23Plants use nitrate and ammonium in the soil as their main nitrogen sources. Recently, 24 ammonium has attracted attention due to evidence suggesting that, in C 3 species, an 25 elevated CO 2 environment inhibits nitrate assimilation. However, high concentrations of 26 ammonium as the sole nitrogen source for plants causes impaired growth, i.e. ammonium 27 toxicity. Although ammonium toxicity has been studied for a long time, the primary cause 28 remains to be elucidated. Here, we show that ammonium assimilation in plastids rather 29 than ammonium accumulation is a primary cause for toxicity. Our genetic screen of 30 ammonium-tolerant Arabidopsis lines with enhanced shoot growth identified plastidic 31 GLUTAMINE SYNTHETASE 2 (GLN2) as the causal gene. Our reciprocal grafting of 32 wild-type and GLN2 or GLN1;2-deficient lines suggested that shoot GLN2 activity results 33 in ammonium toxicity, whilst root GLN1;2 activity prevents it. With exposure to toxic 34 levels of ammonium, the shoot GLN2 reaction produced an abundance of protons within 35 cells, thereby elevating shoot acidity and stimulating expression of acidic stress-36 responsive genes. Application of an alkaline ammonia solution to the toxic ammonium 37 medium efficiently alleviated the ammonium toxicity with a concomitant reduction in 38 shoot acidity. Consequently, we conclude that a primary cause of ammonium toxicity is 39 acidic stress in the shoot. This fundamental insight provides a framework for enhanced 40 understanding of ammonium toxicity in plants. 41 42 43 44Recent studies suggest that elevated CO 2 inhibits nitrate reduction in C 3 species, such as 47 wheat and Arabidopsis, whereas ammonium utilization does not decrease (1). One 48 estimate predicts that only a 1% drop in nitrogen use efficiency could increase worldwide 49 cultivation costs for crops by about $1 billion annually (2). Therefore, increasing 50 ammonium use by crops is an important goal for agriculture as CO 2 levels rise in the 51 world; however, millimolar concentrations of ammonium as the sole N source causes 52 growth suppression and chlorosis in plants, compared with nitrate (3, 4, 5). This 53 phenomenon is widely known as ammonium toxicity, but the primary cause of impaired 54 growth remains to be identified. 55Plants grown in high ammonium conditions show several distinct 56 characteristics from those grown in nitrate (3, 4, 5). These toxic symptoms have evoked 57 several hypotheses about the toxic causes, including futile transmembrane ammonium 58 cycling, deficiencies in inorganic cations and organic acids, impaired hormonal 59 homeostasis, disordered pH regulation, and the uncoupling of photophosphorylation; 60 however, some of the symptoms are not directly associated with growth suppression by 61 ammonium toxicity (6), making it difficult to determine the toxic cause. Several efforts 62 have isolated ammonium-sensitive mutants in Arabidopsis thaliana and determined their 63 causative genes (4, 5). GMP1 is a causal gene whose deficiency causes stunted growth of 6...