The present disclosure provides guided microbial remodeling (GMR) methods for the rational improvement of
plant-associated microbes to perform
plant-beneficial functions. The GMR methods described herein allow for non-intergeneric genetic optimization of key regulatory networks within the microbes, which improve
plant-beneficial functions over wild-type microbes but don't have the risks associated with transgenic approaches (e.g., unpredictable
gene function, public and regulatory concerns, etc.). The present disclosure also provides remodeled microbes and compositions thereof. The utilization of remodeled microbes and compositions thereof will enable farmers to realize more productive and predictable
crop yields without the
nutrient degradation, leaching, or toxic runoff associated with traditional synthetically derived fertilizers.