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The Agriculture Homeland Security Section is responsible for ensuring that Alabama agriculture is as secure as possible. As the threats of this century become broader in their scope and threaten our traditional ways of life, this section was created to help harden our agricultural targets and keep Alabama agriculture as safe as possible. This section manages the Agriculture Emergency Operations Center, which is the hub of agriculture emergency response for the State of Alabama, and develops and administers plans, policies, and training programs for the department, including Food Safety, Animal Health, Pesticide Management, Plant Protection, and other sections. This section coordinates activities with other state and federal agencies such as USDA, FBI, Homeland Security, Emergency Management, universities, commodity groups, trade associations, and others to ensure that plans and policies are effectively communicated, training programs are implemented, and to collaborate in ways that increase the speed and effectiveness of an Agriculture Emergency Response.

This section also manages the Alabama State Agriculture Response Team (SART), which collectively coordinates and manages agriculture emergencies for the department through state employees, private sector employees, and volunteers throughout the state. SART works closely with other agencies to develop plans and protocols that allow for agriculture emergency response to occur, such as developing state disaster animal shelters, responding to motor vehicle crashes involving mass transit of animals, and various other necessary emergency responses.