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Background Ammonium is an indispensable nutrient for crop growth, but anoxic conditions or inappropriate fertilizer usage result in the increase in ammonium content in soil. Excessive ammonium causes phytotoxicity. Thymol is a kind of natural phenolic compound with anti-microbial properties. However, little is known about the role of thymol in modulating plant physiology. Here we find the novel role of thymol in protecting rice from ammonium toxicity. Results Thymol remarkably rescued rice seedlings growth from ammonium stress, which may resulted from the attenuation of reactive oxygen species (ROS) accumulation, oxidative injury, and cell death in both shoots and roots. Polyamine oxidase (PAO) metabolizes polyamines to produce ROS in plants in response to stress conditions. Thymol blocked ammonium-induced upregulation of a set of rice  PAOs , which contributed to the decrease in ROS content. In rice seedlings upon ammonium stress, thymol downregulate the expression of  ammonium transporters  ( AMT1;1  and  AMT1;2 ); thymol upregulated the expression of  calcineurin B-like interacting protein kinase 23  ( CIPK23 ) and  calcineurin B-like binding protein 1  ( CBL1 ), two negative regulators of  AMTs . This may help rice avoid ammonium overload in excessive ammonium environment. Correlation analysis indicated that  PAOs ,  AMTs , and  CBL1  were the targets of thymol in the detoxification of excessive ammonium. Conclusion Thymol facilitates rice tolerance against ammonium toxicity by decreasing PAO-derived ROS and modulating ammonium transporters. Such findings may be applicable in the modulation of nutrient acquisition during crop production. Graphical abstract

Thymol ameliorates ammonium toxicity via repressing polyamine oxidase-derived hydrogen peroxide and modulating ammonium transporters in rice root