Live-exudation assisted phytobiome culturomics system (LEAP-CS): a high-throughput culturomics system for studying plant-microbiome interactions through diffusible metabolites

Chemical exchange between plants and their microbiome influence each other’s functioning, which ultimately determines agricultural productivity. The diffusible nature of these chemicals allow communication from a distance and the chemical milieu at this interface is highly dynamic and complex due to the contribution from both the host plant and the microbiome. However, current methods do not capture such dynamic chemical exchange where the host plant and the microbiome is physically separated. The Live-Exudation Assisted Phytobiome Cultromics System (LEAP-CS) enables the co-cultivation of plants and microbes using a membrane-based setup that permits chemical exchange without direct physical contact. This system captures root–microbiome interactions by harnessing exudates from both partners. LEAP-CS supports a moderately complex microbial community (~ 146 ASVs) for co-cultivation with plants. Using this system, plant growth assays with bulk and rhizospheric soil microbial communities revealed distinct differences in growth promotion compared to the no-microbiome control- with plants treated with the bulk soil microbiome exhibiting higher growth. Furthermore, exometabolomic analysis of plant root and microbial exudates, along with abundance profiling, suggested a potential source–sink transfer of specific metabolites and small peptides between plants and microbes, indicating their role as potential signaling molecules. This novel in vitro plant growth assay system holds significant potential for investigating the chemical dialogue between plants and their microbiomes under various biotic and abiotic stress conditions. Additionally, the system can serve as a high-throughput platform for screening plant phenotypic traits, enabling the assessment of microbiome functionality and associated metabolic signatures. These fundamental insights can subsequently be validated through greenhouse and field trials to support agricultural applications.