The rice circadian clock orchestrates the rhizosphere microbiome to synchronize nitrogen supply with plant demand.
TL;DR
This work uncovers a mechanism by which the plant circadian clock directly coordinates rhizosphere microbial functions to optimize N acquisition, thus providing a tractable strategy for sustainable crop production.
Abstract
Improving nitrogen use efficiency (NUE) is pivotal for sustainable agriculture but is limited by spatiotemporal mismatches between soil N supply and crop N demand. Here, we show that the rice circadian clock component Nhd1 coordinates rhizosphere microbial activity with plant diurnal N uptake. Nhd1 drives a rhythmic root exudation program: quercetin 3-gentiobioside peaks during the day against a constitutive baseline of baimaside secretion, both of which upregulate core microbial N-cycling genes to boost ammonium bioavailability. This Nhd1-orchestrated exudation rhythm aligns microbial N turnover with peak plant N demand. A synchronized microbial community engineered to match this diurnal N release pattern increased grain yield and NUE in field trials, with far greater benefits in cultivars harboring weak versus strong Nhd1 alleles. Our work uncovers a mechanism by which the plant circadian clock directly coordinates rhizosphere microbial functions to optimize N acquisition, thus providing a tractable strategy for sustainable crop production.