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, impacting the plant-associated bacterial community. To explore this, we investigated the combined and individual impacts of HS and osmotic stress on tomato plant physiology and root endophytic communities. Tomatoes were grown within a sterile hydroponic system, which allowed the experiment to focus on seed-transmitted endophytic bacteria. Moreover, sequencing the 16S-ITS-23S region of the <i>rrn</i> operon (~4,500 bp) in a metabarcoding assay using the PNA-chr11 clamp nearly eliminated the reads assigned to <i>Solanum lycopersicum</i> and allowed the species-level identification of these communities. Our findings revealed that HS, osmotic stress, and their combined application induce changes in bacterial endophytic communities. Osmotic stress led to reduced plant growth and a decrease in <i>Bradyrhizobium</i> sp., while the application of HS under osmotic stress resulted in increased tomato growth, accompanied by an increase in <i>Frigoribacterium</i> sp., <i>Roseateles</i> sp., and <i>Hymenobacter</i> sp., along with a decrease in <i>Sphingomonas</i> sp. Finally, HS application under non-stress conditions did not affect plant growth but did alter the endophytic community, increasing <i>Hymenobacter</i> sp. and decreasing <i>Sphingomonas</i> sp. This study enhances the understanding of plant-endophyte interactions under stress and HS application, highlighting the significance of the vertically transmitted core microbiome in tomato roots and suggesting new insights into the mode of action of HS that was used as a biostimulant.