Over the last several years our regional atmospheric measurements and mesocosm experiments have revealed that reactive nitrogen losses associated with corn production are likely to increase as our climate continues to get warmer and wetter. Our mesocosm experiments also indicate that alternative nitrogen management techniques have significant potential to reduce reactive nitrogen losses. Here, we propose to extend our mesocosm experimental approach and analyses to assess if the recoupling of grain and animal production systems via improved manure nitrogen management can help to further mitigate reactive nitrogen losses. Finally, there are emerging and exciting claims that “designer” microbial communities can reduce the demand for synthetic nitrogen inputs in corn systems. We will assess if better manure management and if designer microbial communities are effective and practical strategies for reducing reactive nitrogen losses, while maintaining high corn yields in Minnesota.