Abiotic treatment to common bean plants results in an altered seed microbiome

We performed a pilot study in a controlled growth chamber to investigate how the seed microbiome of the common bean ( (var. Redhawk)) was altered under abiotic treatments relevant for crop management with changing climate. Bean plants were subjected to one of three treatments: 66% water withholding to simulate mild drought, 50 % Hoagland nutrient solution to simulate fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene amplicon sequencing and ITS amplicon sequencing of the endophytic metagenomic DNA to assess seed bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed microbiome structure was high while alpha diversity was low, with tens of taxa present. Water withholding and nutrient addition altered the seed microbiome structure for bacterial/archaeal communities as compared to the untreated control, and each treatment resulted in a distinct microbiome structure. There were no statistically supported differences in the fungal microbiome across treatments. While we discuss several limitations of this study, the promising results suggest that further and more comprehensive investigation is needed to better understand abiotic stress-induced changes in the seed microbiome, the mechanisms that drive those changes, and the implications of seed microbiome changes for the health and stress responses of the next plant generation.