Strategic Enrichment of Endophytic Bacteria and Consortium Design to Enhance Plant Adaptation to Salinity Stress

Background The rice ( Oryza sativa ) root microbiome plays a critical role in plant adaptation to salinity stress, and its targeted manipulation offers a promising strategy to enhance crop resilience. In this study, a multi-generation enrichment approach under saline conditions was used to restructure the rice root endosphere and enrich for salt stress–resistant bacterial taxa. Results Successive reinoculations led to the consistent enrichment of key plant growth–promoting genera detected by 16S rRNA amplicon sequencing analysis, including Rhizobium, Paenibacillus, Pseudomonas, Pantoea , and Kosakonia , indicating adaptation to the root environment under salt stress while maintaining overall microbial diversity. Based on these enriched communities seen in silico , halotolerant bacterial strains were then isolated, characterized, and phenotypically tested in vitro. Strains exhibiting in vitro plant growth promoting and complementary functional traits were selected and combined into synthetic consortia. An eight-strains consortium (C1) significantly improved plant growth under both non-stressed and saline conditions without disrupting the native microbiome, in addition, a reduced three-strains consortium (C5) retained similar beneficial effects. In contrast, individual strain inoculations were less effective and often impaired plant performance. Importantly, colonization assays, monitored through Oxford Nanopore sequencing as a targeted high-resolution approach, revealed that several strains unable to establish efficiently as single inoculants were able to persist when delivered within a consortium. This indicates that consortium assembly does not simply combine individually beneficial strains but can create a supportive microbial context that promotes colonization, persistence, and plant growth promotion. Conclusions This study demonstrates that salinity-driven microbiome enrichment, combined with rational consortium design, can generate effective multi-strain inoculants that outperform single strains in promoting rice growth and salt stress tolerance, highlighting synergistic interactions and strain compatibility as key determinants of successful root establishment and bioinoculant performance.