Root endophyte differentially regulates plant response to NO3− and NH4+ nutrition by modulating N fluxes at the plant–fungal interface

Abstract In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO 3 − )/ammonium (NH 4 + ) 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 3 − or NH 4 + nutrition. Under NO 3 − nutrition, P . liquidambaris inoculation promoted seedling growth, whereas under NH 4 + nutrition, P. liquidambaris suppressed seedling growth. Under high NH 4 + conditions, fungus‐colonized roots displayed increased NH 4 + accumulation and NH 4 + efflux, similar to the effect of ammonium stress caused by elevated NH 4 + levels. Notably, this fungus excluded NH 4 + during interactions with host roots, thereby leading to increased NH 4 + levels at the plant–fungal interface under high NH 4 + conditions. A nitrite reductase‐deficient strain that excludes NO 3 − but absorbs NH 4 + , decreased NH 4 + levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH 4 + 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 3 − /NH 4 + dynamics at the plant–fungal interface alters plant response to NO 3 − /NH 4 + nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients.