Fig. 4

Co-occurrence patterns of cropping sensitive OTUs. a Co-occurrence networks visualizing significant correlations (ρ > 0.7, p < 0.001; indicated with gray lines) between bacteria and fungi OTUs in soil and root communities. Circles indicate bacteria, triangles fungi, and keystone OTUs are represented with asterisks (Table  1 ). OTUs are colored by their association to the different cropping systems (as defined in Additional file 1: Figure S6; gray OTUs are insensitive to cropping practices). Shaded areas represent the network modules containing csOTUs as defined in Additional file 1: Figure S14. b Cumulative relative abundance (as counts per million, CPM; y-axis in ×1000) of all bacteria and fungi of the cropping sensitive modules in soil and root networks. The cumulative relative abundance in samples of C-IT (dark blue), C-NT (light blue), O-IT (dark red), O-RT (light red) cropping systems indicates the overall response of cropping sensitive modules to the different farming practices. c Qualitative taxonomic composition of cropping sensitive modules is reported as proportional OTUs numbers per class (bacteria) and phylum (fungi) and compared to the overall taxonomic distribution in the entire dataset (column “all”)