Nature-Based Microbial Strategies for Enhancing Wheat Salt Tolerance in Coastal Agroecosystems

Global warming and sea-level rise are intensifying soil salinization in coastal regions, threatening food security and ecosystem stability. In coastal areas of Iran, where most of the rainfed farming and cultivation occur, seawater intrusion (EC > 4 dS/m) has severely degraded soils, reducing vegetation cover and carbon sequestration. This creates a dangerous feedback loop, which further amplify climate-change impacts. Developing sustainable, nature-based strategies to maintain crop productivity under these extreme conditions is therefore essential.

In this study, we explored halophyte-associated microbial communities from the Oman Sea coast as a nature-based solution to enhance wheat tolerance to seawater irrigation. A total of 510 bacterial isolates were obtained from halophyte rhizospheres and endospheres, and assembled into salt-tolerant, non-antagonistic consortia. These consortia were inoculated into six wheat cultivars (Pishgam, Narin, Arg, Ofoq, Bam, Barzgar) and irrigated with seawater (EC = 50 dS/m).

Results revealed strong genotype–microbiome interactions. Some consortia significantly increased biomass (up to 228% in Pishgam and 127% in Ofoq with Consortium 3), while others reduced growth (−33% in Arg with Consortium 7). Rhizospheric sequencing identified 122 shared OTUs across treatments, yet β-diversity analyses (UniFrac) showed distinct plant-driven microbial filtering. Ofoq maintained a microbiome closer to its control (0.285 distance), mitigating negative effects, while Bam exhibited a greater divergence (0.401), correlating with poor growth.

These findings highlight that the success of microbial inoculation depends on host genotype compatibility and root-exudate-mediated selection. Leveraging native halophyte-associated microbes offers a promising, ecosystem-based pathway to enhance crop resilience, restore coastal soils, and mitigate carbon loss under salinity stress. Under extreme conditions, a shift from grain to forage-oriented systems may further improve sustainability and align with climate adaptation goals.