Changes in Soil Chemistry and Microbial Communities in Rhizospheres of Planted Gastrodia elata on a Barren Slope and under a Forest

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Changes in Soil Chemistry and Microbial Communities in Rhizospheres of Planted Gastrodia elata on a Barren Slope and under a Forest


Author Contributions

X.X., resources, investigation, methodology and writing—original draft; R.S., formal analysis, methodology, and writing—original draft; X.Y., resources, data curation, and methodology; A.Z., data curation and software; Y.W., data curation and writing—review and editing; J.J., methodology and formal analysis; Y.Y., resources and visualization; A.R.H., data curation, validation, and writing—review and editing; J.L., formal analysis, visualization, writing—review and editing, and supervision; X.H., conceptualization, project administrator, writing—review and editing. All authors have read and agreed to the published version of the manuscript.

Figure 1.
Chemical properties of the four soil groups. (A) pH; (B) Total nitrogen; (C) NO3N; (D) NO4+—N; (E) Organic matter; (F) Total carbon; (G) Organic carbon; (H) Total sulfur; (I) Total phosphorus; (J) Effective boron; (K) Total potassium. Different letters above bars indicate statistical differences at p < 0.05. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

Figure 1.
Chemical properties of the four soil groups. (A) pH; (B) Total nitrogen; (C) NO3N; (D) NO4+—N; (E) Organic matter; (F) Total carbon; (G) Organic carbon; (H) Total sulfur; (I) Total phosphorus; (J) Effective boron; (K) Total potassium. Different letters above bars indicate statistical differences at p < 0.05. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

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Figure 2.
Estimation of similarity and distance between soil groups. (A) Homology analysis; (B) Hierarchical clustering tree of the samples (the length of the branches represents the distance between samples); (C) NMDS plot; (D) Principal coordinate analysis (PCoA). The closer the two samples are on the NMDS and PCoA plots, the more similar the species composition of the two samples. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

Figure 2.
Estimation of similarity and distance between soil groups. (A) Homology analysis; (B) Hierarchical clustering tree of the samples (the length of the branches represents the distance between samples); (C) NMDS plot; (D) Principal coordinate analysis (PCoA). The closer the two samples are on the NMDS and PCoA plots, the more similar the species composition of the two samples. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

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Figure 3.
The composition and structure of the microbial community at the phylum level. (A) Relative abundances of the microbial phyla in different samples. (B,C) Pie plots for microbial community analysis at the phylum level in HPT and HPGJ, respectively. (D,E) Pie plots for microbial community analysis at the phylum level in FLXT and LXT, respectively. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

Figure 3.
The composition and structure of the microbial community at the phylum level. (A) Relative abundances of the microbial phyla in different samples. (B,C) Pie plots for microbial community analysis at the phylum level in HPT and HPGJ, respectively. (D,E) Pie plots for microbial community analysis at the phylum level in FLXT and LXT, respectively. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

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Figure 4.
The composition and structure of the microbial community at the genus level. (A) Relative abundances of the microbial genera in different samples. (B,C) Pie plots for microbial community analysis at the genus level in HPT and HPGJ, respectively. (D,E) Pie plots for microbial community analysis at the genus level in FLXT and LXT, respectively. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

Figure 4.
The composition and structure of the microbial community at the genus level. (A) Relative abundances of the microbial genera in different samples. (B,C) Pie plots for microbial community analysis at the genus level in HPT and HPGJ, respectively. (D,E) Pie plots for microbial community analysis at the genus level in FLXT and LXT, respectively. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

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Figure 5.
KEGG annotation of functional genes in different samples. The scaled Log2 fold change of each annotaion is plotted in a blue-white-red color scale. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

Figure 5.
KEGG annotation of functional genes in different samples. The scaled Log2 fold change of each annotaion is plotted in a blue-white-red color scale. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

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Figure 6.
Effects of G. elata cultivation on N cycling. (A) Expression fold change of N cycling-related genes taking FLXT as the control. (B) Abundance of N cycling-related genes in different samples. The scaled Log2 fold change of the abundance of genes in each process is plotted in a blue-yellow-red color scale. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

Figure 6.
Effects of G. elata cultivation on N cycling. (A) Expression fold change of N cycling-related genes taking FLXT as the control. (B) Abundance of N cycling-related genes in different samples. The scaled Log2 fold change of the abundance of genes in each process is plotted in a blue-yellow-red color scale. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

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Figure 7.
Effects of G. elata cultivation on C and S cycling. (A,C) Expression fold change of C and S cycling-related genes taking FLXT as the control, respectively. (B,D) Abundance of C and S cycling-related genes in different samples, respectively. The scaled Log2 fold change of the abundance of genes in each process is plotted in a blue-yellow-red color scale. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

Figure 7.
Effects of G. elata cultivation on C and S cycling. (A,C) Expression fold change of C and S cycling-related genes taking FLXT as the control, respectively. (B,D) Abundance of C and S cycling-related genes in different samples, respectively. The scaled Log2 fold change of the abundance of genes in each process is plotted in a blue-yellow-red color scale. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

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Figure 8.
Abundance of top 50 pathogenic microbes in different samples. The scaled Log2 fold change of the abundance of each pathogen is plotted in a light blue-white-red color scale. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

Figure 8.
Abundance of top 50 pathogenic microbes in different samples. The scaled Log2 fold change of the abundance of each pathogen is plotted in a light blue-white-red color scale. HPT, barren slope soil; HPGJ, rhizosphere slope soil of wild G. elata rhizosphere; FLXT, understory soil; and LXT, rhizosphere soil of G. elata under forest.

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