Biostimulant endophyte Phomopsis liquidambaris modulates hormone signaling to improve rice nitrogen use under nitrogen-deficiency stress

• Phomopsis liquidambaris enhances rice performance under low nitrogen stress • Fungal endophyte rewires auxin-ethylene-cytokinin crosstalk to boost nitrogen use • Stage-specific hormone regulation coordinates nitrogen transporter expression • Inoculation induces hormonal preferences for nitrate or ammonium uptake Nitrogen (N) deficiency is a major constraint on rice productivity, and improving nitrogen use efficiency (NUE) is essential for sustainable agriculture. Endophytic fungi have emerged as promising biostimulants that enhance nutrient acquisition, yet the hormonal mechanisms underlying their effects remain insufficiently understood. We investigated the endophyte Phomopsis liquidambaris B3 and its role in regulating N use in rice under N-deficiency stress (1.0 mM N in the form of NH₄NO₃). Inoculation increased rice biomass from 7 days after inoculation (dai), accompanied by substantial hormonal changes that auxin (IAA) increased by 39.1% and 46.8% in shoots and roots at 28 dai, ethylene (ETH) by 23.8% and 47.6% at 7 dai, and cytokinin (CTK) elevated from 3-7 dai onward. Transcriptomic and correlation analyses revealed stage-specific regulation, with IAA- and ETH-signaling genes strongly induced and positively associated with N transporters at early and middle stages, whereas CTK signaling predominated at later stages. Hormonal network analyses further demonstrated a dynamic hierarchy of signaling interactions: IAA and ETH act synergistically, with IAA upstream of ETH, whereas IAA and CTK display antagonistic effects, and CTK cooperates with ETH downstream. Quantitative PCR validated these patterns and demonstrated distinct hormonal preferences for N forms: IAA and CTK strongly favored nitrate uptake, with OsNRT2.1 expressed at 2.74-fold and 5.15-fold higher levels than OsAMT1.1 , respectively, whereas ETH favored ammonium uptake, yielding an NRT/AMT ratio of 0.47. These results indicate that P. liquidambaris enhances rice N acquisition by coordinating IAA-ETH-CTK crosstalk to fine-tune transporter expression and N utilization under N deficiency.