Introduction and study design
Understanding how salinity affects plant-associated microbial communities is essential for unraveling plant resilience mechanisms. This study used a controlled hydroponic system with Hoagland’s nutrient solution to isolate the effects of salt (NaCl) on bacterial communities in the rhizosphere of wild soybean (Glycine soja) and its surrounding water environment. Four treatments were applied: a salt-free control (CK), low-salt (LT, 100 mmol/L NaCl), medium-salt (MT, 200 mmol/L NaCl), and high-salt (HT, 300 mmol/L NaCl), each in triplicate. After 21 days, rhizosphere roots and tank water were sampled for high-throughput 16S rRNA gene sequencing to compare community composition and diversity.
The analysis focused on the V3–V4 region of the bacterial 16S rRNA gene, generating a comprehensive dataset of amplicon sequence variants (ASVs) to assess richness (Chao1) and diversity (Shannon), as well as beta diversity through weighted UniFrac distances and PCoA. The goal was to determine how salt stress shapes microbial assembly in two linked but distinct habitats: the plant-adjacent rhizosphere and the surrounding water environment.
Alpha and beta diversity under salt stress
Across samples, Proteobacteria consistently dominated both rhizosphere and water communities, often comprising more than half of the relative abundance. However, salinity shifted the community structure. In the rhizosphere, higher salinity (HT) led to a notable rise in Proteobacteria, with Pseudomonas gaining prominence as salinity increased. The rhizosphere also showed an increase in Shewanella under high salt, signaling enhanced tolerance and possible roles in osmotic balance through EPS production and solute accumulation. In contrast, the surrounding water environment displayed a stronger sensitivity to salt, with Beta diversity shifting more markedly as salinity rose.
Alpha diversity patterns revealed a general decline in diversity with increasing salt in both habitats, though the rhythm of change differed. Shannon diversity in rhizosphere samples showed significant reductions at high salinity relative to controls, while Chao1 richness changes were more nuanced and treatment-dependent. In the water environment, the control group differed strikingly from salt-treated groups in both richness and diversity, suggesting that the aquatic microbiome responds rapidly to ionic changes, potentially altering nutrient cycling and microbial interactions in the tank.
Taxonomic patterns of response to salinity
Phylum-level analyses showed Proteobacteria as a persistent dominant group in both habitats, with its relative abundance increasing with salinity. Bacteroidota tended to decline under higher salt, while Actinobacteriota often rose as salinity intensified, indicating a shift toward salt-tolerant lineages across environments. In the rhizosphere, Cyanobacteria peaked at low-to-medium salt before diminishing at high salinity, a pattern likely tied to niche-specific responses to osmotic stress and nutrient availability.
Genus-level dynamics were illustrative of potential plant-microbe interactions under salt stress. Pseudomonas consistently enriched with increasing salinity in both rhizosphere and water environments, suggesting robust salt tolerance and the ability to form protective biofilms via EPS. Acinetobacter maintained a stable presence in the rhizosphere despite salt changes, consistent with roles as a versatile rhizosphere settler. Rhizobium, Sphingobium, and Shewanella also showed salinity-dependent shifts, with Shewanella notably expanding under high-salt conditions, potentially aiding osmotic balance and stress tolerance through metabolite exchange and biofilm formation.
Implications for plant health and ecosystem function
The observed patterns imply a plant-driven selection of salt-tolerant taxa in the rhizosphere, possibly mediated by root exudates that alter carbon sources and signaling under stress. This selective recruitment can stabilize the rhizosphere microbiome, preserving plant-associated functions such as nutrient acquisition, hormone signaling, and stress mitigation. The surrounding water microbiome, exposed directly to salinity, may experience greater reorganization, affecting nutrient turnover and microbial interactions in the hydroponic system. Together, these results highlight the rhizosphere as a comparatively resilient interface that can maintain beneficial microbial partners under salt stress, while the ambient environment exhibits more pronounced community restructuring.
Conclusions
Salt stress reshapes both rhizosphere and water microbial communities in wild soybeans, with Proteobacteria becoming more dominant and taxa like Pseudomonas and Shewanella responding strongly to elevated salinity. The rhizosphere shows signs of stability through plant-mediated recruitment of salt-tolerant microbes, whereas the surrounding environment demonstrates greater beta diversity changes. These insights inform strategies to harness microbial allies for improving soybean tolerance to salinity in natural and managed ecosystems.
