Diversity, Composition and Resilience of the Root Microbiome of Tomato Plants in a Hydroponic Rockwool System

ABSTRACT

In hydroponic horticulture, where soil is replaced by a sterile artificial substrate, attention to microorganisms is primarily focused on the suppression of plant pathogens and the application of potentially beneficial organisms. This study examined the ecology of the root microbiome of tomato plants which were grown to maturity in a hydroponic rockwool system and then treated with a Trichoderma ‐based biocontrol product. The bacterial community was species‐rich but was dominated by a small number of Alphaproteobacteria, Gammaproteobacteria and Bacteroidia species. The fungal community was less diverse and consisted almost exclusively of Ascomycota and Rozellomycota species. Biocontrol treatment did not have a significant effect on bacterial diversity, but the microbiome composition changed distinctly over the period of sampling in both treated and untreated plants. These results support the view that mineral substrates in a hydroponic system can support a complex and resilient root microbiome. Understanding the microorganisms that thrive in this unique environment may help identify effective biological treatments, and enable the development of rockwool‐specific practices for monitoring, protecting and promoting plant health.