Microbial Assembly and Stress-Tolerance Mechanisms in Salt-Adapted Plants Along the Shore of a Salt Lake: Implications for Saline-Alkaline Soil Remediation

Abstract

Investigating the microbial community structure and stress-tolerance mechanisms in the rhizospheres of salt-adapted plants along saline lakes is critical for understanding plant-microbe interactions in extreme environments and developing effective strategies for saline-alkaline soil remediation. This study explored the rhizosphere microbiomes of four salt-adapted species (Suaeda glauca, Artemisia carvifolia, Chloris virgata, and Limonium bicolor) from the Yuncheng Salt Lake region in China using high-throughput sequencing. Cultivable salt-tolerant plant growth-promoting rhizobacteria (PGPR) were isolated and characterized to identify functional genes related to stress resistance. Results revealed that plant identity and soil physicochemical properties jointly shaped the microbial community composition, with total organic carbon being a dominant driver explaining 17.6% of the variation. Cyanobacteria dominated low-salinity environments, while Firmicutes thrived in high-salinity niches. Isolated PGPR strains exhibited tolerance up to 15% salinity and harbored genes associated with heat (htpX), osmotic stress (otsA), oxidative stress (katE), and UV radiation (uvrA). Notably, Peribacillus and Isoptericola strains demonstrated broad functional versatility and robust halotolerance. Our findings highlight that TOC (total organic carbon) plays a pivotal role in microbial assembly under extreme salinity, surpassing host genetic influences. The identified PGPR strains, with their stress-resistance traits and functional gene repertoires, hold significant promise for biotechnological applications in saline-alkaline soil remediation and sustainable agriculture.

Keywords: Yuncheng salt lake; plant growth-promoting rhizobacteria (PGPR); saline-alkaline soil remediation; salt tolerance mechanisms; salt-adapted plant rhizosphere microbiome; total organic carbon.

Figure 1

Upset diagram illustrating the soil bacterial operational taxonomic units (ASVs) in the rhizosphere soil of five plants. The upper vertical bars represent the number of ASVs shared among different plant rhizospheres, with connected black circles below indicating the specific sets included in each intersection and gray circles showing the sets not involved. The horizontal bars display the size of each ASV set.

Figure 2

Box plots illustrating the alpha (α) diversity of microbial communities in the rhizosphere soils of five plant species. (a) Simpson index; (b) the number of observed ASVs; (c) Shannon index; (d) equitability index. Significant differences between the pairs of plant species are indicated by asterisks (*: p < 0.05, **: p < 0.01, ***: p < 0.001).

Figure 3

Comparative analysis of the rhizosphere microbial assemblages and taxa exhibiting differential abundance. (a) PCoA ordination plot illustrating differences in the species-level microbial community structure across five rhizosphere soil samples. (b) LEfSe analysis identifying differentially abundant microbial taxa in the rhizosphere soils of plants grown under the conditions of SGG versus SGR. Taxa with significantly different relative abundances between the two groups were identified using an LDA > 4.

Figure 4

Correlations between soil physicochemical properties and rhizosphere microbial communities. (a) RDA illustrating the relationships between soil physicochemical properties and microbial community composition. The red arrows indicate physicochemical factors that significantly influence microbial variation, with their length proportional to the strength of the correlation. (b) Spearman correlation analysis examining the relationships between soil physicochemical properties and microbial communities at the class level. Asterisks (*) above the line indicate a statistically significant difference between the compared samples, with * indicating p < 0.05, ** indicating p < 0.01, and *** indicating p < 0.001.

Figure 5

Taxonomic profiling and phylogenetic diversity of the culturable rhizosphere bacteria. Panels (a,b) represent the relative abundances of culturable microorganisms at the phylum and class levels, respectively, found in the rhizosphere soils of the five investigated plant species. Panel (c) represents the phylogenetic tree illustrating 121 bacterial strains isolated from the rhizosphere soils of five plant species. The inner ring, segmented into 39 distinct colors, represents different genera, while the outer ring, colored in five different hues, corresponds to the rhizosphere soil samples. The colors of the outermost branches of the phylogenetic tree match those of the corresponding rhizosphere soil samples.

Figure 6

Phylogenetic analysis and stress resistance profiles of PGPR strains. (a) Phylogenetic tree of 19 PGPR strains. (b) Dot plot showing the presence and distribution of stress resistance genes within each PGPR strain. Dot size may represent gene copy number or relative abundance. (c) Heatmap displaying the functional profiles of the PGPR strains related to stress resistance. The color intensity indicates the relative abundance or expression level of the different stress resistance functions.