Transcriptome analysis Arabidopsis Col-0 plants grown under axenic and holoxenic conditions in FlowPot gnotobiotic growth system

We performed RNA-Seq based gene expression analysis of Arabidopsis Col-0 plants grown under axenic and holoxenic conditions in FlowPot system. Holoxenic plants were grown in the presence of soil slurries containing microbial communities derived from natural soils and under axenic condition in presence of heat-killed soil slurries for three weeks. We identified genes differentially enriched in response to presence of microbial communities. Our results suggested that in presence of microbiota there is a differential expression of immunity/defense-related genes in holoxenic compared to axenic plants. Overall design: Whole rosette tissues of 21-days old plants from three biological replicates each defined as a pool of eight rosettes were collected from four FlowPots within the same microbox. For holoxenic experiments, natural community inputs harvested from soils obtained from two geographical locations (MSU and Laurel) were used. For axenic mock-inoculated plants corresponding autoclaved soil slurries were used.