Endophyte-mediated mechanisms of drought and salinity tolerance in rice: physiological, molecular, and field perspectives

Rice (Oryza sativa L.) is highly susceptible to drought and salinity, two major abiotic stresses that severely constrain global productivity under climate change. Endophytic microorganisms have emerged as promising biological tools for enhancing stress tolerance; however, their mechanisms and field applicability in rice remain insufficiently integrated. This review synthesizes current advances in rice–endophyte interactions with a specific focus on mechanistic and functional outcomes. Evidence from bacterial and fungal endophytes, including Bacillus, Pseudomonas, Enterobacter, and Trichoderma spp., demonstrates improved drought and salinity tolerance through measurable traits such as enhanced root architecture, increased water-use efficiency, maintenance of Na+/K+ homeostasis, and improved biomass and yield stability. These effects are mediated via key pathways including ACC deaminase activity (ethylene regulation), modulation of antioxidant systems (SOD, CAT, APX), osmolyte accumulation, and hormonal crosstalk involving abscisic acid (ABA), indole-3-acetic acid (IAA), and gibberellins. Under salinity, endophytes contribute to ion homeostasis through regulation of transporters such as HKT1;5, while under drought they enhance hydraulic conductivity via aquaporin regulation through plasma membrane intrinsic proteins (PIPs) and tonoplast intrinsic proteins (TIPs). Despite promising results under controlled conditions, inconsistencies in field performance remain a major limitation due to genotype dependence, environmental variability, and challenges in colonization and inoculum stability. This review integrates molecular, physiological, and applied perspectives and proposes a framework for linking rice genotype, endophyte function, and environmental conditions to improve reproducibility and field-scale application. These insights provide a foundation for developing climate-resilient rice systems through targeted microbial inoculants.