Fig. S1 Box plot representation of the distribution of normalized hybridization intensity values for 39 strains according to seven arbitrarily-defined classes of WMM values.

Fig. S2 Box plot representation of the distribution of normalized hybridization intensity values for the TAD stages studied (PI, PV and PX).

Fig. S3 Microarray hybridization patterns for rhizosphere samples. α-prot, Alphaproteobacteria; β-prot, Betaproteobacteria; γ-prot, Gammaproteobacteria; -prot, Epsilonproteobacteria; δ-prot, Deltaproteobacteria; Actino, Actinobacteria; Acido, Acidobacteria; Bac, Bacteroidetes; Flav, Flavobacteria; Sphi, Sphingobacteria; Firm, Firmicutes; Planc, Planctomycetes; Verru, Verrucomicrobia; Nit, Nitrospira; Chlo, Chloroflexi; Cya, Cyanobacteria; Flex, Flexistipes.

Fig. S4 Estimation of the proportion between the total bacterial community and Pseudomonas-related populations, by quantitative PCR, in the three TAD stages.

Table S1 List of 16 rRNA targeted oligonucleotide probes designed in this work [and added to the probe set of Sanguin et al. (2006a) and Sanguin et al. (2008)].

Table S2 16S rRNA sequences used for phylogenetic analysis, which originate from the wheat rhizosphere (i.e. PV and PX clones; this study) or Greengenes and SILVA databases.

Table S3 Affiliation of Pseudomonas-related 16S rRNA clones using Greengenes classify tool.

Table S4 Significance analysis of microarray probe hybridization data from PI, PV and PX stages.

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