Humic substances increase tomato tolerance to osmotic stress while modulating vertically-transmitted endophytic bacterial communities

While humic substances (HS) are recognized for their role in enhancing plant growth under abiotic stress by modulating hormonal and redox metabolisms, a key question remains: how do HS influence the microbiota associated with plants? This study hypothesizes that the effects of HS extend beyond plant physiology, significantly impacting the associated bacterial community. To explore this, we investigated the combined and individual impacts of HS and osmotic stress on tomato plant physiology and roots endophytic communities within a sterile hydroponic system. Growing plants under sterile conditions allowed focusing on seed-transmitted endophytic bacteria, enabling a detailed examination of these interactions. Moreover, sequencing the 16S-ITS-23S region of the rrn operon ~4,500 bp in a metabarcoding assay using the PNA-chr11 clamp nearly eliminated reads assigned to Solanum lycopersicum and allowed species-level identification of these communities. Our findings revealed that osmotic stress, HS, and their combined application induce changes in bacterial endophytic communities. Osmotic stress led to reduced plant growth and a decrease in Bradyrhizobium sp., while HS did not affect plant growth but increased the relative abundance of Hymenobacter sp. and decreased Sphingomonas sp. abundance. Finally, the application of HS under osmotic stress resulted in increased tomato growth, accompanied by an increase in Frigoribacterium sp., Roseateles sp., and Hymenobacter sp., along with a decrease in Sphingomonas sp. This research significantly advances our understanding of the complex dynamics of plant-endophyte interactions under environmental stresses and biostimulant application, highlighting the importance of the vertically-transmitted core microbiome in tomato roots. It underscores the potential of HS to enhance these relationships and opens new perspectives on the mode of action of these substances.