Fig. 3

Results of differential abundance analysis. Dots show the log2 fold change of different bacterial or fungal families and error bars show ± log fold change standard error. Results are from N = 3 replicate plants per treatment. Shown are: A Bacterial and fungal families that were differentially abundant between the bulk soil the rhizosphere, and between the rhizosphere and the endosphere for stem elongation and senesced plants. B Bacterial and fungal taxa that were differentially abundant between the endosphere of stem elongation growth phase plants and senesced plants. C Bacterial and fungal taxa that were differentially abundant regardless of soil type for pot grown wheat. Analysis was performed using DESeq2. If a family had a base mean > 200 and a significant p-value (significance cut-off p < 0.05) in one or more comparison, data for that taxon was plotted for all comparisons, * indicates p < 0.05, ** indicates p < 0.01, *** indicates p < 0.001, and n.s indicates p > 0.05. Data for all pot-grown plants were pooled and taxa which still showed significant fold change across compartments were included. For all complete statistical outputs see Supplementary Tables 10, 11, 12, 13, 14, 15 and 16