Introduction
Wild soybean (Glycine soja) growing in coastal saline habitats relies on a complex microbiome to cope with salt stress. This study uses a hydroponic system with Hoagland’s solution to precisely control NaCl concentrations and to clearly separate rhizosphere bacteria from those in the surrounding water environment. By comparing a control (CK) with low (LT), medium (MT), and high (HT) salt treatments, researchers evaluated how salt stress influences bacterial diversity, community structure, and taxonomic composition in both the rhizosphere and the adjacent aquatic milieu.
Experimental design and sampling
Wild soybean seeds from Binzhou, Shandong, were germinated and grown hydroponically. After establishment, plants were exposed to four salt regimes for 21 days. Roots were collected to isolate rhizosphere bacteria, and the hydroponic tank water was filtered to capture the bacterial community in the surrounding environment. DNA was extracted from 64 samples (32 rhizosphere, 32 environmental) and subjected to 16S rRNA V3–V4 sequencing. The study focused on alpha diversity (Chao1 for richness, Shannon for diversity) and beta diversity (weighted UniFrac) to reveal how salt stress reshapes microbial communities.
Alpha and beta diversity under salt stress
Rhizosphere responses: Across salinity levels, rhizosphere bacterial richness (Chao1) showed limited variation, with significant changes primarily between the low-salt and high-salt groups. By contrast, Shannon diversity declined as salinity increased, particularly when comparing high-salt roots to controls. Principal coordinate analysis (PCoA) and PERMANOVA established clear separation of the high-salt rhizosphere (RootHT) from other groups, indicating strong selective pressure from salt stress on rhizosphere communities. Overall, rhizosphere communities exhibited a trend toward reduced diversity with higher salinity, likely due to plant-mediated selection and microbial competition under osmotic stress.
Environmental responses: The water environment showed more pronounced shifts with salinity. Shannon diversity differed significantly between the control water (WaterCK) and all salt-treated waters, and PCoA separated WaterCK from WaterLT/WaterMT/WaterHT. These results suggest that the surrounding environment is highly sensitive to salt changes, with microbial reassembly occurring as salinity rises.
Community composition and key players
Phylum-level trends: Proteobacteria dominated both rhizosphere and environmental samples (>50% across all groups) and tended to increase with salinity. Bacteroidota generally declined with higher salt, while Actinobacteriota increased under salt stress, indicating niche shifts favoring salt-tolerant taxa. Cyanobacteria surged in the rhizosphere under low- to medium-salt conditions but did not persist at high salinity in the rhizosphere.
Genus-level patterns: In the rhizosphere, Pseudomonas consistently enriched with rising salinity, reaching the highest relative abundance under HT. Acinetobacter and members of the AlloRhizobium-NeoRhizobium-ParaRhizobium-Rhizobium cluster were also prominent under salt stress. The high-salt rhizosphere showed notable enrichment of Shewanella and Sphingobium, suggesting specialized salt-tolerant lineages contribute to plant stress responses. In the water environment, Pseudomonas and Acinetobacter remained dominant, with Shewanella increasing under higher salinity. LEfSe analysis highlighted Shewanella and Pseudomonas as biomarkers in the HT group, underscoring their roles in salt adaptation.
Ecological implications
The rhizosphere and surrounding water host distinct but overlapping microbial dynamics under salt stress. Plants likely regulate rhizosphere communities via root exudates and immune signaling, preferentially enriching salt-tolerant, plant-growth-promoting taxa such as Pseudomonas, which can produce EPS, resist ionic stress, and enhance plant salt tolerance through hormone modulation and nutrient acquisition. In the environment, direct exposure to salinity drives rapid reorganization, with stress-tolerant taxa adapting to changing osmotic conditions. The study supports the idea that salt stress acts as a selective filter, shaping microbiomes in both niches, but plant-mediated sorting may buffer rhizosphere communities against extreme shifts compared with the external environment.
Conclusions
Salt stress distinctly alters the diversity and composition of bacterial communities in the wild soybean rhizosphere and its surrounding water environment. While Proteobacteria dominate across treatments, high-salt conditions strongly reshape rhizosphere structure, favoring Pseudomonas, Acinetobacter, and Shewanella, among others. The environmental bacterial community shows pronounced sensitivity to salinity, with clear differentiation from control conditions. These findings highlight the rhizosphere’s potential to recruit salt-tolerant, plant-beneficial microbes, contributing to wild soybean resilience in saline habitats and offering insights for microbiome-assisted crop improvement under salt stress.
