Bacterial communities in roots and soil from a novel system for studying non-sterile rhizosphere chemistry

A growth system was developed for untargeted metabolome analysis of non-sterile rhizosphere soil. As part of this study modified 30ml plastic tubes were filled with a homogenous 9:1 (v/v) mixture of sand (silica CH52) and dry compost (Levington M3) which were then either sown with Arabidopsis thaliana seeds or left unplanted. The main aim of the experiment was to characterise rhizosphere metabolites by comparing the pots containing plants with those that did not. As the use of suitable non sterile growth substrate was vital to this approach, it was important to determine if the bacterial community in the artificial growth substrate used resembled a natural soil both in its diversity and its response to plant roots. MiSeq 16S rRNA gene sequencing was therefore used to characterise and compare the bacterial communities from the unplanted pots ('control soil' samples) and from roots covered in their associated, tightly bound soil ('root' samples).