The hypoxic niche enclosing the shoot apical meristem is shaped by a combination of morphological features and metabolic activity.

Stem cell niches in both plants and animals are frequently located in low-oxygen microenvironments that support their function. In plants, these hypoxic niches promote local stabilization of several transcriptional regulators that control a range of developmental processes, including shoot apical meristem (SAM) activity, vernalization, lateral root development, and leaf growth and morphogenesis. Despite their importance, however, it remained unclear how these hypoxic niches are maintained. In this study, we employed a combination of experimental and modeling approaches to identify the key features required to establish and sustain the hypoxic niche enclosing the SAM. Using respiration inhibitors, manipulation of resource availability, and mitochondria mutant lines, we found that respiratory oxygen consumption is required to establish the hypoxic niche. Oxygen microprofiling and imaging of hypoxia signaling in cuticle biosynthesis mutants, as well as following targeted cuticle degradation, revealed that a cuticle-like barrier defines the steepness of the oxygen gradient and ensures that even the outermost layer remains hypoxic. Moreover, high tissue compactness in the shoot apex region was visualized using X-ray micro-computed tomography and shown to stabilize the hypoxic microenvironment by limiting internal oxygen diffusion. Finally, sensitivity tests on a novel reaction-diffusion model closely recapitulated oxygen gradients across the SAM and revealed distinct roles of each feature and their combined effect on oxygen distribution. Together, these findings explain how the SAM sustains hypoxia and point to a potential universal strategy used by stem cell niches to maintain low oxygen levels.