Metagenomic analysis of the soil microbial composition and salt tolerance mechanism in Yuncheng Salt Lake, Shanxi Province

Abstract

The soil in Yuncheng Salt Lake has serious salinization and the biogeographic environment affects the composition and distribution of special halophilic and salt-tolerant microbial communities in this area. Therefore, this study collected soils at distances of 15, 30, and 45 m from the Salt Lake and used non-saline soil (60 m) as a control to explore the microbial composition and salt tolerance mechanisms using metagenomics technology. The results showed that the dominant species and abundance of salt-tolerant microorganisms changed gradually with distance from Salt Lake. The salt-tolerant microorganisms can increase the expression of the Na⁺/H⁺ antiporter by upregulating the Na⁺/H⁺ antiporter subunit mnhA-G to respond to salt stress, simultaneously upregulating the genes in the betaine/proline transport system to promote the conversion of choline into betaine, while also upregulating the trehalose/maltose transport system encode genes to promote the synthesis of trehalose to resist a high salt environment.

Keywords: Salt Lake; metagenome; microbial composition; salt tolerance mechanism; soil microorganism.

FIGURE 1

Satellite cloud image and physical and chemical indices of soil sampling points in Yuncheng Salt Lake. (A) Satellite cloud image of Yuncheng Salt Lake, Shanxi Province, China; (B) represents the changes in electrical conductivity, SO4^2–, total potassium and OM content in soil at different distances (15, 30, 45, 60 m) from the lake shore. Data were analyzed by one-way ANOVA (*p < 0.05).

FIGURE 2

Microbial composition of soil in Yuncheng Salt Lake. (A) Relative abundance composition of soil microorganisms at the kingdom level. (B) PCoA (principal coordinate analysis) based on Bray–Curtis at the genus level. (C) The relative contribution of the top 10 phyla at different distances (15, 30, 45, 60 m). (D) The relative contribution of the top 10 genera at different distances (15, 30, 45, 60 m). NE northeast, NW northwest, SE southeast, SW southwest.

FIGURE 3

Differential microorganisms in Salt Lake soil. (A) The 10 most discriminant genera in the models classifying different distances of bacterial microorganisms at the genus level based on the random forest method. The bar lengths indicate the importance of the variable. (B) Evaluation of predictive grouping ability of soil microbiota markers based on receiver operating characteristic (ROC) curve analysis. Draw the curve with sensitivity as the ordinate. The closer the ROC curve is to the upper left corner, the higher the accuracy of the test. If the area under the ROC curve (AUC) value is 1.0, it reflects the perfect distinction between the two groups, and there is no prediction error. Higher accuracy when AUC is above 0.9. (C) Heatmaps of the 10 most discriminant genera at different distances (15, 30, 45, 60 m) and directions (NE, NW, SW, SE) in the model classification.

FIGURE 4

Correlation analysis of phenotypic traits and screening of key regulatory genes. (A) Represents the number of genes in each module divided based on WGCNA (weighted gene coexpression network analysis); (B) represents the correlation heatmap of the soil phenotype and each module, the leftmost color block represents the module, the rightmost color bar represents the correlation range, and the abscissa is the soil phenotype index. The darker the color in the figure is, the higher the correlation; red indicates a positive correlation, and green indicates a negative correlation. The number in each cell indicates correlation and significance, (C) expression pattern of all modules in the sample.

FIGURE 5

The coexpression of genes in the black module. Based on the similarity between genes in the key module, the module network was constructed, and the core genes were screened. Different colors represent genes from different samples, and the size of the circle represents the degree.

FIGURE 6

Salt tolerance-related pathways and mechanisms of salt lake microorganisms.