Micro- and nanobubble aeration improves root–shoot physiology of tomato via enhanced soil oxygenation

• Stage-specific aeration improved tomato dry matter and biomass yield. • Aeration at fruiting ripening stage-maintained root-zone oxygen. • Stage-specific aeration enhanced root growth and nitrogen cycling. • Stage-specific aeration reduced continuous oxygen demand. Micro- and nanobubble (MNB) aeration under subsurface drip irrigation (SDI) has emerged as an effective strategy to alleviate rhizosphere hypoxia. However, the optimal timing of aeration during crop development remains unclear. This study evaluated the effects of crop growth-stage-specific MNB aeration on soil oxygen (SO) dynamics, soil biochemical properties, root architecture, photosynthetic performance, and biomass yield of greenhouse tomato over two cropping seasons. Six treatments were compared, including non-aerated SDI, continuous aeration (A W ), and four stage-specific aeration regimes. Under conventional SDI, SO declined progressively, whereas MNB aeration significantly increased it, with aeration during the pollination–fruit-set stage (A P+FRS ) maintaining oxygen levels comparable to A w . Stage-specific aeration significantly enhanced soil total nitrogen (by 12–26%), microbial biomass carbon and nitrogen (by 18–41%), promoted nitrification, and reduced ammonium accumulation relative to the control. Improved oxygen availability markedly stimulated root development, increasing total root length, surface area, and volume by 35–79%, which translated into higher net photosynthetic rate (+21–38%), leaf water-use efficiency (+19–33%), and chlorophyll content. Biomass yield increased significantly under aerated treatments, with A P+FRS producing the highest and most stable yields (14.46 and 13.31 t ha⁻¹ in Seasons 1 and 2, respectively), exceeding the non-aerated control by 57–90%. Correlation analysis revealed strong positive relationships among SO, microbial activity, root traits, photosynthetic performance, and biomass yield. Overall, targeted MNB aeration during the A P+FRS optimized rhizosphere oxygen supply and crop performance while avoiding the energy costs associated with continuous aeration, providing a physiological basis for precision oxygen management in aerated SDI systems.