This session will emphasize challenges, methods, and case studies of biologically-based agroecosystems that rely or partly rely on soil microbial communities for plant nutrient availability, pathogen control, weed suppression, and other processes that support crop growth. A focus will be on how to manage microbial communities to promote specific activities at specific phases of crop growth. Lessons learned from organic management systems can be applied to conventional systems to develop sustainable hybrid systems or support systems transitioning into organic. Hybrid systems may employ innovative strategies including no-till, diverse crop rotations, integrated crop-livestock, and/or cover crops along with conventional practices. These systems might benefit microbial communities similarly as organic systems.