Artificial Soil (ArtSoil): recreating soil conditions in synthetic plant growth media

Controlled plant growth in laboratories can be achieved by cultivating plants in sterile or axenic conditions on pre-defined synthetic growth media typically supplemented with sugar. In nature, plants do not receive exogenous sugar supply, form symbiosis with microbes, and plant growth is influenced by soil edaphic factors. Thus, physiological and multi-omic analyses from plants grown on synthetic media will differ from those of soil-grown plants due to the influence of sucrose, and the lack of influence from microbiota and soil edaphic factors on plant growth. The rapid advancements in spatial-omics call for accurate characterization of plants grown in conditions similar to soil. To address the issue, we developed Artificial Soil (ArtSoil), a growth medium containing essential nutrients for plant growth, and aqueous soil extract (ASE) to maintain soil microbiomes and edaphic factors, simultaneously eliminating the need for sugar supplementation in the medium. We compared Arabidopsis thaliana grown on conventional media to ArtSoil under various growth conditions, and showed that complex soil microbiota in ArtSoil promote plant growth without physiological side effects induced by sucrose. We demonstrate an application for ArtSoil in single-cell transcriptomics and report microbiota-induced cell-type specificity in immune and nitrogen signaling. We tested ArtSoil with six types of ASEs to present the potential of ArtSoil in decoupling the effects of nutrients from microbiota in plant growth. We conclude that ArtSoil recapitulates the soil environment compared to conventional media, hence, enabling physiologically relevant plant growth.