A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming

Bacterial communities are among the main players in the colonization of arid ecosystems and their importance for soil development and plant fitness is emerging. Traditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, influencing the structure of plant associated microbiome and its functional role in supporting plant development under drought stress. To evaluate the contribute of root microbiome on crop plants growth in arid soils, the bacterial diversity associated to pepper plants cultivated in a Egyptian desert farm was studied. Culture-independent and -dependent analysis of the microbiome associated to root tissues and rhizosphere showed a difference in the spatial distribution of bacterial genera according to the microhabitat, indicating a selective pressure determined by the plant activity. Particularly, the endophytes were dominated by the sporeformer Bacillales order represented by the Bacillus and Paenibacillus genera. On the contrary, Gammaproteobacteria were predominant in the rhizosphere, with many isolates assigned to Enterobacteriaceae family. In order to identify polyvalent isolates capable of expressing multiple activities against drought stress, plant growth promotion (PGP) properties of the isolates were assessed in vitro. The most performing PGP strains showing a close association with the root system were tested in greenhouse experiments demonstrating their capability to enhance the biomass and photosynthetic activity of plants under drought stress. The complex nature of the microbiome associated to the pepper root system suggests the ability of plant root system to attract and select microbial communities endowed with multiple PGP traits that sustain plant development under water limiting conditions