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The Obama administration is losing its most powerful supporter of local and organic foods. Kathleen Merrigan, the No. 2 official at the U.S. Department of Agriculture, announced last week that she would be leaving her post as USDA’s deputy secretary. Sustainable agriculture groups responded with dismay and disappointment to what the

Columbus Dispatch described as her “abrupt” departure. The food industry publication The Packer speculated that this could spell “the end of local food at USDA.”

Merrigan is best known for her local foods initiative called Know Your Farmer, Know Your Food, which brought all of the agency’s efforts to improve regional and local food systems under one conceptual roof. It was a modest program in terms of budget – its funding was measured in mere millions while agribusiness reaped tens of billions in subsidies – but it was the first effort of its kind at an agency long known for its support of large commodity growers. (And small as it was, it was revolutionary enough to draw the ire of Republicans.)

Merrigan is also credited with preserving strong standards for the Organic label, championing a national farm-to-school program, funding hoop houses to allow farmers to grow later into the season, and acting as a key player in the effort to improve the foods sold in school vending machines. Jerry Hagstrom has a good wrap-up in

National Journal.

But it wasn’t just about her favored policies. Merrigan also provided political cover to her boss, Secretary of Agriculture Tom Vilsack. She was a counterweight to the administration’s more industry-friendly moves, especially regarding support for biotech seeds. Decisions like Vilsack’s fast-tracking of approval of so-called Agent Orange corn and USDA’s willingness to ignore a court order and allow farmers to keep growing GMO sugar beets infuriated sustainable-agriculture types. But Merrigan’s presence near the top of USDA’s chain of command convinced them that the agency wasn’t totally in the tank to Big Ag.