Figure Caption
Fig. 1 . The relative abundances of gene modules. The letters a, b, and c indicate statistically significant differences between groups (p < 0.05). Functional modules correspond to the following designations: A-energy production and conversion, B-amino acid transport and metabolism, C-nucleotide transport and metabolism, D-carbohydrate transport and metabolism, E-intracellular trafficking, secretion, and vesicular transport, F-lipid transport and metabolism, G-transcription, H-cell wall or membrane or envelope biogenesis, I-extracellular structures, J-signal transduction mechanisms, K-coenzyme transport and metabolism, L-inorganic ion transport and metabolism, M-RNA processing and modification, N-secondary metabolite biosynthesis, transport, and catabolism, O-cell motility, P-defense mechanisms, Q-general function prediction only, R-function unknown, S-cell cycle control, cell division, chromosome partitioning, T-post-translational modification, protein turnover, and chaperones, U-replication, recombination and repair, V-chromatin structure and dynamics, and W-translation, ribosomal structure, and biogenesis. Gene modules with very low RAs were amplified 10–1000 times to better visualize their relative ratios across groups (M, I and V). The modules can be characterized into six general groups including basic metabolism-related (dark yellow), interaction-related (gray), cofactor metabolite-related (yellow), environmental resistance-related (brown), other (blue), and reproduction-related (green) functions.
Fig. 2 . Important nodes and modules within the soil microbial networks. Fig.2A shows the identity of the module hubs and connectors for the three soil types. The nodes with Zi > 2.5 were considered module hubs, and nodes with Pi > 0.625 were considered connectors, while nodes with both Zi > 2.5 and Pi > 0.625 were considered network hubs. The module hub and connector node identities at the phylum level are shown on the right side of the panels. Fig.2B shows the modularity of soil networks and the location of T.matsutake within the networks. Blue circles show T.matsutake, yellow circles show bacterial OTUs, and green circles show fungal OTUs. Yellow and green lines show positive and negative interactions, respectively. Several smaller modules that were highly marginalized are not included in the figure to allow for better visualization of each stage’s network.
Fig. 3 . The interactions and interactive OTUs associated with T.matsutake. Fig.3A shows the ratio of positive to negative interactions. Fig.3B shows the relative abundances of different interaction types across the T.matsutake habitat degradation gradient. + and - indicate positive and negative interactions, respectively. B and F indicate bacterial and fungal nodes, respectively, wherein B+F indicates inferred positive interactions between bacterial OTUs and fungal OTUs. Fig.3C shows variation in the relative abundances of OTUs that originally interacted with T.matsutake, *** indicates statistically significant differences among groups (p < 0.001).
Fig. 4. The linear relationships between T.matsutake RAs and soil properties, community diversity, community structure, and community network structures. Upward arrows indicate components that were positively related to extraction. BE, BR, and BS indicate bacterial equitability, richness, and Shannon index values, respectively, while FE, FR, and FS indicate the respective fungal counterparts. Community structure was extracted from PC1 of the bacterial and fungal PCoAs, while network structure was comprised of the values from the network indices avgK, avgCC, and Tran. Shaded areas show 95% confidence intervals.