Customizable High-Throughput Chemical Phenotyping of Root Bacteria

Chemical phenotyping is a fundamental technique to study the metabolic properties or chemical sensitivities of bacteria. Traditional methods such as dilution methods, discs, or gradient diffusion assays are labor-intensive, often have high material requirements, and are limited in scalability. High-throughput cultivation approaches based on 96-well plates scale efficiently to large numbers of samples. A stacker, when coupled with a plate reader system (often already available in most laboratories), greatly enhances assay scalability and robustness. Here, we describe a customized high-throughput, flexible, scalable, robust, and affordable method for the chemical phenotyping of bacteria. This liquid culture-based growth system allows screening many bacteria in parallel and in a replicated manner for their tolerance to various chemicals, including specialized metabolites of plants, antibiotics, or pesticides. Compared to commercial solutions, our approach offers high flexibility in experimental conditions while keeping costs for consumables low. Key features • Approach to determine tolerance of bacteria against diverse chemicals, including specialized plant metabolites. • Experimental platform where parameters like strains, media, chemicals, concentrations, or exposure time can be flexibly varied for bacterial phenotyping. • Coupling a stacker to a plate reader permits highly replicated and efficient screenings of large bacterial collections and numerous different compounds.