Streptomyces dominate the soil under betula trees that have naturally colonized a red gypsum landfill

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Abstract

The successful restoration of well-engineered tailings storage facilities is needed to avoid mine tailings problems. This study characterized the bacterial communities from vegetated and non-vegetated soils from a red gypsum landfill resulting from the industrial extraction of titanium. A set of 275 bacteria was isolated from vegetated soil and non-vegetated soil areas and taxonomically characterized using BOX-PCR. The study also evaluated the ability of a subset of 88 isolated bacteria on their ability to produce plant growth promoting (PGP) traits [indoleacetic acid (IAA) production, phosphate solubilization, and siderophore production] and their tolerance to potentially toxic elements (PTEs). Twenty strains were chosen for further analysis to produce inoculum for birch-challenging experiments. Principal component analysis (PCA) showed that the set of pedological parameters (pH, granulometry, carbon, organic matter, and Mg content) alone explained approximately 40% of the differences between the two soils. The highest density of total culturable bacteria was found in the vegetated soil, and it was much higher than that in the non-vegetated soil. The Actinobacteria phyla dominated the culturable soil community (70% in vegetated soil and 95% in non-vegetated soil), while the phyla Firmicutes (including the genus Bacillus) and Bacteroides (including the genera Pedobacter and Olivibacter) were found only in the vegetated soil fraction. Additional genera (Rhizobium, Variovorax, and Ensifer) were found solely in the vegetated soil. The vegetated soil bacteria harbored the most beneficial PGP bacteria with 12% of the isolates showing three or more PGP traits. The strains with higher metal tolerances in our study were Phyllobacterium sp. WR140 (RO1.15), Phyllobacterium sp. WR140 (R01.34), and Streptomyces sp. (R04.15), all isolated from the vegetated soil. Among the isolates tested in challenging experiments, Phyllobacterium (R01.34) and Streptomyces sp. (R05.33) have the greatest potential to act as PGP rhizobacteria and therefore to be used in the biological restoration of tailings dumps.

Figures

  • FIGURE 1 | (A) Diagram of the sampling site with soils taken in a vegetated area under birch trees (VS, top-left photo, green dotted line) or soil taken in a non-vegetated area (NVS, bottom-left photo). (B) PCA carried out with soil data and soil element concentrations discriminating between the two sampling areas, n = 5.
  • TABLE 1 | Physico-chemical parameters of vegetated soils (VS) and non-vegetated soils (NVS).
  • TABLE 2 | Total and CaCl2 extractable element concentrations in vegetated soils (VS) and non-vegetated soils (NVS).
  • FIGURE 2 | CFU culturable bacterial density expressed as UFC g-1 dry soil. The dilution series used to determine the density is represented by the Petri dishes after incubation for the non-vegetated soil (NVS) and the vegetated soil (VS).
  • FIGURE 3 | The cultivable bacterial communities from the VS and NVS fractions. The light-colored histograms at the edge represent the abundance of bacterial phyla expressed as a percentage of the total number of bacteria for the VS (Left) and the NVS (Right). The dark-colored central histogram represents the abundance of bacterial genera expressed as a percentage of the total number of bacteria for the VS (Left) and the NVS (Right). The names in white in the center indicate the shared bacteria between the two habitats.
  • FIGURE 4 | Functional traits of bacterial isolates from the Thann site. Plots representing the percentage of isolates that harbor the positive PGP trait or show metal tolerance. PGP traits were indoleacetic acid (IAA) production, organic acid production (OA), phosphorus solubilization (P), and siderophore production (SID). Metal tolerance was tested for Cr, Mn, and Zn at concentrations ranging from 0.1 to 25 mM. Gray plots indicate non-tested concentrations (nt) for a given metal. Significant differences are indicated (∗P < 0.05; ∗∗P < 0.01).
  • FIGURE 5 | Impact of bacterial inoculation on birch growth. Birch trees were grown for 3 months on the Thann soil inoculated with 20 bacterial isolates collected from the VS fraction. Significant differences are indicated (∗P < 0.05; ∗∗P < 0.01; and ∗∗∗P < 0.001).

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APA

Zappelini, C., Alvarez-Lopez, V., Capelli, N., Guyeux, C., & Chalot, M. (2018). Streptomyces dominate the soil under betula trees that have naturally colonized a red gypsum landfill. Frontiers in Microbiology, 9(AUG). https://doi.org/10.3389/fmicb.2018.01772

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