Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

Abstract

Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices.IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

Keywords: Oryza sativa; SST variation; rhizosphere bacterial community; salt tolerant; soil metabolites.

FIG 1

Phenotypes of WT, mutant (sst), HHZ, HHZcas, ZH11, and ZH11cas rice plants after 20 days of control treatment (A to C) or 150 mM NaCl salt treatment (D to F). Size bars = 50 mm. The bottom of the image is divided into the corresponding local enlarged image. The control treatment was pure water. (G) K⁺ concentrations among the HHZ, HHZcas, ZH11, ZH11cas, WT, and sst plants. (H) Na⁺ concentrations among the HHZ, HHZcas, ZH11, ZH11cas, WT, and sst plants. One-way ANOVA, n = 3, P < 0.05.

FIG 2

(A) Effects of NaCl and the sst gene on rice rhizosphere soil bacterial Shannon diversity index (one-way ANOVA, n = 6, P < 0.05). (B) Principal-coordinate analysis (PCoA) based on Bray-Curtis dissimilarities showing differences in rhizosphere bacterial community structure under the control and 150 mM NaCl salt conditions (PERMANOVA, n = 6, P < 0.05). (C) Canonical correspondence analysis (CCA) based on the bacterial community compositions of samples under the NaCl condition (Mantel test, n = 6, P < 0.05). (D) The relative abundances of the bacterial phyla.

FIG 3

(A) Venn analysis of the OTUs that significantly differed in relative abundance between comparisons of Na-HHZ and Na-HHZcas, Na-ZH11 and Na-ZH11cas, and Na-WT and Na-sst plants. (B to D) The relative abundances of the OTUs that were coenriched in the roots of plants with loss of function of SST under salt stress and coexisted in soils of three pairs of plant materials (B), in soils of Na-ZH11 and Na-ZH11cas and Na-WT and Na-sst plant materials (C), and in soils of Na-HHZ and Na-HHZcas and Na-WT and Na-sst plant materials (D) (DESeq2, n = 6, P < 0.05). In panels B to D, different background colors correspond to different components in the Venn diagram.

FIG 4

Orthogonal partial least-squares discrimination analysis (OPLS-DA) (n = 6, P < 0.05) showing differences in soil metabolites between HHZ and HHZcas plants under the 150 mM NaCl condition.

FIG 5

Screening for maps of metabolic pathways involved in key differentially expressed metabolites. The log₂ fold change (HHZ versus HHZcas) of each metabolite is displayed in the form of a heat map from low (blue) to high (red) as presented in the color scale. The box indicates the HHZcas plants treated with 150 mM NaCl.

FIG 6

Correlation analysis between microbes and soil metabolites with significant differences between HHZ and HHZcas plants under the salinity condition. Red boxes represent positive correlations, while blue boxes represent negative correlations (Pearson's correlation, n = 6, P < 0.05). White asterisks indicate statistical significance: *, P < 0.05; **, P < 0.01.

FIG 7

Schematic representation of how the SST gene shapes the rhizosphere bacterial community by conferring tolerance to salt stress through regulation of soil metabolites.