Understanding the reciprocal interaction between root development and coadapted beneficial microbes in response to elevated CO (eCO) will facilitate the identification of nutrient-efficient cultivars for sustainable agriculture. Here, systematic morphological, anatomical, chemical and gene expression assays performed under low-nitrogen conditions revealed that eCO drove the development of the endodermal barrier with respect to L-/S-shaped lateral roots (LRs) in rice. Next, we applied metabolome and endodermal-cell-specific RNA sequencing and showed that rice adapts to eCO by spatially recruiting diazotrophs via flavonoid secretion in L-shaped LRs. Using the rice Casparian strip mutant Oscasp1-1, we confirmed that reduced lignin deposition selectively recruits the diazotrophic family of Oxalobacteraceae to confer tolerance to low nitrogen availability.
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