Introduction: Why study salt stress and the soybean microbiome?
Salt stress dramatically alters plant performance and microbial communities. In a controlled hydroponic system using Hoagland’s solution, researchers can isolate the direct effects of NaCl concentration on the rhizosphere (root-associated) and the surrounding water environment of wild soybean (Glycine soja) without the confounding variables of soil. This study design enables precise comparisons of microbial diversity, composition, and potential plant–microbe interactions across a gradient of salinity.
Experimental design at a glance
Wild soybean seeds from coastal saline-alkali land were subjected to four treatments: control (CK, no added NaCl), low-salt (LT, 100 mmol/L NaCl), medium-salt (MT, 200 mmol/L NaCl), and high-salt (HT, 300 mmol/L NaCl). Root and water samples were collected after 21 days and processed for high-throughput 16S rRNA gene sequencing, focusing on the V3–V4 region. This approach revealed how salt stress shapes bacterial communities in both the rhizosphere and the water environment, revealing patterns of alpha and beta diversity, as well as shifts in major phyla and genera.
Alpha and beta diversity reveal contrasting responses
Alpha diversity showed that increasing salinity generally reduces bacterial richness and evenness, with distinct patterns between rhizosphere and environment. In the rhizosphere, the Shannon diversity metric declined notably under high salinity (HT) compared with other groups, indicating a selective pressure that narrows community structure. Richness (Chao1) also varied with salinity, most clearly distinguishing Low Salt from High Salt rhizosphere samples. By contrast, environmental (water) communities exhibited more pronounced shifts in both richness and diversity across salt treatments, with WaterCK often separating from the salt-treated groups in beta-diversity analyses.
beta diversity analyses based on weighted UniFrac showed clear separation: RootHT clustered away from other rhizosphere groups, while WaterCK separated from all salt-treated water samples. PERMANOVA confirmed that salinity gradients significantly explain differences in community composition, underscoring that salt stress exerts strong selective pressures on microbial assemblages, particularly in the rhizosphere.
Taxonomic shifts: who dominates as salinity rises?
Phylum-level patterns were consistent across habitats, with Proteobacteria dominating all samples (>50%). In the rhizosphere, Proteobacteria often rose with salinity, from about 85% in CK to over 91% in HT, signaling a robust enrichment of salt-tolerant lineages. Environmental samples showed a similar trend, with Proteobacteria increasing from 58–60% in control to ~88% in HT. Bacteroidota tended to decline as salinity rose, while Actinobacteriota generally increased under higher salinity, suggesting their role in nutrient cycling and stress response in saline environments.
Genus-level dynamics highlighted the prominent role of Pseudomonas in both habitats, rising with salinity and peaking under HT. Acinetobacter and Rhizobium also featured prominently, though their responses varied between rhizosphere and environment. Notably, Shewanella emerged as a key responder in the rhizosphere under high salt, while the environmental community showed increased Shewanella abundance with rising salinity. These taxa are associated with osmotic balance, EPS production, and versatile metabolic capabilities that may support plant stress tolerance.
Implications for plant–microbe interactions under salt stress
The data suggest that wild soybean roots actively recruit salt-tolerant taxa, potentially via altered root exudation under stress. This selective assembly could stabilize the rhizosphere microbiome and bolster plant tolerance through mechanisms such as hormone modulation, nutrient acquisition, and osmoprotectant production. In contrast, the surrounding water environment appears more directly perturbed by salt, with greater shifts in community composition and diversity across the salinity gradient. The juxtaposition of rhizosphere stability and environmental sensitivity underscores the plant’s role in shaping its microbial neighborhood under stress.
Conclusion: salinity reshapes, but plants help stabilize
Salt stress exerts a pronounced, gradient-dependent effect on bacterial communities in both the rhizosphere and surrounding water of wild soybean. While Proteobacteria and other salt-tolerant groups expand under higher salinity, overall diversity tends to decline, especially in the rhizosphere. The plant–microbe interface shows signs of selective recruitment that could contribute to salt tolerance, highlighting the rhizosphere as a resilient zone where plant signals and microbial traits converge to mitigate stress. In the broader environment, salt exposure drives more expansive reorganization of microbial communities, pointing to distinct ecological responses between plant-associated and free-living microbiomes under salinity stress.
