Root endophyte differentially regulates plant response to NO3− and NH4+ 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. Brief Summary We determined how to root endophyte affects plant response to different forms of N. Our results suggest that root endophyte differentially regulates plant response to NO3− and NH4+ nutrition through modulating N fluxes at the plant–fungal interface rather than through regulating defense responses.