Root endophyte differentially regulates plant response to NO and NH nutrition by modulating N fluxes at the plant-fungal interface.

In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO )/ammonium (NH ) 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 NO or NH nutrition. Under NO nutrition, P. liquidambaris inoculation promoted seedling growth, whereas under NH nutrition, P. liquidambaris suppressed seedling growth. Under high NH conditions, fungus-colonized roots displayed increased NH accumulation and NH efflux, similar to the effect of ammonium stress caused by elevated NH levels. Notably, this fungus excluded NH during interactions with host roots, thereby leading to increased NH levels at the plant-fungal interface under high NH conditions. A nitrite reductase-deficient strain that excludes NO but absorbs NH , decreased NH levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH 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 NO /NH dynamics at the plant-fungal interface alters plant response to NO /NH nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients.