Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease (HRD)

The rhizosphere is a complex ecosystem consisting of microbes in the interface between soil and plant roots. Bacterial communities present in the rhizosphere can have an effect on plant health and productivity. Differences in bacterial community diversity and composition could translate into a healthy or diseased plant. Several studies analysing bacterial communities present in the rhizosphere have focused on soil-grown plants. Nevertheless, soilless culture using mineral (rockwool) or organic substrate is an important production system prevalent in several temperate-climate regions. Tomato grown under hydroponic conditions using rockwool has been affected by a disease known as hairy root disease (HRD) that is caused by rhizogenic Agrobacterium biovar 1 strains. In this study, we aimed to characterize bacterial communities in rockwool samples obtained from healthy or HRD-infested tomato growing under hydroponic conditions. Alpha diversity of rockwool increased in direct relation with time and samples obtained from healthy greenhouses presented a significantly lower alpha diversity than those obtained from HRD-infested greenhouses. Beta diversity or bacterial community composition revealed that time is a strong driver of the bacterial community composition. As expected, Amplicon Sequence Variants (ASVs) identified as rhizogenic Agrobacterium bv. 1 were more prevalent in HRD-infected greenhouses. On the other hand, ASVs identified as Paenibacillus, which were previously identified as biocontrol organisms showing antagonistic activity against rhizogenic aAgrobacteria, were more prevalent in healthy greenhouses. This is the first comprehensive study examining the dynamics of bacterial communities in rockwool throughout the growing season. It allowed to identify specific bacterial genera that serve as indicator organisms for either healthy or HRD -infected greenhouses.