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Monitoring Bacterial Colonization and Maintenance on Arabidopsis thaliana Roots in a Floating Hydroponic System

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Customizable High-Throughput Chemical Phenotyping of Root Bacteria.

Lisa Thoenen¹, Caitlin Giroud¹, Claudia Probst¹

¹Department of Environmental Sciences, University of Basel, Basel, Switzerland.

|June 19, 2026

Summary

This study presents a new, affordable method for bacterial chemical phenotyping using high-throughput 96-well plates and a stacker system. It enables efficient screening of bacterial tolerance to various chemicals, including plant metabolites.

Keywords:

Antimicrobials Bacteria phenotyping Bacterial isolates High-throughput Root microbiome Tolerance testing

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Area of Science:

Microbiology
Bacterial Physiology
Chemical Biology

Background:

Chemical phenotyping is crucial for understanding bacterial metabolic properties and sensitivities.
Traditional methods are labor-intensive, require significant materials, and lack scalability.
High-throughput cultivation in 96-well plates offers improved scalability for bacterial studies.

Purpose of the Study:

To develop a customized, high-throughput, flexible, scalable, robust, and affordable method for bacterial chemical phenotyping.
To enable parallel and replicated screening of bacterial tolerance to diverse chemicals.
To provide a cost-effective alternative to commercial solutions with high experimental flexibility.

Main Methods:

Utilizing a liquid culture-based growth system in 96-well plates.
Coupling an automated stacker with a plate reader for enhanced assay throughput.
Implementing a flexible experimental platform allowing variation of strains, media, chemicals, concentrations, and exposure times.

Main Results:

Demonstrated a scalable and robust method for bacterial chemical phenotyping.
Successfully screened bacterial tolerance to various chemicals, including specialized plant metabolites, antibiotics, and pesticides.
Achieved high replication and efficiency in screening large bacterial collections and numerous compounds.

Conclusions:

The developed method offers a flexible, scalable, robust, and affordable approach to bacterial chemical phenotyping.
This system allows for efficient screening of bacterial tolerance to a wide range of chemical compounds.
The integration of a stacker and plate reader significantly enhances the throughput and reliability of bacterial assays.