Last summer the USDA's Microbiological Data Program (MDP) was the agency that ordered cilantro and bagged spinach that had tested positive for salmonella to be removed from grocery store shelves. It also forced a recall of lettuce that had tested positive for E. coli, and started testing cantaloupe regularly for Listeria after an outbreak that left 13 people dead.

(For more, see: Food safety battle rages over funding)

As part of President Obama's 2013 budget, this program will be shut down.

Food and Drug Administration Produce Safety officials say that testing certain high-risk crops such as sprouts, tomatoes, and cantaloupe would now have to be undertaken by state and local agencies, many of which are already cash-strapped and short on staff.

While USDA has made a number of difficult budget cuts in recent months, to its defense it should be noted that almost all the cuts were mandated by lawmakers and policy managers in Washington. The agency seems to be making an effort to cut their budget as effectively as possible.

Providing the keynote address at the Mighty Mo Flood Conference held at the University of South Dakota last week, USDA National Office Food and Agricultural Council Executive Director John Berge said the agency is “doing as well as possible” with required budget cuts.

“Rural Development has lost about 30 percent of its workforce, and the Farm Service Agency (FSA) has lost 14 to 15 percent,” Berge said. “Many of our customers are not really thrilled that we are in the process of closing 259 USDA offices across the country.”

Of more concern are the lawmakers in Congress. Speaking about the 2012 Farm Bill, Congressman Henry Cuellar, D-Texas, a member of the House Agriculture Committee, says it is beginning to look like Congress will be making sweeping reforms in any new legislation if a new Farm Bill will even make it to the Congressional floor this year.

“The remainder of the 112th Congress is likely to be consumed by the debate of a variety of long-term pieces of legislation, including corporate tax reform, surface transportation funding and debt reduction provisions. Unfortunately, the likelihood of Congress taking up long-term agricultural reform legislation is not promising,” Cuellar says.