Plant-microbiome interactions are associated with enhanced salinity tolerance and methane emissions in rice

Salinity is a severe environmental stressor that reduces crop performance, alters soil microbial communities, and influences greenhouse gas emissions such as methane (CH₄). Climate change is expected to further increase salinity globally. Although plants have evolved physiological and molecular mechanisms to cope with salinity, the role of plant-microbiome interactions in salinity tolerance and their link to CH₄ emissions remain poorly understood. Here, we investigated the interactions among plant salinity tolerance, rhizobiome, and CH₄ emission under salinity stress. We used salt-tolerant and salt-sensitive rice genotypes grown in nutrient-poor paddy field soil and nutrient-rich commercial nursery soil under climate-controlled greenhouse conditions with salinity stress until harvesting. Salt-sensitive genotypes exhibited decreases in early biomass and gas exchange due to salinity stress under nutrient-rich nursery soil. However, salinity effects were mitigated by plant-microbiome interactions, which improved plant growth performance. Rhizosphere microbiome analysis revealed that Rhizobacteria, including Cyanobacteria, were associated with plant development and salinity tolerance. Salinity altered methanogenic archaeal communities, especially Methanobacteria and Methanocellia, with salt-tolerant genotypes releasing more CH₄ during stress. Gas exchange and antioxidant enzyme activity were positively correlated with CH₄ emissions, suggesting an association between improved physiological performance under salinity and microbial methanogenesis. Gene expression profiling revealed a significant upregulation of hormone- and ion-transport-related genes in paddy soil, which may be associated with stress tolerance, microbial activity, and CH₄ emissions. This study proposes a mechanistic framework that links plant salinity tolerance, rhizosphere microbial dynamics, and methane production, illustrating how these interconnected processes shape plant performance and the environmental outcomes. These findings emphasize the necessity of balancing agricultural productivity with CH₄ emissions and soil resilience under climate-induced stress.