Disruption of OsNLP4 -mediated nitrate signaling alters root exudate composition and root-associated bacterial communities in rice

Abstract

OsNLP4 is a master regulator of nitrate signaling, but its ecological role in the root-associated bacterial communities is unknown. This study investigated how OsNLP4-mediated nitrate signaling influences root-associated microbial composition and root exudate metabolism. We found that the osnlp4 mutants exhibited distinct root-associated bacterial communities compared to the WT under non-nitrogen-fertilized conditions, with a significant enrichment of Bradyrhizobium and other bacterial taxa with potential roles in nitrogen cycling. Isolated Bradyrhizobium strains showed increased colonization in the osnlp4 mutant. Metabolomic analysis revealed increased secretion of sugars and phosphoric acid, along with a lower C:N ratio, in the osnlp4 mutant root exudates. Bacterial growth and chemotactic responses differed between WT- and osnlp4-derived root exudates, and sugars enriched in osnlp4 exudates elicited chemotactic responses in isolated Bradyrhizobium strains. These metabolic changes were associated with differential bacterial responses to WT and osnlp4 root exudates and may contribute to the altered root-associated bacterial community. Taken together, our results suggest that OsNLP4 links nitrate signaling and nitrogen metabolism with root-associated bacterial community assembly. Disruption of OsNLP4 reprograms root exudation and reshapes root-associated microbial communities, highlighting an association between nitrate signaling, nutrient allocation, and root-associated bacterial community assembly in rice.