Waterlogging-induced hypoxia threatens horticultural crop production by disrupting metabolic processes, nutrient uptake, and plant health. Despite significant progress in model plants, such as Arabidopsis and rice, the unique hypoxia responses and regulatory mechanisms in vegetable and fruit crops remain underexplored. This review bridges critical knowledge gaps by synthesizing recent advances and highlighting species-specific adaptations aimed at enhancing hypoxia tolerance in horticultural crops. Although the central roles of Ethylene response factor group VII (ERF-VIIs), metabolic reprogramming, and redox signaling in oxygen homeostasis have been elucidated in model species, recent studies on horticultural crops have demonstrated the conservation of this core regulatory module and the emergence of unique species-specific adaptations that optimize hypoxia tolerance. Horticultural crops employ diverse morphological, physiological, and molecular strategies to maintain energy homeostasis under hypoxic conditions. In this review, we summarize the key mechanisms, including antioxidant defense activation, dynamic reprogramming of carbon and nitrogen metabolism, and integrated hormonal crosstalk and signaling networks. Plants adapt to hypoxia through a complex molecular network that orchestrates multifaceted responses involving dynamic epigenetic reprogramming, the induction of hypoxia-responsive genes, and translational control to fine-tune protein function and stability. Recent advances in genetics, molecular breeding, and grafting have accelerated the development of hypoxia-tolerant horticultural crops. By integrating adaptive traits from wild relatives through genome editing and multi-omics approaches and optimizing rootstock performance, sustainable productivity can be enhanced under oxygen-limiting conditions. Elucidating these mechanisms provides fundamental insights into plant resilience, and directly informs innovative breeding and biotechnological strategies for climate-smart horticulture.

Fungal endophytes are microorganisms that inhabit plant tissues without causing disease and emerge as critical mediators of plant stress tolerance, nutrient acquisition, and ecosystem resilience under diverse climate change scenarios. Their unique position within the host allows them to modulate physiological responses more closely than external microbiota. This review explores how endophytic fungi contribute to plant adaptation under climate-induced stresses such as heat, salinity, drought, pollution, and nutrient limitation, with a focus on molecular crosstalk, functional trait modules, and metabolic trade-offs. Key findings emphasize multilayered signaling systems, including MAMP/DAMP recognition, phytohormone regulation, immune tuning, ROS dynamics, and effector deployment, while emerging mechanisms such as cross-kingdom RNA and extracellular vesicle (EV)-mediated exchange are discussed as promising but currently limited in empirical validation within many endophytic systems. Endophytes also enhance nutrient exchange through conditional carbon-for-benefit trade and may shape rhizosphere microbiota and soil activities through plant-mediated inputs. Integrative multi-omics approaches provide predominantly correlational insights into the mechanistic basis of these effects, linking molecular function to ecosystem and community outcomes. These insights have potential applications in climate-resilient agriculture, phytoremediation, and ecosystem restoration; however, their large-scale implementation requires further field-based validation and context-specific assessment. Future priorities should focus on trait-based selection, ecological modeling, and biosafety evaluation to translate microbial functions into reliable field-level strategies that support sustainable crop performance under accelerating environmental stress.