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 wanted to know how the wheat rhizosphere microbiome would respond to drought stress applied at key growth stages. We grew wheat in pots and stopped watering them at stem elongation, booting, or flowering. 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 transcripts were differentially abundant at 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 transcripts, taxa and functions that varied from one growth stage to the next in the control were not seen under drought. Our results suggest that the timing of the drought event is paramount to the microbial rhizosphere communities, and that it will be difficult to discern any common response to such events.