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.

微生物共生可以减轻作物的干旱胁迫，但利用这些有益的相互作用需要深入了解根系微生物组对干旱周期的反应。在这里，通过对干旱胁迫和恢复期间水稻根系相关微生物群落的详细时间表征，我们发现再浇水后内层群落的组成仍然发生变化，长期干旱导致恢复力下降。在干旱期间和补水后数周内，几种内球放线菌显着丰富。值得注意的是，这一时期最丰富的内球分类单元是链霉菌属，相应的分离物促进了根系生长。此外，干旱胁迫扰乱了晚期定殖微生物的时间动态，永久改变了根系微生物群的正常演替趋势。这些发现表明，严重干旱会对水稻根系微生物群产生持久影响，包括丰富分类群，从而影响寄主的恢复反应，并对使用根系微生物群的干旱保护策略产生影响。