Variety-dependent microbial community restructuring under salinity stress outweighs direct benefits of native microbe inoculation in Hordeum vulgare

Soil salinization is an escalating threat to global food security under climate change, necessitating innovative strategies to enhance crop resilience. Native microbial inoculants, sourced from salinity-adapted soils, offer a potential avenue for sustainable agricultural adaptation. Here, we evaluated the effects of saline prairie-derived, arbuscular mycorrhizal fungi (AMF)-enriched microbial inoculants on the growth of barley ( Hordeum vulgare) cultivars under a salinity gradient. Greenhouse trials demonstrated that salinity was the dominant constraint on biomass production, but inoculant identity and genotype significantly influenced plant performance and microbial assembly. Inoculant effects on shoot biomass were heterogeneous, with neutral or negative outcomes predominating under saline conditions. Amplicon sequencing of bacterial, fungal, oomycete, and arbuscular mycorrhizal (AMF) communities revealed that salinity strongly restructured microbial diversity and composition, reducing bacterial and fungal evenness. Genotype and inoculant identity shaped fungal communities, while oomycete responses depended on specific plant–microbe pairings. Model selection confirmed that shoot biomass was primarily explained by salinity, with additional contributions from barley genotype, inoculant identity, and fungal evenness. These results demonstrate that microbial community restructuring under salinity stress outweighs direct benefits of native microbial inoculation, and emphasize that successful microbial interventions in salt-affected soils must account for genotype-specific compatibility and stress-driven community dynamics, rather than assuming universal benefits.