Salinity stress reveals keystone metabolites linking rhizosphere metabolomes and microbiomes in Halophyte Suaeda salsa

Abstract

Aim

Halophytes are vital tools for saline-alkali land reclamation, in part due to their ability to establish stable rhizosphere microbial communities in saline environments. However, the mechanisms by which rhizodeposition mediates microbiome enrichment under salt stress remain poorly understood. Our objectives were to assess the impact of salinity on halophyte-rhizosphere microbe interactions and identify potential "keystone metabolites"—compounds with functional links to specific microbial lineages that significantly influence the structure of rhizosphere microbiomes.

Methods

Suaeda salsa was grown in marginal soil under varying salinity levels of control, 0.5%, 1.0%, 1.5%, and 2.5%. We investigated the relationship between rhizosphere metabolites, microbial community composition, and salt stress using 16S rRNA and ITS sequencing combined with LC–MS/MS-based metabolomics,

Results

Increased salinity reduced shoot and root biomass while elevating Na accumulation in both tissues. We identified significant shifts in rhizosphere metabolite profiles and microbial communities through hierarchical clustering and co-occurrence network analysis. At lower salinity levels (0%–0.5%), organic acids and sugars were enriched, aligning with microbial taxa dominated by Actinobacteria and Bacteroidetes. In contrast, higher salinity levels (1.5%–2.5%) favored organic acids and lipids, which were correlated with salt-tolerant microbial taxa such as Truepera, Halomonas, and Fulvivirga. Notably, 5′-methylthioadenosine was prominent at moderate salinity levels (0.5%–1.0%), while oleamide emerged as a keystone metabolite at higher salinity levels (1.0%–2.5%), serving as a network hub that connected microbial taxa and drove community assembly.

Conclusions

This study demonstrates that halophyte metabolites undergo significant alterations under salinity stress, with these changes showing a strong correlation to the composition of the rhizosphere microbial community.