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

Controlled plant growth in laboratories can be achieved by cultivating plants under sterile or axenic conditions on predefined synthetic growth media, typically supplemented with sugar. In nature, plants do not receive exogenous sugar supplies, form symbiosis with microbes, and plant growth is influenced by soil edaphic factors. Thus, physiological and multi-omic analyses of plants grown on synthetic media will differ from those of soil-grown plants due to the influence of sucrose, and the absence of microbiota and soil edaphic factors on plant growth. The rapid advances in spatial omics call for accurate characterization of plants grown under 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 and on ArtSoil under various growth conditions. We 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 demonstrate its potential to decouple nutrient effects from microbiota in plant growth. We conclude that ArtSoil offers a more physiologically relevant alternative to conventional media for studying plant growth within a soil-like context.