Preferential enhancement of nitrate utilization in rice by endophytic Burkholderia vietnamiensis RS1

Burkholderia vietnamiensis RS1 is an endophytic bacterium that promotes rice growth by enhancing nitrogen acquisition. Transcriptomic analysis in our previous study showed that RS1 inoculation induces genes involved in nitrate transport and amino acid metabolism. However, its direct effects on nitrate uptake and the associated physiological mechanisms remained unclear. In this study, we quantitatively demonstrated that RS1 preferentially promotes nitrate uptake even in the presence of both nitrate and ammonium by applying ¹⁵N-labeled ammonium nitrate. Metabolic analysis by LC-MS/MS revealed reduced levels of specific amino acids (e.g., Ala, Ser, and Pro) and organic acids (pyruvic and citric acids) in RS1-inoculated roots, suggesting accelerated amino acid assimilation supported by increased carbon skeleton supply through the TCA cycle. RT-qPCR analysis in rice roots further revealed that inoculation with RS1 upregulated genes involved in the ammonium and nitrate transport, nitrogen assimilation, and the TCA cycle. Field experiments comparing nitrate- and urea-based fertilization revealed that RS1 significantly promoted rice growth under nitrate fertilization, but not under urea fertilization. These findings indicate that RS1 facilitates selective nitrate uptake and assimilation, contributing to improved nitrogen use efficiency and biomass production in rice. This study provides new insights into the functional role of endophytic bacteria in modulating nitrogen metabolism and highlights the potential of RS1 as a bioinoculant for sustainable agriculture, particularly under nitrate-rich conditions.