Figure S2.

Microbial Networks of Soil and A. thaliana Episphere Microbiota, Related to Figure 2

(A) Correlation-based network of microbial episphere-associated (left) and soil-associated (right) OTUs detected in three natural A. thaliana populations (Pulheim, Geyen, Saint-Dié). Each node corresponds to a microbial OTU and edges between nodes correspond to either positive (black) or negative (red) correlations inferred from OTU abundance profiles using the SparCC method (pseudo p-value > 0.05, correlation values < -0.6 or > 0.6). OTUs belonging to the different microbial kingdoms have distinct color codes and node size reflects their relative abundance in the episphere compartment. Intra-kingdom correlations are represented with dotted lines and inter-kingdom correlations by solid lines.

(B) Hub properties of negatively correlated bacterial and fungal OTUs in the episphere (left) and soil (right) networks. For each fungal and bacterial OTU, the frequency of negative inter-kingdom connections is plotted against the betweenness centrality inferred from all negative BF connections (cases in which a node lies on the shortest path between all pairs of other nodes).

(C) Proportion of edges showing positive (black) or negative (red) correlations in the microbial episphere (left) and soil (right) networks. B: bacteria, F: fungi, O: oomycetes.

(D) Cumulative correlation scores measured in the microbial episphere (left) and soil (right) networks between fungal and bacterial OTUs. Fungal OTUs were grouped at the class level (> five OTUs/class) and sorted according to their cumulative correlation scores with bacterial OTUs.

(E) Cumulative correlation scores measured in the microbial episphere (left) and soil (right) networks between bacterial and fungal OTUs. Bacterial OTUs were grouped at the class level (> five OTUs/class) and sorted according to their cumulative correlation scores with fungal OTUs. (F-I) Validation of SparCC-defined (anti-)correlated OTUs using Spearman correlation.

(F) Number of edges that are either unique to one of the two networks or shared by the two (B = connections between bacterial OTUs, F = connections between fungal OTUs, BF = connections between fungal and bacterial OTUs, pos = positively correlated connections, neg = negatively correlated connections).

(G) Cumulative negative correlations across taxonomic groups inferred by Spearman correlation.

(H) The ten most positively correlated OTUs from the sparCC network and the corresponding correlation inferred by Spearman correlation based on the relative abundance of the OTUs.

(I) The ten most negatively correlated OTUs from the sparCC network and the corresponding correlation inferred by Spearman correlation based on the relative abundance of the OTUs.