Drought duration determines the recovery dynamics of rice root microbiomes

Abstract

As extreme droughts become more frequent, dissecting the responses of root-associated microbiomes to drying-wetting events is essential to understand their influence on plant performance. Here, we show that rhizosphere and endosphere communities associated with drought-stressed rice plants display compartment-specific recovery trends. Rhizosphere microorganisms were mostly affected during the stress period, whereas endosphere microorganisms remained altered even after irrigation was resumed. The duration of drought stress determined the stability of these changes, with more prolonged droughts leading to decreased microbiome resilience. Drought stress was also linked to a permanent delay in the temporal development of root microbiomes, mainly driven by a disruption of late colonization dynamics. Furthermore, a root-growth-promoting Streptomyces became the most abundant community member in the endosphere during drought and early recovery. Collectively, these results reveal that severe drought results in enduring impacts on root-associated microbiomes that could potentially reshape the recovery response of rice plants.