Synbio in the Soil: Tools, Models, and Applications

Many engineered organisms have been developed in recent years for soil-related applications including biosensing, bioremediation, and pathogen control. However, it is unclear how to deploy these solutions safely, as it is difficult to predict survival and persistence of a genetically engineered microbe (GEM) in a complex soil environment. Further complicating the issue, many well characterized synthetic genetic circuits function well within the lab but fail when introduced to the natural soil environment. In order to enable deployment of synthetic biology solutions in soil, two developments are needed: 1) improved genetic circuit designs optimized for function in the soil environment; and 2) enhanced laboratory models of the soil environment that permit automated, high throughput assessment of GEM survival and function. Herein we report on our progress in these two key development areas. We have developed an automatable and scalable liquid soil extract model for monitoring survival and genetic circuit function of an engineered soil organism Pseudomonas putida, and have successfully employed this model to examine the relationship of engineered P. putida to dominant soil microbes and the native microbiome. We have employed both targeted design and transcriptomics mining approaches to identify both constitutive and inducible promoters with enhanced performance in P. putida under a variety of environmental conditions. Our improved tools are expanding our understanding of the relationship of GEMs to the native soil microbiome and advancing knowledge that will enable future deployment of synthetic biology solutions to global soil challenges.