Engineering Reliable Genetic Circuits for Characterization and Remediation of Soil Ecologies

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The goal of this project is to develop genetic circuits that can be implemented in engineered microbes operating in (laboratory-based) soil environments that are able to sense and manipulate the concentration of small molecules present in the soil. We plan to use phosphorous as our initial molecule of interest, as a model for other chemical species present in soils.

Current participants:

Additional participants:


  • Dianne Newman

Past participants:



Use of engineered microorganisms for sensing and characterizing rhizosphere properties

​A key element of characterization and remediation of soil ecologies will be developing and understanding of the biology and chemistry of soil ecosystems. Culture and sequencing can provide a broad outline of what is in the rhizosphere. In situ hybridization can contribute to provide some spatial information for specific species and the genes they are expressing. However, much of what we want to know involves understanding the roles of particular genes, and the levels of nutrients and metabolites in specific species in specific microenvironments. While many compounds are found in soils, one of the most important is phosphate, a vital macronutrient. Recently, we have discovered that diverse soil bacteria produce redox-active antibiotics (e.g. phenazines) in response to phosphorus limitations; phenazines help make phosphorus more bioavailable by catalyzing the reductive dissolution of minerals to which phosphorus is adsorbed. Because phenazines biosynthesis is genetically tractable and phenazines can be electrochemically detected, there is an exciting opportunity to build on these discoveries using synthetic biology to detect phosphorus concentration as an exemplar for ​in situ​ detection of other chemical species. Species-specific transgenesis and the creation of reporters and biosensors will contribute to this goal, more broadly showcasing how synthetic biology can be applied to sense compounds of interest in soils.

Use of engineered microorganisms to detect, respond, and manipulate rhizosphere conditions

​In addition to characterization, we ultimately want to be able to perturb the rhizosphere to enhance desired characteristics such as soil material properties or to remediate spills that may have been affected by toxins. Engineered microorganisms provide a mechanism for detecting local environmental conditions and then responding to these conditions by synthesizing and exporting small molecules or proteins that modulate the biological and chemical state of the soil. This work will involve introduction of novel extant wildtype members of other species into environments, and characterization of their fate and influence on other species. It will also involve genetic modification, creation of circuits, and engineering of cooperative and competitive interactions that function in the soil environment. In particular, we plan to demonstrate the ability to sense and respond to the presence of phosphorus, again as an exemplar of manipulation of compounds of interest in soils.


This research is supported by the Institute for Collaborative Biotechnologies through contract W911NF-19-D-0001 from the U.S. Army Research Office. The content of the information on this page does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.

  • Agency: Army Research Office
  • Grant number: W911NF-19-D-0001
  • Start date: 15 Oct 2021
  • End date: 14 Oct 2023
  • Support: 2 graduate students, part-time technician
  • Reporting: Annual reports