Taxonomic Structure of Rhizosphere Bacterial Communities and Its Association With the Accumulation of Alkaloidal Metabolites in Sophora flavescens

Abstract

Plant secondary metabolites (SMs) play a crucial role in plant defense against pathogens and adaptation to environmental stresses, some of which are produced from medicinal plants and are the material basis of clinical efficacy and vital indicators for quality evaluation of corresponding medicinal materials. The influence of plant microbiota on plant nutrient uptake, production, and stress tolerance has been revealed, but the associations between plant microbiota and the accumulation of SMs in medicinal plants remain largely unknown. Plant SMs can vary among individuals, which could be partly ascribed to the shift in microbial community associated with the plant host. In the present study, we sampled fine roots and rhizosphere soils of Sophora flavescens grown in four well-separated cities/counties in China and determined the taxonomic composition of rhizosphere bacterial communities using Illumina 16S amplicon sequencing. In addition, the association of the rhizosphere bacterial microbiota with the accumulation of alkaloids in the roots of S. flavescens was analyzed. The results showed that S. flavescens hosted distinct bacterial communities in the rhizosphere across geographic locations and plant ages, also indicating that geographic location was a larger source of variation than plant age. Moreover, redundancy analysis revealed that spatial, climatic (mean annual temperature and precipitation), and edaphic factors (pH and available N and P) were the key drivers that shape the rhizosphere bacterial communities. Furthermore, the results of the Mantel test demonstrated that the rhizosphere bacterial microbiota was remarkably correlated with the contents of oxymatrine, sophoridine, and matrine + oxymatrine in roots. Specific taxa belonging to Actinobacteria and Chloroflexi were identified as potential beneficial bacteria associated with the total accumulation of matrine and oxymatrine by a random forest machine learning algorithm. Finally, the structural equation modeling indicated that the Actinobacteria phylum had a direct effect on the total accumulation of matrine and oxymatrine. The present study addresses the association between the rhizosphere bacterial communities and the accumulation of alkaloids in the medicinal plant S. flavescens. Our findings may provide a basis for the quality improvement and sustainable utilization of this medicinal plant thorough rhizosphere microbiota manipulation.

Keywords: alkaloids; medicinal plants; plant bacterial community; rhizosphere; secondary metabolites.

Figure 1

Diversity of the rhizosphere bacterial communities of Sophora flavescens. (A,B) The number of specific and shared operational taxonomic units (OTUs) of the rhizosphere bacterial communities from different geographic locations (A) or between different plant ages (B). (C–E) The alpha diversity, including species richness (C), Chao1 index (D), and Shannon index (E), of the bacterial communities in the rhizosphere samples from different geographic locations. Different lowercase letters indicate significant differences among geographical locations (P < 0.05). LN: Lingyuan; CZ: Changzhi; DL: Dali; LN: Luonan. 1Y: 1-year-old; 2Y: 2-year-old; 3Y: 3-year-old.

Figure 2

Taxonomic structure of the bacterial communities in the rhizosphere of S. flavescens from different geographic locations (A,C) or of different ages (B) at the phylum (A,B) or order (C) level. LN: Lingyuan; CZ: Changzhi; DL: Dali; LN: Luonan. 1Y: 1-year-old; 2Y: 2-year-old; 3Y: 3-year-old.

Figure 3

Variation in the rhizosphere bacterial communities of S. flavescens. (A) Nonmetric multidimensional scaling (NMDS) ordination of the rhizosphere bacterial communities based on the Bray-Curtis distance matrix. (B) Redundancy analysis (RDA) revealing significant spatial, climatic, and edaphic variables shaping the rhizosphere bacterial communities. (C) Variation partitioning analysis (VPA) indicating the independent and interactive impacts (the percentage of variation explained) of the spatial, climatic, and edaphic factors on the rhizosphere bacterial communities. LN: Lingyuan; CZ: Changzhi; DL: Dali; LN: Luonan. 1Y: 1-year-old; 2Y: 2-year-old; 3Y: 3-year-old. PCNM: principal coordinates of neighbor matrices; MAT: mean annual temperature; MAP: mean annual precipitation; AN: available N; AP: available P.

Figure 4

Variation in the root alkaloid accumulation of S. flavescens performed by principal coordinate analysis (PCoA) based on the Bray-Curtis distance matrix. LN: Lingyuan; CZ: Changzhi; DL: Dali; LN: Luonan. 1Y: 1-year-old; 2Y: 2-year-old; 3Y: 3-year-old.

Figure 5

The top 30 important bacterial markers associated with the total accumulation of matrine and oxymatrine in the roots of S. flavescens based on a random forest model. (A) The 10-fold cross-validation with five repeats generates 935 bacterial marker OTUs correlated with the total content of matrine and oxymatrine. (B) The peak map plotted according to the relative abundance of the top 30 marker OTUs against the total content of matrine and oxymatrine.

Figure 6

Structural equation model depicting the direct and indirect effects of the spatial, climatic, and edaphic factors and the relative abundance of three preponderant rhizosphere phyla on the accumulation of alkaloids in the roots of S. flavescens (P = 0.385; root-mean-squared error of approximation = 0.027; comparative fit index = 1.000). Black arrow lines: significant correlations; Gray arrow lines: correlations that are not significant; Red arrows: positive correlations; Blue arrows: negative correlations. Numbers between parameter boxes are indicative of the correlations. *P < 0.05; **P < 0.01; ***P < 0.001. MAT: mean annual temperature; MAP: mean annual precipitation; OM: organic matter; AN: available N; AP: available P; AK: available K.