Fig. 2

Comparison of microbial communities in samples from different rootstock root-system compartments (root tissues and rhizospheres). a Principal coordinates analysis (PCoA) for root, rhizosphere and bulk samples. b Constrained analysis of principal coordinates (CAP) was generated from the same OTU table by selecting only those samples influenced by their location within the root system (root tissue or rhizosphere) and constrained to the rootstock grouping factor. Pairwise comparisons using permutational MANOVAs on a distance matrix are shown in Additional file 1: Table S4. c Relative abundance of different bacterial classes in the root tissues and rhizospheres of rootstocks representing OTUs showing more than 1% relative abundance of all reads and present in at least 2/3 of replicates. Classes representing less than 1% of the total reads are grouped in ‘Other’