Prolonged drought imparts lasting compositional changes to the rice root microbiome

Microbial symbioses can help plants mitigate environmental stresses and plant microbiome compositions are influenced, for example, by drought stress. The investigated temporal shifts of the rice root microbiome under various durations of drought show the progression of microbiome composition in response to stress and a long-lasting effect of severe conditions. Microbial symbioses can mitigate drought stress in crops but harnessing these beneficial interactions will require an in-depth understanding of root microbiome responses to drought cycles. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during drought stress and recovery, we find that endosphere communities remained compositionally altered after rewatering, with prolonged droughts leading to decreased resilience. Several endospheric Actinobacteria were significantly enriched during drought and for weeks after rewatering. Notably, the most abundant endosphere taxon during this period was a Streptomyces, and a corresponding isolate promoted root growth. Additionally, drought stress disrupted the temporal dynamics of late-colonizing microorganisms, permanently altering the normal successional trends of root microbiota. These findings reveal that severe drought results in enduring impacts on rice root microbiomes, including enrichment of taxonomic groups that could shape the recovery response of the host, and have implications relevant to drought protection strategies using root microbiota.

Automated summary

The study shows that drought stress can alter the composition of rice root microbiomes, with certain important bacterial groups significantly enriched during drought and maintaining a lasting impact even after rewatering, leading to increased instability in the root microbiota.