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Background and Aims Acidic soils are dominated chemically by more ammonium and more available, so more potentially toxic, aluminium compared with neutral to calcareous soils, which are characterized by more nitrate and less available, so less toxic, aluminium. However, it is not known whether aluminium tolerance and nitrogen source preference are linked in plants. Methods This question was investigated by comparing the responses of 30 rice (Oryza sativa) varieties (15 subsp. japonica cultivars and 15 subsp. indica cultivars) to aluminium, various ammonium/nitrate ratios and their combinations under acidic solution conditions. Key Results indica rice plants were generally found to be aluminium-sensitive and nitrate-preferring, while japonica cultivars were aluminium-tolerant and relatively ammonium-preferring. Aluminium tolerance of different rice varieties was significantly negatively correlated with their nitrate preference. Furthermore, aluminium enhanced ammonium-fed rice growth but inhibited nitrate-fed rice growth. Conclusions The results suggest that aluminium tolerance in rice is antagonistic with nitrate preference and synergistic with ammonium preference under acidic solution conditions. A schematic diagram summarizing the interactions of aluminium and nitrogen in soil–plant ecosystems is presented and provides a new basis for the integrated management of acidic soils. [ABSTRACT FROM AUTHOR]