On September 29, Kevin Shea, Administrator of USDA's APHIS, issued a memo regarding its intention to explore "regulatory alternatives." Specifically, the memo mentions a "series of pilot tests to test the efficacy of the systematic process we’ve set up to consider non-regulatory options for emerging issues, as well as to systematically consider how we can more productively or flexibly use our existing regulations."
One of these pilot tests will involve "issuing a general permit for imports of EPA-registered microbial biopesticides, effective September 17, 2014. These low-risk organisms are regulated by EPA." The Biotechnology Regulatory Service (BRS, within APHIS) has permitting authority for genetically engineered microbes brought into the country, such as for research or registration for use as pathogen control. Here you can find additional details on USDA permitting. The rules are a little different for pesticides, as these are regulated by EPA. Once the EPA-registered microbe is brought into the country, then EPA is responsible for interstate movement, research use, etc. (and of course, since it is registered already with EPA, you will need a Notice of Arrival form from it as well at port, not to mention other submissions depending on what you're doing with it once it arrives ... the regulatory manager's job is never done!)
Information regarding a pilot USDA general permit for imported GE microbial pesticides is scant, but this will likely serve to streamline the overall regulatory process as the federal agencies regulate products of biotechnology per their individual statutory mandate -- which leads to very complex regulatory hurdles for these products.
Both USDA and EPA maintain pages online regarding their joint regulation of products of agricultural biotechnology (which also includes FDA if food) and there is a great recent review paper on the topic, written by staff within the EPA's Biopesticide and Pollution Prevention Division.