High-throughput sequencing analysis provides a comprehensive insight into the complex bacterial relationships in horticultural growing substrates

Despite numerous preventative measures, the hairy roots syndrome is an increasing problem for the greenhouse horticulture in Europe. In this study, we compared the physicochemical and microbial community characteristics of inorganic and organic horticultural substrates in relation to the presence of the plant pathogen Agrobacterium rhizogenes. We aimed to identify how microbial and environmental interactions influenced the development and spread of this disease in a soilless cultivation system. Multivariate statistical analysis performed to assess the characteristics of each growing medium revealed the key variables impacting the resident microbial community, such as potassium and ammonia concentrations. High throughput sequencing analysis of the bacterial abundance of the communities present in organic substrate indicated potential competitive interactions among Methylophilaceae and Actinobacteridae with A. rhizogenes. Based on our hypothesis that horticultural substrates host a particular bacterial population with potential for modulating hairy roots, we determine how the microbe-environment interactions in organic substrates influences the establishment of A. rhizogenes. Our results clarified the complex bacterial relationships in horticultural media. Knowledge regarding these relationships may be used to develop strategies to control the hairy roots syndrome.