Delineating Arabidopsis thaliana growth and root microbiome in two culture systems

Agronomy and plant physiology have different goals and, apart from the scale difference, most of the knowledge on the physiology of plants were obtained under conditions artificial conditions. While the beneficial effects of micro-organisms present in the soil on both plant growth and plant resistance to stress, have long been documented the root microbiome of plants grown in green houses or growth cabinet, have received little attention. Most studies, including those on the model plant Arabidospis thaliana, were conducted on plants in their natural soil environment. In parallel, the role of roots in resistance to stress has received renewed attention . Roots are not easily accessible when plants are growing in soil. Therefore several culture systems such as rhizobox have been designed to monitor growth of root separated from soil. Here we report the first thorough investigation of the rhizobox and pot culture systems which combineing plant growth parameter analysis to awith characterization of the compost- and root-inhabiting bacterial communitiesy. We show that the A. thaliana plants grown in rhizobox displayeding a similar growth pattern than in pots, but with a slowed down leaf initiation and growth over the experiment leading to smaller plants. No nutrient deficiency symptoms were observed. Interestingly, roots from plants in rhizobox supported a distinct root microbiome than plants in pot from the same compost, related to a significant reduction of the bacterial richness and diversity. However, the main phyla recovered were similar to Arabidopsis thaliana grown on natural soils It is concluded that the physical partition between plant roots and compost in rhizobox delay the root bacterial colonization, and may shift signalling occurring in the rhizosphere.