Metagenomic Association Uncovers Host Genotype‐Structured Rhizobacterial Networks and Novel Taxa That Enhance Soybean Salt Tolerance

ABSTRACT Salinity is an escalating agricultural challenge, yet plant microbiomes offer a promising avenue for improving salt tolerance. Nevertheless, most naturally occurring microbes remain unevaluated for plant growth–promoting function, and systematic approaches to uncover salt‐tolerance‐enhancing plant growth–promoting rhizobacteria (PGPR) are limited. Here, using soybean as a model, we implement a quantitative framework to characterize rhizosphere microbial networks and nominate novel taxa functionally associated with plant salt tolerance. We introduced a salt tolerance index (STI) to quantify plant salt tolerance and normalize performance across heterogeneous natural soil salinity. Metagenomic sequencing and co‐occurrence analysis revealed distinct rhizosphere microbiota structures between tolerant and susceptible soybeans. In tolerant soybeans, Pseudomonas dominated as the hub of a highly interconnected network, whereas susceptible accessions showed a fragmented network dominated by Acinetobacter . Correlation analyses identified bacterial taxa positively associated with STI, including documented salt‐tolerant PGPR and novel candidates. Greenhouse experiments showed that one candidate, Thalassospira xiamenensis , enhances soybean salt tolerance and reshapes host ion‐transport and oxidative‐stress gene expression under salinity, validating our screening strategy. Our culture‐independent metagenomic association approach reveals host genotype–structured rhizosphere microbial networks underlying salt tolerance and provides an efficient, labor‐saving means for high‐throughput identification of salt‐tolerant PGPR.