Root endophyte differentially regulates plant response to NO ₃ ⁻ and NH ₄ ⁺ nutrition by modulating N fluxes at the plant–fungal interface

In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO3−)/ammonium (NH4+) patches, but the mechanism underlying N form-influenced plant–fungal interactions remains limited. We inoculated Arabidopsis with a root endophyte Phomopsis liquidambaris, and evaluated the effects of P. liquidambaris on plant performance under NO3− or NH4+ nutrition. Under NO3− nutrition, P. liquidambaris inoculation promoted seedling growth, whereas under NH4+ nutrition, P. liquidambaris suppressed seedling growth. Under high NH4+ conditions, fungus-colonized roots displayed increased NH4+ accumulation and NH4+ efflux, similar to the effect of ammonium stress caused by elevated NH4+ levels. Notably, this fungus excluded NH4+ during interactions with host roots, thereby leading to increased NH4+ levels at the plant–fungal interface under high NH4+ conditions. A nitrite reductase-deficient strain that excludes NO3− but absorbs NH4+, decreased NH4+ levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH4+ levels. Transcriptomic analysis highlighted that P. liquidambaris had altered transcriptional responses associated with plant response to inorganic N forms. Our results demonstrate that fungus-regulated NO3−/NH4+ dynamics at the plant–fungal interface alters plant response to NO3−/NH4+ nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients.