Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Developing a High-Throughput Functional Bioimaging Capability for Rhizosphere Interactions Utilizing Sensor Cells, Microfluidics, Automation, and AI-Guided Analyses


Jessica Johnson1, Chase Akins1, Si Chen1, Tomoya Honda2, Neil Getty1, Rosemarie Wilton1, Fangfang Xia1, Kenneth Kemner1, Jean Greenberg3, Yasuo Yoshikuni2, and Gyorgy Babnigg1* (


1Argonne National Laboratory; 2DOE Joint Genome Institute; and 3University of Chicago


The complex dynamics of root-microbe interactions in the rhizosphere drives recognizable spatial structures. However, knowledge of the specific factors that lead to their development and sustain them for plant health and productivity is sparse.


This project aims to develop a unique functional imaging technique that exploits native sense-and-respond circuits of plant growth–promoting rhizobacteria (PGPR) to monitor chemical exchange between the plant root and microbe during the different phases of colonization. Several native PGPRs will be turned into biosensor cells, and root colonization will be evaluated with Arabidopsis and Camelina. Genetic variants of Arabidopsis with gain or loss of function will provide drastically altered local environments, resulting in colonization patterns that differ from those observed previously. An orthogonal X-ray imaging approach will provide high resolution elemental analysis of the local environment, and imaging throughput in general will be accelerated by automation and artificial intelligence (AI)–driven analysis. In addition, the team aims to advance the throughput of current bioimaging capabilities that leverage imaging chips developed with BER funding with automation, and an AI-guided image analysis strategy.

This combined HTP-AI bioimaging capability, along with advanced analytical techniques offered by the Advanced Photon Source and Environmental Molecular Sciences Laboratory, will capture the dynamic chemical shifts and colonization patterns in the rhizosphere.

Funding Information

Argonne National Laboratory is managed by UChicago Argonne, LLC for DOE under contract number DE-AC02-06CH11357. This program is supported by the U. S. Department of Energy, Office of Science, through the Biomolecular Characterization and Imaging Sciences Program, Biological and Environmental Research (BER) Program, under FWP 39156.