Abstract: 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.

Abstract: Methods of predicting in planta phenotypes of microbial strains are provided. The methods can include culturing microbial strains in a plant exudate medium and assaying in vitro phenotypes of the microbial strains. The methods may also include using the in vitro phenotypes to predict in planta phenotypes of the microbial strains. Methods of using the microbial strains in field trials are also provided.

Abstract: Methods and systems are provided for increasing the phosphate solubilization activity of a microbe. Microbes identified through the use of the disclosed methods and systems are also provided. The methods include the steps of and the systems include instructions for identifying a coding sequence associated with phosphate solubilization, altering the coding sequence associated with phosphate solubilization, functionally linking the altered coding sequence associated with phosphate solubilization to a promoter, and introducing the altered coding sequence associated with phosphate solubilization under the control of the promoter into the microbe. Alterations to the coding sequence can include, e.g., codon randomization of native codons, deletion of coding sequence, and insertion of regulatory sequences.

Abstract: The present disclosure provides the integration of exogenous microbial biofilms to confer increased stability and viability for an extended shelf life of desired microbes (e.g., bacteria), as compared to those microbes in the absence of the exogenous microbial biofilms. The microbes include transgenic microbes, non-transgenic microbes, and non-intergeneric remodeled microbes. The utilization of the taught microbial products will enable a significant expansion of the typical shelf life of microbial compositions. The microbes comprising exogenous biofilms taught herein are able to be combined with other agriculturally beneficial compositions.