Amino-acid-transporter-mediated assembly of rhizosphere microbiota enhances soil organic nitrogen acquisition in rice.

Amino acids are plant-available organic nitrogen (N) that can be directly absorbed, but their availability relies on microbial decomposition of organic matter in the soil. Natural variation in Lysine-Histidine-Type Transporter-1 (OsLHT1) (NCBI Gene ID: 3974662 ) is associated with higher amino acid uptake in japonica rice than in indica. However, how this genetic variation influences rhizosphere microbiome assembly and its subsequent impact on amino acid acquisition remains unclear. In this study, we demonstrate that the OsLHT1a allele in japonica is prevalent in rice grown in high-organic-N soils, where it recruits a distinct rhizosphere microbiome to enhance amino acid acquisition. A synthetic microbiota composed of bacteria enriched by the OsLHT1a allele in japonica enhanced amino acid production in soil through organic matter decomposition and increased root amino acid uptake by upregulating OsLHT1 gene expression. The rhizosphere colonization of the synthetic microbiota was specifically driven by the function of OsLHT1. Notably, organic fertilization facilitated this colonization, thereby improving organic N use efficiency and rice yield. This root-rhizosphere microbiome functional synergy under organic fertilization presents a promising strategy to increase organic fertilizer use efficiency and demonstrates the potential for harnessing plant-gene-associated rhizosphere microbiomes for sustainable agriculture.