would push for a federal cap-and-trade system designed to reduce greenhouse gas emissions to 1990 levels by 2020 and then to cut them an additional 80 percent by 2050, targets Bush has never embraced.

    "Delay is no longer an option. Denial is no longer an acceptable response," Obama said in a videotaped message. "The stakes are too high, the consequences too serious."

    Jamie Rappaport Clark, executive vice president of the advocacy group Defenders of Wildlife, said that together, the two agencies will help shape the government's response to climate change.

    Clark, who headed the Fish and Wildlife Service under President Bill Clinton, is not a formal Obama adviser, but many of her former Clinton colleagues are helping the transition team, including David Hayes, a partner at Latham & Watkins; John Leshy, a professor at the University of California's Hastings College of the Law; and Robert Sussman, a senior fellow at the Center for American Progress.

    "EPA will play the lead role in crafting a regulatory response," Clark said. "Interior has a huge role to play in adaptation" -- the effort to cope with climate changes that are already happening, such as drought and more frequent wildfires.

    EPA spokesman Jonathan Shradar said Wednesday that the agency is focused on finalizing policies on coal-fired power plants and other matters, but he would not speculate on the task the next administration faces: "We'll let the next team decide what their priorities will be when they get here."

    With escalating responsibilities, both agencies will need more resources after years when their budgets shrank, relatively speaking. The EPA received $7.5 billion from Congress in 2008, down from $7.8 billion in 2001. Interior has fared slightly better, getting $11.1 billion compared with $10.4 billion in 2001, but that represents more than a 10 percent cut in inflation-adjusted dollars.

    Sen. Barbara Boxer (D-Calif.), who as chairwoman of the Senate Environment and Public Works Committee has feuded with both Johnson and Interior Secretary Dirk Kempthorne over global warming and other issues, said in an interview that she has high expectations of the people who will take their places.

    "I'm expecting President-elect Obama to select people who really care about the issues they're in charge of, someone who believes in their mission and not someone who's going to undermine their mission," she said. "That's a sea change."

    There is a long list of Democrats vying to take the helm of both agencies. The two leading contenders for EPA administrator are Mary Nichols, a favorite of Boxer's who chairs the California Air Resources Board, and Lisa Jackson, who is in the midst of switching from heading New Jersey's Department of Environmental Protection to serving as chief of staff to New Jersey Gov. Jon S. Corzine. Other possible nominees include Pennsylvania Department of Environmental Protection Secretary Kathleen McGinty; Massachusetts Energy and Environmental Affairs Secretary Ian Bowles; former Sierra Club president and environmental activist Lisa Renstrom; and Robert F. Kennedy Jr., a Pace University law professor and chairman of the Waterkeeper Alliance, another advocacy group.

    The list for Interior is almost as long. Two House Democrats, Raul M. Grijalva (Ariz.) and Mike Thompson (Calif.) are contenders, but Rep. Jay Inslee (D-Wash.), Montana Gov. Brian Schweitzer, former Oregon governor John Kitzhaber, National Trust for Historic Preservation President Richard Moe, as well as three former Interior officials - David Hayes, John Leshy and Clark at Defenders of Wildlife - have all been mentioned.

    Regardless of who takes over at the agencies, the new leaders will face impatient scrutiny from green groups eager to change the government's trajectory on the environment. Frank O'Donnell, who heads the advocacy group Clean Air Watch, ticked off 10 initiatives he expects the new EPA administrator to undertake, including changing rules on emissions from coal-fired power plants and monitoring airborne lead pollution more closely.

    "The Bush administration has cut so many special deals for industry that it could be a Herculean effort reversing them all," O'Donnell said. "The new team is going to have to muck out the regulatory stables."

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    Staff researcher Madonna Lebling contributed to this report.