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bioRxiv · 10.1101/2025.01.30.635401

Genetic memory devices to detect specialized metabolites in plant and soil microbiomes

Hansen, M. L.·Kordatos, K. I.·Norgaard, J.-J. K.·Jorgensen, J. P.·Strube, M. L.·Schostag, M. D.·Yang, L.·Jelsbak, L.
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Abstract

Root-associated microbiomes significantly influence plant growth and resilience through intricate chemical dialogues mediated by plant- and microbe-derived specialized metabolites. These metabolites play pivotal roles in shaping the assembly, dynamics, and ecological functions of soil microbiomes. Despite advances in in vitro and DNA sequencing studies, a comprehensive understanding of in situ chemical signaling within plant and soil microbiomes remains elusive due to experimental constraints. To address this gap, we developed and tuned a set of five whole-cell biosensors in Escherichia coli for spatiotemporal, non-disruptive detection of biologically relevant specialized metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, tetracycline, salicylic acid, and naringenin. Four of these biosensors were successfully adapted to the soil-compatible Pseudomonas putida KT2440 {Delta}all-{Phi} strain. Additionally, the four sensors were shown to respond to their cognate ligand in a non-sterile soil extract medium containing the diverse microbiome found in soil. By employing genetic memory devices with DNA barcodes for readouts, our approach provides a scalable platform for sensing additional specialized metabolites in the future. This work demonstrates the potential of real-time biosensor technologies to unravel the complex chemical interactions driving soil microbiome ecology, with implications for sustainable agricultural practices.

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Hansen, M. L., Kordatos, K. I., Norgaard, J.-J. K., Jorgensen, J. P., Strube, M. L., Schostag, M. D., Yang, L., Jelsbak, L.. 2025-01-30. Genetic memory devices to detect specialized metabolites in plant and soil microbiomes. https://doi.org/10.1101/2025.01.30.635401

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