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Background  Organic acid secretion is a widespread physiological response of plants to alkalinity. However, the characteristics and underlying mechanism of the alkali-induced secretion of organic acids are poorly understood.    Results  Oxalate was the main organic acid synthesized and secreted in grapevine (a hybrid of  Vitis amurensis ,  V. berlandieri  and  V. riparia ) roots, while acetate synthesis and malate secretion were also promoted under NaHCO 3  stress. NaHCO 3  stress enhanced the H +  efflux rate of grapevine roots, which is related to the plasma membrane H + -ATPase activity. Transcriptomic profiling revealed that carbohydrate metabolism was the most significantly altered biological process under NaHCO 3  stress; a total of seven genes related to organic acid metabolism were significantly altered, including two phosphoenolpyruvate carboxylases and phosphoenolpyruvate carboxylase kinases. Additionally, the expression levels of five  ATP-binding cassette transporters , particularly  ATP-binding cassette B19 , and two  Al-activated malate transporter 2 s  were substantially upregulated by NaHCO 3  stress. Phosphoproteomic profiling demonstrated that the altered phosphoproteins were primarily related to binding, catalytic activity and transporter activity in the context of their molecular functions. The phosphorylation levels of phosphoenolpyruvate carboxylase 3, two plasma membrane H + -ATPases 4 and ATP-binding cassette B19 and pleiotropic drug resistance 12 were significantly increased. Additionally, the inhibition of ethylene synthesis and perception completely blocked NaHCO 3 -induced organic acid secretion, while the inhibition of indoleacetic acid synthesis reduced NaHCO 3 -induced organic acid secretion.    Conclusions  Our results demonstrated that oxalate was the main organic acid produced under alkali stress and revealed the necessity of ethylene in mediating organic acid secretion. Additionally, we further identified several candidate genes and phosphoproteins responsible for organic acid metabolism and secretion.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1990-9) contains supplementary material, which is available to authorized users.

Transcriptomic and phosphoproteomic profiling and metabolite analyses reveal the mechanism of NaHCO3-induced organic acid secretion in grapevine roots