Roots, rhizomes and other plant organs usually obtain sufficient oxygen for aerobic respiration directly from gaseous spaces in the soil. However, the diffusion of O2 from the air into the soil can be effectively blocked when soil becomes flooded or waterlogged. In such cases, the respiratory consumption by plant roots, soil fauna and microorganisms can totally deplete the oxygen. Periods of oxygen deficiency can trigger functional and developmental responses that promote acclimation to hypoxic or anoxic conditions. Low oxygen concentrations lead to long-term morphological adaptations such as developing aerenchyma in roots.

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