The molecular and physiological responses of gray poplar (Populus 3 canescens) following root hypoxia were studied in roots and leaves using transcript and metabolite profiling. The results indicate that there were changes in metabolite levels in both organs, but changes in transcript abundance were restricted to the roots. In roots, starch and sucrose degradation were altered under hypoxia, and concurrently, the availability of carbohydrates was enhanced, concomitant with depletion of sucrose from leaves and elevation of sucrose in the phloem. Consistent with the above, glycolytic flux and ethanolic fermentation were stimulated in roots but not in leaves. Various messenger RNAs encoding components of biosynthetic pathways such as secondary cell wall formation (i.e. cellulose and lignin biosynthesis) and other energy-demanding processes such as transport of nutrients were significantly down-regulated in roots but not in leaves. The reduction of biosynthesis was unexpected, as shoot growth was not affected by root hypoxia, suggesting that the up-regulation of glycolysis yields sufficient energy to maintain growth. Besides carbon metabolism, nitrogen metabolism was severely affected in roots, as seen from numerous changes in the transcriptome and the metabolome related to nitrogen uptake, nitrogen assimilation, and amino acid metabolism. The coordinated physiological and molecular responses in leaves and roots, coupled with the transport of metabolites, reveal important stress adaptations to ensure survival during long periods of root hypoxia.Higher plants are aerobic organisms and depend on the availability of O 2 . A lack of O 2 in the rhizosphere affects the maintenance of numerous pathways and is therefore an important environmental stress for vascular plants (Drew, 1997). Plant adaptations to O 2 deprivation include avoidance strategies at the morphological level and physiological tolerance mechanisms (Bailey-Serres and Voesenek, 2008). One of the major cellular pathways dependent on O 2 is mitochondrial respiration. In order to maintain energy generation under conditions of decreased O 2 availability, plants switch from respiration to fermentative metabolism. Fermentation allows regeneration of NAD + in the absence of respiration, thereby maintaining glycolysis and the generation of ATP under anaerobic conditions. As an initial reaction to O 2 deprivation, many plants activate lactic acid fermentation. As generation of lactic acid causes a decrease in cytosolic pH (Roberts et al., 1984), which reduces the activity of the responsible enzyme, lactate dehydrogenase (LDH; Hanson and Jacobson, 1984), lactic acid fermentation is followed by alcoholic fermentation (Davies et al., 1974;Roberts et al., 1984). The significantly lower energy yield of alcoholic fermentation, compared with mitochondrial respiration, causes an energy crisis in anaerobic tissues (Bailey-Serres and Voesenek, 2008).A high rate of fermentation increases the demand for carbohydrates, leading to the hypothesis that carbohydrate supply becomes c...