The Office of Science and Technology Policy accounts for $4.5 million of the $1 trillion "minibus" Congress passed yesterday -- a percentage that hardly registers even in an atmosphere of fiscal restraint.

But that amount is more than 30 percent less than last year's budget for the small White House office, and scientists are worried that the deep cut will cripple the coordination of research governmentwide.

"They're already overworked and spread way too thinly to be effective in the way they should be," said Francesca Grifo, a senior scientist at the Union of Concerned Scientists. "In the worst-case scenario, we could start to see duplication of research. One of the key roles they play is to have one agency talk to another."

The spending bill that passed both the House and Senate yesterday keeps the government running until Dec. 16 and funds the Transportation, Agriculture and Commerce departments through fiscal 2012. The Senate approved it by a vote of 70-30, while the House approved it 298-121.

The measure reflects the $1.043 trillion spending cap that both parties agreed to as part of August's debt deal and squeezes funding for agriculture conservation programs, marine research and high-speed rail.

But OSTP's cuts are not due to spending limits. Instead, they are primarily the work of one Republican lawmaker who thought OSTP Director John Holdren needed to learn a lesson.

Rep. Frank Wolf (R-Va.), who chairs the House Commerce, Justice, Science and Related Agencies Appropriations Subcommittee, took Holdren to task earlier this year for holding a meeting with the Chinese science and technology minister and other officials. That cooperation, Wolf asserted, amounted to a violation of a provision he had inserted into the 2011 spending bill that prevented NASA and OSTP from spending money "to develop, design, plan, promulgate, implement, or execute a bilateral policy, program, order, or contract of any kind to participate, collaborate, or coordinate bilaterally in any way with China or any Chinese-owned company."

At a hearing in May, Holdren said he was counseled to interpret the provision as not prohibiting actions linked to the president's authority to negotiate international agreements, several of which exist in energy and economic spheres.

After a GAO analyst told lawmakers that OSTP had violated the provision, Wolf this summer led efforts to cut OSTP's budget by 55 percent in the House spending bill. The spending bill that passed yesterday splits the difference between that House bill and a Senate version that only cut OSTP's budget by 9 percent.

Grifo characterized the deal as "unbelievably crazy."

But Wolf spokesman Dan Scandling said yesterday that the budget cut is meant to "send the message that you obey the law."

"Do we want to coordinate research with the [People's Liberation Army]? Do we want to coordinate research with a country that is spying on us every single day?" he said. "The office needs to make sure that it's obeying the law and that it's not giving away the store."

Scandling dismissed concerns that the cut would hamper research, pointing to increases in funding for the National Science Foundation and the National Institute of Standards and Technology.

"That's where the real science is being done," he said. "I hope that you're not going to focus on a $2 million cut to an office that does no research."

Advocacy groups paint a much bleaker picture.

Alan Leshner, CEO of the American Association for the Advancement of Science, said in a letter to congressional appropriators earlier this month that deep cuts to OSTP could hamper its ability to minimize waste in federal programs and coordinate national science and technology policies.

"We believe such a drastic reduction to OSTP's budget will dramatically inhibit the ability of the federal government to coordinate, prioritize and manage the federal research and development (R&D) effort," wrote Leshner, referring to the House bill's 55 percent cut. "This kind of reduction would also seriously limit the ability to take appropriate account of science and technology considerations in the formulation of diverse policies."

OSTP spokesman Rick Weiss said Holdren announced at a recent all-staff meeting that the office would avoid layoffs and furloughs by not replacing recent departures and losing additional employees through attrition. But to deal with the significant cuts, the office will also "prioritize existing activities in the areas where it has statutory and executive responsibilities for coordinating federal research programs and developing policies," including advanced manufacturing, sustainable energy and scientific integrity.

NOAA and Agriculture

Many programs within other agencies covered under the "minibus" would also see cuts, and most final budget numbers came in below the White House request.

The budgets for agencies not covered under that measure remain uncertain: Earlier this week, Senate leaders failed in their attempt to merge another trio of appropriations bills and instead began debate on a single energy and water measure, then delayed consideration of that bill to December.

The National Oceanic and Atmospheric Administration fared better than some other agencies that saw steeper cuts -- its bottom line would go up 7 percent, compared to fiscal 2011. The majority of the new funding for the agency would go toward new climate and weather satellites.

The bill includes $924 million for the Joint Polar Satellite System -- enough cash to stabilize the nation's struggling environmental satellite program, which is already facing data gaps due to a lack of funding last year.

The "wet" side of NOAA's science -- its programs overseeing ocean research and fisheries -- would take a hit. The general fund for NOAA fisheries operations and research is cut 6 percent, compared to 2011, and survey and monitoring projects are cut 10 percent. Fisheries advocates say those cuts could slow down efforts to end overfishing and restore stocks.

"What to some in Congress are single line-items in a complex budget are critical investments in the information infrastructure that support the well being of Americans who rely on fisheries," said Matt Tinning, executive director of the Marine Fish Conservation Network.

Not all fisheries research programs would suffer. The NOAA funding portion bill includes a significant bump-up for stock assessments -- from $53 million last year to $64 million in 2012 -- and a slight increase for fisheries statistics.

The Agriculture Department, meanwhile, would receive $136.6 billion in discretionary and mandatory spending, $4.6 billion below what President Obama requested.

In all, conservation and energy funding would lose about $1.25 billion compared to their levels set out in the farm bill. The minibus does not spare programs that are popular with farmers, including the Conservation Stewardship Program and the Rural Energy for America Program. The cap on USDA's only program that gives support to farmers for planting biofuels feedstocks would drop from $112 million to $17 million.

Reporter Amanda Peterka contributed.