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 (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.