Supplementary Table S1 Seed surface sterilization methods. Supplementary Table S2




Дата канвертавання24.04.2016
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Supplementary Table S1 Seed surface sterilization methods.
Supplementary Table S2 in a separate Excel file. The table provides the 454Flx sequencing information: barcode and primers sequence, number of reads, number of OTUs constructed for each sample.

Supplementary Figure S1 Comparison of year to year sampling using Arabidopsis wild type (A_1st_yr and A_2nd_yr) and unplanted control (unplanted_1st_yr and unplanted_2nd_yr). Plants were grown in 10% Bawburgh grass soil and 90 % sand condition (vol/vol) and watered with plant mineral supplement and KNO3 (10mg). Unplanted control was kept using the same conditions. Most of the dominant OTUs were found at both sampling times. However, in the first year of sampling an Achromobacter OTU was over-represented compared to the second year.
Supplementary Figure S2 Different model and crop plants grown in sand and compost establish distinct rhizosphere microbiota. (a) sand: ARISA analysis of all three generations of plants. (b) compost: ARISA analysis of all three generations of model plants. (c) compost: ARISA analysis of three generations of crop plants. (d) sand: ARISA data from (a), grouped for visual clarity into 3 bins of eight plants (± S.E.M.). (e) compost: ARISA data from (b), grouped for visual clarity into 3 bins of eight plants (± S.E.M.). (f) compost: ARISA data from (c), grouped for visual clarity into 3 bins of eight plants (± S.E.M.). (g) sand: 454Flx pyrosequencing analysis of fungi from all three generations. (h) compost: 454Flx pyrosequencing analysis of fungi from three generations of model plants. (i) 454Flx pyrosequencing analysis of fungi from three generations of crop plants. (j) compost: ARISA analysis of the third generation of model plants. (k) compost: 454Flx pyrosequencing analysis of bacteria from three generations of model and crop plants. Data shown as nMDS plots (based on Bray-Curtis dissimilarity), which lack axes and where each data point represents one plant microbiota.
Supplementary Figure S3 MANOVA analysis of plants grown in sand. MANOVA output indicates the significance level between two groups of data on the basis of F-tests performed on Bray-Curtis distance matrices with 1000 permutations using adonis implemented in the vegan package in R. For simplicity, the table indicates the minimum number of plant replicates from each group needed for separation (950 permutations with p < 0.05), A. thaliana (A), M. truncatula (M), B. distachyon (B), B. rapa (Br), P. sativum (P), T. aestivum (W), unplanted control (U), generation (1, 2, 3). Colour was used for visual clarity. Analysis based on ARISA data.
Supplementary Figure S4 Microbiota diversity over three generations of plant growth. (a) Community structure at the phylum level over three generations of model plants in sand, y-axis: abundance. (b) Shannon diversity index of model plant microbiota in sand. (c) Shannon diversity index of model plant microbiota in compost. (d) Shannon diversity index of crop plant microbiota in compost. For (b-d) left side of the graph represents the bacterial community and the right, the fungal community. A. thaliana (A), M. truncatula (M), B. distachyon (B), B. rapa (Br), P. sativum (P), T. aestivum (W), unplanted control (U), generation (1, 2, 3). (e) Richness index (number of OTUs in the most abundant 50% of the community). Stars indicate results of pair-wise t-test (p<0.05) with Bonferroni correction.
Supplementary Figure S5 Bacterial OTUs either selected or depleted in the rhizosphere. (a) Selected in sand. (b) Depleted in sand. (c) Selected in compost. (d) Depleted in compost. The heat maps show bacterial OTUs where fold-abundance was statistically different (t-test with Bonferroni correction; p<0.05) in the rhizosphere compared to unplanted control in at least one generation. Only OTUs with a relative abundance of greater than 0.1% were used, A. thaliana (A), M. truncatula (M), B. distachyon (B), B. rapa (Br), P. sativum (P), T. aestivum (W), generation (1, 2, 3). Dendrograms were removed for visual clarity.
Supplementary Figure S6 Explanatory 2-dimensional ternary plot. Each dot represents a single OTU and its size is proportional to the abundance in all three rhizospheres and unplanted control in a given generation. The colour is used for visual clarity and represents the ratio of the mean rhizosphere abundance against the unplanted control. The location is based on the rhizosphere abundance only (in this case the rhizosphere of Arabidopsis, Medicago and Brachypodium). The green dot represents an OTU that was found 30% of the time in the rhizosphere of Brachypodium, 20% in Medicago and 50% in Arabidopsis. Ternary plots present the rhizosphere selection as well as depletion. For example the big red dot in the Medicago corner is an OTU that was strongly selected in the Medicago rhizosphere. The blue dot in the Brachypodium corner is an example of a predominantly soil microorganism (mostly found in the unplanted control), which was depleted from the rhizospheres of Arabidopsis and Medicago, but not Brachypodium.
Supplementary Figure S7 The effect on the rhizosphere fungal microbiota of plants grown in sand compared with compost. Each sphere represents a single OTU, size represents abundance, position corresponds to the relative abundance in the three rhizospheres and colour reflects the rhizosphere abundance relative to unplanted soil calculated for each generation separately. Please refer to Supplementary Figure S6 for an example explanation. (a) Fungal microbiota of model plants grown in sand. (b) Fungal microbiota of model plants grown in compost. (c) Fungal microbiota of crop plants grown in compost. Only OTUs with a relative abundance of greater than 0.1% were used. Abbreviations are as follows: Alternaria (Al), Cryptococcus (Cr), Fusarium (F), Gibellulopsis (G), Olpidium brassicae (O), Penicillium (Pe), Phoma (Ph) and Arabidopsis (A), Medicago (M), Brachypodium (B), Brassica (Br), Pisum (P), Triticum (W), generation (1, 2, 3).
Supplementary Figure S8 Structure of fungal microbiota. (a) Sand experiment. (b) Compost experiment. A. thaliana (A), M. truncatula (M), B. distachyon (B), B. rapa (Br), P. sativum (P), T. aestivum (W), unplanted control in sand (U50), unplanted control in compost (U100), generation (1, 2, 3). Each of the sequencing read has been identified using the GenBank database and annotated in MEGAN. Analysis has been stopped at the phylum and subphylum level. Saccharomyceta and Agaricomycotina subphyla are shown, as they represent the abundant group of Ascomycota and Basidomycota phyla, respectively.

Supplementary Figure S9 Abundance of two dominant OTUs for which a representative strain was isolated.

Supplementary Figure S10 Plant growth promotion assay for three model plants using isolated bacterial strains. Letters a,b, ab, ac and c represent the statistical differences in plant dry weight for each species (based on t-test with Bonferroni correction, p<0.05).
Supplementary Figure S11 MANOVA analysis of plants grown in compost. (a) Model plants. (b) Crop plants, A. thaliana (A), M. truncatula (M), B. distachyon (B), B. rapa (Br), P. sativum (P), T. aestivum (W), unplanted control (U), generation (1, 2, 3). Colour was used for visual clarity. Analysis based on ARISA data.
Supplementary Figure S12 Neighbor-Joining phylogram of fungal OTU 540 annotated as OTU 540 sequence. Tree was constructed using MEGA6 software using BLAST algorithm against 100 target sequences (default ClustalW settings, bootstrap value of 1000.
Supplementary Word file 1 In a separate Word file. Pictures of the soil sampling site and plant growth.
Supplementary Word file 2 In a separate Word file. A brief report about two isolates: Achromobacter xylosoxidans and Arthrobacter sp., indicating their position in the phylogenetic tree of life.






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