Fig 1.
Illustrative description of study design.
Only one species is represented in the picture; however, all plant hosts underwent the same manipulations. Seeds from each plant host (color of which plant host is depicted by color of the pot) were grown in soil collected from all plant hosts (color of source inoculum is depicted by the color of the soil). Soils were subjected to both an antibiotic treatment (depicted by color of liquid in the pipette) and autoclaved treatment (depicted by striations of the soil).
Fig 2.
Plant host explains variation in root endophytic bacterial community.
(A) CAP plot showing the live soil endophytic root microbiome of Carduus nutans (red), Conyza canadensis (blue), Heliopsis helianthoides (green), Monarda fistulosa (purple) and Ratibida pinnata (orange) [ADONIS p < 0.001, r2 = 0.11, n = 201]. (B) CAP plot showing the endophytic root microbiome clustered by soil history [ADONIS p < 0.001, r2 = 0.03, n = 201] (C) CAP plot showing both the live and autoclaved soil endophytic root microbiome clustered by plant host [ADONIS p< 0.001, r2 = 0.07, n = 247] (D) CAP plot showing both live and autoclaved soil endophytic root microbiome separated by soil history [ADONIS p< 0.001, r2 = 0.02, n = 247].
Fig 3.
Plant biomass is affected by soil treatment.
(A) Bars represent mean total dried biomass across all field soils and all autoclaved field soils with SE. The asterisks indicate statistically significant differences [ANOVA tests with P ≤ 0.05, n = 537]. (B) (C) Box plots of differentially abundant OTUs found across all live soil history [ANCOM (Mann-Whiteny U + FDR correction P ≤ 0.05, n = 201)].
Fig 4.
Root-endophytic bacterial community composition as a function of growth differences.
(A) Bars represent mean total dried biomass across all field soils and all autoclaved field soils with SE. The asterisks indicate statistically significant differences [ANOVA tests with P ≤ 0.05, n = 537]. Difference in total biomass between individuals of the same plant species correlated with difference in endophytic root microbiome composition (calculated using Bray-Curtis dissimilarity). Each point represents two individuals’ difference in root microbiome and biomass. (B) C. nutans (n = 52), (C) M. fistulosa (n = 52), (D) R. pinnata (n = 50), (E) C. canadensis (n = 46), (F) H. helianthoides (n = 47). Differences calculated between samples grown in autoclaved soil are in grey, between samples grown in field soil are in pink, and between one sample grown in field soil and one grown in autoclaved soil in black. Lines and regression statistics are based on Mantel and linear regression.
Fig 5.
Bacterial species abundance with statistically significant (P ≤ 0.05, after Bonferroni correction) correlation with plant log biomass.
Bacterial species within the roots of (A) H. helianthoides (B) M. fistulosa and (C) R. pinnata.
Fig 6.
Significant plant-soil feedback pairs correlated with root-endophytic bacterial community composition.
Plant performance when grown in soil history from conspecifics vs heterospecifics: (A) Performance of C. nutans (n = 37) and C. canadensis (n = 38). The resulting interaction between plant host and soil history defined a significant negative feedback (insert, p = 0.027). (C) Performance of C. nutans (n = 37) and H. helianthoides (n = 38). The resulting interaction defined a significant positive feedback (insert, p = 0.016). (E) Performance of C. nutans (n = 37) and M. fistulosa (n = 38). The resulting interaction defined a significant positive feedback (insert, p = 0.019). (G) Performance of C. canadensis (n = 38) and H. helianthoides (n = 38). The resulting interaction defined a closely significant negative feedback (insert, p = 0.064). (I) Performance of M. fistulosa (n = 37) and H. helianthoides (n = 38). The resulting interaction defined a closely significant positive feedback (insert, p = 0.0001). (K) Performance of M. fistulosa (n = 38) and R. pinnata (n = 37). The resulting interaction defined a closely significant negative feedback (insert, p = 0.07). Difference in total biomass grown in conspecific vs heterospecific soil correlated with difference in endophytic root microbiome composition (calculated using Bray-Curtis dissimilarity). Each point represents two individuals’ difference in root microbiome and biomass: (B) C. canadensis grown in inoculum from C.nutans vs conspecific soil (D) C. nutans grown in inoculum from H. helianthoides vs conspecific soil (F) M. fistulosa grown in inoculum from C. nutans vs conspecific soil (H) C. canadensis grown in inoculum from H. helianthoides vs conspecific soil (J) M. fistulosa grown in inoculum from H. helianthoides vs conspecific soil (L) R. pinnata grown in inoculum from M. fistulosa vs conspecific soil.