The metatranscriptomic response of the wheat rhizosphere to drought varies with growth stages

Microbes can help plant sustain abiotic stresses, such as drought. Plant-microbe interactions are, however, dynamic and the timing of the stress will affect both partners, directly and indirectly. Here, we hypothesize that the effect of drought stress on the wheat rhizosphere microbiome would change between key growth stages. We grew wheat in pots and reduced soil water content for two weeks at stem elongation, booting, or heading. We then sampled the rhizosphere soil and sequenced its metatranscriptome. The timing of the drought strongly affected the transcriptional response of the microbes, but few differentially abundant transcripts were shared across all stages. Some common patterns were, however, observed at higher taxonomical or functional levels. Drought also affected the normal succession across wheat growth stages. Many of the differentially abundant transcripts, taxa, and functions between growth stages of the control plants were not significant anymore for plants that experienced drought. Our results suggest that the timing of the drought event is paramount to the microbial rhizosphere communities and that it could explain the heightened sensitivity of younger plants to stresses.