The microbial community from the early-plant colonizer (Baccharis linearis) is required for plant establishment on copper mine tailings

Abstract

Plants must deal with harsh environmental conditions when colonizing abandoned copper mine tailings. We hypothesized that the presence of a native microbial community can improve the colonization of the pioneer plant, Baccharis linearis, in soils from copper mining tailings. Plant growth and microbial community compositions and dynamics were determined in cultivation pots containing material from two abandoned copper mining tailings (Huana and Tambillos) and compared with pots containing fresh tailings or surrounding agricultural soil. Controls without plants or using irradiated microbe-free substrates, were also performed. Results indicated that bacteria (Actinobacteria, Gammaproteobacteria, and Firmicutes groups) and fungi (Glomus genus) are associated with B. linearis and may support plant acclimation, since growth parameters decreased in both irradiated (transiently without microbial community) and fresh tailing substrates (with a significantly different microbial community). Consistently, the composition of the bacterial community from abandoned copper mining tailings was more impacted by plant establishment than by differences in the physicochemical properties of the substrates. Bacteria located at B. linearis rhizoplane were clearly the most distinct bacterial community compared with those of fresh tailings, surrounding soil and non-rhizosphere abandoned tailings substrates. Beta diversity analyses showed that the rhizoplane bacterial community changed mainly through species replacement (turnover) than species loss (nestedness). In contrast, location/geographical conditions were more relevant than interaction with the plants, to explain fungal community differences.

Figure 1

Non-metric multidimensional scaling (NMDS) analysis of HhaI-terminal restriction fragment length polymorphisms (T-RFLP) profiles of metagenomic DNA from three soil substrates. T-RFLP profiles of 16S rRNA bacterial (A) and internal transcribed spacer fungal (B) community sequences were obtained from the rhizoplane (circles), rhizosphere (triangles), and non-rhizosphere (squares) of Huana tailings (red symbols), Tambillos tailings (blue symbols) and surrounding soil (black symbols). Each symbol corresponds to a single T-RFLP profile (four samples each site). Stress values for NMDS analysis are shown in each upper right corner. This image was created using Primer v6 software, URL https://www.primer-e.com/.

Figure 2

Relative abundance of main bacterial taxa detected by terminal restriction fragment length polymorphisms. Two-way clustering dendrogram obtained using Spearman distance with average grouping algorithm to evaluate the distribution of bacterial communities from the different sites and compartments at the phylum level. The heat map colors represent the relative abundance percentage (right hand legend) of the bacterial phylum (X-axis clustering) within each site/compartment (Y-axis clustering). HT-NR Huana tailings-non rhizosphere, HT-SR Huana tailings rhizosphere, TT-NR Tambillos tailings-non rhizophere, S-NR surrounding soil-non rhizosphere, S-SR surrounding soil rhizosphere, TT-SR Tambillos tailings rhizosphere, S-RP surrounding soil rhizoplane, HT-RP Huana tailings rhizoplane, TT-RP Tambillos tailings rhizoplane. This image was created using RStudio Team. Version 1.0.143. URL http://www.rstudio.com/.

Figure 3

Beta diversity analyses of microbial meta-community of the non-rhizosphere, the rhizosphere and rhizoplane of Baccharis linearis plants inhabiting abandoned tailings and surrounding soil. (A) Non-metric multidimensional scaling analysis of meta-community dissimilarities. Grouping by localization and root compartments was performed by estimation of the total beta diversity distances (β_SOR) between samples. The localization and root compartment are denoted as follows: Huana tailings (blue), Tambillos tailings (dark grey), fresh tailings (green), surrounding soil (red), rhizoplane (filled circle), rhizosphere (x) and non-rhizosphere (□). Each point corresponds to a single T-RFLP profile (n = 4 replicates). (B) Density plots representing the distribution of the total beta diversity (β_SOR), turnover (β_SIM) and nestedness (β_SNE) arising from multiple-site dissimilarity across the samples. Components of multiple-site dissimilarity were computed for microbial community composition (bacteria and fungi) in Huana (blue), and Tambillos (black) tailings and surrounding soil (red). Β_SNE: dashed line; β_SIM: dotted line and β_SOR: solid line. These figures were created using Betapart R Package Version 1.3. URL http://CRAN.R-project.org/package=betapart.

Figure 4

Comparisons of the effects of fresh tailings and a surrounding soil substrate in the growth and the establishment of Baccharis linearis plants in tailing substrates. (A) Growth parameters and (B) pigment contents in 18 weeks old plants that were transferred to a surrounding soil (black bars) or to a substrate derived from Tambillos fresh tailings (grey bars), six weeks after sowing. Bars represent the average ± SE of 24 replicates and asterisks indicate significant differences considering the treatment (surrounding soil or fresh tailings) as factor in each parameter (one-way ANOVA for parametric data or Kruskal–Wallis test for non-parametric data, p < 0.01).

Figure 5

Effects of the microbial community in the establishment of Baccharis linearis plants in non-irradiated or irradiated tailing substrates. Plantlets were transferred to non-irradiated (grey bars) or irradiated (black bars) tailing substrates six weeks after sowing and plant growth parameters (A) height; (B) leaf area; (C) green dry biomass and (D) number of green leaves, were measured 18 weeks after transplantation. Bars represent average ± SE (24 replicates per treatment). Asterisks indicate significant differences according to a one-way ANOVA (for parametric data) or to a Kruskal–Wallis test (for non-parametric data) considering irradiation as factor; *p < 0.05 **p < 0.01. (E). Representative plants grown on each treatment are shown, bars indicate 1 cm.