Soil Microbiome Improves Salinity Tolerance in Rice by Enhancing Chlorophyll Content and Photosynthetic Performance

Salinity is one of the most destructive abiotic stresses limiting rice productivity worldwide. The present study investigates the role of the native soil microbiome in enhancing salinity tolerance of the salt-sensitive Oryza sativa ssp. japonica cv. Nipponbare. Plants were grown under control (0 mM NaCl) and salinity (75 mM NaCl) conditions with microbiome presence (Mb⁺) or absence (Mb⁻). Growth parameters, pigment composition, and gas-exchange traits were quantified, followed by correlation, random forest, and principal component analyses. Salinity stress markedly suppressed plant height, biomass, chlorophyll content, and photosynthetic rate, whereas microbiome inoculation significantly alleviated these effects. Under salinity, Mb⁺ plants exhibited higher plant height, chlorophyll a+b, β-carotene, net photosynthetic rate (Aₙ), and stomatal conductance (gₛ) compared with Mb⁻ plants. Correlation and machine-learning analyses identified Aₙ and chlorophyll a as the most important predictors of microbiome-associated salinity tolerance in rice. Multivariate clustering revealed that Mb⁺ plants under salinity displayed physiological profiles similar to non-stressed controls, suggesting microbiome-mediated buffering of stress responses. Overall, the results indicate that the native soil microbiome enhances photosynthetic resilience and biomass accumulation under salinity, offering a sustainable biological approach to improve rice performance in salt-affected soils.