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Supplementary Table S1 Seed surface sterilization methods.
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Supplementary Table S2 in a separate Excel file. The table provides the 454Flx
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sequencing information: barcode and primers sequence, number of reads, number of
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OTUs constructed for each sample.
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Supplementary Figure S1 Comparison of year to year sampling using Arabidopsis wild
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type (A_1st_yr and A_2nd_yr) and unplanted control (unplanted_1st_yr and
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unplanted_2nd_yr). Plants were grown in 10% Bawburgh grass soil and 90 % sand
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condition (vol/vol) and watered with plant mineral supplement and KNO3 (10mg).
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Unplanted control was kept using the same conditions. Most of the dominant OTUs were
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found at both sampling times. However, in the first year of sampling an Achromobacter
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OTU was over-represented compared to the second year.
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Supplementary Figure S2 Different model and crop plants grown in sand and compost
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establish distinct rhizosphere microbiota. (a) sand: ARISA analysis of all three
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generations of plants. (b) compost: ARISA analysis of all three generations of model
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plants. (c) compost: ARISA analysis of three generations of crop plants. (d) sand: ARISA
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data from (a), grouped for visual clarity into 3 bins of eight plants (± S.E.M.). (e)
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compost: ARISA data from (b), grouped for visual clarity into 3 bins of eight plants (±
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S.E.M.). (f) compost: ARISA data from (c), grouped for visual clarity into 3 bins of eight
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plants (± S.E.M.). (g) sand: 454Flx pyrosequencing analysis of fungi from all three
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generations. (h) compost: 454Flx pyrosequencing analysis of fungi from three
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generations of model plants. (i) 454Flx pyrosequencing analysis of fungi from three
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generations of crop plants. (j) compost: ARISA analysis of the third generation of model
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plants. (k) compost: 454Flx pyrosequencing analysis of bacteria from three generations
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of model and crop plants. Data shown as nMDS plots (based on Bray-Curtis
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dissimilarity), which lack axes and where each data point represents one plant
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microbiota.
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Supplementary Figure S3 MANOVA analysis of plants grown in sand. MANOVA output
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indicates the significance level between two groups of data on the basis of F-tests
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performed on Bray-Curtis distance matrices with 1000 permutations using adonis
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implemented in the vegan package in R. For simplicity, the table indicates the minimum
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number of plant replicates from each group needed for separation (950 permutations
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with p < 0.05), A. thaliana (A), M. truncatula (M), B. distachyon (B), B. rapa (Br), P.
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sativum (P), T. aestivum (W), unplanted control (U), generation (1, 2, 3). Colour was used
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for visual clarity. Analysis based on ARISA data.
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Supplementary Figure S4 Microbiota diversity over three generations of plant growth.
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(a) Community structure at the phylum level over three generations of model plants in
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sand, y-axis: abundance. (b) Shannon diversity index of model plant microbiota in sand.
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(c) Shannon diversity index of model plant microbiota in compost. (d) Shannon
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diversity index of crop plant microbiota in compost. For (b-d) left side of the graph
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represents the bacterial community and the right, the fungal community. A. thaliana (A),
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M. truncatula (M), B. distachyon (B), B. rapa (Br), P. sativum (P), T. aestivum (W),
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unplanted control (U), generation (1, 2, 3). (e) Richness index (number of OTUs in the
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most abundant 50% of the community). Stars indicate results of pair-wise t-test
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(p<0.05) with Bonferroni correction.
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Supplementary Figure S5 Bacterial OTUs either selected or depleted in the
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rhizosphere. (a) Selected in sand. (b) Depleted in sand. (c) Selected in compost. (d)
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Depleted in compost. The heat maps show bacterial OTUs where fold-abundance was
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statistically different (t-test with Bonferroni correction; p<0.05) in the rhizosphere
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compared to unplanted control in at least one generation. Only OTUs with a relative
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abundance of greater than 0.1% were used, A. thaliana (A), M. truncatula (M), B.
