Root inoculation with Herbaspirillum seropedicae RAM10 reveals structural and functional shifts in the wheat seed-borne microbiota associated with improved plant phenotype

Exploiting the beneficial features of the plant microbiota is a promising approach to improve cereal growth and health in a more sustainable manner. Seed-borne endophytic microbiota can intimately colonize the plant’s endosphere and influence plant responses efficiently. Understanding their structure and functions is a critical step towards the formulation of microbial inoculants that can promote plant-beneficial microbiota functions. In this study, both 16S and ITS metabarcoding analyses were employed to explore the structure of the endophytic seed-borne microbiota in wheat seeds as well as in roots either non-inoculated or inoculated with the endophytic bacterium Herbaspirillum seropedicae RAM10. Furthermore, machine learning tools were employed to predict the ecological functions associated to these structural shifts. Inoculation with H. seropedicae markedly changed the composition of the seed-borne endophytic community. This compositional shift mirrored a predicted functional diversification, which was manifested by the differential enrichment of OTUs involved in bacterial nitrogen fixation, nitrate metabolism and aerobic chemoheterotrophy as well as by changes in fungal life strategies. These results suggest that endophytic inoculants could represent suitable vehicles to effectively promote desired plant traits through the modulation of the wheat seed-borne microbiota in the root endosphere.