Soil microbiomes vary in their ability to confer drought tolerance to Arabidopsis

• Sympatric microbiome increases biomass significantly under drought stress.
• Sympatric microbiome dampening the perception of drought stress.
• Drought response marker genes expression was reduced by sympatric microbiome.
• Identified potential microbe(s) modify plant's ability to sense drought stress.

Drought is a major constraint on agricultural production. Crop genetic improvement for drought tolerance has received much attention and there is ample information about the ability of specific soil microbes to influence drought tolerance in plants. However, in nature, plants interact simultaneously with an array of beneficial, benign and pathogenic microbes. There is a need to understand the cumulative effect of these multiple interactions on a plant's ability to overcome abiotic stresses such as drought. The objective of this research was to investigate the potential of whole soil microbiomes to help Arabidopsis thaliana plants deal with drought stress under in vivo conditions. A sympatric microbiome (i.e., having a history of exposure to Arabidopsis at a natural site) significantly increased plant biomass under drought conditions, but caused earlier death rates as a consequence of drought; whereas, the two non-sympatric soils did not influence Arabidopsis biomass. Consistent with this, we observed reduced expression levels for several Arabidopsis drought response marker genes (ATDI21, DREB1A, DREB2A, and NCED3) in the sympatric Arabidopsis soil treatment. Pyrosequencing analysis of the three soil microbiomes used in this study identified 84 bacterial OTUs (3% genetic distance) from 41 genera (Burkholderia, Phormidium, Bacillus, Aminobacter, Acidiphilum and among others) that were significantly higher in the sympatric Arabidopsis soil, as compared to the two non-sympatric soils. In conclusion, we have identified a robust set of Arabidopsis-associated microbes that when present in the soil can modify the plant's ability to sense abiotic stress and increase its biomass production.