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distachyon (B), B. rapa (Br), P. sativum (P), T. aestivum (W), generation (1, 2, 3).
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Dendrograms were removed for visual clarity.
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Supplementary Figure S6 Explanatory 2-dimensional ternary plot. Each dot represents
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a single OTU and its size is proportional to the abundance in all three rhizospheres and
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unplanted control in a given generation. The colour is used for visual clarity and
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represents the ratio of the mean rhizosphere abundance against the unplanted control.
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The location is based on the rhizosphere abundance only (in this case the rhizosphere of
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Arabidopsis, Medicago and Brachypodium). The green dot represents an OTU that was
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found 30% of the time in the rhizosphere of Brachypodium, 20% in Medicago and 50%
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in Arabidopsis. Ternary plots present the rhizosphere selection as well as depletion. For
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example the big red dot in the Medicago corner is an OTU that was strongly selected in
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the Medicago rhizosphere. The blue dot in the Brachypodium corner is an example of a
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predominantly soil microorganism (mostly found in the unplanted control), which was
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depleted from the rhizospheres of Arabidopsis and Medicago, but not Brachypodium.
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Supplementary Figure S7 The effect on the rhizosphere fungal microbiota of plants
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grown in sand compared with compost. Each sphere represents a single OTU, size
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represents abundance, position corresponds to the relative abundance in the three
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rhizospheres and colour reflects the rhizosphere abundance relative to unplanted soil
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calculated for each generation separately. Please refer to Supplementary Figure S6 for
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an example explanation. (a) Fungal microbiota of model plants grown in sand. (b)
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Fungal microbiota of model plants grown in compost. (c) Fungal microbiota of crop
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plants grown in compost. Only OTUs with a relative abundance of greater than 0.1%
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were used. Abbreviations are as follows: Alternaria (Al), Cryptococcus (Cr), Fusarium (F),
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Gibellulopsis (G), Olpidium brassicae (O), Penicillium (Pe), Phoma (Ph) and Arabidopsis
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(A), Medicago (M), Brachypodium (B), Brassica (Br), Pisum (P), Triticum (W), generation
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(1, 2, 3).
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Supplementary Figure S8 Structure of fungal microbiota. (a) Sand experiment. (b)
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Compost experiment. A. thaliana (A), M. truncatula (M), B. distachyon (B), B. rapa (Br), P.
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sativum (P), T. aestivum (W), unplanted control in sand (U50), unplanted control in
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compost (U100), generation (1, 2, 3). Each of the sequencing read has been identified
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using the GenBank database and annotated in MEGAN. Analysis has been stopped at the
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phylum and subphylum level. Saccharomyceta and Agaricomycotina subphyla are
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shown, as they represent the abundant group of Ascomycota and Basidomycota phyla,
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respectively.
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Supplementary Figure S9 Abundance of two dominant OTUs for which a
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representative strain was isolated.
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Supplementary Figure S10 Plant growth promotion assay for three model plants using
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isolated bacterial strains. Letters a,b, ab, ac and c represent the statistical differences in
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plant dry weight for each species (based on t-test with Bonferroni correction, p<0.05).
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Supplementary Figure S11 MANOVA analysis of plants grown in compost. (a) Model
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plants. (b) Crop plants, A. thaliana (A), M. truncatula (M), B. distachyon (B), B. rapa (Br),
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P. sativum (P), T. aestivum (W), unplanted control (U), generation (1, 2, 3). Colour was
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used for visual clarity. Analysis based on ARISA data.
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Supplementary Figure S12 Neighbor-Joining phylogram of fungal OTU 540 annotated
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as OTU 540 sequence. Tree was constructed using MEGA6 software using BLAST
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algorithm against 100 target sequences (default ClustalW settings, bootstrap value of
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1000.
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Supplementary Word file 1 In a separate Word file. Pictures of the soil sampling site
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and plant growth.
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Supplementary Word file 2 In a separate Word file. A brief report about two isolates:
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Achromobacter xylosoxidans and Arthrobacter sp., indicating their position in the
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phylogenetic tree of life.
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